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 408 patients, 300 significant findings detected with P value < 0.05 and Q value < 0.25.

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

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 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, 300 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
9p loss	175 (43%)	233	1e-05 (0.000164)	7e-05 (0.000857)	0.00207 (0.0131)	8e-05 (0.000924)	0.00101 (0.00739)	5e-05 (0.000672)	0.0291 (0.0954)	0.00091 (0.00697)	2e-05 (0.000309)	1e-05 (0.000164)
9q loss	170 (42%)	238	1e-05 (0.000164)	1e-05 (0.000164)	0.00025 (0.0025)	1e-05 (0.000164)	2e-05 (0.000309)	1e-05 (0.000164)	0.0194 (0.0723)	0.00066 (0.00515)	1e-05 (0.000164)	1e-05 (0.000164)
3p loss	53 (13%)	355	0.167 (0.303)	0.0322 (0.101)	0.02 (0.0736)	0.013 (0.0532)	1e-05 (0.000164)	3e-05 (0.000424)	0.633 (0.73)	0.00464 (0.0242)	0.00062 (0.00514)	0.0015 (0.0102)
3p gain	142 (35%)	266	6e-05 (0.000794)	0.0469 (0.13)	0.887 (0.921)	0.692 (0.771)	0.00841 (0.0377)	0.0209 (0.075)	0.031 (0.098)	0.0664 (0.165)	0.0234 (0.082)	0.00043 (0.00379)
4p gain	38 (9%)	370	0.00234 (0.0143)	0.00899 (0.0392)	0.00513 (0.0258)	0.0423 (0.122)	0.00795 (0.0364)	0.0105 (0.044)	0.012 (0.0494)	0.456 (0.585)	0.245 (0.397)	0.462 (0.591)
5p gain	166 (41%)	242	1e-05 (0.000164)	0.0401 (0.117)	0.00023 (0.00236)	0.00207 (0.0131)	0.106 (0.223)	0.00049 (0.00423)	0.835 (0.879)	0.00237 (0.0144)	0.092 (0.207)	0.0043 (0.0226)
9q gain	56 (14%)	352	0.0003 (0.00283)	0.0206 (0.0744)	0.0898 (0.203)	0.00313 (0.0177)	0.00248 (0.0147)	0.00027 (0.00264)	0.866 (0.903)	0.374 (0.523)	0.0003 (0.00283)	1e-05 (0.000164)
4p loss	143 (35%)	265	1e-05 (0.000164)	0.116 (0.237)	0.168 (0.303)	0.0053 (0.0265)	0.00621 (0.0298)	8e-05 (0.000924)	0.0349 (0.107)	0.00966 (0.0415)	0.0139 (0.0566)	0.0639 (0.161)
4q loss	136 (33%)	272	1e-05 (0.000164)	0.0619 (0.159)	0.0731 (0.176)	0.0275 (0.092)	0.0381 (0.114)	0.00114 (0.0082)	0.388 (0.527)	0.0408 (0.119)	0.00208 (0.0131)	0.00311 (0.0177)
8p loss	188 (46%)	220	1e-05 (0.000164)	0.00608 (0.0293)	0.0159 (0.0628)	0.00121 (0.00855)	0.154 (0.285)	0.0216 (0.0768)	0.0996 (0.218)	0.03 (0.0964)	0.306 (0.458)	0.00324 (0.0181)
11p loss	181 (44%)	227	1e-05 (0.000164)	1e-05 (0.000164)	0.118 (0.239)	8e-05 (0.000924)	7e-05 (0.000857)	1e-05 (0.000164)	0.0996 (0.218)	0.0943 (0.21)	0.00013 (0.00137)	0.00066 (0.00515)
14q loss	122 (30%)	286	1e-05 (0.000164)	1e-05 (0.000164)	0.909 (0.932)	0.256 (0.408)	0.157 (0.289)	0.0001 (0.00109)	0.00056 (0.00469)	0.0249 (0.0847)	0.00231 (0.0142)	1e-05 (0.000164)
22q loss	159 (39%)	249	1e-05 (0.000164)	0.0191 (0.0723)	0.142 (0.27)	0.00063 (0.00515)	0.00858 (0.038)	0.00098 (0.00731)	0.233 (0.382)	0.00376 (0.0203)	0.069 (0.169)	1e-05 (0.000164)
21q gain	115 (28%)	293	1e-05 (0.000164)	3e-05 (0.000424)	0.38 (0.523)	0.411 (0.544)	0.00275 (0.0162)	0.00149 (0.0102)	0.00805 (0.0367)	0.00757 (0.0355)	0.0584 (0.152)	0.258 (0.41)
xp gain	66 (16%)	342	0.00045 (0.00393)	0.00066 (0.00515)	0.00095 (0.00715)	0.0084 (0.0377)	0.00769 (0.0358)	0.0566 (0.15)	0.071 (0.172)	0.13 (0.254)	0.0215 (0.0768)	0.115 (0.236)
6p loss	100 (25%)	308	0.0001 (0.00109)	0.0187 (0.0712)	0.121 (0.242)	0.693 (0.772)	0.184 (0.325)	0.0372 (0.111)	0.0476 (0.13)	0.00476 (0.0244)	0.0871 (0.199)	7e-05 (0.000857)
6q loss	159 (39%)	249	1e-05 (0.000164)	0.0142 (0.0571)	0.0177 (0.0685)	0.405 (0.541)	0.385 (0.525)	0.0458 (0.128)	0.0942 (0.21)	0.00306 (0.0175)	0.441 (0.573)	3e-05 (0.000424)
13q loss	86 (21%)	322	1e-05 (0.000164)	0.632 (0.73)	0.00042 (0.00374)	0.539 (0.65)	0.0176 (0.0685)	0.266 (0.419)	0.201 (0.346)	2e-05 (0.000309)	0.0106 (0.0442)	0.001 (0.00739)
15q loss	145 (36%)	263	1e-05 (0.000164)	1e-05 (0.000164)	0.0967 (0.214)	0.0561 (0.15)	0.423 (0.555)	0.305 (0.458)	0.00893 (0.0392)	1e-05 (0.000164)	0.00584 (0.0283)	0.00014 (0.00145)
21q loss	79 (19%)	329	0.211 (0.355)	0.0897 (0.203)	0.0225 (0.0795)	0.0257 (0.0869)	0.0018 (0.0117)	0.01 (0.0422)	0.382 (0.523)	0.144 (0.272)	0.00827 (0.0375)	0.0278 (0.0925)
2p gain	111 (27%)	297	1e-05 (0.000164)	1e-05 (0.000164)	0.189 (0.331)	0.692 (0.771)	0.35 (0.502)	0.0199 (0.0736)	0.116 (0.237)	0.00793 (0.0364)	0.232 (0.382)	0.00132 (0.00916)
3q gain	178 (44%)	230	1e-05 (0.000164)	0.286 (0.439)	0.115 (0.236)	0.627 (0.727)	0.758 (0.822)	0.0835 (0.193)	0.0327 (0.102)	0.0289 (0.0952)	0.0341 (0.105)	3e-05 (0.000424)
8q gain	203 (50%)	205	1e-05 (0.000164)	0.00899 (0.0392)	0.00027 (0.00264)	0.654 (0.748)	0.449 (0.581)	0.815 (0.867)	0.28 (0.434)	0.0346 (0.106)	0.689 (0.771)	0.0422 (0.122)
11p gain	28 (7%)	380	0.0001 (0.00109)	0.184 (0.325)	0.0753 (0.179)	0.00538 (0.0266)	0.0643 (0.161)	0.0073 (0.0344)	0.937 (0.952)	0.569 (0.676)	0.0024 (0.0145)	0.0172 (0.0676)
2q loss	91 (22%)	317	0.00133 (0.00916)	0.0239 (0.0829)	0.322 (0.473)	0.314 (0.465)	0.0629 (0.16)	0.0313 (0.0985)	0.745 (0.811)	0.892 (0.923)	0.0113 (0.0469)	0.00535 (0.0266)
5p loss	56 (14%)	352	0.0586 (0.152)	0.00012 (0.00128)	0.147 (0.274)	0.00119 (0.00849)	0.143 (0.27)	0.00024 (0.00243)	0.636 (0.734)	0.734 (0.803)	0.0177 (0.0685)	0.00993 (0.042)
5q loss	159 (39%)	249	1e-05 (0.000164)	0.00133 (0.00916)	0.494 (0.616)	0.257 (0.409)	0.214 (0.358)	0.0178 (0.0686)	0.211 (0.355)	0.0192 (0.0723)	0.22 (0.367)	0.00779 (0.0361)
18q loss	146 (36%)	262	0.00181 (0.0117)	0.556 (0.664)	0.655 (0.748)	0.273 (0.429)	0.591 (0.696)	0.0445 (0.126)	0.00028 (0.0027)	0.00066 (0.00515)	0.0329 (0.102)	0.163 (0.298)
5q gain	53 (13%)	355	0.00561 (0.0275)	0.0842 (0.194)	0.0004 (0.0036)	0.0241 (0.083)	0.396 (0.532)	0.27 (0.424)	0.344 (0.494)	0.121 (0.242)	0.488 (0.613)	0.0364 (0.11)
7p gain	171 (42%)	237	1e-05 (0.000164)	0.0609 (0.157)	0.00498 (0.0252)	0.146 (0.274)	0.664 (0.752)	0.105 (0.223)	0.365 (0.517)	0.0389 (0.115)	0.204 (0.349)	7e-05 (0.000857)
9p gain	68 (17%)	340	1e-05 (0.000164)	0.114 (0.236)	0.125 (0.247)	0.00853 (0.038)	0.101 (0.218)	0.063 (0.16)	0.317 (0.467)	0.215 (0.359)	7e-05 (0.000857)	1e-05 (0.000164)
10p gain	116 (28%)	292	1e-05 (0.000164)	0.00476 (0.0244)	0.392 (0.531)	0.57 (0.676)	0.747 (0.811)	0.00278 (0.0163)	0.861 (0.902)	0.9 (0.926)	0.807 (0.859)	0.00992 (0.042)
14q gain	58 (14%)	350	5e-05 (0.000672)	0.0457 (0.128)	0.469 (0.598)	0.381 (0.523)	0.0443 (0.126)	0.0436 (0.125)	0.597 (0.7)	0.18 (0.322)	0.369 (0.519)	0.366 (0.518)
17q gain	136 (33%)	272	0.00326 (0.0181)	0.0307 (0.0977)	0.0813 (0.189)	0.989 (0.99)	0.0396 (0.116)	0.305 (0.458)	0.279 (0.433)	0.205 (0.349)	0.293 (0.445)	0.00245 (0.0147)
18p gain	117 (29%)	291	1e-05 (0.000164)	0.00356 (0.0196)	0.544 (0.655)	0.403 (0.54)	0.29 (0.442)	0.0205 (0.0743)	0.329 (0.479)	0.109 (0.226)	0.0585 (0.152)	4e-05 (0.000556)
12p loss	56 (14%)	352	0.00467 (0.0242)	0.00293 (0.017)	0.498 (0.618)	0.106 (0.223)	0.0754 (0.179)	0.0156 (0.0623)	0.259 (0.411)	0.277 (0.433)	0.0292 (0.0954)	0.191 (0.332)
16q loss	103 (25%)	305	1e-05 (0.000164)	0.0204 (0.0743)	0.0141 (0.0571)	0.306 (0.458)	0.613 (0.716)	0.354 (0.505)	0.711 (0.785)	0.1 (0.218)	0.453 (0.583)	0.00377 (0.0203)
xq loss	80 (20%)	328	0.13 (0.254)	9e-05 (0.00102)	0.659 (0.749)	0.0841 (0.194)	0.383 (0.524)	0.297 (0.45)	0.0357 (0.109)	0.116 (0.236)	0.00167 (0.0112)	0.00933 (0.0405)
1p gain	90 (22%)	318	1e-05 (0.000164)	0.0228 (0.0801)	0.456 (0.585)	0.614 (0.716)	0.852 (0.893)	0.688 (0.771)	0.893 (0.924)	0.382 (0.523)	0.746 (0.811)	0.0295 (0.0954)
