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

Stomach Adenocarcinoma (Primary solid tumor)

02 April 2015 | analyses__2015_04_02

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 (2015): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1028QN0

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 81 arm-level events and 10 molecular subtypes across 441 patients, 406 significant findings detected with P value < 0.05 and Q value < 0.25.

1p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
1q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
2p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
2q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
3p gain cnv correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
3q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
4q gain cnv correlated to 'MRNASEQ_CNMF'.
5p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
5q gain cnv correlated to 'CN_CNMF'.
6p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
6q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
7p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
7q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
8p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
8q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
10p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
10q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
11p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
11q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
12p gain cnv correlated to 'CN_CNMF'.
12q gain cnv correlated to 'CN_CNMF'.
13q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
14q gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.
15q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
16p gain cnv correlated to 'CN_CNMF'.
16q gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.
17p gain cnv correlated to 'CN_CNMF'.
17q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
18p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
18q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
19p gain cnv correlated to 'CN_CNMF'.
19q gain cnv correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
20p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
20q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
21q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
22q gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.
xp gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
xq gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
1p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
1q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'RPPA_CNMF'.
2p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.
2q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
3p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
3q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
4p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
4q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
5p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
5q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
6p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
6q loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
7p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
7q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
8p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
8q loss cnv correlated to 'CN_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
9p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
9q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
10p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
10q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
11p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
11q loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
12p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
12q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
13q loss cnv correlated to 'CN_CNMF'.
14q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
15q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
16p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
16q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
17p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
17q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
18p loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.
18q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
19p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
19q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
20p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
21q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
22q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
xp loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
xq loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', '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 81 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, 406 significant findings detected.


