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

Head and Neck Squamous Cell Carcinoma (Primary solid tumor)

28 January 2016 | analyses__2016_01_28

Maintainer Information

Citation Information

Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)

Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1X34WWD

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 522 patients, 341 significant findings detected with P value < 0.05 and Q value < 0.25.

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

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, 341 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
8q gain	318 (61%)	204	1e-05 (8.82e-05)	0.00011 (0.000758)	0.0089 (0.0304)	0.965 (0.977)	0.00031 (0.00183)	2e-05 (0.000164)	0.00668 (0.0239)	0.00418 (0.0161)	0.0377 (0.0956)	0.00588 (0.0218)
16q gain	105 (20%)	417	1e-05 (8.82e-05)	1e-05 (8.82e-05)	0.327 (0.499)	0.891 (0.933)	0.00586 (0.0218)	0.00226 (0.0097)	0.00033 (0.00189)	5e-05 (0.000373)	0.00865 (0.0297)	0.0124 (0.0399)
20q gain	204 (39%)	318	1e-05 (8.82e-05)	1e-05 (8.82e-05)	0.599 (0.732)	0.935 (0.956)	0.0081 (0.0281)	0.00013 (0.000867)	0.0127 (0.0402)	0.00185 (0.00816)	0.0441 (0.109)	0.00033 (0.00189)
4p loss	193 (37%)	329	1e-05 (8.82e-05)	1e-05 (8.82e-05)	0.0404 (0.1)	0.495 (0.648)	0.0182 (0.054)	1e-05 (8.82e-05)	0.0697 (0.156)	0.0103 (0.0341)	0.0328 (0.0861)	0.0231 (0.065)
14q gain	153 (29%)	369	1e-05 (8.82e-05)	1e-05 (8.82e-05)	0.848 (0.908)	0.0974 (0.198)	0.00101 (0.00502)	1e-05 (8.82e-05)	8e-05 (0.000581)	0.00029 (0.00175)	0.094 (0.193)	0.00119 (0.00574)
8p loss	185 (35%)	337	1e-05 (8.82e-05)	1e-05 (8.82e-05)	0.393 (0.558)	0.7 (0.812)	0.00015 (0.000976)	1e-05 (8.82e-05)	0.00065 (0.00342)	0.00109 (0.00538)	0.0689 (0.155)	0.00627 (0.0227)
16q loss	82 (16%)	440	0.00161 (0.00725)	1e-05 (8.82e-05)	0.762 (0.859)	0.131 (0.252)	1e-05 (8.82e-05)	1e-05 (8.82e-05)	1e-05 (8.82e-05)	0.012 (0.0387)	0.335 (0.506)	0.00082 (0.00418)
18q loss	211 (40%)	311	1e-05 (8.82e-05)	1e-05 (8.82e-05)	0.714 (0.823)	0.326 (0.498)	1e-05 (8.82e-05)	1e-05 (8.82e-05)	1e-05 (8.82e-05)	2e-05 (0.000164)	0.676 (0.791)	0.0107 (0.0351)
1q gain	124 (24%)	398	1e-05 (8.82e-05)	1e-05 (8.82e-05)	0.25 (0.413)	0.627 (0.754)	0.00139 (0.00651)	0.00247 (0.0104)	0.00147 (0.00681)	0.00057 (0.00304)	0.54 (0.689)	0.38 (0.547)
2p gain	96 (18%)	426	1e-05 (8.82e-05)	1e-05 (8.82e-05)	0.757 (0.856)	0.424 (0.587)	0.00739 (0.026)	3e-05 (0.000241)	0.00129 (0.00611)	0.0309 (0.0827)	0.0808 (0.173)	0.399 (0.564)
3p gain	82 (16%)	440	9e-05 (0.000647)	0.00013 (0.000867)	0.186 (0.327)	0.756 (0.856)	0.00928 (0.0312)	0.0404 (0.1)	0.00764 (0.0267)	0.115 (0.227)	0.0281 (0.0763)	0.173 (0.308)
9p gain	102 (20%)	420	1e-05 (8.82e-05)	1e-05 (8.82e-05)	0.176 (0.312)	0.092 (0.191)	0.00066 (0.00345)	0.00081 (0.00415)	0.00215 (0.00928)	0.00904 (0.0306)	0.148 (0.272)	0.893 (0.934)
18q gain	53 (10%)	469	0.00029 (0.00175)	4e-05 (0.000309)	0.152 (0.278)	0.017 (0.0508)	0.00011 (0.000758)	0.00052 (0.00282)	0.00018 (0.00114)	0.241 (0.401)	1 (1.00)	0.134 (0.255)
20p gain	192 (37%)	330	1e-05 (8.82e-05)	1e-05 (8.82e-05)	0.501 (0.655)	0.814 (0.883)	0.0377 (0.0956)	0.00316 (0.0128)	0.294 (0.461)	0.00913 (0.0308)	0.216 (0.367)	0.024 (0.0672)
3p loss	296 (57%)	226	1e-05 (8.82e-05)	1e-05 (8.82e-05)	0.629 (0.754)	0.678 (0.792)	0.00342 (0.0137)	1e-05 (8.82e-05)	0.00171 (0.00762)	0.0016 (0.00725)	0.267 (0.428)	0.194 (0.337)
9p loss	186 (36%)	336	1e-05 (8.82e-05)	1e-05 (8.82e-05)	0.189 (0.332)	0.116 (0.227)	0.0141 (0.0436)	1e-05 (8.82e-05)	2e-05 (0.000164)	1e-05 (8.82e-05)	0.811 (0.883)	0.713 (0.823)
18p loss	103 (20%)	419	1e-05 (8.82e-05)	2e-05 (0.000164)	0.898 (0.934)	0.519 (0.668)	0.00473 (0.018)	0.00375 (0.0147)	0.0263 (0.0727)	0.00645 (0.0232)	0.488 (0.641)	0.179 (0.317)
20q loss	27 (5%)	495	0.131 (0.252)	0.00405 (0.0157)	0.417 (0.581)	0.585 (0.725)	0.265 (0.428)	0.0156 (0.048)	0.00055 (0.00297)	0.0225 (0.0642)	0.0326 (0.0859)	0.038 (0.0959)
21q loss	185 (35%)	337	1e-05 (8.82e-05)	1e-05 (8.82e-05)	0.798 (0.878)	0.983 (0.991)	0.00706 (0.0252)	4e-05 (0.000309)	0.00183 (0.00811)	0.00022 (0.00137)	0.197 (0.34)	0.103 (0.207)
xq loss	82 (16%)	440	1e-05 (8.82e-05)	0.00027 (0.00166)	0.196 (0.338)	0.0072 (0.0254)	0.293 (0.459)	0.0228 (0.0648)	0.0186 (0.0548)	0.095 (0.194)	0.02 (0.0581)	0.193 (0.337)
2q gain	73 (14%)	449	1e-05 (8.82e-05)	1e-05 (8.82e-05)	0.629 (0.754)	0.764 (0.859)	0.0281 (0.0763)	1e-05 (8.82e-05)	0.0131 (0.041)	0.144 (0.268)	0.052 (0.124)	0.105 (0.211)
7p gain	184 (35%)	338	1e-05 (8.82e-05)	1e-05 (8.82e-05)	0.905 (0.936)	0.453 (0.612)	0.0945 (0.193)	1e-05 (8.82e-05)	0.00063 (0.00333)	1e-05 (8.82e-05)	0.375 (0.544)	0.609 (0.741)
11q gain	71 (14%)	451	0.00015 (0.000976)	0.00022 (0.00137)	0.458 (0.615)	0.503 (0.655)	0.026 (0.0723)	0.0858 (0.181)	5e-05 (0.000373)	0.0212 (0.0611)	0.46 (0.616)	0.146 (0.269)
16p gain	109 (21%)	413	2e-05 (0.000164)	1e-05 (8.82e-05)	0.472 (0.624)	0.178 (0.314)	0.191 (0.335)	0.00233 (0.0099)	0.00754 (0.0264)	0.00011 (0.000758)	0.271 (0.433)	0.348 (0.519)
17p gain	67 (13%)	455	1e-05 (8.82e-05)	3e-05 (0.000241)	0.81 (0.883)	0.904 (0.935)	0.0362 (0.0928)	0.00299 (0.0123)	0.799 (0.878)	0.046 (0.112)	0.234 (0.392)	0.131 (0.252)
17q gain	86 (16%)	436	1e-05 (8.82e-05)	4e-05 (0.000309)	0.874 (0.925)	0.804 (0.88)	0.0453 (0.111)	0.00097 (0.00485)	0.432 (0.595)	0.00191 (0.00833)	0.642 (0.759)	0.257 (0.418)
18p gain	124 (24%)	398	1e-05 (8.82e-05)	1e-05 (8.82e-05)	0.216 (0.367)	0.238 (0.398)	0.0785 (0.17)	0.00011 (0.000758)	0.0318 (0.0848)	0.0157 (0.048)	0.836 (0.899)	0.515 (0.666)
19p gain	56 (11%)	466	0.0195 (0.057)	1e-05 (8.82e-05)	0.644 (0.759)	0.768 (0.859)	0.0263 (0.0728)	0.0277 (0.0757)	0.00309 (0.0127)	0.0515 (0.123)	0.559 (0.707)	0.0609 (0.142)
22q gain	112 (21%)	410	1e-05 (8.82e-05)	1e-05 (8.82e-05)	0.467 (0.621)	0.518 (0.667)	0.155 (0.283)	0.00029 (0.00175)	0.00016 (0.00103)	0.08 (0.172)	0.0333 (0.087)	0.737 (0.837)
4q loss	151 (29%)	371	1e-05 (8.82e-05)	1e-05 (8.82e-05)	0.452 (0.612)	0.283 (0.446)	0.0207 (0.0599)	1e-05 (8.82e-05)	0.0769 (0.168)	0.0303 (0.0812)	0.0732 (0.161)	0.309 (0.478)
5q loss	160 (31%)	362	1e-05 (8.82e-05)	1e-05 (8.82e-05)	0.0163 (0.0496)	0.782 (0.871)	0.348 (0.519)	1e-05 (8.82e-05)	0.132 (0.252)	0.00021 (0.00132)	0.372 (0.541)	0.158 (0.286)
6p loss	67 (13%)	455	0.0106 (0.035)	0.00197 (0.00855)	0.388 (0.553)	0.0814 (0.174)	0.0457 (0.111)	0.0498 (0.12)	0.0162 (0.0495)	0.625 (0.754)	0.14 (0.264)	0.16 (0.289)
7p loss	29 (6%)	493	0.00715 (0.0254)	0.0169 (0.0508)	0.0102 (0.034)	0.421 (0.584)	0.0383 (0.0965)	0.104 (0.208)	0.144 (0.267)	0.761 (0.858)	0.0155 (0.0477)	0.352 (0.523)
9q loss	83 (16%)	439	1e-05 (8.82e-05)	1e-05 (8.82e-05)	0.846 (0.907)	0.853 (0.911)	0.0484 (0.117)	0.0295 (0.0793)	0.218 (0.368)	0.00547 (0.0205)	0.707 (0.819)	0.228 (0.383)
11q loss	172 (33%)	350	1e-05 (8.82e-05)	1e-05 (8.82e-05)	0.901 (0.935)	0.119 (0.232)	0.00087 (0.00438)	0.00269 (0.0113)	0.00044 (0.00247)	0.399 (0.564)	0.441 (0.602)	0.504 (0.656)
14q loss	56 (11%)	466	0.0126 (0.0402)	0.00045 (0.00251)	0.0782 (0.17)	0.528 (0.677)	0.00451 (0.0173)	0.0019 (0.00833)	0.00112 (0.00547)	0.286 (0.449)	0.794 (0.877)	0.61 (0.741)
22q loss	74 (14%)	448	0.00042 (0.00238)	0.0348 (0.0901)	0.372 (0.541)	0.655 (0.769)	0.0402 (0.1)	0.318 (0.488)	0.00039 (0.00222)	0.417 (0.581)	0.332 (0.503)	0.00466 (0.0178)
3q gain	257 (49%)	265	1e-05 (8.82e-05)	1e-05 (8.82e-05)	0.257 (0.418)	0.28 (0.443)	8e-05 (0.000581)	0.0671 (0.153)	0.00843 (0.029)	0.81 (0.883)	0.135 (0.256)	0.592 (0.727)