7q gain	150 (37%)	258	1e-05 (0.000164)	0.122 (0.243)	0.0387 (0.115)	0.611 (0.715)	0.931 (0.952)	0.659 (0.749)	0.234 (0.382)	0.206 (0.349)	0.804 (0.857)	0.00222 (0.0138)
8p gain	90 (22%)	318	1e-05 (0.000164)	0.286 (0.439)	0.0005 (0.00427)	0.0564 (0.15)	0.332 (0.482)	0.953 (0.962)	0.12 (0.242)	0.0165 (0.0649)	0.352 (0.504)	0.178 (0.32)
10q gain	45 (11%)	363	0.00038 (0.00346)	0.0531 (0.144)	0.889 (0.921)	0.409 (0.544)	0.518 (0.631)	0.0306 (0.0977)	0.438 (0.572)	0.975 (0.979)	0.254 (0.408)	0.028 (0.0929)
11q gain	48 (12%)	360	0.00575 (0.0281)	0.322 (0.473)	0.49 (0.614)	0.0099 (0.042)	0.278 (0.433)	0.14 (0.267)	0.941 (0.953)	0.906 (0.93)	0.0327 (0.102)	0.152 (0.282)
15q gain	35 (9%)	373	0.0583 (0.152)	0.00012 (0.00128)	0.00066 (0.00515)	0.0704 (0.172)	0.334 (0.484)	0.0311 (0.098)	0.0744 (0.178)	0.617 (0.718)	0.146 (0.274)	0.0581 (0.152)
18q gain	63 (15%)	345	0.00383 (0.0205)	0.243 (0.395)	0.185 (0.326)	0.0806 (0.188)	0.585 (0.691)	0.365 (0.517)	0.0386 (0.115)	0.427 (0.56)	0.327 (0.477)	0.00689 (0.0328)
19q gain	134 (33%)	274	1e-05 (0.000164)	0.00393 (0.0209)	0.102 (0.219)	0.802 (0.856)	0.302 (0.454)	0.287 (0.439)	0.481 (0.607)	0.0209 (0.075)	0.165 (0.3)	0.183 (0.325)
20q gain	229 (56%)	179	1e-05 (0.000164)	0.0293 (0.0954)	0.394 (0.531)	0.71 (0.785)	0.5 (0.62)	0.107 (0.224)	0.377 (0.523)	0.191 (0.332)	0.518 (0.631)	0.0237 (0.0828)
10q loss	128 (31%)	280	1e-05 (0.000164)	0.00037 (0.00341)	0.406 (0.542)	0.492 (0.615)	0.0121 (0.0498)	0.723 (0.794)	0.125 (0.247)	0.0531 (0.144)	0.284 (0.438)	0.0645 (0.161)
11q loss	131 (32%)	277	1e-05 (0.000164)	0.0242 (0.083)	0.287 (0.439)	0.0154 (0.0616)	0.335 (0.484)	0.255 (0.408)	0.701 (0.778)	0.538 (0.649)	0.665 (0.752)	0.286 (0.439)
16p loss	107 (26%)	301	1e-05 (0.000164)	0.0559 (0.15)	0.00214 (0.0134)	0.3 (0.454)	0.256 (0.408)	0.203 (0.348)	0.517 (0.631)	0.139 (0.265)	0.0778 (0.183)	0.0199 (0.0736)
17p loss	180 (44%)	228	0.00035 (0.00326)	0.265 (0.419)	0.102 (0.219)	0.112 (0.232)	0.309 (0.46)	0.0693 (0.17)	0.761 (0.824)	0.0363 (0.11)	0.165 (0.3)	0.00421 (0.0223)
19p loss	94 (23%)	314	1e-05 (0.000164)	0.0455 (0.128)	0.106 (0.223)	0.143 (0.27)	0.0987 (0.217)	0.00697 (0.033)	0.254 (0.408)	0.307 (0.458)	0.339 (0.489)	0.0685 (0.169)
19q loss	57 (14%)	351	0.0007 (0.00542)	0.33 (0.479)	0.0462 (0.128)	0.203 (0.348)	0.413 (0.544)	0.137 (0.263)	0.0727 (0.175)	0.628 (0.727)	0.267 (0.421)	0.0194 (0.0723)
2q gain	57 (14%)	351	1e-05 (0.000164)	0.00176 (0.0116)	0.583 (0.689)	0.553 (0.663)	0.655 (0.748)	0.246 (0.398)	0.0643 (0.161)	0.25 (0.404)	0.503 (0.622)	0.277 (0.433)
4q gain	26 (6%)	382	0.00178 (0.0117)	0.101 (0.218)	0.371 (0.521)	0.74 (0.808)	0.0941 (0.21)	0.114 (0.235)	0.0192 (0.0723)	0.494 (0.616)	0.324 (0.475)	0.413 (0.544)
6q gain	41 (10%)	367	0.183 (0.325)	0.862 (0.902)	0.826 (0.872)	0.378 (0.523)	0.389 (0.528)	0.393 (0.531)	0.505 (0.623)	0.505 (0.623)	0.0442 (0.126)	0.0252 (0.0855)
12p gain	115 (28%)	293	0.00486 (0.0248)	0.0636 (0.161)	0.152 (0.282)	0.896 (0.924)	0.701 (0.778)	0.83 (0.876)	0.728 (0.798)	0.0249 (0.0847)	0.301 (0.454)	0.129 (0.253)
13q gain	100 (25%)	308	0.0295 (0.0954)	0.657 (0.749)	0.249 (0.403)	0.816 (0.867)	0.315 (0.465)	0.471 (0.599)	0.776 (0.837)	0.825 (0.872)	0.376 (0.523)	0.0242 (0.083)
20p gain	201 (49%)	207	3e-05 (0.000424)	0.0615 (0.158)	0.252 (0.406)	0.0799 (0.187)	0.6 (0.703)	0.0404 (0.118)	0.509 (0.624)	0.135 (0.261)	0.0629 (0.16)	0.0559 (0.15)
7p loss	21 (5%)	387	0.088 (0.201)	0.463 (0.592)	0.549 (0.66)	0.906 (0.93)	0.41 (0.544)	0.158 (0.291)	0.0974 (0.215)	0.0458 (0.128)	0.0468 (0.13)	0.0688 (0.169)
8q loss	38 (9%)	370	0.00302 (0.0174)	0.618 (0.718)	0.975 (0.979)	0.423 (0.555)	0.0358 (0.109)	0.782 (0.842)	0.121 (0.243)	0.282 (0.437)	0.368 (0.519)	0.381 (0.523)
10p loss	74 (18%)	334	0.0204 (0.0743)	0.0681 (0.169)	0.369 (0.519)	0.849 (0.892)	0.00316 (0.0177)	0.205 (0.349)	0.41 (0.544)	0.106 (0.223)	0.192 (0.334)	0.394 (0.531)
18p loss	99 (24%)	309	0.0186 (0.0712)	0.0894 (0.203)	0.687 (0.771)	0.353 (0.504)	0.977 (0.98)	0.0269 (0.0903)	0.0751 (0.179)	0.654 (0.748)	0.0707 (0.172)	0.175 (0.315)
1q gain	128 (31%)	280	1e-05 (0.000164)	0.687 (0.771)	0.832 (0.877)	0.692 (0.771)	0.78 (0.84)	0.865 (0.903)	0.375 (0.523)	0.77 (0.832)	0.489 (0.613)	0.537 (0.649)
6p gain	78 (19%)	330	0.00052 (0.0044)	0.482 (0.607)	0.464 (0.593)	0.233 (0.382)	0.874 (0.909)	0.638 (0.735)	0.789 (0.846)	0.883 (0.918)	0.187 (0.328)	0.169 (0.304)
12q gain	92 (23%)	316	0.0722 (0.175)	0.227 (0.377)	0.32 (0.471)	0.897 (0.924)	0.381 (0.523)	0.128 (0.252)	0.675 (0.76)	0.0883 (0.201)	0.964 (0.971)	0.0303 (0.0971)
16p gain	74 (18%)	334	0.0491 (0.134)	0.128 (0.252)	0.585 (0.691)	0.528 (0.642)	0.393 (0.531)	0.152 (0.282)	0.515 (0.631)	0.206 (0.349)	0.676 (0.761)	0.384 (0.524)
16q gain	83 (20%)	325	0.0368 (0.11)	0.0514 (0.14)	0.497 (0.618)	0.429 (0.562)	0.38 (0.523)	0.109 (0.226)	0.148 (0.275)	0.0751 (0.179)	0.453 (0.583)	0.124 (0.247)
17p gain	58 (14%)	350	0.00093 (0.00706)	0.0566 (0.15)	0.663 (0.752)	0.45 (0.582)	0.628 (0.727)	0.166 (0.302)	0.326 (0.476)	0.71 (0.785)	0.532 (0.644)	0.181 (0.322)
19p gain	87 (21%)	321	0.00358 (0.0196)	0.0968 (0.214)	0.104 (0.222)	0.554 (0.663)	0.106 (0.223)	0.0961 (0.214)	0.507 (0.624)	0.38 (0.523)	0.184 (0.325)	0.867 (0.903)
22q gain	49 (12%)	359	0.101 (0.218)	0.0572 (0.151)	0.723 (0.794)	0.362 (0.514)	0.00964 (0.0415)	0.132 (0.255)	0.147 (0.274)	0.571 (0.676)	0.179 (0.321)	0.232 (0.382)
1p loss	34 (8%)	374	0.131 (0.255)	0.0475 (0.13)	0.938 (0.952)	0.531 (0.644)	0.441 (0.573)	0.169 (0.304)	0.232 (0.382)	0.667 (0.752)	0.289 (0.441)	0.479 (0.606)
2p loss	45 (11%)	363	0.0762 (0.18)	0.0846 (0.194)	0.824 (0.872)	0.847 (0.891)	0.293 (0.445)	0.0283 (0.0935)	0.518 (0.631)	0.934 (0.952)	0.194 (0.335)	0.213 (0.357)
3q loss	24 (6%)	384	0.1 (0.218)	0.266 (0.419)	0.649 (0.745)	0.2 (0.344)	0.374 (0.523)	0.482 (0.607)	0.766 (0.829)	0.126 (0.248)	0.00112 (0.00813)	0.117 (0.238)
7q loss	27 (7%)	381	0.0017 (0.0113)	0.477 (0.604)	0.509 (0.624)	0.242 (0.395)	0.934 (0.952)	0.819 (0.869)	0.103 (0.221)	0.0829 (0.193)	0.362 (0.514)	0.12 (0.242)
12q loss	60 (15%)	348	8e-05 (0.000924)	0.561 (0.668)	0.496 (0.618)	0.195 (0.336)	0.667 (0.752)	0.518 (0.631)	0.801 (0.856)	0.55 (0.66)	0.663 (0.752)	0.129 (0.253)
17q loss	43 (11%)	365	0.0424 (0.122)	0.486 (0.612)	0.973 (0.979)	0.595 (0.699)	0.732 (0.801)	0.937 (0.952)	0.747 (0.811)	0.914 (0.935)	0.645 (0.742)	0.559 (0.667)
xp loss	71 (17%)	337	0.189 (0.331)	0.0605 (0.156)	0.432 (0.564)	0.347 (0.498)	0.107 (0.224)	0.715 (0.788)	0.314 (0.465)	0.448 (0.581)	0.28 (0.434)	0.0447 (0.126)
xq gain	47 (12%)	361	0.0666 (0.165)	0.382 (0.523)	0.137 (0.262)	0.136 (0.262)	0.0552 (0.149)	0.784 (0.842)	0.229 (0.38)	0.193 (0.335)	0.411 (0.544)	0.423 (0.555)
1q loss	34 (8%)	374	0.234 (0.382)	0.0794 (0.186)	1 (1.00)	0.563 (0.67)	0.441 (0.573)	0.221 (0.367)	0.897 (0.924)	0.213 (0.357)	0.71 (0.785)	0.162 (0.298)
20p loss	33 (8%)	375	0.207 (0.35)	0.105 (0.223)	0.409 (0.544)	0.314 (0.465)	0.946 (0.957)	0.718 (0.79)	0.797 (0.853)	0.956 (0.964)	0.397 (0.533)	0.301 (0.454)
20q loss	14 (3%)	394	0.093 (0.209)	0.475 (0.603)	0.142 (0.27)	0.132 (0.255)	0.783 (0.842)	0.941 (0.953)	0.465 (0.594)	0.341 (0.491)	0.593 (0.697)	0.938 (0.952)