		Clinical Features	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
9p loss	150 (34%)	291	1e-05 (6.69e-05)	1e-05 (6.69e-05)	0.00224 (0.00703)	0.00033 (0.00141)	1e-05 (6.69e-05)	0.00021 (0.00094)	1e-05 (6.69e-05)	1e-05 (6.69e-05)	0.02 (0.0472)	0.0646 (0.124)
19p loss	115 (26%)	326	1e-05 (6.69e-05)	1e-05 (6.69e-05)	0.00635 (0.0179)	0.106 (0.183)	1e-05 (6.69e-05)	1e-05 (6.69e-05)	1e-05 (6.69e-05)	1e-05 (6.69e-05)	9e-05 (0.000439)	0.00681 (0.019)
19q loss	87 (20%)	354	1e-05 (6.69e-05)	1e-05 (6.69e-05)	0.0314 (0.0678)	0.203 (0.301)	1e-05 (6.69e-05)	4e-05 (0.000217)	1e-05 (6.69e-05)	1e-05 (6.69e-05)	0.00026 (0.00114)	0.0127 (0.0322)
22q loss	146 (33%)	295	1e-05 (6.69e-05)	1e-05 (6.69e-05)	0.0154 (0.0384)	0.00708 (0.0196)	0.00104 (0.00383)	0.0043 (0.0125)	2e-05 (0.000119)	1e-05 (6.69e-05)	0.0014 (0.00493)	0.0907 (0.162)
5p gain	102 (23%)	339	1e-05 (6.69e-05)	1e-05 (6.69e-05)	0.261 (0.364)	0.96 (0.971)	2e-05 (0.000119)	0.00545 (0.0156)	0.00024 (0.00106)	1e-05 (6.69e-05)	0.00867 (0.0229)	0.0191 (0.0457)
6p gain	78 (18%)	363	1e-05 (6.69e-05)	1e-05 (6.69e-05)	0.108 (0.185)	0.345 (0.443)	0.0006 (0.00237)	0.00799 (0.0216)	1e-05 (6.69e-05)	1e-05 (6.69e-05)	0.0018 (0.0059)	0.00178 (0.00586)
6q gain	64 (15%)	377	1e-05 (6.69e-05)	1e-05 (6.69e-05)	0.067 (0.126)	0.342 (0.441)	0.00023 (0.00102)	0.0234 (0.0531)	6e-05 (0.000308)	1e-05 (6.69e-05)	0.00118 (0.00423)	0.00365 (0.0108)
18p gain	84 (19%)	357	1e-05 (6.69e-05)	1e-05 (6.69e-05)	0.104 (0.18)	0.0507 (0.1)	0.0089 (0.0235)	0.00144 (0.00501)	0.00019 (0.000865)	2e-05 (0.000119)	0.00379 (0.0111)	0.00999 (0.0259)
4q loss	164 (37%)	277	1e-05 (6.69e-05)	1e-05 (6.69e-05)	0.0801 (0.146)	0.0324 (0.0688)	0.0052 (0.0149)	0.00143 (0.00499)	4e-05 (0.000217)	1e-05 (6.69e-05)	0.0057 (0.0162)	0.212 (0.31)
5q loss	106 (24%)	335	1e-05 (6.69e-05)	1e-05 (6.69e-05)	0.481 (0.572)	0.952 (0.965)	1e-05 (6.69e-05)	3e-05 (0.000168)	1e-05 (6.69e-05)	1e-05 (6.69e-05)	2e-05 (0.000119)	0.00348 (0.0104)
8p loss	88 (20%)	353	1e-05 (6.69e-05)	0.00202 (0.00647)	0.396 (0.494)	0.645 (0.712)	0.0174 (0.0421)	0.00114 (0.0041)	0.00185 (0.00602)	0.00646 (0.0181)	0.0192 (0.0458)	1e-05 (6.69e-05)
9q loss	104 (24%)	337	1e-05 (6.69e-05)	1e-05 (6.69e-05)	0.209 (0.307)	0.0154 (0.0384)	3e-05 (0.000168)	0.00925 (0.0242)	3e-05 (0.000168)	2e-05 (0.000119)	0.0136 (0.0341)	0.194 (0.293)
15q loss	90 (20%)	351	1e-05 (6.69e-05)	0.00174 (0.00578)	0.00488 (0.0141)	0.527 (0.61)	0.00018 (0.000838)	0.00165 (0.00555)	0.0244 (0.0548)	0.0199 (0.0471)	0.15 (0.238)	0.00328 (0.00995)
16q loss	115 (26%)	326	1e-05 (6.69e-05)	1e-05 (6.69e-05)	0.0393 (0.0808)	0.0872 (0.157)	1e-05 (6.69e-05)	1e-05 (6.69e-05)	1e-05 (6.69e-05)	1e-05 (6.69e-05)	0.00011 (0.000524)	0.496 (0.585)
17p loss	164 (37%)	277	1e-05 (6.69e-05)	1e-05 (6.69e-05)	0.583 (0.664)	0.0264 (0.0586)	1e-05 (6.69e-05)	1e-05 (6.69e-05)	1e-05 (6.69e-05)	2e-05 (0.000119)	0.116 (0.195)	0.0007 (0.00267)
18q loss	154 (35%)	287	1e-05 (6.69e-05)	0.0003 (0.0013)	0.342 (0.441)	0.811 (0.849)	0.0228 (0.0521)	0.0251 (0.0561)	8e-05 (4e-04)	0.00067 (0.00257)	0.0447 (0.0903)	0.0222 (0.0516)
1q gain	103 (23%)	338	1e-05 (6.69e-05)	0.00017 (0.000796)	0.0569 (0.111)	0.22 (0.319)	5e-05 (0.000265)	0.00222 (0.007)	0.00078 (0.00295)	5e-05 (0.000265)	0.00336 (0.0101)	0.302 (0.403)
2p gain	77 (17%)	364	1e-05 (6.69e-05)	0.00049 (0.00198)	0.0227 (0.0521)	0.118 (0.197)	0.143 (0.23)	0.0279 (0.0614)	0.00029 (0.00126)	0.00726 (0.0199)	0.142 (0.229)	0.0238 (0.054)
11q gain	74 (17%)	367	1e-05 (6.69e-05)	0.00019 (0.000865)	0.835 (0.869)	1 (1.00)	0.311 (0.414)	0.006 (0.017)	1e-05 (6.69e-05)	0.00048 (0.00195)	0.0119 (0.0304)	0.00945 (0.0247)
13q gain	154 (35%)	287	1e-05 (6.69e-05)	6e-05 (0.000308)	0.676 (0.733)	0.609 (0.684)	0.0231 (0.0528)	6e-05 (0.000308)	0.00086 (0.00324)	6e-05 (0.000308)	0.00131 (0.00465)	0.526 (0.61)
20p gain	243 (55%)	198	1e-05 (6.69e-05)	1e-05 (6.69e-05)	0.0782 (0.143)	0.194 (0.293)	0.0005 (0.00201)	1e-05 (6.69e-05)	3e-05 (0.000168)	1e-05 (6.69e-05)	3e-05 (0.000168)	0.555 (0.638)
20q gain	279 (63%)	162	1e-05 (6.69e-05)	1e-05 (6.69e-05)	0.0523 (0.103)	0.227 (0.325)	1e-05 (6.69e-05)	1e-05 (6.69e-05)	1e-05 (6.69e-05)	1e-05 (6.69e-05)	3e-05 (0.000168)	0.11 (0.188)
1p loss	59 (13%)	382	1e-05 (6.69e-05)	1e-05 (6.69e-05)	0.0318 (0.0683)	0.189 (0.286)	0.0703 (0.131)	0.00762 (0.0208)	0.00898 (0.0236)	0.0038 (0.0111)	0.00723 (0.0199)	0.432 (0.528)
3p loss	91 (21%)	350	1e-05 (6.69e-05)	3e-05 (0.000168)	0.357 (0.457)	0.197 (0.294)	0.00318 (0.00972)	0.00034 (0.00143)	0.00157 (0.00539)	0.00106 (0.00387)	0.156 (0.244)	0.0207 (0.0485)
3q loss	54 (12%)	387	1e-05 (6.69e-05)	5e-05 (0.000265)	0.195 (0.293)	0.274 (0.378)	2e-05 (0.000119)	1e-05 (6.69e-05)	0.0271 (0.06)	0.0124 (0.0314)	0.0806 (0.146)	0.00165 (0.00555)
4p loss	167 (38%)	274	1e-05 (6.69e-05)	1e-05 (6.69e-05)	0.291 (0.393)	0.137 (0.223)	0.00053 (0.0021)	0.00019 (0.000865)	2e-05 (0.000119)	1e-05 (6.69e-05)	0.0004 (0.00165)	0.243 (0.341)
5p loss	60 (14%)	381	1e-05 (6.69e-05)	5e-05 (0.000265)	0.22 (0.319)	0.757 (0.804)	0.00219 (0.00693)	0.012 (0.0306)	0.00037 (0.00154)	0.00012 (0.000568)	0.00342 (0.0103)	0.149 (0.237)
10q loss	67 (15%)	374	1e-05 (6.69e-05)	1e-05 (6.69e-05)	0.674 (0.733)	0.0498 (0.0994)	0.00181 (0.00591)	0.00217 (0.00689)	1e-05 (6.69e-05)	0.0001 (0.000482)	0.277 (0.379)	0.2 (0.298)
12p loss	63 (14%)	378	1e-05 (6.69e-05)	1e-05 (6.69e-05)	0.221 (0.32)	0.136 (0.222)	4e-05 (0.000217)	1e-05 (6.69e-05)	8e-05 (4e-04)	2e-05 (0.000119)	0.097 (0.171)	0.0319 (0.0683)
16p loss	100 (23%)	341	1e-05 (6.69e-05)	1e-05 (6.69e-05)	0.713 (0.762)	0.886 (0.912)	1e-05 (6.69e-05)	1e-05 (6.69e-05)	1e-05 (6.69e-05)	1e-05 (6.69e-05)	1e-05 (6.69e-05)	0.151 (0.238)
17q loss	74 (17%)	367	1e-05 (6.69e-05)	1e-05 (6.69e-05)	0.265 (0.367)	0.032 (0.0683)	0.00241 (0.00754)	0.00799 (0.0216)	0.00051 (0.00205)	0.00017 (0.000796)	0.112 (0.189)	0.638 (0.706)
21q loss	180 (41%)	261	1e-05 (6.69e-05)	1e-05 (6.69e-05)	0.1 (0.175)	0.298 (0.4)	0.0364 (0.076)	0.00173 (0.00577)	0.00067 (0.00257)	0.00442 (0.0128)	0.00161 (0.00546)	0.11 (0.188)
1p gain	51 (12%)	390	1e-05 (6.69e-05)	0.00748 (0.0205)	0.00264 (0.00816)	0.405 (0.504)	0.00143 (0.00499)	0.125 (0.206)	0.00064 (0.0025)	0.0032 (0.00974)	0.0742 (0.137)	0.0634 (0.122)
2q gain	66 (15%)	375	1e-05 (6.69e-05)	0.00866 (0.0229)	0.237 (0.335)	0.555 (0.638)	0.0454 (0.0915)	0.0311 (0.0673)	0.00095 (0.00355)	0.0668 (0.126)	0.0349 (0.0733)	0.284 (0.385)
8q gain	237 (54%)	204	0.00979 (0.0254)	0.0129 (0.0326)	0.679 (0.734)	0.296 (0.398)	0.0369 (0.0766)	0.0176 (0.0425)	0.0413 (0.0846)	0.0381 (0.0789)	0.62 (0.694)	0.374 (0.471)
18q gain	54 (12%)	387	0.00634 (0.0179)	0.00291 (0.00896)	0.595 (0.673)	0.235 (0.333)	0.282 (0.384)	0.0224 (0.0519)	0.0157 (0.0389)	0.0221 (0.0513)	0.282 (0.384)	0.0366 (0.0763)
21q gain	21 (5%)	420	0.0002 (9e-04)	0.00149 (0.00514)	0.145 (0.231)	0.635 (0.704)	0.0103 (0.0266)	0.0305 (0.0662)	0.0899 (0.161)	8e-05 (4e-04)	0.17 (0.262)	0.029 (0.0633)
6p loss	52 (12%)	389	1e-05 (6.69e-05)	0.00019 (0.000865)	0.151 (0.238)	0.911 (0.933)	0.0226 (0.052)	0.00863 (0.0229)	0.0927 (0.165)	0.0161 (0.0395)	0.0334 (0.0706)	0.452 (0.544)
7p loss	20 (5%)	421	0.00047 (0.00192)	0.00161 (0.00546)	0.441 (0.536)	0.432 (0.528)	0.00161 (0.00546)	0.338 (0.44)	0.0002 (9e-04)	0.0225 (0.0519)	0.00196 (0.00635)	0.221 (0.32)
14q loss	111 (25%)	330	1e-05 (6.69e-05)	1e-05 (6.69e-05)	0.562 (0.642)	0.532 (0.615)	0.00111 (0.00403)	0.00845 (0.0227)	2e-05 (0.000119)	2e-05 (0.000119)	0.139 (0.226)	0.0602 (0.116)
7p gain	197 (45%)	244	1e-05 (6.69e-05)	0.00028 (0.00123)	0.676 (0.733)	0.5 (0.587)	0.339 (0.44)	0.00052 (0.00207)	0.223 (0.321)	0.0281 (0.0616)	0.367 (0.467)	0.00311 (0.00954)
11p gain	64 (15%)	377	1e-05 (6.69e-05)	0.00067 (0.00257)	0.935 (0.95)	0.845 (0.878)	0.283 (0.384)	0.394 (0.493)	2e-05 (0.000119)	0.00172 (0.00576)	0.0389 (0.0802)	0.123 (0.203)
19q gain	78 (18%)	363	1e-05 (6.69e-05)	0.111 (0.188)	0.151 (0.238)	0.0435 (0.0884)	0.0161 (0.0395)	0.251 (0.351)	0.0163 (0.0398)	0.0575 (0.112)	0.00723 (0.0199)	0.0876 (0.158)
2q loss	33 (7%)	408	1e-05 (6.69e-05)	0.00033 (0.00141)	0.666 (0.729)	0.804 (0.846)	0.00964 (0.0251)	0.263 (0.365)	0.0233 (0.0531)	0.0329 (0.0698)	0.607 (0.682)	0.207 (0.305)
7q loss	30 (7%)	411	1e-05 (6.69e-05)	0.00215 (0.00686)	0.485 (0.577)	0.783 (0.826)	0.00561 (0.016)	0.28 (0.382)	0.00791 (0.0215)	0.0506 (0.1)	0.0469 (0.0942)	0.413 (0.511)
10p loss	64 (15%)	377	1e-05 (6.69e-05)	0.00066 (0.00257)	0.708 (0.758)	0.0953 (0.168)	0.015 (0.0374)	0.0739 (0.136)	2e-05 (0.000119)	0.00034 (0.00143)	0.214 (0.313)	0.354 (0.453)
12q loss	52 (12%)	389	1e-05 (6.69e-05)	1e-05 (6.69e-05)	0.279 (0.382)	0.113 (0.19)	0.00044 (0.00181)	0.00061 (0.0024)	0.0762 (0.14)	0.00106 (0.00387)	0.371 (0.47)	0.198 (0.295)
xq loss	50 (11%)	391	1e-05 (6.69e-05)	0.00426 (0.0124)	0.51 (0.597)	0.0671 (0.126)	0.032 (0.0683)	0.111 (0.188)	0.0273 (0.0603)	0.136 (0.222)	0.0185 (0.0444)	0.099 (0.174)
7q gain	169 (38%)	272	1e-05 (6.69e-05)	0.00075 (0.00285)	0.924 (0.944)	0.438 (0.534)	0.334 (0.437)	0.00177 (0.00585)	0.316 (0.417)	0.178 (0.272)	0.541 (0.625)	0.0422 (0.0861)
10p gain	98 (22%)	343	1e-05 (6.69e-05)	0.00011 (0.000524)	0.131 (0.215)	0.527 (0.61)	0.00149 (0.00514)	0.149 (0.237)	0.153 (0.24)	0.00335 (0.0101)	0.229 (0.327)	0.42 (0.518)
15q gain	39 (9%)	402	3e-05 (0.000168)	9e-05 (0.000439)	0.348 (0.446)	0.828 (0.862)	0.0354 (0.0742)	0.224 (0.323)	0.117 (0.195)	0.00855 (0.0229)	0.599 (0.676)	0.475 (0.567)
17q gain	62 (14%)	379	4e-05 (0.000217)	0.0472 (0.0947)	0.944 (0.958)	0.965 (0.974)	0.485 (0.577)	0.206 (0.305)	0.0435 (0.0884)	0.342 (0.441)	0.072 (0.133)	0.00707 (0.0196)
xp gain	48 (11%)	393	1e-05 (6.69e-05)	0.00103 (0.00381)	0.452 (0.544)	0.85 (0.881)	0.0661 (0.125)	0.0206 (0.0484)	0.0247 (0.0555)	0.34 (0.441)	0.0671 (0.126)	0.115 (0.194)
xq gain	56 (13%)	385	1e-05 (6.69e-05)	0.0264 (0.0586)	0.505 (0.592)	0.733 (0.781)	0.0345 (0.0726)	0.00038 (0.00158)	0.167 (0.258)	0.0803 (0.146)	0.492 (0.583)	0.0661 (0.125)
2p loss	26 (6%)	415	2e-05 (0.000119)	0.00033 (0.00141)	0.375 (0.471)	0.473 (0.565)	0.0119 (0.0304)	0.299 (0.4)	0.0414 (0.0848)	0.142 (0.23)	0.468 (0.56)	0.335 (0.438)
11p loss	62 (14%)	379	1e-05 (6.69e-05)	0.00112 (0.00405)	0.0177 (0.0427)	0.0693 (0.129)	0.167 (0.258)	0.319 (0.42)	0.0524 (0.103)	0.017 (0.0415)	0.171 (0.263)	0.294 (0.397)
3p gain	53 (12%)	388	0.00202 (0.00647)	0.406 (0.505)	0.793 (0.835)	0.025 (0.0559)	0.624 (0.696)	0.225 (0.324)	0.188 (0.286)	0.589 (0.669)	0.372 (0.47)	0.0286 (0.0625)
3q gain	93 (21%)	348	1e-05 (6.69e-05)	0.118 (0.197)	0.875 (0.901)	0.15 (0.238)	0.143 (0.23)	0.0196 (0.0467)	0.0576 (0.112)	0.341 (0.441)	0.0952 (0.168)	0.019 (0.0455)
10q gain	70 (16%)	371	1e-05 (6.69e-05)	0.0382 (0.0789)	0.124 (0.204)	0.853 (0.882)	0.0132 (0.0331)	0.122 (0.203)	0.464 (0.555)	0.338 (0.44)	0.677 (0.733)	0.447 (0.54)
1q loss	28 (6%)	413	2e-05 (0.000119)	9e-05 (0.000439)	0.0339 (0.0715)	0.298 (0.4)	0.592 (0.671)	0.152 (0.239)	0.0716 (0.133)	0.314 (0.417)	0.519 (0.604)	0.556 (0.638)
8q loss	33 (7%)	408	0.0009 (0.00337)	0.591 (0.67)	0.826 (0.861)	0.375 (0.471)	0.755 (0.804)	0.985 (0.988)	0.0244 (0.0548)	0.511 (0.597)	0.0319 (0.0683)	0.226 (0.324)
20p loss	22 (5%)	419	0.00246 (0.00766)	0.0158 (0.0389)	0.815 (0.851)	0.312 (0.416)	0.00037 (0.00154)	0.0561 (0.11)	0.18 (0.274)	0.413 (0.511)	0.56 (0.641)	0.668 (0.729)
8p gain	182 (41%)	259	3e-05 (0.000168)	0.0445 (0.0901)	0.6 (0.676)	0.24 (0.339)	0.446 (0.54)	0.104 (0.181)	0.208 (0.307)	0.406 (0.505)	0.453 (0.544)	0.316 (0.417)
14q gain	29 (7%)	412	6e-05 (0.000308)	0.15 (0.238)	0.816 (0.851)	0.928 (0.945)	0.195 (0.293)	0.765 (0.811)	0.00821 (0.0221)	0.511 (0.597)	0.204 (0.303)	0.596 (0.673)
16q gain	47 (11%)	394	0.00255 (0.00791)	0.807 (0.847)	0.672 (0.732)	0.262 (0.364)	0.186 (0.283)	0.625 (0.696)	0.706 (0.757)	0.956 (0.968)	0.0506 (0.1)	0.0172 (0.0418)
22q gain	32 (7%)	409	0.00197 (0.00636)	0.124 (0.204)	0.848 (0.879)	0.221 (0.32)	0.257 (0.359)	0.0668 (0.126)	0.235 (0.333)	0.621 (0.694)	0.028 (0.0614)	0.171 (0.263)
6q loss	70 (16%)	371	1e-05 (6.69e-05)	0.00131 (0.00465)	0.901 (0.926)	0.812 (0.849)	0.0625 (0.12)	0.14 (0.227)	0.556 (0.638)	0.0626 (0.12)	0.108 (0.185)	0.446 (0.54)
11q loss	61 (14%)	380	9e-05 (0.000439)	0.02 (0.0472)	0.674 (0.733)	0.452 (0.544)	0.626 (0.696)	0.629 (0.698)	0.0658 (0.125)	0.369 (0.469)	0.17 (0.262)	0.233 (0.331)
18p loss	119 (27%)	322	1e-05 (6.69e-05)	0.166 (0.258)	0.773 (0.818)	0.657 (0.722)	0.559 (0.64)	0.25 (0.35)	0.0483 (0.0967)	0.11 (0.188)	0.372 (0.471)	0.274 (0.378)
xp loss	59 (13%)	382	1e-05 (6.69e-05)	0.0036 (0.0106)	0.646 (0.712)	0.12 (0.2)	0.142 (0.229)	0.0715 (0.133)	0.103 (0.18)	0.315 (0.417)	0.334 (0.437)	0.0992 (0.174)
4q gain	16 (4%)	425	0.429 (0.528)	0.667 (0.729)	0.69 (0.743)	0.0901 (0.162)	0.0211 (0.0493)	0.431 (0.528)	0.495 (0.585)	0.0678 (0.127)	0.615 (0.689)	0.666 (0.729)
5q gain	44 (10%)	397	0.0112 (0.0288)	0.323 (0.424)	0.851 (0.881)	0.275 (0.378)	0.197 (0.294)	0.368 (0.468)	0.418 (0.516)	0.64 (0.707)	0.15 (0.238)	0.805 (0.846)
12p gain	90 (20%)	351	8e-05 (4e-04)	0.197 (0.294)	0.241 (0.34)	0.336 (0.438)	0.166 (0.258)	0.102 (0.178)	0.0572 (0.111)	0.174 (0.267)	0.128 (0.21)	0.0831 (0.15)
12q gain	77 (17%)	364	0.0035 (0.0104)	0.0924 (0.164)	0.438 (0.534)	0.42 (0.518)	0.967 (0.975)	0.276 (0.379)	0.156 (0.244)	0.385 (0.483)	0.231 (0.329)	0.107 (0.185)
16p gain	59 (13%)	382	0.00135 (0.00478)	0.0922 (0.164)	0.396 (0.494)	0.115 (0.193)	0.0756 (0.139)	0.286 (0.387)	0.905 (0.928)	0.977 (0.983)	0.244 (0.342)	0.0989 (0.174)
17p gain	29 (7%)	412	0.00103 (0.00381)	0.0532 (0.104)	0.667 (0.729)	0.687 (0.741)	0.193 (0.292)	0.217 (0.316)	0.0512 (0.101)	0.196 (0.294)	0.108 (0.185)	0.314 (0.417)
19p gain	54 (12%)	387	0.0001 (0.000482)	0.652 (0.718)	0.498 (0.586)	0.0659 (0.125)	0.489 (0.58)	0.905 (0.928)	0.577 (0.658)	0.462 (0.554)	0.543 (0.626)	0.432 (0.528)
13q loss	36 (8%)	405	0.00349 (0.0104)	0.732 (0.781)	0.686 (0.741)	0.302 (0.403)	0.28 (0.382)	0.602 (0.677)	0.7 (0.753)	0.446 (0.54)	0.761 (0.808)	0.143 (0.23)
4p gain	21 (5%)	420	0.0769 (0.141)	0.707 (0.757)	0.912 (0.933)	0.27 (0.373)	0.209 (0.307)	0.321 (0.422)	0.513 (0.598)	0.162 (0.252)	0.352 (0.451)	0.232 (0.331)
9p gain	60 (14%)	381	0.0952 (0.168)	0.986 (0.988)	0.375 (0.471)	0.858 (0.886)	0.581 (0.662)	0.494 (0.585)	0.703 (0.756)	0.774 (0.818)	0.502 (0.589)	1 (1.00)
9q gain	78 (18%)	363	0.215 (0.314)	0.629 (0.698)	0.251 (0.351)	0.983 (0.988)	0.428 (0.527)	0.928 (0.945)	0.974 (0.981)	0.93 (0.946)	0.358 (0.457)	0.776 (0.82)