5p gain	201 (39%)	321	1e-05 (8.82e-05)	0.00419 (0.0161)	0.911 (0.939)	0.834 (0.898)	0.0109 (0.0355)	0.922 (0.948)	0.725 (0.833)	0.032 (0.0849)	0.409 (0.574)	0.368 (0.537)
7q gain	128 (25%)	394	1e-05 (8.82e-05)	1e-05 (8.82e-05)	0.875 (0.925)	0.729 (0.833)	0.433 (0.595)	0.00047 (0.00259)	0.0643 (0.148)	8e-05 (0.000581)	0.368 (0.537)	0.961 (0.975)
10p gain	42 (8%)	480	0.0405 (0.1)	1e-05 (8.82e-05)	0.139 (0.262)	0.0698 (0.156)	0.368 (0.537)	0.00149 (0.00686)	0.319 (0.489)	0.0468 (0.113)	0.91 (0.938)	0.47 (0.623)
11p gain	68 (13%)	454	4e-05 (0.000309)	1e-05 (8.82e-05)	0.84 (0.902)	0.529 (0.677)	0.159 (0.289)	0.209 (0.357)	0.005 (0.0188)	0.34 (0.511)	0.636 (0.758)	0.0192 (0.0563)
12p gain	148 (28%)	374	1e-05 (8.82e-05)	2e-05 (0.000164)	0.172 (0.307)	0.824 (0.892)	0.0141 (0.0436)	0.0001 (0.000713)	0.0721 (0.159)	0.0983 (0.199)	0.958 (0.973)	0.956 (0.972)
15q gain	72 (14%)	450	0.00047 (0.00259)	0.00353 (0.0141)	0.242 (0.402)	0.586 (0.725)	0.352 (0.523)	0.035 (0.0902)	0.0719 (0.159)	0.00624 (0.0227)	0.489 (0.641)	0.167 (0.3)
5p loss	51 (10%)	471	0.00014 (0.000926)	5e-05 (0.000373)	0.0194 (0.0569)	0.385 (0.55)	0.796 (0.877)	0.0129 (0.0406)	0.367 (0.537)	0.256 (0.418)	0.331 (0.503)	0.194 (0.337)
10p loss	156 (30%)	366	1e-05 (8.82e-05)	0.00325 (0.0131)	0.586 (0.725)	0.232 (0.389)	0.0129 (0.0406)	0.0649 (0.149)	0.00389 (0.0152)	0.0925 (0.191)	0.0855 (0.181)	0.598 (0.732)
11p loss	137 (26%)	385	1e-05 (8.82e-05)	0.00057 (0.00304)	0.903 (0.935)	0.415 (0.581)	0.0215 (0.0616)	0.171 (0.307)	0.0184 (0.0544)	0.173 (0.308)	0.602 (0.735)	0.194 (0.337)
13q loss	168 (32%)	354	1e-05 (8.82e-05)	1e-05 (8.82e-05)	0.579 (0.723)	0.826 (0.892)	0.0488 (0.118)	0.00286 (0.0118)	0.2 (0.344)	0.143 (0.266)	0.417 (0.581)	0.0798 (0.172)
19p loss	100 (19%)	422	1e-05 (8.82e-05)	0.00085 (0.0043)	0.63 (0.754)	0.712 (0.823)	0.09 (0.188)	0.0203 (0.0589)	0.637 (0.758)	0.00316 (0.0128)	0.238 (0.398)	0.0858 (0.181)
19q loss	88 (17%)	434	1e-05 (8.82e-05)	0.00017 (0.00109)	0.0684 (0.154)	0.521 (0.67)	0.108 (0.215)	0.00476 (0.018)	0.28 (0.443)	0.023 (0.065)	0.547 (0.696)	0.54 (0.689)
20p loss	46 (9%)	476	0.0127 (0.0402)	0.026 (0.0723)	0.505 (0.656)	0.766 (0.859)	0.0825 (0.176)	0.0989 (0.2)	0.0841 (0.179)	0.0112 (0.0365)	0.00233 (0.0099)	0.468 (0.621)
xp loss	136 (26%)	386	1e-05 (8.82e-05)	1e-05 (8.82e-05)	0.639 (0.758)	0.037 (0.0946)	0.566 (0.711)	0.0346 (0.0897)	0.0544 (0.129)	0.255 (0.417)	0.0714 (0.159)	0.953 (0.971)
1p gain	74 (14%)	448	0.00274 (0.0114)	0.00147 (0.00681)	0.766 (0.859)	0.564 (0.71)	0.284 (0.447)	0.769 (0.86)	0.59 (0.726)	0.00352 (0.0141)	0.577 (0.723)	0.803 (0.88)
6q gain	64 (12%)	458	0.00032 (0.00187)	0.00899 (0.0306)	0.733 (0.834)	0.105 (0.211)	0.058 (0.136)	0.0454 (0.111)	0.116 (0.227)	0.902 (0.935)	0.0656 (0.15)	0.409 (0.574)
9q gain	145 (28%)	377	1e-05 (8.82e-05)	0.00154 (0.00705)	0.27 (0.433)	0.177 (0.313)	0.0696 (0.156)	0.0025 (0.0105)	0.28 (0.443)	0.0633 (0.147)	0.58 (0.723)	0.85 (0.909)
10q gain	34 (7%)	488	0.00076 (0.00392)	0.0781 (0.17)	0.0387 (0.0971)	0.3 (0.467)	0.361 (0.531)	0.142 (0.266)	0.526 (0.674)	0.0378 (0.0956)	0.679 (0.792)	0.5 (0.653)
12q gain	92 (18%)	430	2e-05 (0.000164)	0.00012 (0.000813)	0.145 (0.268)	0.266 (0.428)	0.066 (0.15)	0.00988 (0.0329)	0.203 (0.347)	0.63 (0.754)	0.549 (0.697)	0.643 (0.759)
13q gain	57 (11%)	465	1e-05 (8.82e-05)	0.117 (0.229)	0.972 (0.983)	0.735 (0.836)	0.0356 (0.0914)	0.00611 (0.0225)	0.264 (0.426)	0.244 (0.403)	0.442 (0.603)	0.0634 (0.147)
19q gain	77 (15%)	445	0.136 (0.259)	5e-05 (0.000373)	0.731 (0.834)	0.791 (0.877)	0.027 (0.074)	0.0656 (0.15)	0.00157 (0.00715)	0.0973 (0.198)	0.61 (0.741)	0.314 (0.483)
xq gain	96 (18%)	426	1e-05 (8.82e-05)	1e-05 (8.82e-05)	0.773 (0.862)	0.86 (0.916)	0.15 (0.274)	0.0169 (0.0508)	0.891 (0.933)	0.464 (0.62)	0.435 (0.597)	0.242 (0.402)
1p loss	56 (11%)	466	0.0003 (0.0018)	1e-05 (8.82e-05)	0.0529 (0.126)	0.205 (0.35)	0.163 (0.295)	1e-05 (8.82e-05)	0.358 (0.529)	0.201 (0.345)	0.334 (0.505)	0.339 (0.51)
1q loss	39 (7%)	483	0.00625 (0.0227)	0.138 (0.261)	0.563 (0.71)	0.377 (0.545)	0.361 (0.531)	0.00355 (0.0141)	0.147 (0.271)	0.00113 (0.00548)	0.377 (0.545)	0.299 (0.467)
2p loss	32 (6%)	490	0.033 (0.0865)	0.00841 (0.029)	0.0758 (0.166)	0.0446 (0.11)	0.195 (0.337)	0.0921 (0.191)	0.648 (0.762)	0.824 (0.892)	0.0702 (0.156)	0.869 (0.922)
10q loss	114 (22%)	408	1e-05 (8.82e-05)	0.00033 (0.00189)	0.383 (0.549)	0.302 (0.47)	0.119 (0.232)	0.0932 (0.192)	0.0233 (0.0655)	0.119 (0.232)	0.435 (0.597)	0.889 (0.933)
4p gain	41 (8%)	481	0.0012 (0.00575)	0.00134 (0.00631)	0.143 (0.266)	0.457 (0.615)	0.0887 (0.186)	0.467 (0.621)	0.642 (0.759)	0.594 (0.729)	0.404 (0.57)	0.589 (0.726)
4q gain	37 (7%)	485	0.00607 (0.0224)	0.378 (0.545)	0.832 (0.898)	1 (1.00)	0.0288 (0.0778)	0.479 (0.632)	0.69 (0.804)	1 (1.00)	0.458 (0.615)	0.895 (0.934)
6p gain	85 (16%)	437	0.00012 (0.000813)	0.00031 (0.00183)	0.376 (0.545)	0.746 (0.846)	0.11 (0.217)	0.194 (0.337)	0.663 (0.778)	0.0932 (0.192)	0.139 (0.262)	0.315 (0.483)
21q gain	35 (7%)	487	0.0754 (0.165)	0.0135 (0.0422)	0.0858 (0.181)	0.129 (0.249)	0.0284 (0.0768)	0.0744 (0.164)	0.244 (0.403)	0.251 (0.414)	0.864 (0.919)	0.544 (0.693)
xp gain	51 (10%)	471	0.149 (0.273)	0.0127 (0.0402)	0.416 (0.581)	0.224 (0.379)	0.508 (0.658)	0.577 (0.723)	0.274 (0.436)	0.566 (0.711)	0.353 (0.523)	0.0321 (0.0849)
3q loss	58 (11%)	464	0.00111 (0.00545)	0.791 (0.877)	0.585 (0.725)	0.393 (0.558)	0.382 (0.548)	0.426 (0.588)	0.638 (0.758)	0.00358 (0.0141)	0.312 (0.482)	0.599 (0.732)
8q loss	25 (5%)	497	0.0181 (0.054)	0.0265 (0.0729)	0.795 (0.877)	1 (1.00)	0.897 (0.934)	0.462 (0.619)	0.881 (0.927)	0.367 (0.537)	0.962 (0.975)	0.807 (0.883)
12q loss	31 (6%)	491	0.00049 (0.00268)	0.0116 (0.0376)	0.858 (0.915)	0.116 (0.227)	0.447 (0.607)	0.987 (0.993)	0.878 (0.926)	0.26 (0.423)	0.306 (0.474)	0.898 (0.934)
16p loss	62 (12%)	460	1e-05 (8.82e-05)	0.00633 (0.0229)	0.984 (0.991)	0.0943 (0.193)	0.0677 (0.153)	0.263 (0.425)	0.465 (0.62)	0.557 (0.705)	0.478 (0.631)	0.948 (0.967)
17p loss	107 (20%)	415	1e-05 (8.82e-05)	0.00075 (0.00389)	0.451 (0.611)	0.759 (0.858)	0.626 (0.754)	0.164 (0.295)	0.278 (0.441)	0.108 (0.215)	0.928 (0.953)	0.793 (0.877)
5q gain	75 (14%)	447	0.00171 (0.00762)	0.314 (0.483)	0.589 (0.726)	0.699 (0.812)	0.195 (0.337)	0.554 (0.702)	0.947 (0.967)	0.353 (0.523)	0.346 (0.519)	0.0567 (0.134)
8p gain	158 (30%)	364	0.00935 (0.0313)	0.637 (0.758)	0.512 (0.663)	0.642 (0.759)	0.889 (0.933)	0.714 (0.823)	0.437 (0.599)	0.625 (0.754)	0.447 (0.607)	0.674 (0.789)
2q loss	44 (8%)	478	0.0629 (0.147)	0.253 (0.416)	0.879 (0.926)	0.622 (0.753)	0.934 (0.956)	0.801 (0.879)	0.447 (0.607)	0.814 (0.883)	0.0344 (0.0896)	0.585 (0.725)
6q loss	70 (13%)	452	0.116 (0.227)	0.0166 (0.0502)	0.906 (0.936)	0.264 (0.426)	0.336 (0.507)	0.768 (0.859)	0.254 (0.417)	0.212 (0.36)	0.508 (0.658)	0.488 (0.641)
7q loss	41 (8%)	481	0.0217 (0.062)	0.619 (0.751)	0.306 (0.474)	0.912 (0.939)	0.73 (0.833)	0.454 (0.612)	0.58 (0.723)	0.979 (0.988)	0.876 (0.925)	0.717 (0.824)
15q loss	103 (20%)	419	1e-05 (8.82e-05)	0.0888 (0.186)	0.772 (0.862)	0.348 (0.519)	0.13 (0.251)	0.137 (0.26)	0.423 (0.586)	0.275 (0.438)	0.631 (0.754)	0.418 (0.581)
17q loss	32 (6%)	490	0.00126 (0.00601)	0.0648 (0.149)	0.399 (0.564)	0.694 (0.807)	0.0534 (0.127)	0.0585 (0.137)	0.785 (0.872)	0.869 (0.922)	1 (1.00)	0.729 (0.833)
12p loss	36 (7%)	486	0.0818 (0.175)	0.328 (0.499)	0.729 (0.833)	0.11 (0.217)	0.381 (0.547)	0.0522 (0.125)	0.932 (0.955)	0.813 (0.883)	0.389 (0.554)	0.834 (0.898)