'1p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	169	140	59	40
1P GAIN MUTATED	15	50	13	12
1P GAIN WILD-TYPE	154	90	46	28

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

'1p gain' versus 'METHLYATION_CNMF'

P value = 0.0228 (Fisher's exact test), Q value = 0.08

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	138	116	69	85
1P GAIN MUTATED	27	35	8	20
1P GAIN WILD-TYPE	111	81	61	65

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

'1p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0295 (Fisher's exact test), Q value = 0.095

Table S3. Gene #1: '1p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
1P GAIN MUTATED	16	11	28	12	1	22
1P GAIN WILD-TYPE	58	35	65	54	30	62

Figure S3. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	169	140	59	40
1Q GAIN MUTATED	32	62	16	18
1Q GAIN WILD-TYPE	137	78	43	22

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

'2p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	169	140	59	40
2P GAIN MUTATED	14	64	12	21
2P GAIN WILD-TYPE	155	76	47	19

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

'2p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	138	116	69	85
2P GAIN MUTATED	27	56	11	17
2P GAIN WILD-TYPE	111	60	58	68

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

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0199 (Fisher's exact test), Q value = 0.074

Table S7. Gene #3: '2p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	112	174
2P GAIN MUTATED	44	26	41
2P GAIN WILD-TYPE	74	86	133

Figure S7. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00793 (Fisher's exact test), Q value = 0.036

Table S8. Gene #3: '2p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	89	99	93	70	54
2P GAIN MUTATED	23	32	15	28	12
2P GAIN WILD-TYPE	66	67	78	42	42

Figure S8. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00132 (Fisher's exact test), Q value = 0.0092

Table S9. 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	74	46	93	66	31	84
2P GAIN MUTATED	17	19	35	18	2	17
2P GAIN WILD-TYPE	57	27	58	48	29	67

Figure S9. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	169	140	59	40
2Q GAIN MUTATED	9	31	5	12
2Q GAIN WILD-TYPE	160	109	54	28

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

'2q gain' versus 'METHLYATION_CNMF'

P value = 0.00176 (Fisher's exact test), Q value = 0.012

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	138	116	69	85
2Q GAIN MUTATED	12	29	7	9
2Q GAIN WILD-TYPE	126	87	62	76

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

'3p gain' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00079

Table S12. Gene #5: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	169	140	59	40
3P GAIN MUTATED	40	63	18	21
3P GAIN WILD-TYPE	129	77	41	19

Figure S12. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'

'3p gain' versus 'METHLYATION_CNMF'

P value = 0.0469 (Fisher's exact test), Q value = 0.13

Table S13. Gene #5: '3p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	138	116	69	85
3P GAIN MUTATED	39	52	24	27
3P GAIN WILD-TYPE	99	64	45	58

Figure S13. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p gain' versus 'MRNASEQ_CNMF'

P value = 0.00841 (Fisher's exact test), Q value = 0.038

Table S14. Gene #5: '3p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	116	180	108
3P GAIN MUTATED	42	73	25
3P GAIN WILD-TYPE	74	107	83

Figure S14. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0209 (Fisher's exact test), Q value = 0.075

Table S15. Gene #5: '3p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	112	174
3P GAIN MUTATED	51	41	48
3P GAIN WILD-TYPE	67	71	126

Figure S15. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3p gain' versus 'MIRSEQ_CNMF'

P value = 0.031 (Fisher's exact test), Q value = 0.098

Table S16. Gene #5: '3p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	96	189
3P GAIN MUTATED	40	44	57
3P GAIN WILD-TYPE	80	52	132

Figure S16. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0234 (Fisher's exact test), Q value = 0.082

Table S17. Gene #5: '3p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	43	134	119
3P GAIN MUTATED	28	23	41	45
3P GAIN WILD-TYPE	70	20	93	74

Figure S17. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'3p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00043 (Fisher's exact test), Q value = 0.0038

Table S18. Gene #5: '3p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
3P GAIN MUTATED	27	24	37	24	2	23
3P GAIN WILD-TYPE	47	22	56	42	29	61

Figure S18. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S19. Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	169	140	59	40
3Q GAIN MUTATED	50	81	22	25
3Q GAIN WILD-TYPE	119	59	37	15

Figure S19. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

'3q gain' versus 'MIRSEQ_CNMF'

P value = 0.0327 (Fisher's exact test), Q value = 0.1

Table S20. Gene #6: '3q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	96	189
3Q GAIN MUTATED	49	53	75
3Q GAIN WILD-TYPE	71	43	114

Figure S20. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0289 (Fisher's exact test), Q value = 0.095

Table S21. Gene #6: '3q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	89	99	93	70	54
3Q GAIN MUTATED	39	52	28	32	26
3Q GAIN WILD-TYPE	50	47	65	38	28

Figure S21. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0341 (Fisher's exact test), Q value = 0.11

Table S22. Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	43	134	119
3Q GAIN MUTATED	37	27	53	54
3Q GAIN WILD-TYPE	61	16	81	65

Figure S22. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'3q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00042

Table S23. Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
3Q GAIN MUTATED	30	28	49	32	3	29
3Q GAIN WILD-TYPE	44	18	44	34	28	55

Figure S23. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p gain' versus 'CN_CNMF'

P value = 0.00234 (Fisher's exact test), Q value = 0.014

Table S24. Gene #7: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	169	140	59	40
4P GAIN MUTATED	7	23	4	4
4P GAIN WILD-TYPE	162	117	55	36

Figure S24. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

'4p gain' versus 'METHLYATION_CNMF'

P value = 0.00899 (Fisher's exact test), Q value = 0.039

Table S25. Gene #7: '4p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	138	116	69	85
4P GAIN MUTATED	7	20	4	7
4P GAIN WILD-TYPE	131	96	65	78

Figure S25. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4p gain' versus 'RPPA_CNMF'

P value = 0.00513 (Fisher's exact test), Q value = 0.026

Table S26. Gene #7: '4p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	114	104
4P GAIN MUTATED	4	12	16
4P GAIN WILD-TYPE	118	102	88

Figure S26. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'4p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0423 (Fisher's exact test), Q value = 0.12

Table S27. Gene #7: '4p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	121	98	31
4P GAIN MUTATED	6	19	6	1
4P GAIN WILD-TYPE	84	102	92	30

Figure S27. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'4p gain' versus 'MRNASEQ_CNMF'

P value = 0.00795 (Fisher's exact test), Q value = 0.036

Table S28. Gene #7: '4p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	116	180	108
4P GAIN MUTATED	7	26	5
4P GAIN WILD-TYPE	109	154	103

Figure S28. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0105 (Fisher's exact test), Q value = 0.044

Table S29. Gene #7: '4p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	112	174
4P GAIN MUTATED	11	18	9
4P GAIN WILD-TYPE	107	94	165

Figure S29. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4p gain' versus 'MIRSEQ_CNMF'

P value = 0.012 (Fisher's exact test), Q value = 0.049

Table S30. Gene #7: '4p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	96	189
4P GAIN MUTATED	4	13	21
4P GAIN WILD-TYPE	116	83	168

Figure S30. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'4q gain' versus 'CN_CNMF'

P value = 0.00178 (Fisher's exact test), Q value = 0.012

Table S31. Gene #8: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	169	140	59	40
4Q GAIN MUTATED	6	17	0	3
4Q GAIN WILD-TYPE	163	123	59	37

Figure S31. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

'4q gain' versus 'MIRSEQ_CNMF'

P value = 0.0192 (Fisher's exact test), Q value = 0.072

Table S32. Gene #8: '4q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	96	189
4Q GAIN MUTATED	2	9	15
4Q GAIN WILD-TYPE	118	87	174

Figure S32. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'5p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S33. Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	169	140	59	40
5P GAIN MUTATED	36	73	36	21
5P GAIN WILD-TYPE	133	67	23	19

Figure S33. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'METHLYATION_CNMF'

P value = 0.0401 (Fisher's exact test), Q value = 0.12

Table S34. Gene #9: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	138	116	69	85
5P GAIN MUTATED	65	44	19	38
5P GAIN WILD-TYPE	73	72	50	47

Figure S34. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p gain' versus 'RPPA_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.0024

Table S35. Gene #9: '5p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	114	104
5P GAIN MUTATED	43	31	56
5P GAIN WILD-TYPE	79	83	48

Figure S35. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'5p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00207 (Fisher's exact test), Q value = 0.013

Table S36. Gene #9: '5p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	121	98	31
5P GAIN MUTATED	27	37	51	15
5P GAIN WILD-TYPE	63	84	47	16

Figure S36. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00049 (Fisher's exact test), Q value = 0.0042

Table S37. Gene #9: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	112	174
5P GAIN MUTATED	34	41	89
5P GAIN WILD-TYPE	84	71	85

Figure S37. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00237 (Fisher's exact test), Q value = 0.014

Table S38. Gene #9: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	89	99	93	70	54
5P GAIN MUTATED	40	49	22	32	22
5P GAIN WILD-TYPE	49	50	71	38	32

Figure S38. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0043 (Fisher's exact test), Q value = 0.023

Table S39. Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
5P GAIN MUTATED	23	20	39	31	5	44
5P GAIN WILD-TYPE	51	26	54	35	26	40

Figure S39. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q gain' versus 'CN_CNMF'

P value = 0.00561 (Fisher's exact test), Q value = 0.028

Table S40. Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	169	140	59	40
5Q GAIN MUTATED	12	20	11	10
5Q GAIN WILD-TYPE	157	120	48	30

Figure S40. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

'5q gain' versus 'RPPA_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.0036

Table S41. Gene #10: '5q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	114	104
5Q GAIN MUTATED	8	11	25
5Q GAIN WILD-TYPE	114	103	79

Figure S41. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'5q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0241 (Fisher's exact test), Q value = 0.083

Table S42. Gene #10: '5q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	121	98	31
5Q GAIN MUTATED	6	14	21	3
5Q GAIN WILD-TYPE	84	107	77	28

Figure S42. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0364 (Fisher's exact test), Q value = 0.11

Table S43. Gene #10: '5q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
5Q GAIN MUTATED	7	5	11	13	0	16
5Q GAIN WILD-TYPE	67	41	82	53	31	68

Figure S43. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p gain' versus 'CN_CNMF'

P value = 0.00052 (Fisher's exact test), Q value = 0.0044

Table S44. Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	169	140	59	40
6P GAIN MUTATED	17	35	17	9
6P GAIN WILD-TYPE	152	105	42	31

Figure S44. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

'6q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0442 (Fisher's exact test), Q value = 0.13

Table S45. Gene #12: '6q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	43	134	119
6Q GAIN MUTATED	13	4	18	5
6Q GAIN WILD-TYPE	85	39	116	114

Figure S45. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'6q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0252 (Fisher's exact test), Q value = 0.085