'1p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
1P GAIN MUTATED	27	5	4	12	3
1P GAIN WILD-TYPE	96	182	32	64	16

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

'1p gain' versus 'METHLYATION_CNMF'

P value = 0.00748 (Fisher's exact test), Q value = 0.02

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
1P GAIN MUTATED	23	15	1	7
1P GAIN WILD-TYPE	101	106	41	99

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

'1p gain' versus 'RPPA_CNMF'

P value = 0.00264 (Fisher's exact test), Q value = 0.0082

Table S3. Gene #1: '1p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	90	91
1P GAIN MUTATED	17	4	8
1P GAIN WILD-TYPE	65	86	83

Figure S3. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'1p gain' versus 'MRNASEQ_CNMF'

P value = 0.00143 (Fisher's exact test), Q value = 0.005

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
1P GAIN MUTATED	3	2	6	3	15
1P GAIN WILD-TYPE	62	60	40	34	47

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

'1p gain' versus 'MIRSEQ_CNMF'

P value = 0.00064 (Fisher's exact test), Q value = 0.0025

Table S5. Gene #1: '1p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
1P GAIN MUTATED	15	10	26
1P GAIN WILD-TYPE	171	123	95

Figure S5. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'1p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0032 (Fisher's exact test), Q value = 0.0097

Table S6. Gene #1: '1p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
1P GAIN MUTATED	9	12	7	23
1P GAIN WILD-TYPE	70	163	72	84

Figure S6. 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 = 6.7e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
1Q GAIN MUTATED	53	12	10	22	6
1Q GAIN WILD-TYPE	70	175	26	54	13

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

'1q gain' versus 'METHLYATION_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 8e-04

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
1Q GAIN MUTATED	44	31	5	13
1Q GAIN WILD-TYPE	80	90	37	93

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

'1q gain' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00026

Table S9. Gene #2: '1q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
1Q GAIN MUTATED	10	7	9	9	30
1Q GAIN WILD-TYPE	55	55	37	28	32

Figure S9. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'1q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00222 (Fisher's exact test), Q value = 0.007

Table S10. Gene #2: '1q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
1Q GAIN MUTATED	5	3	7	18	16	15	1
1Q GAIN WILD-TYPE	33	18	42	44	25	25	20

Figure S10. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_CNMF'

P value = 0.00078 (Fisher's exact test), Q value = 0.003

Table S11. Gene #2: '1q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
1Q GAIN MUTATED	34	25	44
1Q GAIN WILD-TYPE	152	108	77

Figure S11. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'1q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00026

Table S12. Gene #2: '1q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
1Q GAIN MUTATED	23	23	17	40
1Q GAIN WILD-TYPE	56	152	62	67

Figure S12. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00336 (Fisher's exact test), Q value = 0.01

Table S13. Gene #2: '1q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
1Q GAIN MUTATED	29	9	10	11	12	8
1Q GAIN WILD-TYPE	47	49	50	47	24	50

Figure S13. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'2p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S14. Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
2P GAIN MUTATED	35	8	12	16	6
2P GAIN WILD-TYPE	88	179	24	60	13

Figure S14. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

'2p gain' versus 'METHLYATION_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.002

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
2P GAIN MUTATED	35	23	5	8
2P GAIN WILD-TYPE	89	98	37	98

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

'2p gain' versus 'RPPA_CNMF'

P value = 0.0227 (Fisher's exact test), Q value = 0.052

Table S16. Gene #3: '2p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	90	91
2P GAIN MUTATED	6	18	19
2P GAIN WILD-TYPE	76	72	72

Figure S16. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0279 (Fisher's exact test), Q value = 0.061

Table S17. Gene #3: '2p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
2P GAIN MUTATED	6	4	3	13	6	11	0
2P GAIN WILD-TYPE	32	17	46	49	35	29	21

Figure S17. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.0013

Table S18. Gene #3: '2p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
2P GAIN MUTATED	29	13	35
2P GAIN WILD-TYPE	157	120	86

Figure S18. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'2p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00726 (Fisher's exact test), Q value = 0.02

Table S19. Gene #3: '2p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
2P GAIN MUTATED	12	24	10	31
2P GAIN WILD-TYPE	67	151	69	76

Figure S19. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0238 (Fisher's exact test), Q value = 0.054

Table S20. Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
2P GAIN MUTATED	36	6	18
2P GAIN WILD-TYPE	165	67	54

Figure S20. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S21. Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
2Q GAIN MUTATED	28	8	10	15	5
2Q GAIN WILD-TYPE	95	179	26	61	14

Figure S21. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

'2q gain' versus 'METHLYATION_CNMF'

P value = 0.00866 (Fisher's exact test), Q value = 0.023

Table S22. Gene #4: '2q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
2Q GAIN MUTATED	29	19	5	8
2Q GAIN WILD-TYPE	95	102	37	98

Figure S22. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2q gain' versus 'MRNASEQ_CNMF'

P value = 0.0454 (Fisher's exact test), Q value = 0.091

Table S23. Gene #4: '2q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
2Q GAIN MUTATED	10	6	5	3	17
2Q GAIN WILD-TYPE	55	56	41	34	45

Figure S23. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0311 (Fisher's exact test), Q value = 0.067

Table S24. Gene #4: '2q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
2Q GAIN MUTATED	8	4	3	9	6	11	0
2Q GAIN WILD-TYPE	30	17	46	53	35	29	21

Figure S24. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_CNMF'

P value = 0.00095 (Fisher's exact test), Q value = 0.0035

Table S25. Gene #4: '2q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
2Q GAIN MUTATED	22	13	31
2Q GAIN WILD-TYPE	164	120	90

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

'2q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0349 (Fisher's exact test), Q value = 0.073

Table S26. Gene #4: '2q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
2Q GAIN MUTATED	17	6	7	5	11	8
2Q GAIN WILD-TYPE	59	52	53	53	25	50

Figure S26. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'3p gain' versus 'CN_CNMF'

P value = 0.00202 (Fisher's exact test), Q value = 0.0065

Table S27. Gene #5: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
3P GAIN MUTATED	18	11	6	12	6
3P GAIN WILD-TYPE	105	176	30	64	13

Figure S27. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'

'3p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.025 (Fisher's exact test), Q value = 0.056

Table S28. Gene #5: '3p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	83	55	91
3P GAIN MUTATED	9	7	3	12
3P GAIN WILD-TYPE	25	76	52	79

Figure S28. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'3p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0286 (Fisher's exact test), Q value = 0.062

Table S29. Gene #5: '3p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
3P GAIN MUTATED	20	4	14
3P GAIN WILD-TYPE	181	69	58

Figure S29. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S30. Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
3Q GAIN MUTATED	27	20	11	25	10
3Q GAIN WILD-TYPE	96	167	25	51	9

Figure S30. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

'3q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0196 (Fisher's exact test), Q value = 0.047

Table S31. Gene #6: '3q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
3Q GAIN MUTATED	5	9	6	18	8	4	3
3Q GAIN WILD-TYPE	33	12	43	44	33	36	18

Figure S31. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.019 (Fisher's exact test), Q value = 0.046

Table S32. Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
3Q GAIN MUTATED	37	7	20
3Q GAIN WILD-TYPE	164	66	52

Figure S32. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q gain' versus 'MRNASEQ_CNMF'

P value = 0.0211 (Fisher's exact test), Q value = 0.049

Table S33. Gene #8: '4q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
4Q GAIN MUTATED	0	0	2	3	1
4Q GAIN WILD-TYPE	65	62	44	34	61

Figure S33. 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 = 6.7e-05

Table S34. Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
5P GAIN MUTATED	59	16	7	17	3
5P GAIN WILD-TYPE	64	171	29	59	16

Figure S34. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S35. Gene #9: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
5P GAIN MUTATED	49	19	6	14
5P GAIN WILD-TYPE	75	102	36	92

Figure S35. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
5P GAIN MUTATED	10	5	8	8	29
5P GAIN WILD-TYPE	55	57	38	29	33

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

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00545 (Fisher's exact test), Q value = 0.016

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
5P GAIN MUTATED	8	4	4	13	12	17	2
5P GAIN WILD-TYPE	30	17	45	49	29	23	19

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

'5p gain' versus 'MIRSEQ_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.0011

Table S38. Gene #9: '5p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
5P GAIN MUTATED	41	18	43
5P GAIN WILD-TYPE	145	115	78

Figure S38. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'5p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S39. Gene #9: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
5P GAIN MUTATED	14	32	10	46
5P GAIN WILD-TYPE	65	143	69	61

Figure S39. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00867 (Fisher's exact test), Q value = 0.023

Table S40. Gene #9: '5p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
5P GAIN MUTATED	26	9	15	14	10	5
5P GAIN WILD-TYPE	50	49	45	44	26	53

Figure S40. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'5p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0191 (Fisher's exact test), Q value = 0.046

Table S41. Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
5P GAIN MUTATED	53	8	18
5P GAIN WILD-TYPE	148	65	54

Figure S41. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q gain' versus 'CN_CNMF'

P value = 0.0112 (Fisher's exact test), Q value = 0.029

Table S42. Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
5Q GAIN MUTATED	20	11	1	11	1
5Q GAIN WILD-TYPE	103	176	35	65	18

Figure S42. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

'6p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
6P GAIN MUTATED	53	6	1	14	4
6P GAIN WILD-TYPE	70	181	35	62	15

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

'6p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S44. Gene #11: '6p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
6P GAIN MUTATED	45	13	1	6
6P GAIN WILD-TYPE	79	108	41	100

Figure S44. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p gain' versus 'MRNASEQ_CNMF'

P value = 6e-04 (Fisher's exact test), Q value = 0.0024

Table S45. Gene #11: '6p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
6P GAIN MUTATED	9	5	6	5	23
6P GAIN WILD-TYPE	56	57	40	32	39

Figure S45. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'6p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00799 (Fisher's exact test), Q value = 0.022

Table S46. Gene #11: '6p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
6P GAIN MUTATED	7	1	2	12	10	13	3
6P GAIN WILD-TYPE	31	20	47	50	31	27	18

Figure S46. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S47. Gene #11: '6p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
6P GAIN MUTATED	27	10	40
6P GAIN WILD-TYPE	159	123	81

Figure S47. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'6p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S48. Gene #11: '6p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
6P GAIN MUTATED	19	13	7	38
6P GAIN WILD-TYPE	60	162	72	69

Figure S48. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0018 (Fisher's exact test), Q value = 0.0059

Table S49. Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
6P GAIN MUTATED	25	6	7	9	6	4
6P GAIN WILD-TYPE	51	52	53	49	30	54

Figure S49. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'6p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00178 (Fisher's exact test), Q value = 0.0059

Table S50. Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
6P GAIN MUTATED	42	3	12
6P GAIN WILD-TYPE	159	70	60

Figure S50. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S51. Gene #12: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
6Q GAIN MUTATED	45	5	0	11	3
6Q GAIN WILD-TYPE	78	182	36	65	16

Figure S51. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

'6q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S52. Gene #12: '6q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
6Q GAIN MUTATED	36	12	1	4
6Q GAIN WILD-TYPE	88	109	41	102

Figure S52. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q gain' versus 'MRNASEQ_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.001

Table S53. Gene #12: '6q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

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

Figure S53. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'6q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0234 (Fisher's exact test), Q value = 0.053

Table S54. Gene #12: '6q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
6Q GAIN MUTATED	5	1	3	8	8	13	2
6Q GAIN WILD-TYPE	33	20	46	54	33	27	19

Figure S54. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6q gain' versus 'MIRSEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00031

Table S55. Gene #12: '6q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
6Q GAIN MUTATED	24	8	31
6Q GAIN WILD-TYPE	162	125	90

Figure S55. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'6q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S56. Gene #12: '6q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
6Q GAIN MUTATED	17	11	6	29
6Q GAIN WILD-TYPE	62	164	73	78

Figure S56. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00118 (Fisher's exact test), Q value = 0.0042

Table S57. Gene #12: '6q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
6Q GAIN MUTATED	21	4	4	9	6	3
6Q GAIN WILD-TYPE	55	54	56	49	30	55

Figure S57. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'6q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00365 (Fisher's exact test), Q value = 0.011

Table S58. Gene #12: '6q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
6Q GAIN MUTATED	33	2	12
6Q GAIN WILD-TYPE	168	71	60

Figure S58. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S59. Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
7P GAIN MUTATED	67	44	34	40	12
7P GAIN WILD-TYPE	56	143	2	36	7