'1p gain' versus 'CN_CNMF'

P value = 0.00274 (Fisher's exact test), Q value = 0.011

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
1P GAIN MUTATED	39	22	10	3
1P GAIN WILD-TYPE	164	106	135	43

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

'1p gain' versus 'METHLYATION_CNMF'

P value = 0.00147 (Fisher's exact test), Q value = 0.0068

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
1P GAIN MUTATED	5	16	8	14	9	20	2
1P GAIN WILD-TYPE	79	71	95	75	69	55	4

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

'1p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00352 (Fisher's exact test), Q value = 0.014

Table S3. Gene #1: '1p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
1P GAIN MUTATED	27	31	16
1P GAIN WILD-TYPE	163	111	170

Figure S3. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'1q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
1Q GAIN MUTATED	55	47	15	7
1Q GAIN WILD-TYPE	148	81	130	39

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

'1q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S5. Gene #2: '1q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
1Q GAIN MUTATED	7	30	10	36	17	21	3
1Q GAIN WILD-TYPE	77	57	93	53	61	54	3

Figure S5. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1q gain' versus 'MRNASEQ_CNMF'

P value = 0.00139 (Fisher's exact test), Q value = 0.0065

Table S6. Gene #2: '1q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
1Q GAIN MUTATED	36	17	55	15
1Q GAIN WILD-TYPE	99	96	116	80

Figure S6. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'1q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00247 (Fisher's exact test), Q value = 0.01

Table S7. Gene #2: '1q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
1Q GAIN MUTATED	31	39	38	15
1Q GAIN WILD-TYPE	145	64	132	50

Figure S7. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_CNMF'

P value = 0.00147 (Fisher's exact test), Q value = 0.0068

Table S8. Gene #2: '1q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
1Q GAIN MUTATED	24	19	41	27	13
1Q GAIN WILD-TYPE	57	120	90	64	63

Figure S8. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'1q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00057 (Fisher's exact test), Q value = 0.003

Table S9. Gene #2: '1q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
1Q GAIN MUTATED	36	51	37
1Q GAIN WILD-TYPE	154	91	149

Figure S9. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S10. Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
2P GAIN MUTATED	45	41	3	7
2P GAIN WILD-TYPE	158	87	142	39

Figure S10. 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 = 8.8e-05

Table S11. Gene #3: '2p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
2P GAIN MUTATED	5	31	7	34	3	15	1
2P GAIN WILD-TYPE	79	56	96	55	75	60	5

Figure S11. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2p gain' versus 'MRNASEQ_CNMF'

P value = 0.00739 (Fisher's exact test), Q value = 0.026

Table S12. Gene #3: '2p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
2P GAIN MUTATED	24	10	40	22
2P GAIN WILD-TYPE	111	103	131	73

Figure S12. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00024

Table S13. Gene #3: '2p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
2P GAIN MUTATED	34	35	24	3
2P GAIN WILD-TYPE	142	68	146	62

Figure S13. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_CNMF'

P value = 0.00129 (Fisher's exact test), Q value = 0.0061

Table S14. Gene #3: '2p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
2P GAIN MUTATED	28	19	16	18	14
2P GAIN WILD-TYPE	53	120	115	73	62

Figure S14. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'2p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0309 (Fisher's exact test), Q value = 0.083

Table S15. Gene #3: '2p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
2P GAIN MUTATED	33	36	26
2P GAIN WILD-TYPE	157	106	160

Figure S15. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S16. Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
2Q GAIN MUTATED	34	32	2	5
2Q GAIN WILD-TYPE	169	96	143	41

Figure S16. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

'2q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
2Q GAIN MUTATED	3	26	5	25	1	12	1
2Q GAIN WILD-TYPE	81	61	98	64	77	63	5

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

'2q gain' versus 'MRNASEQ_CNMF'

P value = 0.0281 (Fisher's exact test), Q value = 0.076

Table S18. Gene #4: '2q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
2Q GAIN MUTATED	17	8	29	19
2Q GAIN WILD-TYPE	118	105	142	76

Figure S18. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S19. Gene #4: '2q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
2Q GAIN MUTATED	30	27	15	1
2Q GAIN WILD-TYPE	146	76	155	64

Figure S19. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_CNMF'

P value = 0.0131 (Fisher's exact test), Q value = 0.041

Table S20. Gene #4: '2q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
2Q GAIN MUTATED	21	15	13	10	13
2Q GAIN WILD-TYPE	60	124	118	81	63

Figure S20. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3p gain' versus 'CN_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00065

Table S21. Gene #5: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
3P GAIN MUTATED	25	34	12	11
3P GAIN WILD-TYPE	178	94	133	35

Figure S21. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'

'3p gain' versus 'METHLYATION_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00087

Table S22. Gene #5: '3p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
3P GAIN MUTATED	11	14	6	16	26	9	0
3P GAIN WILD-TYPE	73	73	97	73	52	66	6

Figure S22. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p gain' versus 'MRNASEQ_CNMF'

P value = 0.00928 (Fisher's exact test), Q value = 0.031

Table S23. Gene #5: '3p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
3P GAIN MUTATED	14	13	40	14
3P GAIN WILD-TYPE	121	100	131	81

Figure S23. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0404 (Fisher's exact test), Q value = 0.1

Table S24. Gene #5: '3p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
3P GAIN MUTATED	20	19	25	17
3P GAIN WILD-TYPE	156	84	145	48

Figure S24. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3p gain' versus 'MIRSEQ_CNMF'

P value = 0.00764 (Fisher's exact test), Q value = 0.027

Table S25. Gene #5: '3p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
3P GAIN MUTATED	14	14	31	17	6
3P GAIN WILD-TYPE	67	125	100	74	70

Figure S25. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0281 (Fisher's exact test), Q value = 0.076

Table S26. Gene #5: '3p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	189	143
3P GAIN MUTATED	18	23	32
3P GAIN WILD-TYPE	123	166	111

Figure S26. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'3q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S27. Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
3Q GAIN MUTATED	114	79	40	24
3Q GAIN WILD-TYPE	89	49	105	22

Figure S27. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

'3q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S28. Gene #6: '3q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
3Q GAIN MUTATED	29	51	26	56	46	44	5
3Q GAIN WILD-TYPE	55	36	77	33	32	31	1

Figure S28. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3q gain' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00058

Table S29. Gene #6: '3q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
3Q GAIN MUTATED	60	40	106	48
3Q GAIN WILD-TYPE	75	73	65	47

Figure S29. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3q gain' versus 'MIRSEQ_CNMF'

P value = 0.00843 (Fisher's exact test), Q value = 0.029

Table S30. Gene #6: '3q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
3Q GAIN MUTATED	45	55	79	42	35
3Q GAIN WILD-TYPE	36	84	52	49	41

Figure S30. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'4p gain' versus 'CN_CNMF'

P value = 0.0012 (Fisher's exact test), Q value = 0.0058

Table S31. Gene #7: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
4P GAIN MUTATED	28	7	5	1
4P GAIN WILD-TYPE	175	121	140	45

Figure S31. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

'4p gain' versus 'METHLYATION_CNMF'

P value = 0.00134 (Fisher's exact test), Q value = 0.0063

Table S32. Gene #7: '4p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
4P GAIN MUTATED	1	9	5	7	4	15	0
4P GAIN WILD-TYPE	83	78	98	82	74	60	6

Figure S32. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4q gain' versus 'CN_CNMF'

P value = 0.00607 (Fisher's exact test), Q value = 0.022

Table S33. Gene #8: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
4Q GAIN MUTATED	23	9	5	0
4Q GAIN WILD-TYPE	180	119	140	46

Figure S33. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

'4q gain' versus 'MRNASEQ_CNMF'

P value = 0.0288 (Fisher's exact test), Q value = 0.078

Table S34. Gene #8: '4q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
4Q GAIN MUTATED	17	5	11	3
4Q GAIN WILD-TYPE	118	108	160	92

Figure S34. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S35. Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
5P GAIN MUTATED	95	67	21	18
5P GAIN WILD-TYPE	108	61	124	28

Figure S35. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'METHLYATION_CNMF'

P value = 0.00419 (Fisher's exact test), Q value = 0.016

Table S36. Gene #9: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
5P GAIN MUTATED	23	40	28	41	29	37	3
5P GAIN WILD-TYPE	61	47	75	48	49	38	3

Figure S36. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p gain' versus 'MRNASEQ_CNMF'

P value = 0.0109 (Fisher's exact test), Q value = 0.035

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
5P GAIN MUTATED	63	30	70	37
5P GAIN WILD-TYPE	72	83	101	58

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

'5p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.032 (Fisher's exact test), Q value = 0.085

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
5P GAIN MUTATED	72	66	60
5P GAIN WILD-TYPE	118	76	126

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

'5q gain' versus 'CN_CNMF'

P value = 0.00171 (Fisher's exact test), Q value = 0.0076

Table S39. Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
5Q GAIN MUTATED	37	22	8	8
5Q GAIN WILD-TYPE	166	106	137	38

Figure S39. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

'6p gain' versus 'CN_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00081

Table S40. Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
6P GAIN MUTATED	46	21	8	10
6P GAIN WILD-TYPE	157	107	137	36

Figure S40. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

'6p gain' versus 'METHLYATION_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.0018

Table S41. Gene #11: '6p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
6P GAIN MUTATED	6	21	12	17	6	22	1
6P GAIN WILD-TYPE	78	66	91	72	72	53	5

Figure S41. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q gain' versus 'CN_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.0019

Table S42. Gene #12: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
6Q GAIN MUTATED	37	13	6	8
6Q GAIN WILD-TYPE	166	115	139	38

Figure S42. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

'6q gain' versus 'METHLYATION_CNMF'

P value = 0.00899 (Fisher's exact test), Q value = 0.031

Table S43. Gene #12: '6q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
6Q GAIN MUTATED	6	14	11	12	3	17	1
6Q GAIN WILD-TYPE	78	73	92	77	75	58	5

Figure S43. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0454 (Fisher's exact test), Q value = 0.11

Table S44. Gene #12: '6q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
6Q GAIN MUTATED	21	13	27	2
6Q GAIN WILD-TYPE	155	90	143	63

Figure S44. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S45. Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
7P GAIN MUTATED	90	55	24	15
7P GAIN WILD-TYPE	113	73	121	31

Figure S45. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S46. Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
7P GAIN MUTATED	22	39	34	48	5	33	3
7P GAIN WILD-TYPE	62	48	69	41	73	42	3

Figure S46. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S47. Gene #13: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
7P GAIN MUTATED	62	46	68	5
7P GAIN WILD-TYPE	114	57	102	60

Figure S47. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_CNMF'

P value = 0.00063 (Fisher's exact test), Q value = 0.0033

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
7P GAIN MUTATED	41	51	31	37	21
7P GAIN WILD-TYPE	40	88	100	54	55

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

'7p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
7P GAIN MUTATED	68	70	43
7P GAIN WILD-TYPE	122	72	143

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

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S50. Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
7Q GAIN MUTATED	58	46	15	9
7Q GAIN WILD-TYPE	145	82	130	37

Figure S50. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S51. Gene #14: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
7Q GAIN MUTATED	9	30	18	43	5	22	1
7Q GAIN WILD-TYPE	75	57	85	46	73	53	5

Figure S51. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00047 (Fisher's exact test), Q value = 0.0026

Table S52. Gene #14: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
7Q GAIN MUTATED	37	37	46	6
7Q GAIN WILD-TYPE	139	66	124	59

Figure S52. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00058

Table S53. Gene #14: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
7Q GAIN MUTATED	44	53	30
7Q GAIN WILD-TYPE	146	89	156

Figure S53. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

P value = 0.00935 (Fisher's exact test), Q value = 0.031

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
8P GAIN MUTATED	58	51	32	17
8P GAIN WILD-TYPE	145	77	113	29

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

'8q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S55. Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
8Q GAIN MUTATED	149	74	64	31
8Q GAIN WILD-TYPE	54	54	81	15