Table S46. Gene #12: '6q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
6Q GAIN MUTATED	3	5	15	2	3	12
6Q GAIN WILD-TYPE	71	41	78	64	28	72

Figure S46. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	169	140	59	40
7P GAIN MUTATED	36	76	32	27
7P GAIN WILD-TYPE	133	64	27	13

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

'7p gain' versus 'RPPA_CNMF'

P value = 0.00498 (Fisher's exact test), Q value = 0.025

Table S48. Gene #13: '7p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	114	104
7P GAIN MUTATED	42	40	56
7P GAIN WILD-TYPE	80	74	48

Figure S48. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'7p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0389 (Fisher's exact test), Q value = 0.11

Table S49. Gene #13: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	89	99	93	70	54
7P GAIN MUTATED	43	44	28	35	19
7P GAIN WILD-TYPE	46	55	65	35	35

Figure S49. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00086

Table S50. Gene #13: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
7P GAIN MUTATED	24	16	45	32	3	44
7P GAIN WILD-TYPE	50	30	48	34	28	40

Figure S50. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S51. Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	169	140	59	40
7Q GAIN MUTATED	39	63	23	25
7Q GAIN WILD-TYPE	130	77	36	15

Figure S51. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'RPPA_CNMF'

P value = 0.0387 (Fisher's exact test), Q value = 0.11

Table S52. Gene #14: '7q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	114	104
7Q GAIN MUTATED	34	40	46
7Q GAIN WILD-TYPE	88	74	58

Figure S52. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'7q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00222 (Fisher's exact test), Q value = 0.014

Table S53. 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	74	46	93	66	31	84
7Q GAIN MUTATED	21	15	42	28	3	35
7Q GAIN WILD-TYPE	53	31	51	38	28	49

Figure S53. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S54. Gene #15: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	169	140	59	40
8P GAIN MUTATED	28	27	11	24
8P GAIN WILD-TYPE	141	113	48	16

Figure S54. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

'8p gain' versus 'RPPA_CNMF'

P value = 5e-04 (Fisher's exact test), Q value = 0.0043

Table S55. Gene #15: '8p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	114	104
8P GAIN MUTATED	17	22	37
8P GAIN WILD-TYPE	105	92	67

Figure S55. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'8p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0165 (Fisher's exact test), Q value = 0.065

Table S56. Gene #15: '8p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	89	99	93	70	54
8P GAIN MUTATED	26	16	19	22	6
8P GAIN WILD-TYPE	63	83	74	48	48

Figure S56. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'8q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S57. Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	169	140	59	40
8Q GAIN MUTATED	64	73	31	35
8Q GAIN WILD-TYPE	105	67	28	5

Figure S57. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 0.00899 (Fisher's exact test), Q value = 0.039

Table S58. Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	138	116	69	85
8Q GAIN MUTATED	67	70	24	42
8Q GAIN WILD-TYPE	71	46	45	43

Figure S58. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8q gain' versus 'RPPA_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.0026

Table S59. Gene #16: '8q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	114	104
8Q GAIN MUTATED	55	46	69
8Q GAIN WILD-TYPE	67	68	35

Figure S59. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'8q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0346 (Fisher's exact test), Q value = 0.11

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	89	99	93	70	54
8Q GAIN MUTATED	47	47	43	45	20
8Q GAIN WILD-TYPE	42	52	50	25	34

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

'8q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0422 (Fisher's exact test), Q value = 0.12

Table S61. Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
8Q GAIN MUTATED	31	21	54	36	9	46
8Q GAIN WILD-TYPE	43	25	39	30	22	38

Figure S61. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S62. Gene #17: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	169	140	59	40
9P GAIN MUTATED	11	24	25	8
9P GAIN WILD-TYPE	158	116	34	32

Figure S62. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

'9p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00853 (Fisher's exact test), Q value = 0.038

Table S63. Gene #17: '9p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	121	98	31
9P GAIN MUTATED	18	10	19	9
9P GAIN WILD-TYPE	72	111	79	22

Figure S63. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'9p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00086

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	43	134	119
9P GAIN MUTATED	32	4	14	15
9P GAIN WILD-TYPE	66	39	120	104

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

'9p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S65. Gene #17: '9p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
9P GAIN MUTATED	14	5	13	2	1	30
9P GAIN WILD-TYPE	60	41	80	64	30	54

Figure S65. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q gain' versus 'CN_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.0028

Table S66. Gene #18: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	169	140	59	40
9Q GAIN MUTATED	12	21	18	5
9Q GAIN WILD-TYPE	157	119	41	35

Figure S66. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

'9q gain' versus 'METHLYATION_CNMF'

P value = 0.0206 (Fisher's exact test), Q value = 0.074

Table S67. Gene #18: '9q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	138	116	69	85
9Q GAIN MUTATED	28	12	4	12
9Q GAIN WILD-TYPE	110	104	65	73

Figure S67. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00313 (Fisher's exact test), Q value = 0.018

Table S68. Gene #18: '9q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	121	98	31
9Q GAIN MUTATED	13	8	19	9
9Q GAIN WILD-TYPE	77	113	79	22

Figure S68. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'9q gain' versus 'MRNASEQ_CNMF'

P value = 0.00248 (Fisher's exact test), Q value = 0.015

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	116	180	108
9Q GAIN MUTATED	16	14	24
9Q GAIN WILD-TYPE	100	166	84

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

'9q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 0.0026

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	112	174
9Q GAIN MUTATED	7	10	37
9Q GAIN WILD-TYPE	111	102	137

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

'9q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.0028

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	43	134	119
9Q GAIN MUTATED	26	3	10	14
9Q GAIN WILD-TYPE	72	40	124	105

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

'9q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S72. Gene #18: '9q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
9Q GAIN MUTATED	10	5	10	2	0	26
9Q GAIN WILD-TYPE	64	41	83	64	31	58

Figure S72. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	169	140	59	40
10P GAIN MUTATED	15	60	19	22
10P GAIN WILD-TYPE	154	80	40	18

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

'10p gain' versus 'METHLYATION_CNMF'

P value = 0.00476 (Fisher's exact test), Q value = 0.024

Table S74. Gene #19: '10p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	138	116	69	85
10P GAIN MUTATED	34	48	15	19
10P GAIN WILD-TYPE	104	68	54	66

Figure S74. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00278 (Fisher's exact test), Q value = 0.016

Table S75. Gene #19: '10p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	112	174
10P GAIN MUTATED	48	24	44
10P GAIN WILD-TYPE	70	88	130

Figure S75. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00992 (Fisher's exact test), Q value = 0.042

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
10P GAIN MUTATED	23	14	30	23	1	21
10P GAIN WILD-TYPE	51	32	63	43	30	63

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

'10q gain' versus 'CN_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.0035

Table S77. Gene #20: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	169	140	59	40
10Q GAIN MUTATED	7	24	6	8
10Q GAIN WILD-TYPE	162	116	53	32

Figure S77. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

'10q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0306 (Fisher's exact test), Q value = 0.098

Table S78. Gene #20: '10q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	112	174
10Q GAIN MUTATED	21	10	14
10Q GAIN WILD-TYPE	97	102	160

Figure S78. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.028 (Fisher's exact test), Q value = 0.093

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
10Q GAIN MUTATED	9	7	13	11	0	4
10Q GAIN WILD-TYPE	65	39	80	55	31	80

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

'11p gain' versus 'CN_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.0011

Table S80. Gene #21: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	169	140	59	40
11P GAIN MUTATED	6	5	12	5
11P GAIN WILD-TYPE	163	135	47	35

Figure S80. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

'11p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00538 (Fisher's exact test), Q value = 0.027

Table S81. Gene #21: '11p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	121	98	31
11P GAIN MUTATED	3	4	10	6
11P GAIN WILD-TYPE	87	117	88	25

Figure S81. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'11p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0073 (Fisher's exact test), Q value = 0.034

Table S82. Gene #21: '11p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	112	174
11P GAIN MUTATED	5	3	20
11P GAIN WILD-TYPE	113	109	154

Figure S82. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0024 (Fisher's exact test), Q value = 0.014

Table S83. Gene #21: '11p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	43	134	119
11P GAIN MUTATED	16	1	6	5
11P GAIN WILD-TYPE	82	42	128	114

Figure S83. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'11p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0172 (Fisher's exact test), Q value = 0.068

Table S84. Gene #21: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
11P GAIN MUTATED	3	1	4	5	1	14
11P GAIN WILD-TYPE	71	45	89	61	30	70

Figure S84. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q gain' versus 'CN_CNMF'

P value = 0.00575 (Fisher's exact test), Q value = 0.028

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	169	140	59	40
11Q GAIN MUTATED	10	19	11	8
11Q GAIN WILD-TYPE	159	121	48	32

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

'11q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0099 (Fisher's exact test), Q value = 0.042

Table S86. Gene #22: '11q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	121	98	31
11Q GAIN MUTATED	5	15	10	9
11Q GAIN WILD-TYPE	85	106	88	22

Figure S86. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0327 (Fisher's exact test), Q value = 0.1

Table S87. Gene #22: '11q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	43	134	119
11Q GAIN MUTATED	20	6	11	11
11Q GAIN WILD-TYPE	78	37	123	108

Figure S87. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 0.00486 (Fisher's exact test), Q value = 0.025

Table S88. Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	169	140	59	40
12P GAIN MUTATED	32	50	19	14
12P GAIN WILD-TYPE	137	90	40	26

Figure S88. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

'12p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0249 (Fisher's exact test), Q value = 0.085

Table S89. Gene #23: '12p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	89	99	93	70	54
12P GAIN MUTATED	27	29	17	29	13
12P GAIN WILD-TYPE	62	70	76	41	41

Figure S89. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0303 (Fisher's exact test), Q value = 0.097

Table S90. Gene #24: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
12Q GAIN MUTATED	11	12	26	23	6	13
12Q GAIN WILD-TYPE	63	34	67	43	25	71

Figure S90. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q gain' versus 'CN_CNMF'

P value = 0.0295 (Fisher's exact test), Q value = 0.095

Table S91. Gene #25: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	169	140	59	40
13Q GAIN MUTATED	29	41	18	12
13Q GAIN WILD-TYPE	140	99	41	28

Figure S91. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

'13q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0242 (Fisher's exact test), Q value = 0.083

Table S92. Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
13Q GAIN MUTATED	20	10	32	18	2	16
13Q GAIN WILD-TYPE	54	36	61	48	29	68

Figure S92. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q gain' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00067

Table S93. Gene #26: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	169	140	59	40
14Q GAIN MUTATED	14	16	14	14
14Q GAIN WILD-TYPE	155	124	45	26

Figure S93. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

'14q gain' versus 'METHLYATION_CNMF'

P value = 0.0457 (Fisher's exact test), Q value = 0.13

Table S94. Gene #26: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	138	116	69	85
14Q GAIN MUTATED	21	20	3	14
14Q GAIN WILD-TYPE	117	96	66	71

Figure S94. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'14q gain' versus 'MRNASEQ_CNMF'

P value = 0.0443 (Fisher's exact test), Q value = 0.13

Table S95. Gene #26: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	116	180	108
14Q GAIN MUTATED	18	17	21
14Q GAIN WILD-TYPE	98	163	87

Figure S95. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0436 (Fisher's exact test), Q value = 0.13

Table S96. Gene #26: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	112	174
14Q GAIN MUTATED	12	11	33
14Q GAIN WILD-TYPE	106	101	141

Figure S96. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'15q gain' versus 'METHLYATION_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.0013

Table S97. Gene #27: '15q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	138	116	69	85
15Q GAIN MUTATED	4	6	14	11
15Q GAIN WILD-TYPE	134	110	55	74

Figure S97. Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'15q gain' versus 'RPPA_CNMF'

P value = 0.00066 (Fisher's exact test), Q value = 0.0052

Table S98. Gene #27: '15q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	114	104
15Q GAIN MUTATED	2	16	11
15Q GAIN WILD-TYPE	120	98	93