Figure S59. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.0012

Table S60. Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
7P GAIN MUTATED	69	59	19	30
7P GAIN WILD-TYPE	55	62	23	76

Figure S60. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00052 (Fisher's exact test), Q value = 0.0021

Table S61. Gene #13: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
7P GAIN MUTATED	13	12	13	29	27	21	4
7P GAIN WILD-TYPE	25	9	36	33	14	19	17

Figure S61. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0281 (Fisher's exact test), Q value = 0.062

Table S62. Gene #13: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
7P GAIN MUTATED	39	72	27	58
7P GAIN WILD-TYPE	40	103	52	49

Figure S62. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00311 (Fisher's exact test), Q value = 0.0095

Table S63. Gene #13: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
7P GAIN MUTATED	97	20	37
7P GAIN WILD-TYPE	104	53	35

Figure S63. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S64. Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
7Q GAIN MUTATED	53	43	34	30	9
7Q GAIN WILD-TYPE	70	144	2	46	10

Figure S64. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 0.00075 (Fisher's exact test), Q value = 0.0029

Table S65. Gene #14: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
7Q GAIN MUTATED	58	46	20	24
7Q GAIN WILD-TYPE	66	75	22	82

Figure S65. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00177 (Fisher's exact test), Q value = 0.0059

Table S66. Gene #14: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
7Q GAIN MUTATED	13	12	11	22	25	15	4
7Q GAIN WILD-TYPE	25	9	38	40	16	25	17

Figure S66. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0422 (Fisher's exact test), Q value = 0.086

Table S67. Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
7Q GAIN MUTATED	78	18	31
7Q GAIN WILD-TYPE	123	55	41

Figure S67. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00017

Table S68. Gene #15: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
8P GAIN MUTATED	44	82	16	23	17
8P GAIN WILD-TYPE	79	105	20	53	2

Figure S68. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

'8p gain' versus 'METHLYATION_CNMF'

P value = 0.0445 (Fisher's exact test), Q value = 0.09

Table S69. Gene #15: '8p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
8P GAIN MUTATED	44	61	16	36
8P GAIN WILD-TYPE	80	60	26	70

Figure S69. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8q gain' versus 'CN_CNMF'

P value = 0.00979 (Fisher's exact test), Q value = 0.025

Table S70. Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
8Q GAIN MUTATED	71	93	19	37	17
8Q GAIN WILD-TYPE	52	94	17	39	2

Figure S70. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 0.0129 (Fisher's exact test), Q value = 0.033

Table S71. Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
8Q GAIN MUTATED	69	75	17	46
8Q GAIN WILD-TYPE	55	46	25	60

Figure S71. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 0.0369 (Fisher's exact test), Q value = 0.077

Table S72. Gene #16: '8q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
8Q GAIN MUTATED	34	30	17	22	41
8Q GAIN WILD-TYPE	31	32	29	15	21

Figure S72. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0176 (Fisher's exact test), Q value = 0.042

Table S73. Gene #16: '8q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
8Q GAIN MUTATED	14	8	25	29	25	28	15
8Q GAIN WILD-TYPE	24	13	24	33	16	12	6

Figure S73. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_CNMF'

P value = 0.0413 (Fisher's exact test), Q value = 0.085

Table S74. Gene #16: '8q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
8Q GAIN MUTATED	104	60	73
8Q GAIN WILD-TYPE	82	73	48

Figure S74. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'8q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0381 (Fisher's exact test), Q value = 0.079

Table S75. Gene #16: '8q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
8Q GAIN MUTATED	50	85	37	65
8Q GAIN WILD-TYPE	29	90	42	42

Figure S75. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'10p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S76. Gene #19: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
10P GAIN MUTATED	39	9	14	35	1
10P GAIN WILD-TYPE	84	178	22	41	18

Figure S76. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

'10p gain' versus 'METHLYATION_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00052

Table S77. Gene #19: '10p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
10P GAIN MUTATED	43	24	2	17
10P GAIN WILD-TYPE	81	97	40	89

Figure S77. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10p gain' versus 'MRNASEQ_CNMF'

P value = 0.00149 (Fisher's exact test), Q value = 0.0051

Table S78. Gene #19: '10p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
10P GAIN MUTATED	10	14	7	6	27
10P GAIN WILD-TYPE	55	48	39	31	35

Figure S78. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00335 (Fisher's exact test), Q value = 0.01

Table S79. Gene #19: '10p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
10P GAIN MUTATED	14	28	18	37
10P GAIN WILD-TYPE	65	147	61	70

Figure S79. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'10q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S80. Gene #20: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
10Q GAIN MUTATED	20	7	6	33	4
10Q GAIN WILD-TYPE	103	180	30	43	15

Figure S80. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

'10q gain' versus 'METHLYATION_CNMF'

P value = 0.0382 (Fisher's exact test), Q value = 0.079

Table S81. Gene #20: '10q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
10Q GAIN MUTATED	27	19	2	13
10Q GAIN WILD-TYPE	97	102	40	93

Figure S81. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10q gain' versus 'MRNASEQ_CNMF'

P value = 0.0132 (Fisher's exact test), Q value = 0.033

Table S82. Gene #20: '10q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
10Q GAIN MUTATED	9	9	5	3	20
10Q GAIN WILD-TYPE	56	53	41	34	42

Figure S82. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'11p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S83. Gene #21: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
11P GAIN MUTATED	35	10	3	13	3
11P GAIN WILD-TYPE	88	177	33	63	16

Figure S83. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

'11p gain' versus 'METHLYATION_CNMF'

P value = 0.00067 (Fisher's exact test), Q value = 0.0026

Table S84. Gene #21: '11p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
11P GAIN MUTATED	32	10	6	10
11P GAIN WILD-TYPE	92	111	36	96

Figure S84. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11p gain' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

Table S85. Gene #21: '11p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
11P GAIN MUTATED	23	8	32
11P GAIN WILD-TYPE	163	125	89

Figure S85. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'11p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00172 (Fisher's exact test), Q value = 0.0058

Table S86. Gene #21: '11p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
11P GAIN MUTATED	9	20	6	28
11P GAIN WILD-TYPE	70	155	73	79

Figure S86. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'11p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0389 (Fisher's exact test), Q value = 0.08

Table S87. Gene #21: '11p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
11P GAIN MUTATED	17	10	4	6	7	4
11P GAIN WILD-TYPE	59	48	56	52	29	54

Figure S87. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'11q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S88. Gene #22: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
11Q GAIN MUTATED	39	10	2	18	5
11Q GAIN WILD-TYPE	84	177	34	58	14

Figure S88. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

'11q gain' versus 'METHLYATION_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.00086

Table S89. Gene #22: '11q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
11Q GAIN MUTATED	36	14	6	9
11Q GAIN WILD-TYPE	88	107	36	97

Figure S89. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.006 (Fisher's exact test), Q value = 0.017

Table S90. Gene #22: '11q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
11Q GAIN MUTATED	6	4	0	5	7	9	2
11Q GAIN WILD-TYPE	32	17	49	57	34	31	19

Figure S90. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S91. Gene #22: '11q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
11Q GAIN MUTATED	28	7	38
11Q GAIN WILD-TYPE	158	126	83

Figure S91. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'11q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00048 (Fisher's exact test), Q value = 0.002

Table S92. Gene #22: '11q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
11Q GAIN MUTATED	11	26	5	31
11Q GAIN WILD-TYPE	68	149	74	76

Figure S92. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0119 (Fisher's exact test), Q value = 0.03

Table S93. Gene #22: '11q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
11Q GAIN MUTATED	19	11	5	9	8	3
11Q GAIN WILD-TYPE	57	47	55	49	28	55

Figure S93. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'11q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00945 (Fisher's exact test), Q value = 0.025

Table S94. Gene #22: '11q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
11Q GAIN MUTATED	32	5	18
11Q GAIN WILD-TYPE	169	68	54

Figure S94. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12p gain' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 4e-04

Table S95. Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
12P GAIN MUTATED	27	21	11	27	4
12P GAIN WILD-TYPE	96	166	25	49	15

Figure S95. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

'12q gain' versus 'CN_CNMF'

P value = 0.0035 (Fisher's exact test), Q value = 0.01

Table S96. Gene #24: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
12Q GAIN MUTATED	20	21	9	23	4
12Q GAIN WILD-TYPE	103	166	27	53	15

Figure S96. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

'13q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S97. Gene #25: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
13Q GAIN MUTATED	71	36	23	17	7
13Q GAIN WILD-TYPE	52	151	13	59	12

Figure S97. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

'13q gain' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00031

Table S98. Gene #25: '13q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
13Q GAIN MUTATED	63	36	8	29
13Q GAIN WILD-TYPE	61	85	34	77

Figure S98. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q gain' versus 'MRNASEQ_CNMF'

P value = 0.0231 (Fisher's exact test), Q value = 0.053

Table S99. Gene #25: '13q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
13Q GAIN MUTATED	19	17	9	18	26
13Q GAIN WILD-TYPE	46	45	37	19	36

Figure S99. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'13q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00031

Table S100. Gene #25: '13q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

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

Figure S100. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'13q gain' versus 'MIRSEQ_CNMF'

P value = 0.00086 (Fisher's exact test), Q value = 0.0032

Table S101. Gene #25: '13q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
13Q GAIN MUTATED	56	38	59
13Q GAIN WILD-TYPE	130	95	62

Figure S101. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'13q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00031

Table S102. Gene #25: '13q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
13Q GAIN MUTATED	34	43	23	53
13Q GAIN WILD-TYPE	45	132	56	54

Figure S102. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'13q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00131 (Fisher's exact test), Q value = 0.0047

Table S103. Gene #25: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
13Q GAIN MUTATED	36	18	17	16	19	11
13Q GAIN WILD-TYPE	40	40	43	42	17	47

Figure S103. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'14q gain' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00031

Table S104. Gene #26: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
14Q GAIN MUTATED	19	5	4	1	0
14Q GAIN WILD-TYPE	104	182	32	75	19

Figure S104. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

'14q gain' versus 'MIRSEQ_CNMF'

P value = 0.00821 (Fisher's exact test), Q value = 0.022

Table S105. Gene #26: '14q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
14Q GAIN MUTATED	6	8	15
14Q GAIN WILD-TYPE	180	125	106

Figure S105. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'15q gain' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00017

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
15Q GAIN MUTATED	16	5	3	15	0
15Q GAIN WILD-TYPE	107	182	33	61	19

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

'15q gain' versus 'METHLYATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00044

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
15Q GAIN MUTATED	24	5	1	5
15Q GAIN WILD-TYPE	100	116	41	101

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

'15q gain' versus 'MRNASEQ_CNMF'

P value = 0.0354 (Fisher's exact test), Q value = 0.074

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
15Q GAIN MUTATED	5	1	1	5	8
15Q GAIN WILD-TYPE	60	61	45	32	54

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

'15q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00855 (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	CLUS_4
ALL	79	175	79	107
15Q GAIN MUTATED	4	13	3	18
15Q GAIN WILD-TYPE	75	162	76	89

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

'16p gain' versus 'CN_CNMF'

P value = 0.00135 (Fisher's exact test), Q value = 0.0048

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
16P GAIN MUTATED	23	12	4	17	3
16P GAIN WILD-TYPE	100	175	32	59	16

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

'16q gain' versus 'CN_CNMF'

P value = 0.00255 (Fisher's exact test), Q value = 0.0079

Table S111. Gene #29: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
16Q GAIN MUTATED	19	9	4	14	1
16Q GAIN WILD-TYPE	104	178	32	62	18

Figure S111. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0172 (Fisher's exact test), Q value = 0.042

Table S112. Gene #29: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
16Q GAIN MUTATED	27	3	3
16Q GAIN WILD-TYPE	174	70	69

Figure S112. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p gain' versus 'CN_CNMF'

P value = 0.00103 (Fisher's exact test), Q value = 0.0038

Table S113. Gene #30: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
17P GAIN MUTATED	17	5	3	2	2
17P GAIN WILD-TYPE	106	182	33	74	17

Figure S113. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

'17q gain' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00022

Table S114. Gene #31: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
17Q GAIN MUTATED	30	10	6	12	4
17Q GAIN WILD-TYPE	93	177	30	64	15

Figure S114. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 0.0472 (Fisher's exact test), Q value = 0.095

Table S115. Gene #31: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
17Q GAIN MUTATED	23	17	9	8
17Q GAIN WILD-TYPE	101	104	33	98

Figure S115. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q gain' versus 'MIRSEQ_CNMF'

P value = 0.0435 (Fisher's exact test), Q value = 0.088

Table S116. Gene #31: '17q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
17Q GAIN MUTATED	24	13	25
17Q GAIN WILD-TYPE	162	120	96

Figure S116. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00707 (Fisher's exact test), Q value = 0.02

Table S117. Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
17Q GAIN MUTATED	37	4	6
17Q GAIN WILD-TYPE	164	69	66

Figure S117. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S118. Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
18P GAIN MUTATED	42	14	7	17	4
18P GAIN WILD-TYPE	81	173	29	59	15

Figure S118. 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 = 6.7e-05

Table S119. Gene #32: '18p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
18P GAIN MUTATED	45	20	0	11
18P GAIN WILD-TYPE	79	101	42	95