Figure S55. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00076

Table S56. Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
8Q GAIN MUTATED	57	48	61	54	33	60	5
8Q GAIN WILD-TYPE	27	39	42	35	45	15	1

Figure S56. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8q gain' versus 'RPPA_CNMF'

P value = 0.0089 (Fisher's exact test), Q value = 0.03

Table S57. Gene #16: '8q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	29	31	29	67
8Q GAIN MUTATED	27	12	17	20	51
8Q GAIN WILD-TYPE	23	17	14	9	16

Figure S57. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.0018

Table S58. Gene #16: '8q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
8Q GAIN MUTATED	91	69	84	70
8Q GAIN WILD-TYPE	44	44	87	25

Figure S58. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00016

Table S59. Gene #16: '8q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
8Q GAIN MUTATED	121	55	114	24
8Q GAIN WILD-TYPE	55	48	56	41

Figure S59. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_CNMF'

P value = 0.00668 (Fisher's exact test), Q value = 0.024

Table S60. Gene #16: '8q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
8Q GAIN MUTATED	57	88	63	62	46
8Q GAIN WILD-TYPE	24	51	68	29	30

Figure S60. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'8q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00418 (Fisher's exact test), Q value = 0.016

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
8Q GAIN MUTATED	132	86	98
8Q GAIN WILD-TYPE	58	56	88

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

'8q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0377 (Fisher's exact test), Q value = 0.096

Table S62. Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	189	143
8Q GAIN MUTATED	93	121	75
8Q GAIN WILD-TYPE	48	68	68

Figure S62. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'8q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00588 (Fisher's exact test), Q value = 0.022

Table S63. Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	104	198
8Q GAIN MUTATED	118	66	105
8Q GAIN WILD-TYPE	53	38	93

Figure S63. 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 = 8.8e-05

Table S64. Gene #17: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
9P GAIN MUTATED	29	15	26	32
9P GAIN WILD-TYPE	174	113	119	14

Figure S64. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

'9p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S65. Gene #17: '9p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
9P GAIN MUTATED	11	6	41	17	13	12	2
9P GAIN WILD-TYPE	73	81	62	72	65	63	4

Figure S65. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p gain' versus 'MRNASEQ_CNMF'

P value = 0.00066 (Fisher's exact test), Q value = 0.0034

Table S66. Gene #17: '9p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
9P GAIN MUTATED	25	36	20	17
9P GAIN WILD-TYPE	110	77	151	78

Figure S66. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00081 (Fisher's exact test), Q value = 0.0042

Table S67. Gene #17: '9p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
9P GAIN MUTATED	31	16	47	4
9P GAIN WILD-TYPE	145	87	123	61

Figure S67. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9p gain' versus 'MIRSEQ_CNMF'

P value = 0.00215 (Fisher's exact test), Q value = 0.0093

Table S68. Gene #17: '9p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
9P GAIN MUTATED	6	41	24	17	14
9P GAIN WILD-TYPE	75	98	107	74	62

Figure S68. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'9p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00904 (Fisher's exact test), Q value = 0.031

Table S69. Gene #17: '9p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
9P GAIN MUTATED	38	17	47
9P GAIN WILD-TYPE	152	125	139

Figure S69. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'9q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S70. Gene #18: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
9Q GAIN MUTATED	46	37	30	32
9Q GAIN WILD-TYPE	157	91	115	14

Figure S70. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

'9q gain' versus 'METHLYATION_CNMF'

P value = 0.00154 (Fisher's exact test), Q value = 0.0071

Table S71. Gene #18: '9q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
9Q GAIN MUTATED	16	20	46	25	18	17	3
9Q GAIN WILD-TYPE	68	67	57	64	60	58	3

Figure S71. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0025 (Fisher's exact test), Q value = 0.011

Table S72. Gene #18: '9q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
9Q GAIN MUTATED	46	27	61	8
9Q GAIN WILD-TYPE	130	76	109	57

Figure S72. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10p gain' versus 'CN_CNMF'

P value = 0.0405 (Fisher's exact test), Q value = 0.1

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
10P GAIN MUTATED	18	16	5	3
10P GAIN WILD-TYPE	185	112	140	43

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

'10p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
10P GAIN MUTATED	2	20	4	6	5	3	2
10P GAIN WILD-TYPE	82	67	99	83	73	72	4

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

'10p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00149 (Fisher's exact test), Q value = 0.0069

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
10P GAIN MUTATED	10	19	10	3
10P GAIN WILD-TYPE	166	84	160	62

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

'10p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0468 (Fisher's exact test), Q value = 0.11

Table S76. Gene #19: '10p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
10P GAIN MUTATED	10	18	13
10P GAIN WILD-TYPE	180	124	173

Figure S76. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'10q gain' versus 'CN_CNMF'

P value = 0.00076 (Fisher's exact test), Q value = 0.0039

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
10Q GAIN MUTATED	15	12	1	6
10Q GAIN WILD-TYPE	188	116	144	40

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

'10q gain' versus 'RPPA_CNMF'

P value = 0.0387 (Fisher's exact test), Q value = 0.097

Table S78. Gene #20: '10q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	29	31	29	67
10Q GAIN MUTATED	3	4	2	6	2
10Q GAIN WILD-TYPE	47	25	29	23	65

Figure S78. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'10q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0378 (Fisher's exact test), Q value = 0.096

Table S79. Gene #20: '10q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
10Q GAIN MUTATED	14	14	6
10Q GAIN WILD-TYPE	176	128	180

Figure S79. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'11p gain' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00031

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
11P GAIN MUTATED	43	6	12	7
11P GAIN WILD-TYPE	160	122	133	39

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

'11p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S81. Gene #21: '11p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
11P GAIN MUTATED	2	5	17	15	5	23	1
11P GAIN WILD-TYPE	82	82	86	74	73	52	5

Figure S81. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11p gain' versus 'MIRSEQ_CNMF'

P value = 0.005 (Fisher's exact test), Q value = 0.019

Table S82. Gene #21: '11p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
11P GAIN MUTATED	9	31	12	9	5
11P GAIN WILD-TYPE	72	108	119	82	71

Figure S82. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'11p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0192 (Fisher's exact test), Q value = 0.056

Table S83. Gene #21: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	104	198
11P GAIN MUTATED	20	22	19
11P GAIN WILD-TYPE	151	82	179

Figure S83. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q gain' versus 'CN_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.00098

Table S84. Gene #22: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
11Q GAIN MUTATED	45	11	10	5
11Q GAIN WILD-TYPE	158	117	135	41

Figure S84. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

'11q gain' versus 'METHLYATION_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.0014

Table S85. Gene #22: '11q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
11Q GAIN MUTATED	5	13	16	14	2	20	1
11Q GAIN WILD-TYPE	79	74	87	75	76	55	5

Figure S85. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11q gain' versus 'MRNASEQ_CNMF'

P value = 0.026 (Fisher's exact test), Q value = 0.072

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
11Q GAIN MUTATED	25	20	16	8
11Q GAIN WILD-TYPE	110	93	155	87

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

'11q gain' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00037

Table S87. Gene #22: '11q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
11Q GAIN MUTATED	18	29	7	11	4
11Q GAIN WILD-TYPE	63	110	124	80	72

Figure S87. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'11q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0212 (Fisher's exact test), Q value = 0.061

Table S88. Gene #22: '11q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
11Q GAIN MUTATED	29	25	15
11Q GAIN WILD-TYPE	161	117	171

Figure S88. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S89. Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
12P GAIN MUTATED	66	55	10	17
12P GAIN WILD-TYPE	137	73	135	29

Figure S89. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00016

Table S90. Gene #23: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
12P GAIN MUTATED	12	38	13	41	18	25	1
12P GAIN WILD-TYPE	72	49	90	48	60	50	5

Figure S90. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 0.0141 (Fisher's exact test), Q value = 0.044

Table S91. Gene #23: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
12P GAIN MUTATED	38	20	60	29
12P GAIN WILD-TYPE	97	93	111	66

Figure S91. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00071

Table S92. Gene #23: '12p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
12P GAIN MUTATED	50	48	35	14
12P GAIN WILD-TYPE	126	55	135	51

Figure S92. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12q gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00016

Table S93. Gene #24: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
12Q GAIN MUTATED	38	34	8	12
12Q GAIN WILD-TYPE	165	94	137	34

Figure S93. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

'12q gain' versus 'METHLYATION_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00081

Table S94. Gene #24: '12q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
12Q GAIN MUTATED	5	24	8	21	14	19	1
12Q GAIN WILD-TYPE	79	63	95	68	64	56	5

Figure S94. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00988 (Fisher's exact test), Q value = 0.033

Table S95. Gene #24: '12q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
12Q GAIN MUTATED	29	30	22	10
12Q GAIN WILD-TYPE	147	73	148	55

Figure S95. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'13q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S96. Gene #25: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
13Q GAIN MUTATED	42	6	6	3
13Q GAIN WILD-TYPE	161	122	139	43

Figure S96. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

'13q gain' versus 'MRNASEQ_CNMF'

P value = 0.0356 (Fisher's exact test), Q value = 0.091

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
13Q GAIN MUTATED	13	16	11	16
13Q GAIN WILD-TYPE	122	97	160	79

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

'13q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00611 (Fisher's exact test), Q value = 0.022

Table S98. Gene #25: '13q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
13Q GAIN MUTATED	28	12	15	1
13Q GAIN WILD-TYPE	148	91	155	64

Figure S98. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'14q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S99. Gene #26: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
14Q GAIN MUTATED	87	38	12	16
14Q GAIN WILD-TYPE	116	90	133	30

Figure S99. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

'14q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S100. Gene #26: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
14Q GAIN MUTATED	19	31	27	34	4	36	2
14Q GAIN WILD-TYPE	65	56	76	55	74	39	4

Figure S100. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'14q gain' versus 'MRNASEQ_CNMF'

P value = 0.00101 (Fisher's exact test), Q value = 0.005

Table S101. Gene #26: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
14Q GAIN MUTATED	53	28	35	34
14Q GAIN WILD-TYPE	82	85	136	61

Figure S101. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S102. Gene #26: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
14Q GAIN MUTATED	60	37	51	2
14Q GAIN WILD-TYPE	116	66	119	63

Figure S102. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00058

Table S103. Gene #26: '14q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
14Q GAIN MUTATED	31	47	18	32	24
14Q GAIN WILD-TYPE	50	92	113	59	52

Figure S103. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'14q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.0017

Table S104. Gene #26: '14q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
14Q GAIN MUTATED	70	47	35
14Q GAIN WILD-TYPE	120	95	151

Figure S104. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00119 (Fisher's exact test), Q value = 0.0057

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	104	198
14Q GAIN MUTATED	64	37	42
14Q GAIN WILD-TYPE	107	67	156

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

'15q gain' versus 'CN_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.0026

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
15Q GAIN MUTATED	36	25	9	2
15Q GAIN WILD-TYPE	167	103	136	44

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

'15q gain' versus 'METHLYATION_CNMF'

P value = 0.00353 (Fisher's exact test), Q value = 0.014

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
15Q GAIN MUTATED	6	15	16	14	3	18	0
15Q GAIN WILD-TYPE	78	72	87	75	75	57	6

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

'15q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.035 (Fisher's exact test), Q value = 0.09

Table S108. Gene #27: '15q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
15Q GAIN MUTATED	21	19	28	3
15Q GAIN WILD-TYPE	155	84	142	62

Figure S108. Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'15q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00624 (Fisher's exact test), Q value = 0.023

Table S109. Gene #27: '15q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
15Q GAIN MUTATED	23	31	18
15Q GAIN WILD-TYPE	167	111	168

Figure S109. Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16p gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00016

Table S110. Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
16P GAIN MUTATED	59	30	10	10
16P GAIN WILD-TYPE	144	98	135	36

Figure S110. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

'16p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S111. Gene #28: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
16P GAIN MUTATED	12	41	10	18	6	21	1
16P GAIN WILD-TYPE	72	46	93	71	72	54	5

Figure S111. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00233 (Fisher's exact test), Q value = 0.0099

Table S112. Gene #28: '16p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
16P GAIN MUTATED	39	30	35	4
16P GAIN WILD-TYPE	137	73	135	61

Figure S112. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_CNMF'

P value = 0.00754 (Fisher's exact test), Q value = 0.026

Table S113. Gene #28: '16p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
16P GAIN MUTATED	26	32	18	22	10
16P GAIN WILD-TYPE	55	107	113	69	66