Figure S98. Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'15q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0311 (Fisher's exact test), Q value = 0.098

Table S99. Gene #27: '15q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	112	174
15Q GAIN MUTATED	14	13	8
15Q GAIN WILD-TYPE	104	99	166

Figure S99. Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'CN_CNMF'

P value = 0.0491 (Fisher's exact test), Q value = 0.13

Table S100. Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	169	140	59	40
16P GAIN MUTATED	24	36	9	5
16P GAIN WILD-TYPE	145	104	50	35

Figure S100. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

'16q gain' versus 'CN_CNMF'

P value = 0.0368 (Fisher's exact test), Q value = 0.11

Table S101. Gene #29: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	169	140	59	40
16Q GAIN MUTATED	27	40	10	6
16Q GAIN WILD-TYPE	142	100	49	34

Figure S101. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

'17p gain' versus 'CN_CNMF'

P value = 0.00093 (Fisher's exact test), Q value = 0.0071

Table S102. Gene #30: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	169	140	59	40
17P GAIN MUTATED	12	31	11	4
17P GAIN WILD-TYPE	157	109	48	36

Figure S102. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

'17q gain' versus 'CN_CNMF'

P value = 0.00326 (Fisher's exact test), Q value = 0.018

Table S103. Gene #31: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	169	140	59	40
17Q GAIN MUTATED	42	58	17	19
17Q GAIN WILD-TYPE	127	82	42	21

Figure S103. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 0.0307 (Fisher's exact test), Q value = 0.098

Table S104. Gene #31: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	138	116	69	85
17Q GAIN MUTATED	36	50	20	30
17Q GAIN WILD-TYPE	102	66	49	55

Figure S104. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 0.0396 (Fisher's exact test), Q value = 0.12

Table S105. Gene #31: '17q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	116	180	108
17Q GAIN MUTATED	31	72	32
17Q GAIN WILD-TYPE	85	108	76

Figure S105. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00245 (Fisher's exact test), Q value = 0.015

Table S106. Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
17Q GAIN MUTATED	18	21	42	22	4	25
17Q GAIN WILD-TYPE	56	25	51	44	27	59

Figure S106. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S107. Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	169	140	59	40
18P GAIN MUTATED	16	54	31	16
18P GAIN WILD-TYPE	153	86	28	24

Figure S107. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 0.00356 (Fisher's exact test), Q value = 0.02

Table S108. Gene #32: '18p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	138	116	69	85
18P GAIN MUTATED	42	43	9	23
18P GAIN WILD-TYPE	96	73	60	62

Figure S108. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0205 (Fisher's exact test), Q value = 0.074

Table S109. Gene #32: '18p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	112	174
18P GAIN MUTATED	29	25	63
18P GAIN WILD-TYPE	89	87	111

Figure S109. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00056

Table S110. Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
18P GAIN MUTATED	15	10	36	21	0	30
18P GAIN WILD-TYPE	59	36	57	45	31	54

Figure S110. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q gain' versus 'CN_CNMF'

P value = 0.00383 (Fisher's exact test), Q value = 0.021

Table S111. Gene #33: '18q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	169	140	59	40
18Q GAIN MUTATED	14	26	14	9
18Q GAIN WILD-TYPE	155	114	45	31

Figure S111. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #1: 'CN_CNMF'

'18q gain' versus 'MIRSEQ_CNMF'

P value = 0.0386 (Fisher's exact test), Q value = 0.11

Table S112. Gene #33: '18q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	96	189
18Q GAIN MUTATED	15	9	38
18Q GAIN WILD-TYPE	105	87	151

Figure S112. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'18q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00689 (Fisher's exact test), Q value = 0.033

Table S113. Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
18Q GAIN MUTATED	7	4	17	16	0	15
18Q GAIN WILD-TYPE	67	42	76	50	31	69

Figure S113. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p gain' versus 'CN_CNMF'

P value = 0.00358 (Fisher's exact test), Q value = 0.02

Table S114. Gene #34: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	169	140	59	40
19P GAIN MUTATED	24	44	11	8
19P GAIN WILD-TYPE	145	96	48	32

Figure S114. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

'19q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S115. Gene #35: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	169	140	59	40
19Q GAIN MUTATED	34	68	15	17
19Q GAIN WILD-TYPE	135	72	44	23

Figure S115. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

'19q gain' versus 'METHLYATION_CNMF'

P value = 0.00393 (Fisher's exact test), Q value = 0.021

Table S116. Gene #35: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	138	116	69	85
19Q GAIN MUTATED	32	52	23	27
19Q GAIN WILD-TYPE	106	64	46	58

Figure S116. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0209 (Fisher's exact test), Q value = 0.075

Table S117. Gene #35: '19q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	89	99	93	70	54
19Q GAIN MUTATED	27	34	20	31	22
19Q GAIN WILD-TYPE	62	65	73	39	32

Figure S117. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00042

Table S118. Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	169	140	59	40
20P GAIN MUTATED	59	79	36	27
20P GAIN WILD-TYPE	110	61	23	13

Figure S118. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0404 (Fisher's exact test), Q value = 0.12

Table S119. Gene #36: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	112	174
20P GAIN MUTATED	69	47	84
20P GAIN WILD-TYPE	49	65	90

Figure S119. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S120. Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	169	140	59	40
20Q GAIN MUTATED	69	92	39	29
20Q GAIN WILD-TYPE	100	48	20	11

Figure S120. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 0.0293 (Fisher's exact test), Q value = 0.095

Table S121. Gene #37: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	138	116	69	85
20Q GAIN MUTATED	71	77	32	49
20Q GAIN WILD-TYPE	67	39	37	36

Figure S121. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0237 (Fisher's exact test), Q value = 0.083

Table S122. 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	74	46	93	66	31	84
20Q GAIN MUTATED	42	28	61	38	9	47
20Q GAIN WILD-TYPE	32	18	32	28	22	37

Figure S122. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S123. Gene #38: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	169	140	59	40
21Q GAIN MUTATED	19	70	15	11
21Q GAIN WILD-TYPE	150	70	44	29

Figure S123. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

'21q gain' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00042

Table S124. Gene #38: '21q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	138	116	69	85
21Q GAIN MUTATED	25	54	16	20
21Q GAIN WILD-TYPE	113	62	53	65

Figure S124. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'21q gain' versus 'MRNASEQ_CNMF'

P value = 0.00275 (Fisher's exact test), Q value = 0.016

Table S125. Gene #38: '21q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	116	180	108
21Q GAIN MUTATED	31	65	19
21Q GAIN WILD-TYPE	85	115	89

Figure S125. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'21q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00149 (Fisher's exact test), Q value = 0.01

Table S126. Gene #38: '21q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	112	174
21Q GAIN MUTATED	48	30	37
21Q GAIN WILD-TYPE	70	82	137

Figure S126. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'21q gain' versus 'MIRSEQ_CNMF'

P value = 0.00805 (Fisher's exact test), Q value = 0.037

Table S127. Gene #38: '21q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	96	189
21Q GAIN MUTATED	28	39	46
21Q GAIN WILD-TYPE	92	57	143

Figure S127. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'21q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00757 (Fisher's exact test), Q value = 0.035

Table S128. Gene #38: '21q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	89	99	93	70	54
21Q GAIN MUTATED	15	34	20	27	17
21Q GAIN WILD-TYPE	74	65	73	43	37

Figure S128. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'22q gain' versus 'MRNASEQ_CNMF'

P value = 0.00964 (Fisher's exact test), Q value = 0.041

Table S129. Gene #39: '22q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	116	180	108
22Q GAIN MUTATED	9	32	8
22Q GAIN WILD-TYPE	107	148	100

Figure S129. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xp gain' versus 'CN_CNMF'

P value = 0.00045 (Fisher's exact test), Q value = 0.0039

Table S130. Gene #40: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	169	140	59	40
XP GAIN MUTATED	16	37	6	7
XP GAIN WILD-TYPE	153	103	53	33

Figure S130. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'

'xp gain' versus 'METHLYATION_CNMF'

P value = 0.00066 (Fisher's exact test), Q value = 0.0052

Table S131. Gene #40: 'xp gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	138	116	69	85
XP GAIN MUTATED	10	29	10	17
XP GAIN WILD-TYPE	128	87	59	68

Figure S131. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xp gain' versus 'RPPA_CNMF'

P value = 0.00095 (Fisher's exact test), Q value = 0.0071

Table S132. Gene #40: 'xp gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	114	104
XP GAIN MUTATED	8	23	23
XP GAIN WILD-TYPE	114	91	81

Figure S132. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'xp gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0084 (Fisher's exact test), Q value = 0.038

Table S133. Gene #40: 'xp gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	121	98	31
XP GAIN MUTATED	7	28	17	2
XP GAIN WILD-TYPE	83	93	81	29

Figure S133. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'xp gain' versus 'MRNASEQ_CNMF'

P value = 0.00769 (Fisher's exact test), Q value = 0.036

Table S134. Gene #40: 'xp gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	116	180	108
XP GAIN MUTATED	12	41	13
XP GAIN WILD-TYPE	104	139	95

Figure S134. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xp gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0215 (Fisher's exact test), Q value = 0.077

Table S135. Gene #40: 'xp gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	43	134	119
XP GAIN MUTATED	12	9	32	13
XP GAIN WILD-TYPE	86	34	102	106

Figure S135. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 0.0475 (Fisher's exact test), Q value = 0.13

Table S136. Gene #42: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	138	116	69	85
1P LOSS MUTATED	8	15	8	3
1P LOSS WILD-TYPE	130	101	61	82

Figure S136. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0283 (Fisher's exact test), Q value = 0.093

Table S137. Gene #44: '2p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	112	174
2P LOSS MUTATED	14	18	11
2P LOSS WILD-TYPE	104	94	163

Figure S137. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'CN_CNMF'

P value = 0.00133 (Fisher's exact test), Q value = 0.0092

Table S138. Gene #45: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	169	140	59	40
2Q LOSS MUTATED	22	40	19	10
2Q LOSS WILD-TYPE	147	100	40	30

Figure S138. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

'2q loss' versus 'METHLYATION_CNMF'

P value = 0.0239 (Fisher's exact test), Q value = 0.083

Table S139. Gene #45: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	138	116	69	85
2Q LOSS MUTATED	22	36	12	21
2Q LOSS WILD-TYPE	116	80	57	64

Figure S139. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0313 (Fisher's exact test), Q value = 0.098

Table S140. Gene #45: '2q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	112	174
2Q LOSS MUTATED	29	32	28
2Q LOSS WILD-TYPE	89	80	146

Figure S140. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0113 (Fisher's exact test), Q value = 0.047

Table S141. Gene #45: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	43	134	119
2Q LOSS MUTATED	12	13	38	23
2Q LOSS WILD-TYPE	86	30	96	96

Figure S141. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'2q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00535 (Fisher's exact test), Q value = 0.027

Table S142. Gene #45: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
2Q LOSS MUTATED	14	15	30	13	2	12
2Q LOSS WILD-TYPE	60	31	63	53	29	72

Figure S142. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3p loss' versus 'METHLYATION_CNMF'

P value = 0.0322 (Fisher's exact test), Q value = 0.1

Table S143. Gene #46: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	138	116	69	85
3P LOSS MUTATED	27	10	5	11
3P LOSS WILD-TYPE	111	106	64	74

Figure S143. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p loss' versus 'RPPA_CNMF'

P value = 0.02 (Fisher's exact test), Q value = 0.074

Table S144. Gene #46: '3p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	114	104
3P LOSS MUTATED	17	9	22
3P LOSS WILD-TYPE	105	105	82

Figure S144. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'3p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.013 (Fisher's exact test), Q value = 0.053