Figure S119. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18p gain' versus 'MRNASEQ_CNMF'

P value = 0.0089 (Fisher's exact test), Q value = 0.023

Table S120. Gene #32: '18p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
18P GAIN MUTATED	5	6	10	6	18
18P GAIN WILD-TYPE	60	56	36	31	44

Figure S120. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'18p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00144 (Fisher's exact test), Q value = 0.005

Table S121. Gene #32: '18p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
18P GAIN MUTATED	3	0	4	16	9	12	1
18P GAIN WILD-TYPE	35	21	45	46	32	28	20

Figure S121. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.00086

Table S122. Gene #32: '18p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
18P GAIN MUTATED	27	18	39
18P GAIN WILD-TYPE	159	115	82

Figure S122. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'18p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

Table S123. Gene #32: '18p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
18P GAIN MUTATED	14	23	9	38
18P GAIN WILD-TYPE	65	152	70	69

Figure S123. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00379 (Fisher's exact test), Q value = 0.011

Table S124. Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
18P GAIN MUTATED	27	7	12	10	3	8
18P GAIN WILD-TYPE	49	51	48	48	33	50

Figure S124. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'18p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00999 (Fisher's exact test), Q value = 0.026

Table S125. Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
18P GAIN MUTATED	39	7	21
18P GAIN WILD-TYPE	162	66	51

Figure S125. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q gain' versus 'CN_CNMF'

P value = 0.00634 (Fisher's exact test), Q value = 0.018

Table S126. Gene #33: '18q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
18Q GAIN MUTATED	22	12	3	13	4
18Q GAIN WILD-TYPE	101	175	33	63	15

Figure S126. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #1: 'CN_CNMF'

'18q gain' versus 'METHLYATION_CNMF'

P value = 0.00291 (Fisher's exact test), Q value = 0.009

Table S127. Gene #33: '18q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
18Q GAIN MUTATED	24	13	0	11
18Q GAIN WILD-TYPE	100	108	42	95

Figure S127. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0224 (Fisher's exact test), Q value = 0.052

Table S128. Gene #33: '18q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
18Q GAIN MUTATED	1	0	4	12	7	8	1
18Q GAIN WILD-TYPE	37	21	45	50	34	32	20

Figure S128. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_CNMF'

P value = 0.0157 (Fisher's exact test), Q value = 0.039

Table S129. Gene #33: '18q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
18Q GAIN MUTATED	17	13	24
18Q GAIN WILD-TYPE	169	120	97

Figure S129. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'18q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0221 (Fisher's exact test), Q value = 0.051

Table S130. Gene #33: '18q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
18Q GAIN MUTATED	10	14	8	22
18Q GAIN WILD-TYPE	69	161	71	85

Figure S130. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0366 (Fisher's exact test), Q value = 0.076

Table S131. Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
18Q GAIN MUTATED	19	7	15
18Q GAIN WILD-TYPE	182	66	57

Figure S131. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p gain' versus 'CN_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00048

Table S132. Gene #34: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
19P GAIN MUTATED	22	9	8	15	0
19P GAIN WILD-TYPE	101	178	28	61	19

Figure S132. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

'19q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S133. Gene #35: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
19Q GAIN MUTATED	36	13	9	20	0
19Q GAIN WILD-TYPE	87	174	27	56	19

Figure S133. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

'19q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0435 (Fisher's exact test), Q value = 0.088

Table S134. Gene #35: '19q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	83	55	91
19Q GAIN MUTATED	3	21	11	10
19Q GAIN WILD-TYPE	31	62	44	81

Figure S134. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 0.0161 (Fisher's exact test), Q value = 0.04

Table S135. Gene #35: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
19Q GAIN MUTATED	10	6	8	4	20
19Q GAIN WILD-TYPE	55	56	38	33	42

Figure S135. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19q gain' versus 'MIRSEQ_CNMF'

P value = 0.0163 (Fisher's exact test), Q value = 0.04

Table S136. Gene #35: '19q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
19Q GAIN MUTATED	30	16	31
19Q GAIN WILD-TYPE	156	117	90

Figure S136. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'19q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00723 (Fisher's exact test), Q value = 0.02

Table S137. Gene #35: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
19Q GAIN MUTATED	22	6	5	11	9	6
19Q GAIN WILD-TYPE	54	52	55	47	27	52

Figure S137. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S138. Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
20P GAIN MUTATED	93	58	25	52	15
20P GAIN WILD-TYPE	30	129	11	24	4

Figure S138. 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 = 6.7e-05

Table S139. Gene #36: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
20P GAIN MUTATED	92	53	29	42
20P GAIN WILD-TYPE	32	68	13	64

Figure S139. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 5e-04 (Fisher's exact test), Q value = 0.002

Table S140. Gene #36: '20p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
20P GAIN MUTATED	27	27	20	23	46
20P GAIN WILD-TYPE	38	35	26	14	16

Figure S140. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S141. Gene #36: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
20P GAIN MUTATED	16	19	17	28	29	32	2
20P GAIN WILD-TYPE	22	2	32	34	12	8	19

Figure S141. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00017

Table S142. Gene #36: '20p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
20P GAIN MUTATED	89	64	89
20P GAIN WILD-TYPE	97	69	32

Figure S142. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S143. Gene #36: '20p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
20P GAIN MUTATED	39	84	36	83
20P GAIN WILD-TYPE	40	91	43	24

Figure S143. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00017

Table S144. Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
20P GAIN MUTATED	59	24	28	26	23	25
20P GAIN WILD-TYPE	17	34	32	32	13	33

Figure S144. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S145. Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
20Q GAIN MUTATED	108	66	31	59	15
20Q GAIN WILD-TYPE	15	121	5	17	4

Figure S145. 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 = 6.7e-05

Table S146. Gene #37: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
20Q GAIN MUTATED	112	58	31	50
20Q GAIN WILD-TYPE	12	63	11	56

Figure S146. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S147. Gene #37: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

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

Figure S147. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S148. Gene #37: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

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

Figure S148. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S149. Gene #37: '20q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
20Q GAIN MUTATED	102	74	102
20Q GAIN WILD-TYPE	84	59	19

Figure S149. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S150. Gene #37: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
20Q GAIN MUTATED	41	100	40	97
20Q GAIN WILD-TYPE	38	75	39	10

Figure S150. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00017

Table S151. Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
20Q GAIN MUTATED	64	28	34	35	27	29
20Q GAIN WILD-TYPE	12	30	26	23	9	29

Figure S151. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'21q gain' versus 'CN_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 9e-04

Table S152. Gene #38: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
21Q GAIN MUTATED	14	1	1	5	0
21Q GAIN WILD-TYPE	109	186	35	71	19

Figure S152. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

'21q gain' versus 'METHLYATION_CNMF'

P value = 0.00149 (Fisher's exact test), Q value = 0.0051

Table S153. Gene #38: '21q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
21Q GAIN MUTATED	14	5	0	1
21Q GAIN WILD-TYPE	110	116	42	105

Figure S153. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'21q gain' versus 'MRNASEQ_CNMF'

P value = 0.0103 (Fisher's exact test), Q value = 0.027

Table S154. Gene #38: '21q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
21Q GAIN MUTATED	1	1	1	4	8
21Q GAIN WILD-TYPE	64	61	45	33	54

Figure S154. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'21q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0305 (Fisher's exact test), Q value = 0.066

Table S155. Gene #38: '21q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
21Q GAIN MUTATED	0	0	0	6	3	5	1
21Q GAIN WILD-TYPE	38	21	49	56	38	35	20

Figure S155. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'21q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 4e-04

Table S156. Gene #38: '21q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
21Q GAIN MUTATED	5	3	0	13
21Q GAIN WILD-TYPE	74	172	79	94

Figure S156. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'21q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.029 (Fisher's exact test), Q value = 0.063

Table S157. Gene #38: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
21Q GAIN MUTATED	12	0	6
21Q GAIN WILD-TYPE	189	73	66

Figure S157. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q gain' versus 'CN_CNMF'

P value = 0.00197 (Fisher's exact test), Q value = 0.0064

Table S158. Gene #39: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
22Q GAIN MUTATED	17	5	4	6	0
22Q GAIN WILD-TYPE	106	182	32	70	19

Figure S158. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

'22q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.028 (Fisher's exact test), Q value = 0.061

Table S159. Gene #39: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
22Q GAIN MUTATED	8	2	4	10	0	3
22Q GAIN WILD-TYPE	68	56	56	48	36	55

Figure S159. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xp gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S160. Gene #40: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
XP GAIN MUTATED	20	6	10	7	5
XP GAIN WILD-TYPE	103	181	26	69	14

Figure S160. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'

'xp gain' versus 'METHLYATION_CNMF'

P value = 0.00103 (Fisher's exact test), Q value = 0.0038

Table S161. Gene #40: 'xp gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
XP GAIN MUTATED	22	14	2	3
XP GAIN WILD-TYPE	102	107	40	103

Figure S161. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xp gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0206 (Fisher's exact test), Q value = 0.048

Table S162. Gene #40: 'xp gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
XP GAIN MUTATED	6	2	2	8	11	7	0
XP GAIN WILD-TYPE	32	19	47	54	30	33	21

Figure S162. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xp gain' versus 'MIRSEQ_CNMF'

P value = 0.0247 (Fisher's exact test), Q value = 0.056

Table S163. Gene #40: 'xp gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
XP GAIN MUTATED	18	9	21
XP GAIN WILD-TYPE	168	124	100

Figure S163. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'xq gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S164. Gene #41: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
XQ GAIN MUTATED	27	9	11	5	4
XQ GAIN WILD-TYPE	96	178	25	71	15

Figure S164. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

'xq gain' versus 'METHLYATION_CNMF'

P value = 0.0264 (Fisher's exact test), Q value = 0.059

Table S165. Gene #41: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
XQ GAIN MUTATED	21	19	2	7
XQ GAIN WILD-TYPE	103	102	40	99

Figure S165. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq gain' versus 'MRNASEQ_CNMF'

P value = 0.0345 (Fisher's exact test), Q value = 0.073

Table S166. Gene #41: 'xq gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
XQ GAIN MUTATED	3	8	7	9	12
XQ GAIN WILD-TYPE	62	54	39	28	50

Figure S166. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xq gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00038 (Fisher's exact test), Q value = 0.0016

Table S167. Gene #41: 'xq gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
XQ GAIN MUTATED	6	2	3	8	16	4	0
XQ GAIN WILD-TYPE	32	19	46	54	25	36	21

Figure S167. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
1P LOSS MUTATED	38	2	3	15	1
1P LOSS WILD-TYPE	85	185	33	61	18

Figure S168. 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 = 6.7e-05

Table S169. Gene #42: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
1P LOSS MUTATED	34	12	2	6
1P LOSS WILD-TYPE	90	109	40	100

Figure S169. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1p loss' versus 'RPPA_CNMF'

P value = 0.0318 (Fisher's exact test), Q value = 0.068

Table S170. Gene #42: '1p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	90	91
1P LOSS MUTATED	5	11	18
1P LOSS WILD-TYPE	77	79	73

Figure S170. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00762 (Fisher's exact test), Q value = 0.021

Table S171. Gene #42: '1p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
1P LOSS MUTATED	5	1	1	5	8	9	0
1P LOSS WILD-TYPE	33	20	48	57	33	31	21

Figure S171. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_CNMF'

P value = 0.00898 (Fisher's exact test), Q value = 0.024

Table S172. Gene #42: '1p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
1P LOSS MUTATED	20	12	26
1P LOSS WILD-TYPE	166	121	95

Figure S172. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'1p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0038 (Fisher's exact test), Q value = 0.011

Table S173. Gene #42: '1p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
1P LOSS MUTATED	11	15	7	25
1P LOSS WILD-TYPE	68	160	72	82

Figure S173. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00723 (Fisher's exact test), Q value = 0.02

Table S174. Gene #42: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
1P LOSS MUTATED	18	2	11	5	5	5
1P LOSS WILD-TYPE	58	56	49	53	31	53

Figure S174. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'1q loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

Table S175. Gene #43: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
1Q LOSS MUTATED	16	1	1	9	1
1Q LOSS WILD-TYPE	107	186	35	67	18

Figure S175. Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

'1q loss' versus 'METHLYATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00044

Table S176. Gene #43: '1q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
1Q LOSS MUTATED	20	4	1	2
1Q LOSS WILD-TYPE	104	117	41	104

Figure S176. Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1q loss' versus 'RPPA_CNMF'

P value = 0.0339 (Fisher's exact test), Q value = 0.071

Table S177. Gene #43: '1q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	90	91
1Q LOSS MUTATED	2	4	11
1Q LOSS WILD-TYPE	80	86	80

Figure S177. Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'2p loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

Table S178. Gene #44: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
2P LOSS MUTATED	15	1	2	8	0
2P LOSS WILD-TYPE	108	186	34	68	19

Figure S178. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

'2p loss' versus 'METHLYATION_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.0014

Table S179. Gene #44: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
2P LOSS MUTATED	18	4	0	3
2P LOSS WILD-TYPE	106	117	42	103

Figure S179. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2p loss' versus 'MRNASEQ_CNMF'