Figure S113. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.00076

Table S114. Gene #28: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
16P GAIN MUTATED	42	44	22
16P GAIN WILD-TYPE	148	98	164

Figure S114. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S115. Gene #29: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
16Q GAIN MUTATED	63	25	9	8
16Q GAIN WILD-TYPE	140	103	136	38

Figure S115. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S116. Gene #29: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
16Q GAIN MUTATED	11	34	9	19	6	25	1
16Q GAIN WILD-TYPE	73	53	94	70	72	50	5

Figure S116. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q gain' versus 'MRNASEQ_CNMF'

P value = 0.00586 (Fisher's exact test), Q value = 0.022

Table S117. Gene #29: '16q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
16Q GAIN MUTATED	38	25	21	19
16Q GAIN WILD-TYPE	97	88	150	76

Figure S117. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00226 (Fisher's exact test), Q value = 0.0097

Table S118. Gene #29: '16q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
16Q GAIN MUTATED	43	23	34	3
16Q GAIN WILD-TYPE	133	80	136	62

Figure S118. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.0019

Table S119. Gene #29: '16q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
16Q GAIN MUTATED	25	30	12	25	12
16Q GAIN WILD-TYPE	56	109	119	66	64

Figure S119. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00037

Table S120. Gene #29: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
16Q GAIN MUTATED	47	38	19
16Q GAIN WILD-TYPE	143	104	167

Figure S120. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00865 (Fisher's exact test), Q value = 0.03

Table S121. Gene #29: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	189	143
16Q GAIN MUTATED	42	32	24
16Q GAIN WILD-TYPE	99	157	119

Figure S121. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0124 (Fisher's exact test), Q value = 0.04

Table S122. Gene #29: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	104	198
16Q GAIN MUTATED	48	19	31
16Q GAIN WILD-TYPE	123	85	167

Figure S122. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S123. Gene #30: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
17P GAIN MUTATED	35	23	1	8
17P GAIN WILD-TYPE	168	105	144	38

Figure S123. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

'17p gain' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00024

Table S124. Gene #30: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
17P GAIN MUTATED	6	14	6	26	3	12	0
17P GAIN WILD-TYPE	78	73	97	63	75	63	6

Figure S124. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p gain' versus 'MRNASEQ_CNMF'

P value = 0.0362 (Fisher's exact test), Q value = 0.093

Table S125. Gene #30: '17p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
17P GAIN MUTATED	15	7	28	16
17P GAIN WILD-TYPE	120	106	143	79

Figure S125. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00299 (Fisher's exact test), Q value = 0.012

Table S126. Gene #30: '17p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
17P GAIN MUTATED	25	23	14	4
17P GAIN WILD-TYPE	151	80	156	61

Figure S126. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.046 (Fisher's exact test), Q value = 0.11

Table S127. Gene #30: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
17P GAIN MUTATED	31	19	15
17P GAIN WILD-TYPE	159	123	171

Figure S127. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S128. Gene #31: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
17Q GAIN MUTATED	40	31	5	10
17Q GAIN WILD-TYPE	163	97	140	36

Figure S128. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00031

Table S129. Gene #31: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
17Q GAIN MUTATED	8	22	8	24	6	18	0
17Q GAIN WILD-TYPE	76	65	95	65	72	57	6

Figure S129. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 0.0453 (Fisher's exact test), Q value = 0.11

Table S130. Gene #31: '17q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
17Q GAIN MUTATED	22	11	38	14
17Q GAIN WILD-TYPE	113	102	133	81

Figure S130. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00097 (Fisher's exact test), Q value = 0.0048

Table S131. Gene #31: '17q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
17Q GAIN MUTATED	27	31	20	7
17Q GAIN WILD-TYPE	149	72	150	58

Figure S131. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00191 (Fisher's exact test), Q value = 0.0083

Table S132. Gene #31: '17q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
17Q GAIN MUTATED	33	34	18
17Q GAIN WILD-TYPE	157	108	168

Figure S132. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'18p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S133. Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
18P GAIN MUTATED	57	48	13	6
18P GAIN WILD-TYPE	146	80	132	40

Figure S133. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S134. Gene #32: '18p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
18P GAIN MUTATED	7	39	10	27	18	21	2
18P GAIN WILD-TYPE	77	48	93	62	60	54	4

Figure S134. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.00076

Table S135. Gene #32: '18p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
18P GAIN MUTATED	39	42	27	14
18P GAIN WILD-TYPE	137	61	143	51

Figure S135. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_CNMF'

P value = 0.0318 (Fisher's exact test), Q value = 0.085

Table S136. Gene #32: '18p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
18P GAIN MUTATED	30	30	32	20	12
18P GAIN WILD-TYPE	51	109	99	71	64

Figure S136. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'18p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0157 (Fisher's exact test), Q value = 0.048

Table S137. Gene #32: '18p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
18P GAIN MUTATED	43	46	35
18P GAIN WILD-TYPE	147	96	151

Figure S137. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'18q gain' versus 'CN_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.0017

Table S138. Gene #33: '18q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
18Q GAIN MUTATED	9	25	14	5
18Q GAIN WILD-TYPE	194	103	131	41

Figure S138. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #1: 'CN_CNMF'

'18q gain' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00031

Table S139. Gene #33: '18q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
18Q GAIN MUTATED	1	14	6	11	18	3	0
18Q GAIN WILD-TYPE	83	73	97	78	60	72	6

Figure S139. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.017 (Fisher's exact test), Q value = 0.051

Table S140. Gene #33: '18q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	76	82	48
18Q GAIN MUTATED	6	14	1
18Q GAIN WILD-TYPE	70	68	47

Figure S140. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'18q gain' versus 'MRNASEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00076

Table S141. Gene #33: '18q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
18Q GAIN MUTATED	9	4	33	7
18Q GAIN WILD-TYPE	126	109	138	88

Figure S141. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'18q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00052 (Fisher's exact test), Q value = 0.0028

Table S142. Gene #33: '18q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
18Q GAIN MUTATED	13	17	9	14
18Q GAIN WILD-TYPE	163	86	161	51

Figure S142. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.0011

Table S143. Gene #33: '18q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
18Q GAIN MUTATED	10	4	25	10	4
18Q GAIN WILD-TYPE	71	135	106	81	72

Figure S143. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'19p gain' versus 'CN_CNMF'

P value = 0.0195 (Fisher's exact test), Q value = 0.057

Table S144. Gene #34: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
19P GAIN MUTATED	20	23	9	4
19P GAIN WILD-TYPE	183	105	136	42

Figure S144. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

'19p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S145. Gene #34: '19p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
19P GAIN MUTATED	3	7	3	21	17	4	1
19P GAIN WILD-TYPE	81	80	100	68	61	71	5

Figure S145. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19p gain' versus 'MRNASEQ_CNMF'

P value = 0.0263 (Fisher's exact test), Q value = 0.073

Table S146. Gene #34: '19p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
19P GAIN MUTATED	15	5	26	8
19P GAIN WILD-TYPE	120	108	145	87

Figure S146. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0277 (Fisher's exact test), Q value = 0.076

Table S147. Gene #34: '19p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
19P GAIN MUTATED	12	15	15	12
19P GAIN WILD-TYPE	164	88	155	53

Figure S147. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_CNMF'

P value = 0.00309 (Fisher's exact test), Q value = 0.013

Table S148. Gene #34: '19p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
19P GAIN MUTATED	14	6	22	8	6
19P GAIN WILD-TYPE	67	133	109	83	70

Figure S148. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'19q gain' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00037

Table S149. Gene #35: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
19Q GAIN MUTATED	5	11	7	24	20	9	1
19Q GAIN WILD-TYPE	79	76	96	65	58	66	5

Figure S149. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 0.027 (Fisher's exact test), Q value = 0.074

Table S150. Gene #35: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
19Q GAIN MUTATED	22	8	33	12
19Q GAIN WILD-TYPE	113	105	138	83

Figure S150. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19q gain' versus 'MIRSEQ_CNMF'

P value = 0.00157 (Fisher's exact test), Q value = 0.0072

Table S151. Gene #35: '19q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
19Q GAIN MUTATED	19	9	27	13	9
19Q GAIN WILD-TYPE	62	130	104	78	67

Figure S151. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S152. Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
20P GAIN MUTATED	99	48	29	16
20P GAIN WILD-TYPE	104	80	116	30

Figure S152. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S153. Gene #36: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
20P GAIN MUTATED	25	31	27	41	19	46	3
20P GAIN WILD-TYPE	59	56	76	48	59	29	3

Figure S153. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 0.0377 (Fisher's exact test), Q value = 0.096

Table S154. Gene #36: '20p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
20P GAIN MUTATED	51	38	53	46
20P GAIN WILD-TYPE	84	75	118	49

Figure S154. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00316 (Fisher's exact test), Q value = 0.013

Table S155. Gene #36: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
20P GAIN MUTATED	79	34	62	13
20P GAIN WILD-TYPE	97	69	108	52

Figure S155. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00913 (Fisher's exact test), Q value = 0.031

Table S156. Gene #36: '20p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
20P GAIN MUTATED	84	53	54
20P GAIN WILD-TYPE	106	89	132

Figure S156. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.024 (Fisher's exact test), Q value = 0.067

Table S157. Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	104	198
20P GAIN MUTATED	70	44	58
20P GAIN WILD-TYPE	101	60	140

Figure S157. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S158. Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
20Q GAIN MUTATED	109	50	26	19
20Q GAIN WILD-TYPE	94	78	119	27

Figure S158. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S159. Gene #37: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
20Q GAIN MUTATED	27	41	30	43	15	45	3
20Q GAIN WILD-TYPE	57	46	73	46	63	30	3

Figure S159. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 0.0081 (Fisher's exact test), Q value = 0.028

Table S160. Gene #37: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
20Q GAIN MUTATED	61	36	56	47
20Q GAIN WILD-TYPE	74	77	115	48

Figure S160. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.00087

Table S161. Gene #37: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
20Q GAIN MUTATED	85	39	65	11
20Q GAIN WILD-TYPE	91	64	105	54

Figure S161. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 0.0127 (Fisher's exact test), Q value = 0.04

Table S162. Gene #37: '20q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
20Q GAIN MUTATED	37	63	35	35	32
20Q GAIN WILD-TYPE	44	76	96	56	44

Figure S162. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00185 (Fisher's exact test), Q value = 0.0082

Table S163. Gene #37: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
20Q GAIN MUTATED	91	55	56
20Q GAIN WILD-TYPE	99	87	130

Figure S163. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0441 (Fisher's exact test), Q value = 0.11

Table S164. Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	189	143
20Q GAIN MUTATED	63	77	44
20Q GAIN WILD-TYPE	78	112	99

Figure S164. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00033 (Fisher's exact test), Q value = 0.0019

Table S165. Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	104	198
20Q GAIN MUTATED	79	49	56
20Q GAIN WILD-TYPE	92	55	142

Figure S165. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q gain' versus 'METHLYATION_CNMF'

P value = 0.0135 (Fisher's exact test), Q value = 0.042

Table S166. Gene #38: '21q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
21Q GAIN MUTATED	3	11	2	10	7	2	0
21Q GAIN WILD-TYPE	81	76	101	79	71	73	6

Figure S166. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'21q gain' versus 'MRNASEQ_CNMF'

P value = 0.0284 (Fisher's exact test), Q value = 0.077

Table S167. Gene #38: '21q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
21Q GAIN MUTATED	9	2	18	6
21Q GAIN WILD-TYPE	126	111	153	89

Figure S167. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'22q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S168. Gene #39: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
22Q GAIN MUTATED	52	42	10	8
22Q GAIN WILD-TYPE	151	86	135	38

Figure S168. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

'22q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S169. Gene #39: '22q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
22Q GAIN MUTATED	15	26	4	40	5	20	2
22Q GAIN WILD-TYPE	69	61	99	49	73	55	4

Figure S169. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.0017

Table S170. Gene #39: '22q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
22Q GAIN MUTATED	38	37	30	6
22Q GAIN WILD-TYPE	138	66	140	59

Figure S170. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.001

Table S171. Gene #39: '22q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
22Q GAIN MUTATED	32	17	25	23	15
22Q GAIN WILD-TYPE	49	122	106	68	61

Figure S171. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'22q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0333 (Fisher's exact test), Q value = 0.087

Table S172. Gene #39: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	189	143
22Q GAIN MUTATED	41	34	26
22Q GAIN WILD-TYPE	100	155	117

Figure S172. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xp gain' versus 'METHLYATION_CNMF'