Table S145. Gene #46: '3p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	121	98	31
3P LOSS MUTATED	14	8	20	6
3P LOSS WILD-TYPE	76	113	78	25

Figure S145. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S146. Gene #46: '3p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	116	180	108
3P LOSS MUTATED	5	13	34
3P LOSS WILD-TYPE	111	167	74

Figure S146. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00042

Table S147. Gene #46: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	112	174
3P LOSS MUTATED	5	8	39
3P LOSS WILD-TYPE	113	104	135

Figure S147. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00464 (Fisher's exact test), Q value = 0.024

Table S148. Gene #46: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	89	99	93	70	54
3P LOSS MUTATED	22	9	7	11	4
3P LOSS WILD-TYPE	67	90	86	59	50

Figure S148. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00062 (Fisher's exact test), Q value = 0.0051

Table S149. Gene #46: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	43	134	119
3P LOSS MUTATED	25	3	15	8
3P LOSS WILD-TYPE	73	40	119	111

Figure S149. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'3p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0015 (Fisher's exact test), Q value = 0.01

Table S150. Gene #46: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
3P LOSS MUTATED	2	4	15	10	1	19
3P LOSS WILD-TYPE	72	42	78	56	30	65

Figure S150. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00112 (Fisher's exact test), Q value = 0.0081

Table S151. Gene #47: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	43	134	119
3Q LOSS MUTATED	13	3	7	1
3Q LOSS WILD-TYPE	85	40	127	118

Figure S151. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S152. Gene #48: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	169	140	59	40
4P LOSS MUTATED	28	60	33	22
4P LOSS WILD-TYPE	141	80	26	18

Figure S152. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

'4p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0053 (Fisher's exact test), Q value = 0.026

Table S153. Gene #48: '4p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	121	98	31
4P LOSS MUTATED	41	32	39	6
4P LOSS WILD-TYPE	49	89	59	25

Figure S153. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 0.00621 (Fisher's exact test), Q value = 0.03

Table S154. Gene #48: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	116	180	108
4P LOSS MUTATED	46	48	47
4P LOSS WILD-TYPE	70	132	61

Figure S154. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00092

Table S155. Gene #48: '4p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	112	174
4P LOSS MUTATED	49	21	71
4P LOSS WILD-TYPE	69	91	103

Figure S155. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_CNMF'

P value = 0.0349 (Fisher's exact test), Q value = 0.11

Table S156. Gene #48: '4p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	96	189
4P LOSS MUTATED	48	40	54
4P LOSS WILD-TYPE	72	56	135

Figure S156. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'4p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00966 (Fisher's exact test), Q value = 0.041

Table S157. Gene #48: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	89	99	93	70	54
4P LOSS MUTATED	37	42	19	25	19
4P LOSS WILD-TYPE	52	57	74	45	35

Figure S157. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0139 (Fisher's exact test), Q value = 0.057

Table S158. Gene #48: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	43	134	119
4P LOSS MUTATED	42	18	33	45
4P LOSS WILD-TYPE	56	25	101	74

Figure S158. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'4q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S159. Gene #49: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	169	140	59	40
4Q LOSS MUTATED	25	57	35	19
4Q LOSS WILD-TYPE	144	83	24	21

Figure S159. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

'4q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0275 (Fisher's exact test), Q value = 0.092

Table S160. Gene #49: '4q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	121	98	31
4Q LOSS MUTATED	39	32	33	6
4Q LOSS WILD-TYPE	51	89	65	25

Figure S160. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 0.0381 (Fisher's exact test), Q value = 0.11

Table S161. Gene #49: '4q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	116	180	108
4Q LOSS MUTATED	40	49	45
4Q LOSS WILD-TYPE	76	131	63

Figure S161. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00114 (Fisher's exact test), Q value = 0.0082

Table S162. Gene #49: '4q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	112	174
4Q LOSS MUTATED	46	22	66
4Q LOSS WILD-TYPE	72	90	108

Figure S162. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0408 (Fisher's exact test), Q value = 0.12

Table S163. Gene #49: '4q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	89	99	93	70	54
4Q LOSS MUTATED	37	35	20	27	17
4Q LOSS WILD-TYPE	52	64	73	43	37

Figure S163. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00208 (Fisher's exact test), Q value = 0.013

Table S164. Gene #49: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	43	134	119
4Q LOSS MUTATED	43	13	29	45
4Q LOSS WILD-TYPE	55	30	105	74

Figure S164. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'4q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00311 (Fisher's exact test), Q value = 0.018

Table S165. Gene #49: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
4Q LOSS MUTATED	22	15	28	28	2	35
4Q LOSS WILD-TYPE	52	31	65	38	29	49

Figure S165. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p loss' versus 'METHLYATION_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.0013

Table S166. Gene #50: '5p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	138	116	69	85
5P LOSS MUTATED	15	29	9	3
5P LOSS WILD-TYPE	123	87	60	82

Figure S166. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00119 (Fisher's exact test), Q value = 0.0085

Table S167. Gene #50: '5p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	121	98	31
5P LOSS MUTATED	24	17	6	4
5P LOSS WILD-TYPE	66	104	92	27

Figure S167. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.0024

Table S168. Gene #50: '5p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	112	174
5P LOSS MUTATED	29	14	13
5P LOSS WILD-TYPE	89	98	161

Figure S168. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0177 (Fisher's exact test), Q value = 0.069

Table S169. Gene #50: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	43	134	119
5P LOSS MUTATED	8	11	14	21
5P LOSS WILD-TYPE	90	32	120	98

Figure S169. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'5p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00993 (Fisher's exact test), Q value = 0.042

Table S170. Gene #50: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
5P LOSS MUTATED	15	11	13	8	0	7
5P LOSS WILD-TYPE	59	35	80	58	31	77

Figure S170. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S171. Gene #51: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	169	140	59	40
5Q LOSS MUTATED	37	77	26	19
5Q LOSS WILD-TYPE	132	63	33	21

Figure S171. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 0.00133 (Fisher's exact test), Q value = 0.0092

Table S172. Gene #51: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	138	116	69	85
5Q LOSS MUTATED	52	61	17	29
5Q LOSS WILD-TYPE	86	55	52	56

Figure S172. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0178 (Fisher's exact test), Q value = 0.069

Table S173. Gene #51: '5q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	112	174
5Q LOSS MUTATED	59	39	60
5Q LOSS WILD-TYPE	59	73	114

Figure S173. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0192 (Fisher's exact test), Q value = 0.072

Table S174. Gene #51: '5q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	89	99	93	70	54
5Q LOSS MUTATED	33	44	24	34	24
5Q LOSS WILD-TYPE	56	55	69	36	30

Figure S174. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00779 (Fisher's exact test), Q value = 0.036

Table S175. Gene #51: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
5Q LOSS MUTATED	27	24	42	31	5	27
5Q LOSS WILD-TYPE	47	22	51	35	26	57

Figure S175. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p loss' versus 'CN_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.0011

Table S176. Gene #52: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	169	140	59	40
6P LOSS MUTATED	24	51	12	13
6P LOSS WILD-TYPE	145	89	47	27

Figure S176. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

'6p loss' versus 'METHLYATION_CNMF'

P value = 0.0187 (Fisher's exact test), Q value = 0.071

Table S177. Gene #52: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	138	116	69	85
6P LOSS MUTATED	23	39	18	20
6P LOSS WILD-TYPE	115	77	51	65

Figure S177. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0372 (Fisher's exact test), Q value = 0.11

Table S178. Gene #52: '6p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	112	174
6P LOSS MUTATED	36	31	32
6P LOSS WILD-TYPE	82	81	142

Figure S178. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_CNMF'

P value = 0.0476 (Fisher's exact test), Q value = 0.13

Table S179. Gene #52: '6p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	96	189
6P LOSS MUTATED	26	33	41
6P LOSS WILD-TYPE	94	63	148

Figure S179. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'6p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00476 (Fisher's exact test), Q value = 0.024

Table S180. Gene #52: '6p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	89	99	93	70	54
6P LOSS MUTATED	17	32	13	25	13
6P LOSS WILD-TYPE	72	67	80	45	41

Figure S180. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00086

Table S181. Gene #52: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
6P LOSS MUTATED	15	19	32	19	1	12
6P LOSS WILD-TYPE	59	27	61	47	30	72

Figure S181. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S182. Gene #53: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	169	140	59	40
6Q LOSS MUTATED	34	83	20	22
6Q LOSS WILD-TYPE	135	57	39	18

Figure S182. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

'6q loss' versus 'METHLYATION_CNMF'

P value = 0.0142 (Fisher's exact test), Q value = 0.057

Table S183. Gene #53: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	138	116	69	85
6Q LOSS MUTATED	43	59	25	32
6Q LOSS WILD-TYPE	95	57	44	53

Figure S183. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q loss' versus 'RPPA_CNMF'

P value = 0.0177 (Fisher's exact test), Q value = 0.069

Table S184. Gene #53: '6q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	114	104
6Q LOSS MUTATED	40	37	51
6Q LOSS WILD-TYPE	82	77	53

Figure S184. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0458 (Fisher's exact test), Q value = 0.13

Table S185. Gene #53: '6q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	112	174
6Q LOSS MUTATED	57	42	59
6Q LOSS WILD-TYPE	61	70	115

Figure S185. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00306 (Fisher's exact test), Q value = 0.018

Table S186. Gene #53: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	89	99	93	70	54
6Q LOSS MUTATED	30	48	23	34	23
6Q LOSS WILD-TYPE	59	51	70	36	31

Figure S186. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00042

Table S187. Gene #53: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
6Q LOSS MUTATED	26	25	46	31	2	26
6Q LOSS WILD-TYPE	48	21	47	35	29	58

Figure S187. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0458 (Fisher's exact test), Q value = 0.13

Table S188. Gene #54: '7p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	89	99	93	70	54
7P LOSS MUTATED	2	9	4	6	0
7P LOSS WILD-TYPE	87	90	89	64	54

Figure S188. Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0468 (Fisher's exact test), Q value = 0.13

Table S189. Gene #54: '7p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	43	134	119
7P LOSS MUTATED	4	6	8	3
7P LOSS WILD-TYPE	94	37	126	116

Figure S189. Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'7q loss' versus 'CN_CNMF'

P value = 0.0017 (Fisher's exact test), Q value = 0.011

Table S190. Gene #55: '7q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	169	140	59	40
7Q LOSS MUTATED	3	16	6	2
7Q LOSS WILD-TYPE	166	124	53	38

Figure S190. Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #1: 'CN_CNMF'

'8p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S191. Gene #56: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	169	140	59	40
8P LOSS MUTATED	48	94	38	8
8P LOSS WILD-TYPE	121	46	21	32

Figure S191. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 0.00608 (Fisher's exact test), Q value = 0.029

Table S192. Gene #56: '8p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	138	116	69	85
8P LOSS MUTATED	67	66	24	31
8P LOSS WILD-TYPE	71	50	45	54

Figure S192. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8p loss' versus 'RPPA_CNMF'

P value = 0.0159 (Fisher's exact test), Q value = 0.063

Table S193. Gene #56: '8p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	114	104
8P LOSS MUTATED	69	44	45
8P LOSS WILD-TYPE	53	70	59

Figure S193. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'8p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00121 (Fisher's exact test), Q value = 0.0086

Table S194. Gene #56: '8p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	121	98	31
8P LOSS MUTATED	50	39	52	17
8P LOSS WILD-TYPE	40	82	46	14

Figure S194. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0216 (Fisher's exact test), Q value = 0.077

Table S195. Gene #56: '8p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	112	174
8P LOSS MUTATED	62	40	86
8P LOSS WILD-TYPE	56	72	88

Figure S195. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.03 (Fisher's exact test), Q value = 0.096

Table S196. Gene #56: '8p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	89	99	93	70	54
8P LOSS MUTATED	35	57	34	33	27
8P LOSS WILD-TYPE	54	42	59	37	27