P value = 0.0119 (Fisher's exact test), Q value = 0.03

Table S180. Gene #44: '2p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
2P LOSS MUTATED	0	1	3	3	7
2P LOSS WILD-TYPE	65	61	43	34	55

Figure S180. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2p loss' versus 'MIRSEQ_CNMF'

P value = 0.0414 (Fisher's exact test), Q value = 0.085

Table S181. Gene #44: '2p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
2P LOSS MUTATED	7	6	13
2P LOSS WILD-TYPE	179	127	108

Figure S181. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'2q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S182. Gene #45: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
2Q LOSS MUTATED	20	1	3	9	0
2Q LOSS WILD-TYPE	103	186	33	67	19

Figure S182. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

'2q loss' versus 'METHLYATION_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.0014

Table S183. Gene #45: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
2Q LOSS MUTATED	20	6	0	4
2Q LOSS WILD-TYPE	104	115	42	102

Figure S183. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2q loss' versus 'MRNASEQ_CNMF'

P value = 0.00964 (Fisher's exact test), Q value = 0.025

Table S184. Gene #45: '2q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
2Q LOSS MUTATED	0	1	4	3	7
2Q LOSS WILD-TYPE	65	61	42	34	55

Figure S184. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2q loss' versus 'MIRSEQ_CNMF'

P value = 0.0233 (Fisher's exact test), Q value = 0.053

Table S185. Gene #45: '2q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
2Q LOSS MUTATED	9	8	16
2Q LOSS WILD-TYPE	177	125	105

Figure S185. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'2q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0329 (Fisher's exact test), Q value = 0.07

Table S186. Gene #45: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
2Q LOSS MUTATED	3	12	3	15
2Q LOSS WILD-TYPE	76	163	76	92

Figure S186. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S187. Gene #46: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
3P LOSS MUTATED	45	10	8	24	4
3P LOSS WILD-TYPE	78	177	28	52	15

Figure S187. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00017

Table S188. Gene #46: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
3P LOSS MUTATED	43	26	4	11
3P LOSS WILD-TYPE	81	95	38	95

Figure S188. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 0.00318 (Fisher's exact test), Q value = 0.0097

Table S189. Gene #46: '3p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
3P LOSS MUTATED	6	7	6	8	21
3P LOSS WILD-TYPE	59	55	40	29	41

Figure S189. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00034 (Fisher's exact test), Q value = 0.0014

Table S190. Gene #46: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

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

Figure S190. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CNMF'

P value = 0.00157 (Fisher's exact test), Q value = 0.0054

Table S191. Gene #46: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
3P LOSS MUTATED	29	23	39
3P LOSS WILD-TYPE	157	110	82

Figure S191. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00106 (Fisher's exact test), Q value = 0.0039

Table S192. Gene #46: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
3P LOSS MUTATED	18	25	12	36
3P LOSS WILD-TYPE	61	150	67	71

Figure S192. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0207 (Fisher's exact test), Q value = 0.048

Table S193. Gene #46: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
3P LOSS MUTATED	50	8	11
3P LOSS WILD-TYPE	151	65	61

Figure S193. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
3Q LOSS MUTATED	32	3	7	11	1
3Q LOSS WILD-TYPE	91	184	29	65	18

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

'3q loss' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00026

Table S195. Gene #47: '3q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
3Q LOSS MUTATED	29	15	1	5
3Q LOSS WILD-TYPE	95	106	41	101

Figure S195. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3q loss' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

Table S196. Gene #47: '3q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
3Q LOSS MUTATED	2	3	0	6	17
3Q LOSS WILD-TYPE	63	59	46	31	45

Figure S196. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S197. Gene #47: '3q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
3Q LOSS MUTATED	3	0	1	1	10	13	0
3Q LOSS WILD-TYPE	35	21	48	61	31	27	21

Figure S197. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_CNMF'

P value = 0.0271 (Fisher's exact test), Q value = 0.06

Table S198. Gene #47: '3q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
3Q LOSS MUTATED	16	15	23
3Q LOSS WILD-TYPE	170	118	98

Figure S198. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0124 (Fisher's exact test), Q value = 0.031

Table S199. Gene #47: '3q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
3Q LOSS MUTATED	9	14	8	23
3Q LOSS WILD-TYPE	70	161	71	84

Figure S199. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00165 (Fisher's exact test), Q value = 0.0055

Table S200. Gene #47: '3q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
3Q LOSS MUTATED	34	5	2
3Q LOSS WILD-TYPE	167	68	70

Figure S200. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S201. Gene #48: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
4P LOSS MUTATED	76	27	12	47	5
4P LOSS WILD-TYPE	47	160	24	29	14

Figure S201. 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 = 6.7e-05

Table S202. Gene #48: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
4P LOSS MUTATED	73	38	4	33
4P LOSS WILD-TYPE	51	83	38	73

Figure S202. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 0.00053 (Fisher's exact test), Q value = 0.0021

Table S203. Gene #48: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
4P LOSS MUTATED	12	22	15	10	34
4P LOSS WILD-TYPE	53	40	31	27	28

Figure S203. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.00086

Table S204. Gene #48: '4p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
4P LOSS MUTATED	11	2	18	17	17	25	3
4P LOSS WILD-TYPE	27	19	31	45	24	15	18

Figure S204. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

Table S205. Gene #48: '4p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
4P LOSS MUTATED	55	42	70
4P LOSS WILD-TYPE	131	91	51

Figure S205. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'4p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S206. Gene #48: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
4P LOSS MUTATED	22	51	25	69
4P LOSS WILD-TYPE	57	124	54	38

Figure S206. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.0017

Table S207. Gene #48: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
4P LOSS MUTATED	46	19	15	17	13	22
4P LOSS WILD-TYPE	30	39	45	41	23	36

Figure S207. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'4q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S208. Gene #49: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
4Q LOSS MUTATED	72	26	10	51	5
4Q LOSS WILD-TYPE	51	161	26	25	14

Figure S208. 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 = 6.7e-05

Table S209. Gene #49: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
4Q LOSS MUTATED	71	39	4	34
4Q LOSS WILD-TYPE	53	82	38	72

Figure S209. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0324 (Fisher's exact test), Q value = 0.069

Table S210. Gene #49: '4q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	83	55	91
4Q LOSS MUTATED	11	38	12	35
4Q LOSS WILD-TYPE	23	45	43	56

Figure S210. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 0.0052 (Fisher's exact test), Q value = 0.015

Table S211. Gene #49: '4q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
4Q LOSS MUTATED	12	22	16	11	31
4Q LOSS WILD-TYPE	53	40	30	26	31

Figure S211. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00143 (Fisher's exact test), Q value = 0.005

Table S212. Gene #49: '4q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
4Q LOSS MUTATED	13	2	17	17	17	23	3
4Q LOSS WILD-TYPE	25	19	32	45	24	17	18

Figure S212. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00022

Table S213. Gene #49: '4q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
4Q LOSS MUTATED	54	44	66
4Q LOSS WILD-TYPE	132	89	55

Figure S213. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'4q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S214. Gene #49: '4q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
4Q LOSS MUTATED	23	51	24	66
4Q LOSS WILD-TYPE	56	124	55	41

Figure S214. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0057 (Fisher's exact test), Q value = 0.016

Table S215. Gene #49: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
4Q LOSS MUTATED	44	18	17	20	12	22
4Q LOSS WILD-TYPE	32	40	43	38	24	36

Figure S215. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'5p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S216. Gene #50: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
5P LOSS MUTATED	28	5	4	19	4
5P LOSS WILD-TYPE	95	182	32	57	15

Figure S216. 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 = 0.00026

Table S217. Gene #50: '5p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
5P LOSS MUTATED	31	17	1	6
5P LOSS WILD-TYPE	93	104	41	100

Figure S217. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p loss' versus 'MRNASEQ_CNMF'

P value = 0.00219 (Fisher's exact test), Q value = 0.0069

Table S218. Gene #50: '5p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
5P LOSS MUTATED	6	2	2	5	15
5P LOSS WILD-TYPE	59	60	44	32	47

Figure S218. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.012 (Fisher's exact test), Q value = 0.031

Table S219. Gene #50: '5p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
5P LOSS MUTATED	4	1	1	6	6	11	1
5P LOSS WILD-TYPE	34	20	48	56	35	29	20

Figure S219. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.0015

Table S220. Gene #50: '5p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
5P LOSS MUTATED	17	13	30
5P LOSS WILD-TYPE	169	120	91

Figure S220. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'5p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.00057

Table S221. Gene #50: '5p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
5P LOSS MUTATED	10	15	6	29
5P LOSS WILD-TYPE	69	160	73	78

Figure S221. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00342 (Fisher's exact test), Q value = 0.01

Table S222. Gene #50: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
5P LOSS MUTATED	23	6	6	5	6	5
5P LOSS WILD-TYPE	53	52	54	53	30	53

Figure S222. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'5q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S223. Gene #51: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
5Q LOSS MUTATED	58	6	9	27	6
5Q LOSS WILD-TYPE	65	181	27	49	13

Figure S223. 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 = 6.7e-05

Table S224. Gene #51: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
5Q LOSS MUTATED	61	24	3	11
5Q LOSS WILD-TYPE	63	97	39	95

Figure S224. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S225. Gene #51: '5q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
5Q LOSS MUTATED	10	3	5	7	28
5Q LOSS WILD-TYPE	55	59	41	30	34

Figure S225. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00017

Table S226. Gene #51: '5q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

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

Figure S226. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S227. Gene #51: '5q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
5Q LOSS MUTATED	33	20	53
5Q LOSS WILD-TYPE	153	113	68

Figure S227. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S228. Gene #51: '5q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
5Q LOSS MUTATED	13	30	9	54
5Q LOSS WILD-TYPE	66	145	70	53

Figure S228. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

Table S229. Gene #51: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
5Q LOSS MUTATED	39	12	11	10	9	10
5Q LOSS WILD-TYPE	37	46	49	48	27	48

Figure S229. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'5q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00348 (Fisher's exact test), Q value = 0.01

Table S230. Gene #51: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
5Q LOSS MUTATED	64	9	18
5Q LOSS WILD-TYPE	137	64	54

Figure S230. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S231. Gene #52: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
6P LOSS MUTATED	17	7	5	20	3
6P LOSS WILD-TYPE	106	180	31	56	16

Figure S231. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

'6p loss' versus 'METHLYATION_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.00086

Table S232. Gene #52: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
6P LOSS MUTATED	28	12	0	9
6P LOSS WILD-TYPE	96	109	42	97

Figure S232. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p loss' versus 'MRNASEQ_CNMF'

P value = 0.0226 (Fisher's exact test), Q value = 0.052

Table S233. Gene #52: '6p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
6P LOSS MUTATED	3	2	7	3	11
6P LOSS WILD-TYPE	62	60	39	34	51

Figure S233. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00863 (Fisher's exact test), Q value = 0.023

Table S234. Gene #52: '6p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
6P LOSS MUTATED	6	0	1	6	4	9	0
6P LOSS WILD-TYPE	32	21	48	56	37	31	21

Figure S234. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0161 (Fisher's exact test), Q value = 0.04

Table S235. Gene #52: '6p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
6P LOSS MUTATED	5	21	5	21
6P LOSS WILD-TYPE	74	154	74	86

Figure S235. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0334 (Fisher's exact test), Q value = 0.071

Table S236. Gene #52: '6p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
6P LOSS MUTATED	14	10	7	2	5	3
6P LOSS WILD-TYPE	62	48	53	56	31	55

Figure S236. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'6q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S237. Gene #53: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
6Q LOSS MUTATED	22	11	8	25	4
6Q LOSS WILD-TYPE	101	176	28	51	15

Figure S237. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

'6q loss' versus 'METHLYATION_CNMF'

P value = 0.00131 (Fisher's exact test), Q value = 0.0047

Table S238. Gene #53: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
6Q LOSS MUTATED	33	14	2	14
6Q LOSS WILD-TYPE	91	107	40	92

Figure S238. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p loss' versus 'CN_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.0019

Table S239. Gene #54: '7p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
7P LOSS MUTATED	12	1	1	6	0
7P LOSS WILD-TYPE	111	186	35	70	19

Figure S239. Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #1: 'CN_CNMF'

'7p loss' versus 'METHLYATION_CNMF'

P value = 0.00161 (Fisher's exact test), Q value = 0.0055

Table S240. Gene #54: '7p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
7P LOSS MUTATED	13	2	1	1
7P LOSS WILD-TYPE	111	119	41	105

Figure S240. Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p loss' versus 'MRNASEQ_CNMF'

P value = 0.00161 (Fisher's exact test), Q value = 0.0055

Table S241. Gene #54: '7p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
7P LOSS MUTATED	1	1	0	0	8
7P LOSS WILD-TYPE	64	61	46	37	54

Figure S241. Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7p loss' versus 'MIRSEQ_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 9e-04

Table S242. Gene #54: '7p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
7P LOSS MUTATED	3	3	14
7P LOSS WILD-TYPE	183	130	107

Figure S242. Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'7p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0225 (Fisher's exact test), Q value = 0.052

Table S243. Gene #54: '7p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
7P LOSS MUTATED	2	4	3	11
7P LOSS WILD-TYPE	77	171	76	96