P value = 0.0127 (Fisher's exact test), Q value = 0.04

Table S173. Gene #40: 'xp gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
XP GAIN MUTATED	2	8	6	13	8	13	1
XP GAIN WILD-TYPE	82	79	97	76	70	62	5

Figure S173. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xp gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0321 (Fisher's exact test), Q value = 0.085

Table S174. Gene #40: 'xp gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	104	198
XP GAIN MUTATED	14	17	14
XP GAIN WILD-TYPE	157	87	184

Figure S174. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S175. Gene #41: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
XQ GAIN MUTATED	58	18	11	9
XQ GAIN WILD-TYPE	145	110	134	37

Figure S175. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

'xq gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S176. Gene #41: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
XQ GAIN MUTATED	5	20	13	24	9	25	0
XQ GAIN WILD-TYPE	79	67	90	65	69	50	6

Figure S176. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0169 (Fisher's exact test), Q value = 0.051

Table S177. Gene #41: 'xq gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
XQ GAIN MUTATED	39	23	30	4
XQ GAIN WILD-TYPE	137	80	140	61

Figure S177. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.0018

Table S178. Gene #42: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
1P LOSS MUTATED	24	22	4	6
1P LOSS WILD-TYPE	179	106	141	40

Figure S178. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S179. Gene #42: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
1P LOSS MUTATED	7	7	7	27	2	6	0
1P LOSS WILD-TYPE	77	80	96	62	76	69	6

Figure S179. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S180. Gene #42: '1p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
1P LOSS MUTATED	25	22	6	2
1P LOSS WILD-TYPE	151	81	164	63

Figure S180. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'1q loss' versus 'CN_CNMF'

P value = 0.00625 (Fisher's exact test), Q value = 0.023

Table S181. Gene #43: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
1Q LOSS MUTATED	21	9	3	6
1Q LOSS WILD-TYPE	182	119	142	40

Figure S181. Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

'1q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00355 (Fisher's exact test), Q value = 0.014

Table S182. Gene #43: '1q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
1Q LOSS MUTATED	21	10	6	1
1Q LOSS WILD-TYPE	155	93	164	64

Figure S182. Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'1q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00113 (Fisher's exact test), Q value = 0.0055

Table S183. Gene #43: '1q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
1Q LOSS MUTATED	21	13	4
1Q LOSS WILD-TYPE	169	129	182

Figure S183. Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2p loss' versus 'CN_CNMF'

P value = 0.033 (Fisher's exact test), Q value = 0.087

Table S184. Gene #44: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
2P LOSS MUTATED	19	7	3	3
2P LOSS WILD-TYPE	184	121	142	43

Figure S184. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

'2p loss' versus 'METHLYATION_CNMF'

P value = 0.00841 (Fisher's exact test), Q value = 0.029

Table S185. Gene #44: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
2P LOSS MUTATED	2	2	6	4	5	13	0
2P LOSS WILD-TYPE	82	85	97	85	73	62	6

Figure S185. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2p loss' versus 'RPPA_CHIERARCHICAL'

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

Table S186. Gene #44: '2p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	76	82	48
2P LOSS MUTATED	7	1	4
2P LOSS WILD-TYPE	69	81	44

Figure S186. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0344 (Fisher's exact test), Q value = 0.09

Table S187. Gene #45: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	189	143
2Q LOSS MUTATED	6	18	18
2Q LOSS WILD-TYPE	135	171	125

Figure S187. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'3p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S188. Gene #46: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
3P LOSS MUTATED	164	80	25	27
3P LOSS WILD-TYPE	39	48	120	19

Figure S188. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S189. Gene #46: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
3P LOSS MUTATED	37	64	50	66	15	58	6
3P LOSS WILD-TYPE	47	23	53	23	63	17	0

Figure S189. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 0.00342 (Fisher's exact test), Q value = 0.014

Table S190. Gene #46: '3p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
3P LOSS MUTATED	90	54	87	61
3P LOSS WILD-TYPE	45	59	84	34

Figure S190. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S191. Gene #46: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
3P LOSS MUTATED	115	74	86	17
3P LOSS WILD-TYPE	61	29	84	48

Figure S191. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CNMF'

P value = 0.00171 (Fisher's exact test), Q value = 0.0076

Table S192. Gene #46: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
3P LOSS MUTATED	57	74	59	52	51
3P LOSS WILD-TYPE	24	65	72	39	25

Figure S192. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0016 (Fisher's exact test), Q value = 0.0072

Table S193. Gene #46: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
3P LOSS MUTATED	121	86	86
3P LOSS WILD-TYPE	69	56	100

Figure S193. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

P value = 0.00111 (Fisher's exact test), Q value = 0.0055

Table S194. Gene #47: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
3Q LOSS MUTATED	31	14	5	8
3Q LOSS WILD-TYPE	172	114	140	38

Figure S194. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

'3q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00358 (Fisher's exact test), Q value = 0.014

Table S195. Gene #47: '3q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
3Q LOSS MUTATED	19	26	12
3Q LOSS WILD-TYPE	171	116	174

Figure S195. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S196. Gene #48: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
4P LOSS MUTATED	89	81	6	17
4P LOSS WILD-TYPE	114	47	139	29

Figure S196. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S197. Gene #48: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
4P LOSS MUTATED	18	44	24	61	20	21	5
4P LOSS WILD-TYPE	66	43	79	28	58	54	1

Figure S197. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4p loss' versus 'RPPA_CNMF'

P value = 0.0404 (Fisher's exact test), Q value = 0.1

Table S198. Gene #48: '4p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	29	31	29	67
4P LOSS MUTATED	21	11	20	9	22
4P LOSS WILD-TYPE	29	18	11	20	45

Figure S198. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 0.0182 (Fisher's exact test), Q value = 0.054

Table S199. Gene #48: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
4P LOSS MUTATED	52	29	75	34
4P LOSS WILD-TYPE	83	84	96	61

Figure S199. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S200. Gene #48: '4p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
4P LOSS MUTATED	72	59	41	18
4P LOSS WILD-TYPE	104	44	129	47

Figure S200. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0103 (Fisher's exact test), Q value = 0.034

Table S201. Gene #48: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
4P LOSS MUTATED	71	65	55
4P LOSS WILD-TYPE	119	77	131

Figure S201. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0328 (Fisher's exact test), Q value = 0.086

Table S202. Gene #48: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	189	143
4P LOSS MUTATED	58	55	58
4P LOSS WILD-TYPE	83	134	85

Figure S202. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0231 (Fisher's exact test), Q value = 0.065

Table S203. Gene #48: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	104	198
4P LOSS MUTATED	69	26	76
4P LOSS WILD-TYPE	102	78	122

Figure S203. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S204. Gene #49: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
4Q LOSS MUTATED	64	63	6	18
4Q LOSS WILD-TYPE	139	65	139	28

Figure S204. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S205. Gene #49: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
4Q LOSS MUTATED	14	36	17	46	14	22	2
4Q LOSS WILD-TYPE	70	51	86	43	64	53	4

Figure S205. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 0.0207 (Fisher's exact test), Q value = 0.06

Table S206. Gene #49: '4q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
4Q LOSS MUTATED	37	21	60	30
4Q LOSS WILD-TYPE	98	92	111	65

Figure S206. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S207. Gene #49: '4q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
4Q LOSS MUTATED	58	47	30	13
4Q LOSS WILD-TYPE	118	56	140	52

Figure S207. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0303 (Fisher's exact test), Q value = 0.081

Table S208. Gene #49: '4q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
4Q LOSS MUTATED	59	49	41
4Q LOSS WILD-TYPE	131	93	145

Figure S208. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5p loss' versus 'CN_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00093

Table S209. Gene #50: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
5P LOSS MUTATED	26	17	2	6
5P LOSS WILD-TYPE	177	111	143	40

Figure S209. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'

'5p loss' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00037

Table S210. Gene #50: '5p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
5P LOSS MUTATED	1	15	6	15	2	12	0
5P LOSS WILD-TYPE	83	72	97	74	76	63	6

Figure S210. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p loss' versus 'RPPA_CNMF'

P value = 0.0194 (Fisher's exact test), Q value = 0.057

Table S211. Gene #50: '5p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	29	31	29	67
5P LOSS MUTATED	4	1	9	4	5
5P LOSS WILD-TYPE	46	28	22	25	62

Figure S211. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0129 (Fisher's exact test), Q value = 0.041

Table S212. Gene #50: '5p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
5P LOSS MUTATED	21	17	10	3
5P LOSS WILD-TYPE	155	86	160	62

Figure S212. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S213. Gene #51: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
5Q LOSS MUTATED	80	68	4	8
5Q LOSS WILD-TYPE	123	60	141	38

Figure S213. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S214. Gene #51: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
5Q LOSS MUTATED	14	47	12	43	6	35	3
5Q LOSS WILD-TYPE	70	40	91	46	72	40	3

Figure S214. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q loss' versus 'RPPA_CNMF'

P value = 0.0163 (Fisher's exact test), Q value = 0.05

Table S215. Gene #51: '5q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	29	31	29	67
5Q LOSS MUTATED	15	4	17	8	23
5Q LOSS WILD-TYPE	35	25	14	21	44

Figure S215. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S216. Gene #51: '5q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
5Q LOSS MUTATED	62	58	30	9
5Q LOSS WILD-TYPE	114	45	140	56

Figure S216. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.0013

Table S217. Gene #51: '5q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
5Q LOSS MUTATED	66	55	37
5Q LOSS WILD-TYPE	124	87	149

Figure S217. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6p loss' versus 'CN_CNMF'

P value = 0.0106 (Fisher's exact test), Q value = 0.035

Table S218. Gene #52: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
6P LOSS MUTATED	31	21	8	7
6P LOSS WILD-TYPE	172	107	137	39

Figure S218. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

'6p loss' versus 'METHLYATION_CNMF'

P value = 0.00197 (Fisher's exact test), Q value = 0.0085

Table S219. Gene #52: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
6P LOSS MUTATED	4	10	8	23	11	10	1
6P LOSS WILD-TYPE	80	77	95	66	67	65	5

Figure S219. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p loss' versus 'MRNASEQ_CNMF'

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

Table S220. Gene #52: '6p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
6P LOSS MUTATED	15	7	28	15
6P LOSS WILD-TYPE	120	106	143	80

Figure S220. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0498 (Fisher's exact test), Q value = 0.12

Table S221. Gene #52: '6p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
6P LOSS MUTATED	20	21	15	9
6P LOSS WILD-TYPE	156	82	155	56

Figure S221. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_CNMF'

P value = 0.0162 (Fisher's exact test), Q value = 0.05

Table S222. Gene #52: '6p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
6P LOSS MUTATED	10	12	26	6	13
6P LOSS WILD-TYPE	71	127	105	85	63

Figure S222. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'6q loss' versus 'METHLYATION_CNMF'

P value = 0.0166 (Fisher's exact test), Q value = 0.05

Table S223. Gene #53: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
6Q LOSS MUTATED	3	13	13	18	15	8	0
6Q LOSS WILD-TYPE	81	74	90	71	63	67	6

Figure S223. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p loss' versus 'CN_CNMF'

P value = 0.00715 (Fisher's exact test), Q value = 0.025

Table S224. Gene #54: '7p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
7P LOSS MUTATED	10	13	2	4
7P LOSS WILD-TYPE	193	115	143	42

Figure S224. Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #1: 'CN_CNMF'

'7p loss' versus 'METHLYATION_CNMF'

P value = 0.0169 (Fisher's exact test), Q value = 0.051

Table S225. Gene #54: '7p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
7P LOSS MUTATED	1	7	1	8	8	4	0
7P LOSS WILD-TYPE	83	80	102	81	70	71	6

Figure S225. Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p loss' versus 'RPPA_CNMF'

P value = 0.0102 (Fisher's exact test), Q value = 0.034

Table S226. Gene #54: '7p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	29	31	29	67
7P LOSS MUTATED	0	4	3	2	1
7P LOSS WILD-TYPE	50	25	28	27	66

Figure S226. Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'7p loss' versus 'MRNASEQ_CNMF'

P value = 0.0383 (Fisher's exact test), Q value = 0.096

Table S227. Gene #54: '7p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
7P LOSS MUTATED	6	3	17	3
7P LOSS WILD-TYPE	129	110	154	92

Figure S227. Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0155 (Fisher's exact test), Q value = 0.048

Table S228. Gene #54: '7p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	189	143
7P LOSS MUTATED	2	13	12
7P LOSS WILD-TYPE	139	176	131