Figure S196. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00324 (Fisher's exact test), Q value = 0.018

Table S197. 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	74	46	93	66	31	84
8P LOSS MUTATED	34	27	48	26	5	42
8P LOSS WILD-TYPE	40	19	45	40	26	42

Figure S197. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q loss' versus 'CN_CNMF'

P value = 0.00302 (Fisher's exact test), Q value = 0.017

Table S198. Gene #57: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	169	140	59	40
8Q LOSS MUTATED	10	22	6	0
8Q LOSS WILD-TYPE	159	118	53	40

Figure S198. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

'8q loss' versus 'MRNASEQ_CNMF'

P value = 0.0358 (Fisher's exact test), Q value = 0.11

Table S199. Gene #57: '8q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	116	180	108
8Q LOSS MUTATED	18	13	7
8Q LOSS WILD-TYPE	98	167	101

Figure S199. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S200. Gene #58: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	169	140	59	40
9P LOSS MUTATED	79	73	3	20
9P LOSS WILD-TYPE	90	67	56	20

Figure S200. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00086

Table S201. Gene #58: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	138	116	69	85
9P LOSS MUTATED	37	61	34	43
9P LOSS WILD-TYPE	101	55	35	42

Figure S201. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p loss' versus 'RPPA_CNMF'

P value = 0.00207 (Fisher's exact test), Q value = 0.013

Table S202. Gene #58: '9p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	114	104
9P LOSS MUTATED	40	63	42
9P LOSS WILD-TYPE	82	51	62

Figure S202. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'9p loss' versus 'RPPA_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00092

Table S203. Gene #58: '9p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	121	98	31
9P LOSS MUTATED	37	70	29	9
9P LOSS WILD-TYPE	53	51	69	22

Figure S203. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 0.00101 (Fisher's exact test), Q value = 0.0074

Table S204. Gene #58: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	116	180	108
9P LOSS MUTATED	44	96	35
9P LOSS WILD-TYPE	72	84	73

Figure S204. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00067

Table S205. Gene #58: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	112	174
9P LOSS MUTATED	63	60	52
9P LOSS WILD-TYPE	55	52	122

Figure S205. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_CNMF'

P value = 0.0291 (Fisher's exact test), Q value = 0.095

Table S206. Gene #58: '9p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	96	189
9P LOSS MUTATED	42	51	82
9P LOSS WILD-TYPE	78	45	107

Figure S206. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'9p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00091 (Fisher's exact test), Q value = 0.007

Table S207. Gene #58: '9p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	89	99	93	70	54
9P LOSS MUTATED	26	48	37	43	21
9P LOSS WILD-TYPE	63	51	56	27	33

Figure S207. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00031

Table S208. Gene #58: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	43	134	119
9P LOSS MUTATED	23	25	70	53
9P LOSS WILD-TYPE	75	18	64	66

Figure S208. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'9p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S209. Gene #58: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
9P LOSS MUTATED	24	25	43	39	21	19
9P LOSS WILD-TYPE	50	21	50	27	10	65

Figure S209. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S210. Gene #59: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	169	140	59	40
9Q LOSS MUTATED	79	65	4	22
9Q LOSS WILD-TYPE	90	75	55	18

Figure S210. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S211. Gene #59: '9q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	138	116	69	85
9Q LOSS MUTATED	33	57	37	43
9Q LOSS WILD-TYPE	105	59	32	42

Figure S211. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9q loss' versus 'RPPA_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.0025

Table S212. Gene #59: '9q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	114	104
9Q LOSS MUTATED	42	65	34
9Q LOSS WILD-TYPE	80	49	70

Figure S212. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'9q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S213. Gene #59: '9q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	121	98	31
9Q LOSS MUTATED	40	72	22	7
9Q LOSS WILD-TYPE	50	49	76	24

Figure S213. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00031

Table S214. Gene #59: '9q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	116	180	108
9Q LOSS MUTATED	39	100	31
9Q LOSS WILD-TYPE	77	80	77

Figure S214. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S215. Gene #59: '9q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	112	174
9Q LOSS MUTATED	62	65	43
9Q LOSS WILD-TYPE	56	47	131

Figure S215. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_CNMF'

P value = 0.0194 (Fisher's exact test), Q value = 0.072

Table S216. Gene #59: '9q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	96	189
9Q LOSS MUTATED	39	49	82
9Q LOSS WILD-TYPE	81	47	107

Figure S216. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'9q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00066 (Fisher's exact test), Q value = 0.0052

Table S217. Gene #59: '9q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	89	99	93	70	54
9Q LOSS MUTATED	22	43	40	41	24
9Q LOSS WILD-TYPE	67	56	53	29	30

Figure S217. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S218. Gene #59: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	43	134	119
9Q LOSS MUTATED	17	25	76	49
9Q LOSS WILD-TYPE	81	18	58	70

Figure S218. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'9q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S219. Gene #59: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
9Q LOSS MUTATED	28	24	43	35	25	12
9Q LOSS WILD-TYPE	46	22	50	31	6	72

Figure S219. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 0.0204 (Fisher's exact test), Q value = 0.074

Table S220. Gene #60: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	169	140	59	40
10P LOSS MUTATED	20	34	14	6
10P LOSS WILD-TYPE	149	106	45	34

Figure S220. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 0.00316 (Fisher's exact test), Q value = 0.018

Table S221. Gene #60: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	116	180	108
10P LOSS MUTATED	10	35	27
10P LOSS WILD-TYPE	106	145	81

Figure S221. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S222. Gene #61: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	169	140	59	40
10Q LOSS MUTATED	23	68	24	13
10Q LOSS WILD-TYPE	146	72	35	27

Figure S222. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.0034

Table S223. Gene #61: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	138	116	69	85
10Q LOSS MUTATED	30	52	16	30
10Q LOSS WILD-TYPE	108	64	53	55

Figure S223. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 0.0121 (Fisher's exact test), Q value = 0.05

Table S224. Gene #61: '10q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	116	180	108
10Q LOSS MUTATED	24	66	35
10Q LOSS WILD-TYPE	92	114	73

Figure S224. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'11p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S225. Gene #62: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	169	140	59	40
11P LOSS MUTATED	58	90	11	22
11P LOSS WILD-TYPE	111	50	48	18

Figure S225. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S226. Gene #62: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	138	116	69	85
11P LOSS MUTATED	33	67	39	42
11P LOSS WILD-TYPE	105	49	30	43

Figure S226. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11p loss' versus 'RPPA_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00092

Table S227. Gene #62: '11p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	121	98	31
11P LOSS MUTATED	46	68	29	8
11P LOSS WILD-TYPE	44	53	69	23

Figure S227. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'11p loss' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00086

Table S228. Gene #62: '11p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	116	180	108
11P LOSS MUTATED	41	101	37
11P LOSS WILD-TYPE	75	79	71

Figure S228. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'11p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S229. Gene #62: '11p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	112	174
11P LOSS MUTATED	64	62	53
11P LOSS WILD-TYPE	54	50	121

Figure S229. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.0014

Table S230. Gene #62: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	43	134	119
11P LOSS MUTATED	25	23	70	57
11P LOSS WILD-TYPE	73	20	64	62

Figure S230. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'11p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00066 (Fisher's exact test), Q value = 0.0052

Table S231. Gene #62: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
11P LOSS MUTATED	29	24	49	37	15	21
11P LOSS WILD-TYPE	45	22	44	29	16	63

Figure S231. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S232. Gene #63: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	169	140	59	40
11Q LOSS MUTATED	36	63	12	20
11Q LOSS WILD-TYPE	133	77	47	20

Figure S232. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

P value = 0.0242 (Fisher's exact test), Q value = 0.083

Table S233. Gene #63: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	138	116	69	85
11Q LOSS MUTATED	32	44	21	34
11Q LOSS WILD-TYPE	106	72	48	51

Figure S233. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0154 (Fisher's exact test), Q value = 0.062

Table S234. Gene #63: '11q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	121	98	31
11Q LOSS MUTATED	37	41	26	4
11Q LOSS WILD-TYPE	53	80	72	27

Figure S234. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'12p loss' versus 'CN_CNMF'

P value = 0.00467 (Fisher's exact test), Q value = 0.024

Table S235. Gene #64: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	169	140	59	40
12P LOSS MUTATED	12	29	9	6
12P LOSS WILD-TYPE	157	111	50	34

Figure S235. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

'12p loss' versus 'METHLYATION_CNMF'

P value = 0.00293 (Fisher's exact test), Q value = 0.017

Table S236. Gene #64: '12p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	138	116	69	85
12P LOSS MUTATED	10	25	13	8
12P LOSS WILD-TYPE	128	91	56	77

Figure S236. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0156 (Fisher's exact test), Q value = 0.062

Table S237. Gene #64: '12p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	112	174
12P LOSS MUTATED	25	14	16
12P LOSS WILD-TYPE	93	98	158

Figure S237. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0292 (Fisher's exact test), Q value = 0.095

Table S238. Gene #64: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	43	134	119
12P LOSS MUTATED	7	11	21	16
12P LOSS WILD-TYPE	91	32	113	103

Figure S238. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'12q loss' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00092

Table S239. Gene #65: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	169	140	59	40
12Q LOSS MUTATED	10	25	16	9
12Q LOSS WILD-TYPE	159	115	43	31

Figure S239. Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'

'13q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S240. Gene #66: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	169	140	59	40
13Q LOSS MUTATED	15	42	17	12
13Q LOSS WILD-TYPE	154	98	42	28

Figure S240. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

'13q loss' versus 'RPPA_CNMF'

P value = 0.00042 (Fisher's exact test), Q value = 0.0037

Table S241. Gene #66: '13q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	114	104
13Q LOSS MUTATED	20	17	37
13Q LOSS WILD-TYPE	102	97	67

Figure S241. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 0.0176 (Fisher's exact test), Q value = 0.069

Table S242. Gene #66: '13q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	116	180	108
13Q LOSS MUTATED	20	31	33
13Q LOSS WILD-TYPE	96	149	75

Figure S242. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'13q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00031

Table S243. Gene #66: '13q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	89	99	93	70	54
13Q LOSS MUTATED	28	29	8	18	3
13Q LOSS WILD-TYPE	61	70	85	52	51

Figure S243. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0106 (Fisher's exact test), Q value = 0.044

Table S244. Gene #66: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	43	134	119
13Q LOSS MUTATED	32	11	24	18
13Q LOSS WILD-TYPE	66	32	110	101

Figure S244. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'13q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.001 (Fisher's exact test), Q value = 0.0074

Table S245. Gene #66: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
13Q LOSS MUTATED	6	14	21	13	3	28
13Q LOSS WILD-TYPE	68	32	72	53	28	56

Figure S245. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S246. Gene #67: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	169	140	59	40
14Q LOSS MUTATED	29	75	11	7
14Q LOSS WILD-TYPE	140	65	48	33

Figure S246. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S247. Gene #67: '14q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	138	116	69	85
14Q LOSS MUTATED	34	53	24	11
14Q LOSS WILD-TYPE	104	63	45	74

Figure S247. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.0011

Table S248. Gene #67: '14q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	112	174
14Q LOSS MUTATED	53	31	37
14Q LOSS WILD-TYPE	65	81	137

Figure S248. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_CNMF'

P value = 0.00056 (Fisher's exact test), Q value = 0.0047

Table S249. Gene #67: '14q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	96	189
14Q LOSS MUTATED	32	44	45
14Q LOSS WILD-TYPE	88	52	144

Figure S249. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'14q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0249 (Fisher's exact test), Q value = 0.085

Table S250. Gene #67: '14q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	89	99	93	70	54
14Q LOSS MUTATED	21	39	19	25	17
14Q LOSS WILD-TYPE	68	60	74	45	37

Figure S250. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00231 (Fisher's exact test), Q value = 0.014