Figure S243. Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00196 (Fisher's exact test), Q value = 0.0064

Table S244. Gene #54: '7p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
7P LOSS MUTATED	10	1	1	1	1	0
7P LOSS WILD-TYPE	66	57	59	57	35	58

Figure S244. Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'7q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S245. Gene #55: '7q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
7Q LOSS MUTATED	16	1	0	12	1
7Q LOSS WILD-TYPE	107	186	36	64	18

Figure S245. Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #1: 'CN_CNMF'

'7q loss' versus 'METHLYATION_CNMF'

P value = 0.00215 (Fisher's exact test), Q value = 0.0069

Table S246. Gene #55: '7q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
7Q LOSS MUTATED	16	9	0	2
7Q LOSS WILD-TYPE	108	112	42	104

Figure S246. Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q loss' versus 'MRNASEQ_CNMF'

P value = 0.00561 (Fisher's exact test), Q value = 0.016

Table S247. Gene #55: '7q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
7Q LOSS MUTATED	1	3	2	1	11
7Q LOSS WILD-TYPE	64	59	44	36	51

Figure S247. Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7q loss' versus 'MIRSEQ_CNMF'

P value = 0.00791 (Fisher's exact test), Q value = 0.022

Table S248. Gene #55: '7q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
7Q LOSS MUTATED	9	5	16
7Q LOSS WILD-TYPE	177	128	105

Figure S248. Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'7q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0469 (Fisher's exact test), Q value = 0.094

Table S249. Gene #55: '7q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
7Q LOSS MUTATED	12	2	2	3	3	2
7Q LOSS WILD-TYPE	64	56	58	55	33	56

Figure S249. Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'8p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S250. Gene #56: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
8P LOSS MUTATED	38	13	9	27	1
8P LOSS WILD-TYPE	85	174	27	49	18

Figure S250. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 0.00202 (Fisher's exact test), Q value = 0.0065

Table S251. Gene #56: '8p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
8P LOSS MUTATED	38	24	3	15
8P LOSS WILD-TYPE	86	97	39	91

Figure S251. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 0.0174 (Fisher's exact test), Q value = 0.042

Table S252. Gene #56: '8p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
8P LOSS MUTATED	9	5	6	6	19
8P LOSS WILD-TYPE	56	57	40	31	43

Figure S252. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00114 (Fisher's exact test), Q value = 0.0041

Table S253. Gene #56: '8p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
8P LOSS MUTATED	7	2	2	8	11	14	1
8P LOSS WILD-TYPE	31	19	47	54	30	26	20

Figure S253. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_CNMF'

P value = 0.00185 (Fisher's exact test), Q value = 0.006

Table S254. Gene #56: '8p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
8P LOSS MUTATED	40	14	33
8P LOSS WILD-TYPE	146	119	88

Figure S254. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'8p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00646 (Fisher's exact test), Q value = 0.018

Table S255. Gene #56: '8p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
8P LOSS MUTATED	20	34	6	27
8P LOSS WILD-TYPE	59	141	73	80

Figure S255. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0192 (Fisher's exact test), Q value = 0.046

Table S256. Gene #56: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
8P LOSS MUTATED	25	15	9	9	7	6
8P LOSS WILD-TYPE	51	43	51	49	29	52

Figure S256. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'8p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S257. Gene #56: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
8P LOSS MUTATED	53	2	16
8P LOSS WILD-TYPE	148	71	56

Figure S257. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q loss' versus 'CN_CNMF'

P value = 9e-04 (Fisher's exact test), Q value = 0.0034

Table S258. Gene #57: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
8Q LOSS MUTATED	13	5	7	8	0
8Q LOSS WILD-TYPE	110	182	29	68	19

Figure S258. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

'8q loss' versus 'MIRSEQ_CNMF'

P value = 0.0244 (Fisher's exact test), Q value = 0.055

Table S259. Gene #57: '8q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
8Q LOSS MUTATED	21	6	5
8Q LOSS WILD-TYPE	165	127	116

Figure S259. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'8q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0319 (Fisher's exact test), Q value = 0.068

Table S260. Gene #57: '8q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
8Q LOSS MUTATED	7	10	3	2	3	1
8Q LOSS WILD-TYPE	69	48	57	56	33	57

Figure S260. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S261. Gene #58: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
9P LOSS MUTATED	58	14	16	53	9
9P LOSS WILD-TYPE	65	173	20	23	10

Figure S261. 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 = 6.7e-05

Table S262. Gene #58: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
9P LOSS MUTATED	73	34	1	28
9P LOSS WILD-TYPE	51	87	41	78

Figure S262. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p loss' versus 'RPPA_CNMF'

P value = 0.00224 (Fisher's exact test), Q value = 0.007

Table S263. Gene #58: '9p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	90	91
9P LOSS MUTATED	15	28	39
9P LOSS WILD-TYPE	67	62	52

Figure S263. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'9p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00033 (Fisher's exact test), Q value = 0.0014

Table S264. Gene #58: '9p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	83	55	91
9P LOSS MUTATED	6	38	8	30
9P LOSS WILD-TYPE	28	45	47	61

Figure S264. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S265. Gene #58: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
9P LOSS MUTATED	7	12	19	9	36
9P LOSS WILD-TYPE	58	50	27	28	26

Figure S265. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.00094

Table S266. Gene #58: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
9P LOSS MUTATED	12	1	10	24	13	21	2
9P LOSS WILD-TYPE	26	20	39	38	28	19	19

Figure S266. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S267. Gene #58: '9p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
9P LOSS MUTATED	48	38	63
9P LOSS WILD-TYPE	138	95	58

Figure S267. 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 = 6.7e-05

Table S268. Gene #58: '9p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
9P LOSS MUTATED	21	49	19	60
9P LOSS WILD-TYPE	58	126	60	47

Figure S268. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.02 (Fisher's exact test), Q value = 0.047

Table S269. Gene #58: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
9P LOSS MUTATED	40	17	18	18	14	16
9P LOSS WILD-TYPE	36	41	42	40	22	42

Figure S269. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'9q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S270. Gene #59: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
9Q LOSS MUTATED	41	12	11	35	5
9Q LOSS WILD-TYPE	82	175	25	41	14

Figure S270. 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 = 6.7e-05

Table S271. Gene #59: '9q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
9Q LOSS MUTATED	49	21	2	22
9Q LOSS WILD-TYPE	75	100	40	84

Figure S271. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0154 (Fisher's exact test), Q value = 0.038

Table S272. Gene #59: '9q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	83	55	91
9Q LOSS MUTATED	5	27	6	22
9Q LOSS WILD-TYPE	29	56	49	69

Figure S272. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00017

Table S273. Gene #59: '9q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
9Q LOSS MUTATED	7	10	14	4	28
9Q LOSS WILD-TYPE	58	52	32	33	34

Figure S273. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00925 (Fisher's exact test), Q value = 0.024

Table S274. Gene #59: '9q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
9Q LOSS MUTATED	6	2	9	18	8	18	2
9Q LOSS WILD-TYPE	32	19	40	44	33	22	19

Figure S274. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00017

Table S275. Gene #59: '9q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
9Q LOSS MUTATED	31	24	49
9Q LOSS WILD-TYPE	155	109	72

Figure S275. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'9q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

Table S276. Gene #59: '9q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
9Q LOSS MUTATED	13	33	12	46
9Q LOSS WILD-TYPE	66	142	67	61

Figure S276. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0136 (Fisher's exact test), Q value = 0.034

Table S277. Gene #59: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
9Q LOSS MUTATED	30	9	10	13	10	11
9Q LOSS WILD-TYPE	46	49	50	45	26	47

Figure S277. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'10p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S278. Gene #60: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
10P LOSS MUTATED	34	8	3	12	7
10P LOSS WILD-TYPE	89	179	33	64	12

Figure S278. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 0.00066 (Fisher's exact test), Q value = 0.0026

Table S279. Gene #60: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
10P LOSS MUTATED	30	15	1	10
10P LOSS WILD-TYPE	94	106	41	96

Figure S279. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 0.015 (Fisher's exact test), Q value = 0.037

Table S280. Gene #60: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
10P LOSS MUTATED	4	2	8	5	12
10P LOSS WILD-TYPE	61	60	38	32	50

Figure S280. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10p loss' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

Table S281. Gene #60: '10p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
10P LOSS MUTATED	24	8	32
10P LOSS WILD-TYPE	162	125	89

Figure S281. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'10p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00034 (Fisher's exact test), Q value = 0.0014

Table S282. Gene #60: '10p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
10P LOSS MUTATED	12	25	2	25
10P LOSS WILD-TYPE	67	150	77	82

Figure S282. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S283. Gene #61: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
10Q LOSS MUTATED	42	6	7	7	5
10Q LOSS WILD-TYPE	81	181	29	69	14

Figure S283. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S284. Gene #61: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
10Q LOSS MUTATED	35	13	1	9
10Q LOSS WILD-TYPE	89	108	41	97

Figure S284. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0498 (Fisher's exact test), Q value = 0.099

Table S285. Gene #61: '10q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	83	55	91
10Q LOSS MUTATED	4	16	2	11
10Q LOSS WILD-TYPE	30	67	53	80

Figure S285. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 0.00181 (Fisher's exact test), Q value = 0.0059

Table S286. Gene #61: '10q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
10Q LOSS MUTATED	4	2	5	7	15
10Q LOSS WILD-TYPE	61	60	41	30	47

Figure S286. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00217 (Fisher's exact test), Q value = 0.0069

Table S287. Gene #61: '10q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
10Q LOSS MUTATED	3	0	3	7	12	8	0
10Q LOSS WILD-TYPE	35	21	46	55	29	32	21

Figure S287. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S288. Gene #61: '10q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
10Q LOSS MUTATED	27	8	32
10Q LOSS WILD-TYPE	159	125	89

Figure S288. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00048

Table S289. Gene #61: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
10Q LOSS MUTATED	14	18	5	30
10Q LOSS WILD-TYPE	65	157	74	77

Figure S289. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S290. Gene #62: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
11P LOSS MUTATED	33	7	6	16	0
11P LOSS WILD-TYPE	90	180	30	60	19

Figure S290. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 0.00112 (Fisher's exact test), Q value = 0.004

Table S291. Gene #62: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
11P LOSS MUTATED	29	13	1	11
11P LOSS WILD-TYPE	95	108	41	95

Figure S291. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11p loss' versus 'RPPA_CNMF'

P value = 0.0177 (Fisher's exact test), Q value = 0.043

Table S292. Gene #62: '11p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	90	91
11P LOSS MUTATED	5	11	19
11P LOSS WILD-TYPE	77	79	72

Figure S292. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'11p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.017 (Fisher's exact test), Q value = 0.041

Table S293. Gene #62: '11p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
11P LOSS MUTATED	7	25	6	24
11P LOSS WILD-TYPE	72	150	73	83

Figure S293. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00044

Table S294. Gene #63: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
11Q LOSS MUTATED	28	10	6	15	2
11Q LOSS WILD-TYPE	95	177	30	61	17

Figure S294. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

P value = 0.02 (Fisher's exact test), Q value = 0.047

Table S295. Gene #63: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
11Q LOSS MUTATED	27	14	2	12
11Q LOSS WILD-TYPE	97	107	40	94

Figure S295. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S296. Gene #64: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
12P LOSS MUTATED	41	2	5	13	2
12P LOSS WILD-TYPE	82	185	31	63	17

Figure S296. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

'12p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S297. Gene #64: '12p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
12P LOSS MUTATED	41	6	1	5
12P LOSS WILD-TYPE	83	115	41	101

Figure S297. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p loss' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00022

Table S298. Gene #64: '12p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
12P LOSS MUTATED	3	3	6	3	20
12P LOSS WILD-TYPE	62	59	40	34	42

Figure S298. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S299. Gene #64: '12p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
12P LOSS MUTATED	2	0	2	10	4	17	0
12P LOSS WILD-TYPE	36	21	47	52	37	23	21

Figure S299. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12p loss' versus 'MIRSEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 4e-04

Table S300. Gene #64: '12p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
12P LOSS MUTATED	20	11	32
12P LOSS WILD-TYPE	166	122	89

Figure S300. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'12p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

Table S301. Gene #64: '12p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
12P LOSS MUTATED	6	19	6	32
12P LOSS WILD-TYPE	73	156	73	75

Figure S301. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0319 (Fisher's exact test), Q value = 0.068

Table S302. Gene #64: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
12P LOSS MUTATED	33	4	13
12P LOSS WILD-TYPE	168	69	59

Figure S302. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S303. Gene #65: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
12Q LOSS MUTATED	34	1	3	12	2
12Q LOSS WILD-TYPE	89	186	33	64	17

Figure S303. Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'

'12q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S304. Gene #65: '12q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
12Q LOSS MUTATED	33	5	0	7
12Q LOSS WILD-TYPE	91	116	42	99

Figure S304. Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12q loss' versus 'MRNASEQ_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.0018

Table S305. Gene #65: '12q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
12Q LOSS MUTATED	2	2	6	3	15
12Q LOSS WILD-TYPE	63	60	40	34	47

Figure S305. Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00061 (Fisher's exact test), Q value = 0.0024