Figure S228. Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'7q loss' versus 'CN_CNMF'

P value = 0.0217 (Fisher's exact test), Q value = 0.062

Table S229. Gene #55: '7q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
7Q LOSS MUTATED	15	14	5	7
7Q LOSS WILD-TYPE	188	114	140	39

Figure S229. 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 = 8.8e-05

Table S230. Gene #56: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
8P LOSS MUTATED	109	34	25	17
8P LOSS WILD-TYPE	94	94	120	29

Figure S230. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S231. Gene #56: '8p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
8P LOSS MUTATED	28	31	35	35	10	42	4
8P LOSS WILD-TYPE	56	56	68	54	68	33	2

Figure S231. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.00098

Table S232. Gene #56: '8p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
8P LOSS MUTATED	65	35	42	39
8P LOSS WILD-TYPE	70	78	129	56

Figure S232. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S233. Gene #56: '8p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
8P LOSS MUTATED	73	37	65	6
8P LOSS WILD-TYPE	103	66	105	59

Figure S233. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_CNMF'

P value = 0.00065 (Fisher's exact test), Q value = 0.0034

Table S234. Gene #56: '8p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
8P LOSS MUTATED	34	53	27	41	29
8P LOSS WILD-TYPE	47	86	104	50	47

Figure S234. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'8p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00109 (Fisher's exact test), Q value = 0.0054

Table S235. Gene #56: '8p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
8P LOSS MUTATED	83	53	48
8P LOSS WILD-TYPE	107	89	138

Figure S235. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00627 (Fisher's exact test), Q value = 0.023

Table S236. Gene #56: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	104	198
8P LOSS MUTATED	74	40	55
8P LOSS WILD-TYPE	97	64	143

Figure S236. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q loss' versus 'CN_CNMF'

P value = 0.0181 (Fisher's exact test), Q value = 0.054

Table S237. Gene #57: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
8Q LOSS MUTATED	12	9	1	3
8Q LOSS WILD-TYPE	191	119	144	43

Figure S237. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

'8q loss' versus 'METHLYATION_CNMF'

P value = 0.0265 (Fisher's exact test), Q value = 0.073

Table S238. Gene #57: '8q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
8Q LOSS MUTATED	1	9	7	4	1	2	1
8Q LOSS WILD-TYPE	83	78	96	85	77	73	5

Figure S238. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S239. Gene #58: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
9P LOSS MUTATED	107	63	15	1
9P LOSS WILD-TYPE	96	65	130	45

Figure S239. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S240. Gene #58: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
9P LOSS MUTATED	21	57	19	51	9	27	2
9P LOSS WILD-TYPE	63	30	84	38	69	48	4

Figure S240. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 0.0141 (Fisher's exact test), Q value = 0.044

Table S241. Gene #58: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
9P LOSS MUTATED	60	28	63	33
9P LOSS WILD-TYPE	75	85	108	62

Figure S241. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S242. Gene #58: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
9P LOSS MUTATED	61	57	54	12
9P LOSS WILD-TYPE	115	46	116	53

Figure S242. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00016

Table S243. Gene #58: '9p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
9P LOSS MUTATED	49	45	36	28	26
9P LOSS WILD-TYPE	32	94	95	63	50

Figure S243. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'9p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S244. Gene #58: '9p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
9P LOSS MUTATED	64	72	48
9P LOSS WILD-TYPE	126	70	138

Figure S244. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S245. Gene #59: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
9Q LOSS MUTATED	54	22	6	1
9Q LOSS WILD-TYPE	149	106	139	45

Figure S245. 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 = 8.8e-05

Table S246. Gene #59: '9q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
9Q LOSS MUTATED	6	27	7	25	4	13	1
9Q LOSS WILD-TYPE	78	60	96	64	74	62	5

Figure S246. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 0.0484 (Fisher's exact test), Q value = 0.12

Table S247. Gene #59: '9q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
9Q LOSS MUTATED	30	11	24	17
9Q LOSS WILD-TYPE	105	102	147	78

Figure S247. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0295 (Fisher's exact test), Q value = 0.079

Table S248. Gene #59: '9q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
9Q LOSS MUTATED	31	23	24	4
9Q LOSS WILD-TYPE	145	80	146	61

Figure S248. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00547 (Fisher's exact test), Q value = 0.02

Table S249. Gene #59: '9q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
9Q LOSS MUTATED	32	32	18
9Q LOSS WILD-TYPE	158	110	168

Figure S249. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S250. Gene #60: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
10P LOSS MUTATED	87	38	13	18
10P LOSS WILD-TYPE	116	90	132	28

Figure S250. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 0.00325 (Fisher's exact test), Q value = 0.013

Table S251. Gene #60: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
10P LOSS MUTATED	16	27	32	35	14	31	1
10P LOSS WILD-TYPE	68	60	71	54	64	44	5

Figure S251. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 0.0129 (Fisher's exact test), Q value = 0.041

Table S252. Gene #60: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
10P LOSS MUTATED	53	24	46	31
10P LOSS WILD-TYPE	82	89	125	64

Figure S252. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10p loss' versus 'MIRSEQ_CNMF'

P value = 0.00389 (Fisher's exact test), Q value = 0.015

Table S253. Gene #60: '10p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
10P LOSS MUTATED	35	31	34	35	19
10P LOSS WILD-TYPE	46	108	97	56	57

Figure S253. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'10q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S254. Gene #61: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
10Q LOSS MUTATED	55	39	10	10
10Q LOSS WILD-TYPE	148	89	135	36

Figure S254. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.0019

Table S255. Gene #61: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
10Q LOSS MUTATED	9	23	14	31	13	22	2
10Q LOSS WILD-TYPE	75	64	89	58	65	53	4

Figure S255. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10q loss' versus 'MIRSEQ_CNMF'

P value = 0.0233 (Fisher's exact test), Q value = 0.065

Table S256. Gene #61: '10q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
10Q LOSS MUTATED	25	22	33	21	10
10Q LOSS WILD-TYPE	56	117	98	70	66

Figure S256. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'11p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S257. Gene #62: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
11P LOSS MUTATED	63	60	8	6
11P LOSS WILD-TYPE	140	68	137	40

Figure S257. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 0.00057 (Fisher's exact test), Q value = 0.003

Table S258. Gene #62: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
11P LOSS MUTATED	20	28	13	37	21	17	1
11P LOSS WILD-TYPE	64	59	90	52	57	58	5

Figure S258. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11p loss' versus 'MRNASEQ_CNMF'

P value = 0.0215 (Fisher's exact test), Q value = 0.062

Table S259. Gene #62: '11p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
11P LOSS MUTATED	43	18	50	24
11P LOSS WILD-TYPE	92	95	121	71

Figure S259. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'11p loss' versus 'MIRSEQ_CNMF'

P value = 0.0184 (Fisher's exact test), Q value = 0.054

Table S260. Gene #62: '11p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
11P LOSS MUTATED	29	23	38	25	22
11P LOSS WILD-TYPE	52	116	93	66	54

Figure S260. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'11q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S261. Gene #63: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
11Q LOSS MUTATED	76	58	27	11
11Q LOSS WILD-TYPE	127	70	118	35

Figure S261. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S262. Gene #63: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
11Q LOSS MUTATED	21	27	19	38	44	22	1
11Q LOSS WILD-TYPE	63	60	84	51	34	53	5

Figure S262. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11q loss' versus 'MRNASEQ_CNMF'

P value = 0.00087 (Fisher's exact test), Q value = 0.0044

Table S263. Gene #63: '11q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
11Q LOSS MUTATED	51	22	69	27
11Q LOSS WILD-TYPE	84	91	102	68

Figure S263. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'11q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00269 (Fisher's exact test), Q value = 0.011

Table S264. Gene #63: '11q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
11Q LOSS MUTATED	51	31	52	35
11Q LOSS WILD-TYPE	125	72	118	30

Figure S264. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.0025

Table S265. Gene #63: '11q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
11Q LOSS MUTATED	28	32	61	23	27
11Q LOSS WILD-TYPE	53	107	70	68	49

Figure S265. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'12q loss' versus 'CN_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.0027

Table S266. Gene #65: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
12Q LOSS MUTATED	21	8	1	1
12Q LOSS WILD-TYPE	182	120	144	45

Figure S266. Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'

'12q loss' versus 'METHLYATION_CNMF'

P value = 0.0116 (Fisher's exact test), Q value = 0.038

Table S267. Gene #65: '12q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
12Q LOSS MUTATED	1	4	3	12	4	6	1
12Q LOSS WILD-TYPE	83	83	100	77	74	69	5

Figure S267. Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S268. Gene #66: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
13Q LOSS MUTATED	52	82	18	16
13Q LOSS WILD-TYPE	151	46	127	30

Figure S268. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S269. Gene #66: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
13Q LOSS MUTATED	17	41	15	42	25	27	1
13Q LOSS WILD-TYPE	67	46	88	47	53	48	5

Figure S269. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q loss' versus 'MRNASEQ_CNMF'

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

Table S270. Gene #66: '13q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
13Q LOSS MUTATED	47	26	65	28
13Q LOSS WILD-TYPE	88	87	106	67

Figure S270. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00286 (Fisher's exact test), Q value = 0.012

Table S271. Gene #66: '13q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
13Q LOSS MUTATED	56	48	42	20
13Q LOSS WILD-TYPE	120	55	128	45

Figure S271. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 0.0126 (Fisher's exact test), Q value = 0.04

Table S272. Gene #67: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
14Q LOSS MUTATED	15	24	14	3
14Q LOSS WILD-TYPE	188	104	131	43

Figure S272. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 0.00045 (Fisher's exact test), Q value = 0.0025

Table S273. Gene #67: '14q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
14Q LOSS MUTATED	3	15	6	14	15	3	0
14Q LOSS WILD-TYPE	81	72	97	75	63	72	6

Figure S273. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 0.00451 (Fisher's exact test), Q value = 0.017

Table S274. Gene #67: '14q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
14Q LOSS MUTATED	13	6	30	6
14Q LOSS WILD-TYPE	122	107	141	89

Figure S274. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0019 (Fisher's exact test), Q value = 0.0083

Table S275. Gene #67: '14q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
14Q LOSS MUTATED	15	16	10	14
14Q LOSS WILD-TYPE	161	87	160	51

Figure S275. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_CNMF'

P value = 0.00112 (Fisher's exact test), Q value = 0.0055

Table S276. Gene #67: '14q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
14Q LOSS MUTATED	13	7	24	5	6
14Q LOSS WILD-TYPE	68	132	107	86	70

Figure S276. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'15q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S277. Gene #68: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
15Q LOSS MUTATED	57	19	8	19
15Q LOSS WILD-TYPE	146	109	137	27

Figure S277. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'16p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S278. Gene #69: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
16P LOSS MUTATED	27	23	2	10
16P LOSS WILD-TYPE	176	105	143	36

Figure S278. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

'16p loss' versus 'METHLYATION_CNMF'

P value = 0.00633 (Fisher's exact test), Q value = 0.023

Table S279. Gene #69: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
16P LOSS MUTATED	7	6	8	22	11	7	1
16P LOSS WILD-TYPE	77	81	95	67	67	68	5

Figure S279. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q loss' versus 'CN_CNMF'

P value = 0.00161 (Fisher's exact test), Q value = 0.0073

Table S280. Gene #70: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
16Q LOSS MUTATED	22	31	17	12
16Q LOSS WILD-TYPE	181	97	128	34

Figure S280. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S281. Gene #70: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
16Q LOSS MUTATED	5	13	7	25	28	4	0
16Q LOSS WILD-TYPE	79	74	96	64	50	71	6

Figure S281. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S282. Gene #70: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
16Q LOSS MUTATED	13	5	54	10
16Q LOSS WILD-TYPE	122	108	117	85

Figure S282. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S283. Gene #70: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
16Q LOSS MUTATED	18	25	12	27
16Q LOSS WILD-TYPE	158	78	158	38

Figure S283. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S284. Gene #70: '16q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
16Q LOSS MUTATED	10	9	43	9	10
16Q LOSS WILD-TYPE	71	130	88	82	66

Figure S284. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.012 (Fisher's exact test), Q value = 0.039

Table S285. Gene #70: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
16Q LOSS MUTATED	19	23	39
16Q LOSS WILD-TYPE	171	119	147

Figure S285. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00082 (Fisher's exact test), Q value = 0.0042

Table S286. Gene #70: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	104	198
16Q LOSS MUTATED	16	11	45
16Q LOSS WILD-TYPE	155	93	153