Table S251. Gene #67: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	43	134	119
14Q LOSS MUTATED	23	22	32	42
14Q LOSS WILD-TYPE	75	21	102	77

Figure S251. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'14q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S252. Gene #67: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
14Q LOSS MUTATED	19	22	33	28	1	16
14Q LOSS WILD-TYPE	55	24	60	38	30	68

Figure S252. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S253. Gene #68: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	169	140	59	40
15Q LOSS MUTATED	23	76	32	14
15Q LOSS WILD-TYPE	146	64	27	26

Figure S253. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S254. Gene #68: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	138	116	69	85
15Q LOSS MUTATED	59	57	9	20
15Q LOSS WILD-TYPE	79	59	60	65

Figure S254. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'15q loss' versus 'MIRSEQ_CNMF'

P value = 0.00893 (Fisher's exact test), Q value = 0.039

Table S255. Gene #68: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	96	189
15Q LOSS MUTATED	40	47	58
15Q LOSS WILD-TYPE	80	49	131

Figure S255. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S256. Gene #68: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	89	99	93	70	54
15Q LOSS MUTATED	29	50	17	34	15
15Q LOSS WILD-TYPE	60	49	76	36	39

Figure S256. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00584 (Fisher's exact test), Q value = 0.028

Table S257. Gene #68: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	43	134	119
15Q LOSS MUTATED	41	24	40	36
15Q LOSS WILD-TYPE	57	19	94	83

Figure S257. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.0015

Table S258. 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	74	46	93	66	31	84
15Q LOSS MUTATED	23	24	37	21	1	35
15Q LOSS WILD-TYPE	51	22	56	45	30	49

Figure S258. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S259. Gene #69: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	169	140	59	40
16P LOSS MUTATED	16	41	36	14
16P LOSS WILD-TYPE	153	99	23	26

Figure S259. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

'16p loss' versus 'RPPA_CNMF'

P value = 0.00214 (Fisher's exact test), Q value = 0.013

Table S260. Gene #69: '16p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	114	104
16P LOSS MUTATED	34	18	38
16P LOSS WILD-TYPE	88	96	66

Figure S260. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'16p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0199 (Fisher's exact test), Q value = 0.074

Table S261. Gene #69: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
16P LOSS MUTATED	16	11	25	14	3	33
16P LOSS WILD-TYPE	58	35	68	52	28	51

Figure S261. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S262. Gene #70: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	169	140	59	40
16Q LOSS MUTATED	9	44	32	18
16Q LOSS WILD-TYPE	160	96	27	22

Figure S262. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 0.0204 (Fisher's exact test), Q value = 0.074

Table S263. Gene #70: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	138	116	69	85
16Q LOSS MUTATED	31	41	11	20
16Q LOSS WILD-TYPE	107	75	58	65

Figure S263. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q loss' versus 'RPPA_CNMF'

P value = 0.0141 (Fisher's exact test), Q value = 0.057

Table S264. Gene #70: '16q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	114	104
16Q LOSS MUTATED	32	19	35
16Q LOSS WILD-TYPE	90	95	69

Figure S264. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00377 (Fisher's exact test), Q value = 0.02

Table S265. Gene #70: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
16Q LOSS MUTATED	11	14	29	13	2	28
16Q LOSS WILD-TYPE	63	32	64	53	29	56

Figure S265. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.0033

Table S266. Gene #71: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	169	140	59	40
17P LOSS MUTATED	58	72	23	27
17P LOSS WILD-TYPE	111	68	36	13

Figure S266. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0363 (Fisher's exact test), Q value = 0.11

Table S267. Gene #71: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	89	99	93	70	54
17P LOSS MUTATED	44	40	30	38	26
17P LOSS WILD-TYPE	45	59	63	32	28

Figure S267. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00421 (Fisher's exact test), Q value = 0.022

Table S268. 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	74	46	93	66	31	84
17P LOSS MUTATED	28	20	45	40	6	35
17P LOSS WILD-TYPE	46	26	48	26	25	49

Figure S268. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

P value = 0.0424 (Fisher's exact test), Q value = 0.12

Table S269. Gene #72: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	169	140	59	40
17Q LOSS MUTATED	10	22	7	4
17Q LOSS WILD-TYPE	159	118	52	36

Figure S269. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

'18p loss' versus 'CN_CNMF'

P value = 0.0186 (Fisher's exact test), Q value = 0.071

Table S270. Gene #73: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	169	140	59	40
18P LOSS MUTATED	36	46	8	9
18P LOSS WILD-TYPE	133	94	51	31

Figure S270. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

'18p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0269 (Fisher's exact test), Q value = 0.09

Table S271. Gene #73: '18p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	112	174
18P LOSS MUTATED	38	27	32
18P LOSS WILD-TYPE	80	85	142

Figure S271. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'CN_CNMF'

P value = 0.00181 (Fisher's exact test), Q value = 0.012

Table S272. Gene #74: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	169	140	59	40
18Q LOSS MUTATED	44	66	21	15
18Q LOSS WILD-TYPE	125	74	38	25

Figure S272. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0445 (Fisher's exact test), Q value = 0.13

Table S273. Gene #74: '18q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	112	174
18Q LOSS MUTATED	53	37	54
18Q LOSS WILD-TYPE	65	75	120

Figure S273. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.0027

Table S274. Gene #74: '18q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	96	189
18Q LOSS MUTATED	42	51	53
18Q LOSS WILD-TYPE	78	45	136

Figure S274. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'18q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00066 (Fisher's exact test), Q value = 0.0052

Table S275. Gene #74: '18q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	89	99	93	70	54
18Q LOSS MUTATED	24	53	26	27	16
18Q LOSS WILD-TYPE	65	46	67	43	38

Figure S275. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0329 (Fisher's exact test), Q value = 0.1

Table S276. Gene #74: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	43	134	119
18Q LOSS MUTATED	29	23	45	49
18Q LOSS WILD-TYPE	69	20	89	70

Figure S276. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'19p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S277. Gene #75: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	169	140	59	40
19P LOSS MUTATED	22	44	10	18
19P LOSS WILD-TYPE	147	96	49	22

Figure S277. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

P value = 0.0455 (Fisher's exact test), Q value = 0.13

Table S278. Gene #75: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	138	116	69	85
19P LOSS MUTATED	35	33	8	18
19P LOSS WILD-TYPE	103	83	61	67

Figure S278. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00697 (Fisher's exact test), Q value = 0.033

Table S279. Gene #75: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	112	174
19P LOSS MUTATED	32	14	46
19P LOSS WILD-TYPE	86	98	128

Figure S279. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 7e-04 (Fisher's exact test), Q value = 0.0054

Table S280. Gene #76: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	169	140	59	40
19Q LOSS MUTATED	11	25	10	11
19Q LOSS WILD-TYPE	158	115	49	29

Figure S280. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

'19q loss' versus 'RPPA_CNMF'

P value = 0.0462 (Fisher's exact test), Q value = 0.13

Table S281. Gene #76: '19q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	114	104
19Q LOSS MUTATED	20	8	17
19Q LOSS WILD-TYPE	102	106	87

Figure S281. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'19q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0194 (Fisher's exact test), Q value = 0.072

Table S282. 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	74	46	93	66	31	84
19Q LOSS MUTATED	8	6	17	5	0	17
19Q LOSS WILD-TYPE	66	40	76	61	31	67

Figure S282. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q loss' versus 'RPPA_CNMF'

P value = 0.0225 (Fisher's exact test), Q value = 0.08

Table S283. Gene #79: '21q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	114	104
21Q LOSS MUTATED	22	14	28
21Q LOSS WILD-TYPE	100	100	76

Figure S283. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'21q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0257 (Fisher's exact test), Q value = 0.087

Table S284. Gene #79: '21q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	121	98	31
21Q LOSS MUTATED	18	14	27	5
21Q LOSS WILD-TYPE	72	107	71	26

Figure S284. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'21q loss' versus 'MRNASEQ_CNMF'

P value = 0.0018 (Fisher's exact test), Q value = 0.012

Table S285. Gene #79: '21q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	116	180	108
21Q LOSS MUTATED	17	28	34
21Q LOSS WILD-TYPE	99	152	74

Figure S285. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'21q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.01 (Fisher's exact test), Q value = 0.042

Table S286. Gene #79: '21q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	112	174
21Q LOSS MUTATED	14	20	45
21Q LOSS WILD-TYPE	104	92	129

Figure S286. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00827 (Fisher's exact test), Q value = 0.037

Table S287. Gene #79: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	43	134	119
21Q LOSS MUTATED	31	6	21	18
21Q LOSS WILD-TYPE	67	37	113	101

Figure S287. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'21q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0278 (Fisher's exact test), Q value = 0.093

Table S288. Gene #79: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
21Q LOSS MUTATED	12	8	15	12	2	27
21Q LOSS WILD-TYPE	62	38	78	54	29	57

Figure S288. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S289. Gene #80: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	169	140	59	40
22Q LOSS MUTATED	24	73	44	18
22Q LOSS WILD-TYPE	145	67	15	22

Figure S289. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 0.0191 (Fisher's exact test), Q value = 0.072

Table S290. Gene #80: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	138	116	69	85
22Q LOSS MUTATED	62	48	16	33
22Q LOSS WILD-TYPE	76	68	53	52

Figure S290. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00063 (Fisher's exact test), Q value = 0.0052

Table S291. Gene #80: '22q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	121	98	31
22Q LOSS MUTATED	47	32	44	9
22Q LOSS WILD-TYPE	43	89	54	22

Figure S291. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 0.00858 (Fisher's exact test), Q value = 0.038

Table S292. Gene #80: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	116	180	108
22Q LOSS MUTATED	50	55	51
22Q LOSS WILD-TYPE	66	125	57

Figure S292. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00098 (Fisher's exact test), Q value = 0.0073

Table S293. Gene #80: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	112	174
22Q LOSS MUTATED	44	29	83
22Q LOSS WILD-TYPE	74	83	91

Figure S293. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00376 (Fisher's exact test), Q value = 0.02

Table S294. Gene #80: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	89	99	93	70	54
22Q LOSS MUTATED	39	47	21	29	22
22Q LOSS WILD-TYPE	50	52	72	41	32

Figure S294. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S295. Gene #80: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
22Q LOSS MUTATED	23	13	45	30	1	42
22Q LOSS WILD-TYPE	51	33	48	36	30	42

Figure S295. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0447 (Fisher's exact test), Q value = 0.13

Table S296. Gene #81: 'xp loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
XP LOSS MUTATED	8	4	21	16	8	11
XP LOSS WILD-TYPE	66	42	72	50	23	73

Figure S296. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq loss' versus 'METHLYATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.001

Table S297. Gene #82: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	138	116	69	85
XQ LOSS MUTATED	12	32	12	24
XQ LOSS WILD-TYPE	126	84	57	61

Figure S297. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq loss' versus 'MIRSEQ_CNMF'

P value = 0.0357 (Fisher's exact test), Q value = 0.11

Table S298. Gene #82: 'xq loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	96	189
XQ LOSS MUTATED	15	19	46
XQ LOSS WILD-TYPE	105	77	143

Figure S298. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'xq loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00167 (Fisher's exact test), Q value = 0.011

Table S299. Gene #82: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	43	134	119
XQ LOSS MUTATED	10	10	39	18
XQ LOSS WILD-TYPE	88	33	95	101

Figure S299. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xq loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00933 (Fisher's exact test), Q value = 0.04

Table S300. Gene #82: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
XQ LOSS MUTATED	8	9	28	13	9	10
XQ LOSS WILD-TYPE	66	37	65	53	22	74

Figure S300. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_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/BLCA-TP/19780561/transformed.cor.cli.txt
Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/BLCA-TP/20125359/BLCA-TP.transferedmergedcluster.txt
Number of patients = 408
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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