Figure S286. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S287. Gene #71: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
17P LOSS MUTATED	51	36	10	10
17P LOSS WILD-TYPE	152	92	135	36

Figure S287. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 0.00075 (Fisher's exact test), Q value = 0.0039

Table S288. Gene #71: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
17P LOSS MUTATED	8	27	12	22	17	18	3
17P LOSS WILD-TYPE	76	60	91	67	61	57	3

Figure S288. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q loss' versus 'CN_CNMF'

P value = 0.00126 (Fisher's exact test), Q value = 0.006

Table S289. Gene #72: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
17Q LOSS MUTATED	16	9	1	6
17Q LOSS WILD-TYPE	187	119	144	40

Figure S289. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

'18p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S290. Gene #73: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
18P LOSS MUTATED	50	21	13	19
18P LOSS WILD-TYPE	153	107	132	27

Figure S290. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00016

Table S291. Gene #73: '18p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
18P LOSS MUTATED	18	15	18	30	2	20	0
18P LOSS WILD-TYPE	66	72	85	59	76	55	6

Figure S291. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18p loss' versus 'MRNASEQ_CNMF'

P value = 0.00473 (Fisher's exact test), Q value = 0.018

Table S292. Gene #73: '18p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
18P LOSS MUTATED	40	16	25	20
18P LOSS WILD-TYPE	95	97	146	75

Figure S292. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'18p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00375 (Fisher's exact test), Q value = 0.015

Table S293. Gene #73: '18p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
18P LOSS MUTATED	37	21	40	3
18P LOSS WILD-TYPE	139	82	130	62

Figure S293. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_CNMF'

P value = 0.0263 (Fisher's exact test), Q value = 0.073

Table S294. Gene #73: '18p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
18P LOSS MUTATED	22	24	15	21	18
18P LOSS WILD-TYPE	59	115	116	70	58

Figure S294. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'18p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00645 (Fisher's exact test), Q value = 0.023

Table S295. Gene #73: '18p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
18P LOSS MUTATED	41	36	23
18P LOSS WILD-TYPE	149	106	163

Figure S295. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'18q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S296. Gene #74: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
18Q LOSS MUTATED	124	45	18	24
18Q LOSS WILD-TYPE	79	83	127	22

Figure S296. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S297. Gene #74: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
18Q LOSS MUTATED	34	44	37	46	2	45	3
18Q LOSS WILD-TYPE	50	43	66	43	76	30	3

Figure S297. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S298. Gene #74: '18q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
18Q LOSS MUTATED	75	42	42	48
18Q LOSS WILD-TYPE	60	71	129	47

Figure S298. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S299. Gene #74: '18q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
18Q LOSS MUTATED	85	47	72	3
18Q LOSS WILD-TYPE	91	56	98	62

Figure S299. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S300. Gene #74: '18q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
18Q LOSS MUTATED	42	64	23	43	37
18Q LOSS WILD-TYPE	39	75	108	48	39

Figure S300. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'18q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00016

Table S301. Gene #74: '18q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
18Q LOSS MUTATED	92	67	50
18Q LOSS WILD-TYPE	98	75	136

Figure S301. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0107 (Fisher's exact test), Q value = 0.035

Table S302. Gene #74: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	104	198
18Q LOSS MUTATED	80	46	64
18Q LOSS WILD-TYPE	91	58	134

Figure S302. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S303. Gene #75: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
19P LOSS MUTATED	59	23	8	10
19P LOSS WILD-TYPE	144	105	137	36

Figure S303. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

P value = 0.00085 (Fisher's exact test), Q value = 0.0043

Table S304. Gene #75: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
19P LOSS MUTATED	9	17	18	21	8	27	0
19P LOSS WILD-TYPE	75	70	85	68	70	48	6

Figure S304. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0203 (Fisher's exact test), Q value = 0.059

Table S305. Gene #75: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
19P LOSS MUTATED	43	21	29	5
19P LOSS WILD-TYPE	133	82	141	60

Figure S305. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00316 (Fisher's exact test), Q value = 0.013

Table S306. Gene #75: '19p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
19P LOSS MUTATED	45	32	21
19P LOSS WILD-TYPE	145	110	165

Figure S306. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S307. Gene #76: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
19Q LOSS MUTATED	48	26	4	10
19Q LOSS WILD-TYPE	155	102	141	36

Figure S307. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.0011

Table S308. Gene #76: '19q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
19Q LOSS MUTATED	7	18	13	23	5	22	0
19Q LOSS WILD-TYPE	77	69	90	66	73	53	6

Figure S308. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00476 (Fisher's exact test), Q value = 0.018

Table S309. Gene #76: '19q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
19Q LOSS MUTATED	36	23	24	3
19Q LOSS WILD-TYPE	140	80	146	62

Figure S309. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.023 (Fisher's exact test), Q value = 0.065

Table S310. Gene #76: '19q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
19Q LOSS MUTATED	38	28	20
19Q LOSS WILD-TYPE	152	114	166

Figure S310. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20p loss' versus 'CN_CNMF'

P value = 0.0127 (Fisher's exact test), Q value = 0.04

Table S311. Gene #77: '20p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
20P LOSS MUTATED	19	19	6	2
20P LOSS WILD-TYPE	184	109	139	44

Figure S311. Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #1: 'CN_CNMF'

'20p loss' versus 'METHLYATION_CNMF'

P value = 0.026 (Fisher's exact test), Q value = 0.072

Table S312. Gene #77: '20p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
20P LOSS MUTATED	3	10	5	16	6	6	0
20P LOSS WILD-TYPE	81	77	98	73	72	69	6

Figure S312. Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0112 (Fisher's exact test), Q value = 0.036

Table S313. Gene #77: '20p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
20P LOSS MUTATED	9	20	16
20P LOSS WILD-TYPE	181	122	170

Figure S313. Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00233 (Fisher's exact test), Q value = 0.0099

Table S314. Gene #77: '20p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	189	143
20P LOSS MUTATED	14	7	20
20P LOSS WILD-TYPE	127	182	123

Figure S314. Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'20q loss' versus 'METHLYATION_CNMF'

P value = 0.00405 (Fisher's exact test), Q value = 0.016

Table S315. Gene #78: '20q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
20Q LOSS MUTATED	0	6	3	10	7	1	0
20Q LOSS WILD-TYPE	84	81	100	79	71	74	6

Figure S315. Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0156 (Fisher's exact test), Q value = 0.048

Table S316. Gene #78: '20q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
20Q LOSS MUTATED	4	9	7	7
20Q LOSS WILD-TYPE	172	94	163	58

Figure S316. Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20q loss' versus 'MIRSEQ_CNMF'

P value = 0.00055 (Fisher's exact test), Q value = 0.003

Table S317. Gene #78: '20q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
20Q LOSS MUTATED	2	2	17	4	2
20Q LOSS WILD-TYPE	79	137	114	87	74

Figure S317. Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'20q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0225 (Fisher's exact test), Q value = 0.064

Table S318. Gene #78: '20q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
20Q LOSS MUTATED	4	12	11
20Q LOSS WILD-TYPE	186	130	175

Figure S318. Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0326 (Fisher's exact test), Q value = 0.086

Table S319. Gene #78: '20q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	189	143
20Q LOSS MUTATED	6	5	13
20Q LOSS WILD-TYPE	135	184	130

Figure S319. Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'20q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.038 (Fisher's exact test), Q value = 0.096

Table S320. Gene #78: '20q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	104	198
20Q LOSS MUTATED	4	4	16
20Q LOSS WILD-TYPE	167	100	182

Figure S320. Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S321. Gene #79: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
21Q LOSS MUTATED	97	53	10	25
21Q LOSS WILD-TYPE	106	75	135	21

Figure S321. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

'21q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S322. Gene #79: '21q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
21Q LOSS MUTATED	22	34	31	44	9	43	2
21Q LOSS WILD-TYPE	62	53	72	45	69	32	4

Figure S322. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'21q loss' versus 'MRNASEQ_CNMF'

P value = 0.00706 (Fisher's exact test), Q value = 0.025

Table S323. Gene #79: '21q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
21Q LOSS MUTATED	62	34	49	38
21Q LOSS WILD-TYPE	73	79	122	57

Figure S323. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'21q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00031

Table S324. Gene #79: '21q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
21Q LOSS MUTATED	80	41	53	9
21Q LOSS WILD-TYPE	96	62	117	56

Figure S324. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_CNMF'

P value = 0.00183 (Fisher's exact test), Q value = 0.0081

Table S325. Gene #79: '21q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
21Q LOSS MUTATED	39	53	31	28	33
21Q LOSS WILD-TYPE	42	86	100	63	43

Figure S325. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'21q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.0014

Table S326. Gene #79: '21q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	142	186
21Q LOSS MUTATED	79	60	45
21Q LOSS WILD-TYPE	111	82	141

Figure S326. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 0.00042 (Fisher's exact test), Q value = 0.0024

Table S327. Gene #80: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
22Q LOSS MUTATED	39	16	8	11
22Q LOSS WILD-TYPE	164	112	137	35

Figure S327. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 0.0348 (Fisher's exact test), Q value = 0.09

Table S328. Gene #80: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
22Q LOSS MUTATED	6	12	16	10	10	20	0
22Q LOSS WILD-TYPE	78	75	87	79	68	55	6

Figure S328. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 0.0402 (Fisher's exact test), Q value = 0.1

Table S329. Gene #80: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	171	95
22Q LOSS MUTATED	25	21	16	10
22Q LOSS WILD-TYPE	110	92	155	85

Figure S329. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'22q loss' versus 'MIRSEQ_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.0022

Table S330. Gene #80: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
22Q LOSS MUTATED	8	36	13	8	7
22Q LOSS WILD-TYPE	73	103	118	83	69

Figure S330. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'22q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00466 (Fisher's exact test), Q value = 0.018

Table S331. Gene #80: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	104	198
22Q LOSS MUTATED	23	24	18
22Q LOSS WILD-TYPE	148	80	180

Figure S331. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xp loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S332. Gene #81: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
XP LOSS MUTATED	75	38	14	9
XP LOSS WILD-TYPE	128	90	131	37

Figure S332. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'

'xp loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S333. Gene #81: 'xp loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
XP LOSS MUTATED	15	26	18	44	12	20	1
XP LOSS WILD-TYPE	69	61	85	45	66	55	5

Figure S333. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xp loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.037 (Fisher's exact test), Q value = 0.095

Table S334. Gene #81: 'xp loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	76	82	48
XP LOSS MUTATED	18	31	9
XP LOSS WILD-TYPE	58	51	39

Figure S334. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'xp loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0346 (Fisher's exact test), Q value = 0.09

Table S335. Gene #81: 'xp loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
XP LOSS MUTATED	52	35	33	15
XP LOSS WILD-TYPE	124	68	137	50

Figure S335. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xq loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.8e-05

Table S336. Gene #82: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	203	128	145	46
XQ LOSS MUTATED	41	30	10	1
XQ LOSS WILD-TYPE	162	98	135	45

Figure S336. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.0017

Table S337. Gene #82: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	84	87	103	89	78	75	6
XQ LOSS MUTATED	5	14	11	28	11	11	2
XQ LOSS WILD-TYPE	79	73	92	61	67	64	4

Figure S337. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0072 (Fisher's exact test), Q value = 0.025

Table S338. Gene #82: 'xq loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	76	82	48
XQ LOSS MUTATED	7	21	4
XQ LOSS WILD-TYPE	69	61	44

Figure S338. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'xq loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0228 (Fisher's exact test), Q value = 0.065

Table S339. Gene #82: 'xq loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	176	103	170	65
XQ LOSS MUTATED	23	24	19	14
XQ LOSS WILD-TYPE	153	79	151	51

Figure S339. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_CNMF'

P value = 0.0186 (Fisher's exact test), Q value = 0.055

Table S340. Gene #82: 'xq loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	139	131	91	76
XQ LOSS MUTATED	22	16	23	11	8
XQ LOSS WILD-TYPE	59	123	108	80	68

Figure S340. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'xq loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.02 (Fisher's exact test), Q value = 0.058

Table S341. Gene #82: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	189	143
XQ LOSS MUTATED	14	26	31
XQ LOSS WILD-TYPE	127	163	112

Figure S341. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

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/HNSC-TP/22508725/transformed.cor.cli.txt
Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/HNSC-TP/22541004/HNSC-TP.transferedmergedcluster.txt
Number of patients = 522
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.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

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)

Made with Nozzle