Table S306. Gene #65: '12q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
12Q LOSS MUTATED	1	0	1	10	4	11	1
12Q LOSS WILD-TYPE	37	21	48	52	37	29	20

Figure S306. Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00106 (Fisher's exact test), Q value = 0.0039

Table S307. Gene #65: '12q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
12Q LOSS MUTATED	7	15	5	25
12Q LOSS WILD-TYPE	72	160	74	82

Figure S307. Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 0.00349 (Fisher's exact test), Q value = 0.01

Table S308. Gene #66: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
13Q LOSS MUTATED	12	7	2	14	1
13Q LOSS WILD-TYPE	111	180	34	62	18

Figure S308. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

'14q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S309. Gene #67: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
14Q LOSS MUTATED	47	17	5	37	5
14Q LOSS WILD-TYPE	76	170	31	39	14

Figure S309. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S310. Gene #67: '14q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
14Q LOSS MUTATED	55	24	5	16
14Q LOSS WILD-TYPE	69	97	37	90

Figure S310. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 0.00111 (Fisher's exact test), Q value = 0.004

Table S311. Gene #67: '14q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
14Q LOSS MUTATED	9	13	11	5	27
14Q LOSS WILD-TYPE	56	49	35	32	35

Figure S311. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00845 (Fisher's exact test), Q value = 0.023

Table S312. Gene #67: '14q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
14Q LOSS MUTATED	9	4	10	13	7	20	2
14Q LOSS WILD-TYPE	29	17	39	49	34	20	19

Figure S312. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

Table S313. Gene #67: '14q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
14Q LOSS MUTATED	37	24	50
14Q LOSS WILD-TYPE	149	109	71

Figure S313. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'14q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

Table S314. Gene #67: '14q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
14Q LOSS MUTATED	14	36	15	46
14Q LOSS WILD-TYPE	65	139	64	61

Figure S314. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S315. Gene #68: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
15Q LOSS MUTATED	43	13	9	22	3
15Q LOSS WILD-TYPE	80	174	27	54	16

Figure S315. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 0.00174 (Fisher's exact test), Q value = 0.0058

Table S316. Gene #68: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
15Q LOSS MUTATED	41	20	5	17
15Q LOSS WILD-TYPE	83	101	37	89

Figure S316. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'15q loss' versus 'RPPA_CNMF'

P value = 0.00488 (Fisher's exact test), Q value = 0.014

Table S317. Gene #68: '15q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	90	91
15Q LOSS MUTATED	16	7	23
15Q LOSS WILD-TYPE	66	83	68

Figure S317. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.00084

Table S318. Gene #68: '15q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

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

Figure S318. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00165 (Fisher's exact test), Q value = 0.0055

Table S319. Gene #68: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
15Q LOSS MUTATED	7	4	1	12	10	13	1
15Q LOSS WILD-TYPE	31	17	48	50	31	27	20

Figure S319. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_CNMF'

P value = 0.0244 (Fisher's exact test), Q value = 0.055

Table S320. Gene #68: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
15Q LOSS MUTATED	37	19	34
15Q LOSS WILD-TYPE	149	114	87

Figure S320. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0199 (Fisher's exact test), Q value = 0.047

Table S321. Gene #68: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
15Q LOSS MUTATED	16	30	11	33
15Q LOSS WILD-TYPE	63	145	68	74

Figure S321. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00328 (Fisher's exact test), Q value = 0.01

Table S322. Gene #68: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
15Q LOSS MUTATED	52	6	13
15Q LOSS WILD-TYPE	149	67	59

Figure S322. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S323. Gene #69: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
16P LOSS MUTATED	55	10	4	29	2
16P LOSS WILD-TYPE	68	177	32	47	17

Figure S323. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

'16p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S324. Gene #69: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
16P LOSS MUTATED	51	23	1	15
16P LOSS WILD-TYPE	73	98	41	91

Figure S324. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S325. Gene #69: '16p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
16P LOSS MUTATED	7	5	5	4	32
16P LOSS WILD-TYPE	58	57	41	33	30

Figure S325. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S326. Gene #69: '16p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
16P LOSS MUTATED	7	0	4	9	8	22	3
16P LOSS WILD-TYPE	31	21	45	53	33	18	18

Figure S326. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S327. Gene #69: '16p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
16P LOSS MUTATED	31	17	52
16P LOSS WILD-TYPE	155	116	69

Figure S327. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S328. Gene #69: '16p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
16P LOSS MUTATED	12	32	10	46
16P LOSS WILD-TYPE	67	143	69	61

Figure S328. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S329. Gene #69: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
16P LOSS MUTATED	33	12	6	8	15	6
16P LOSS WILD-TYPE	43	46	54	50	21	52

Figure S329. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S330. Gene #70: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
16Q LOSS MUTATED	60	16	3	32	4
16Q LOSS WILD-TYPE	63	171	33	44	15

Figure S330. 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 = 6.7e-05

Table S331. Gene #70: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
16Q LOSS MUTATED	60	20	1	22
16Q LOSS WILD-TYPE	64	101	41	84

Figure S331. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q loss' versus 'RPPA_CNMF'

P value = 0.0393 (Fisher's exact test), Q value = 0.081

Table S332. Gene #70: '16q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	90	91
16Q LOSS MUTATED	12	25	27
16Q LOSS WILD-TYPE	70	65	64

Figure S332. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S333. Gene #70: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
16Q LOSS MUTATED	6	10	10	5	33
16Q LOSS WILD-TYPE	59	52	36	32	29

Figure S333. 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 = 6.7e-05

Table S334. Gene #70: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
16Q LOSS MUTATED	8	0	8	14	8	24	2
16Q LOSS WILD-TYPE	30	21	41	48	33	16	19

Figure S334. 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 = 6.7e-05

Table S335. Gene #70: '16q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
16Q LOSS MUTATED	36	24	55
16Q LOSS WILD-TYPE	150	109	66

Figure S335. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S336. Gene #70: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
16Q LOSS MUTATED	14	37	14	50
16Q LOSS WILD-TYPE	65	138	65	57

Figure S336. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00052

Table S337. Gene #70: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
16Q LOSS MUTATED	36	12	10	9	13	12
16Q LOSS WILD-TYPE	40	46	50	49	23	46

Figure S337. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S338. Gene #71: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
17P LOSS MUTATED	76	17	16	48	7
17P LOSS WILD-TYPE	47	170	20	28	12

Figure S338. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S339. Gene #71: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
17P LOSS MUTATED	78	42	4	24
17P LOSS WILD-TYPE	46	79	38	82

Figure S339. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0264 (Fisher's exact test), Q value = 0.059

Table S340. Gene #71: '17p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	83	55	91
17P LOSS MUTATED	12	38	12	28
17P LOSS WILD-TYPE	22	45	43	63

Figure S340. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S341. Gene #71: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
17P LOSS MUTATED	14	10	18	12	35
17P LOSS WILD-TYPE	51	52	28	25	27

Figure S341. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S342. Gene #71: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
17P LOSS MUTATED	14	2	7	22	17	25	2
17P LOSS WILD-TYPE	24	19	42	40	24	15	19

Figure S342. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S343. Gene #71: '17p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
17P LOSS MUTATED	67	30	66
17P LOSS WILD-TYPE	119	103	55

Figure S343. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

Table S344. Gene #71: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
17P LOSS MUTATED	26	62	16	59
17P LOSS WILD-TYPE	53	113	63	48

Figure S344. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-04 (Fisher's exact test), Q value = 0.0027

Table S345. Gene #71: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
17P LOSS MUTATED	88	14	27
17P LOSS WILD-TYPE	113	59	45

Figure S345. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S346. Gene #72: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
17Q LOSS MUTATED	39	8	5	18	4
17Q LOSS WILD-TYPE	84	179	31	58	15

Figure S346. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

'17q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S347. Gene #72: '17q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
17Q LOSS MUTATED	37	14	0	13
17Q LOSS WILD-TYPE	87	107	42	93

Figure S347. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.032 (Fisher's exact test), Q value = 0.068

Table S348. Gene #72: '17q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	83	55	91
17Q LOSS MUTATED	5	20	4	10
17Q LOSS WILD-TYPE	29	63	51	81

Figure S348. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'17q loss' versus 'MRNASEQ_CNMF'

P value = 0.00241 (Fisher's exact test), Q value = 0.0075

Table S349. Gene #72: '17q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
17Q LOSS MUTATED	6	3	7	6	18
17Q LOSS WILD-TYPE	59	59	39	31	44

Figure S349. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00799 (Fisher's exact test), Q value = 0.022

Table S350. Gene #72: '17q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
17Q LOSS MUTATED	7	0	3	8	11	10	1
17Q LOSS WILD-TYPE	31	21	46	54	30	30	20

Figure S350. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_CNMF'

P value = 0.00051 (Fisher's exact test), Q value = 0.002

Table S351. Gene #72: '17q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
17Q LOSS MUTATED	28	12	33
17Q LOSS WILD-TYPE	158	121	88

Figure S351. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 8e-04

Table S352. Gene #72: '17q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
17Q LOSS MUTATED	12	21	7	33
17Q LOSS WILD-TYPE	67	154	72	74

Figure S352. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S353. Gene #73: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
18P LOSS MUTATED	42	28	13	33	3
18P LOSS WILD-TYPE	81	159	23	43	16

Figure S353. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

'18p loss' versus 'MIRSEQ_CNMF'

P value = 0.0483 (Fisher's exact test), Q value = 0.097

Table S354. Gene #73: '18p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
18P LOSS MUTATED	43	33	43
18P LOSS WILD-TYPE	143	100	78

Figure S354. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S355. Gene #74: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
18Q LOSS MUTATED	66	30	17	38	3
18Q LOSS WILD-TYPE	57	157	19	38	16

Figure S355. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.0013

Table S356. Gene #74: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
18Q LOSS MUTATED	59	31	19	27
18Q LOSS WILD-TYPE	65	90	23	79

Figure S356. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 0.0228 (Fisher's exact test), Q value = 0.052

Table S357. Gene #74: '18q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
18Q LOSS MUTATED	19	16	15	7	30
18Q LOSS WILD-TYPE	46	46	31	30	32

Figure S357. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0251 (Fisher's exact test), Q value = 0.056

Table S358. Gene #74: '18q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
18Q LOSS MUTATED	14	11	12	16	15	17	2
18Q LOSS WILD-TYPE	24	10	37	46	26	23	19

Figure S358. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 4e-04

Table S359. Gene #74: '18q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
18Q LOSS MUTATED	59	34	61
18Q LOSS WILD-TYPE	127	99	60

Figure S359. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'18q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00067 (Fisher's exact test), Q value = 0.0026

Table S360. Gene #74: '18q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
18Q LOSS MUTATED	19	62	20	53
18Q LOSS WILD-TYPE	60	113	59	54

Figure S360. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0447 (Fisher's exact test), Q value = 0.09

Table S361. Gene #74: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
18Q LOSS MUTATED	35	15	17	22	13	13
18Q LOSS WILD-TYPE	41	43	43	36	23	45

Figure S361. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'18q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0222 (Fisher's exact test), Q value = 0.052

Table S362. Gene #74: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
18Q LOSS MUTATED	78	16	21
18Q LOSS WILD-TYPE	123	57	51

Figure S362. 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 = 6.7e-05

Table S363. Gene #75: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
19P LOSS MUTATED	66	4	8	30	7
19P LOSS WILD-TYPE	57	183	28	46	12

Figure S363. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S364. Gene #75: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
19P LOSS MUTATED	70	22	4	9
19P LOSS WILD-TYPE	54	99	38	97

Figure S364. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19p loss' versus 'RPPA_CNMF'

P value = 0.00635 (Fisher's exact test), Q value = 0.018

Table S365. Gene #75: '19p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	90	91
19P LOSS MUTATED	14	12	29
19P LOSS WILD-TYPE	68	78	62

Figure S365. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'19p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S366. Gene #75: '19p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
19P LOSS MUTATED	8	3	8	4	32
19P LOSS WILD-TYPE	57	59	38	33	30

Figure S366. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S367. Gene #75: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
19P LOSS MUTATED	5	2	3	14	9	22	0
19P LOSS WILD-TYPE	33	19	46	48	32	18	21

Figure S367. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S368. Gene #75: '19p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
19P LOSS MUTATED	35	16	63
19P LOSS WILD-TYPE	151	117	58

Figure S368. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'19p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S369. Gene #75: '19p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
19P LOSS MUTATED	12	31	9	62
19P LOSS WILD-TYPE	67	144	70	45

Figure S369. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00044

Table S370. Gene #75: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
19P LOSS MUTATED	37	14	12	12	8	7
19P LOSS WILD-TYPE	39	44	48	46	28	51

Figure S370. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'19p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00681 (Fisher's exact test), Q value = 0.019

Table S371. Gene #75: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
19P LOSS MUTATED	61	9	20
19P LOSS WILD-TYPE	140	64	52

Figure S371. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S372. Gene #76: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
19Q LOSS MUTATED	51	4	7	18	7
19Q LOSS WILD-TYPE	72	183	29	58	12

Figure S372. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S373. Gene #76: '19q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
19Q LOSS MUTATED	53	16	1	7
19Q LOSS WILD-TYPE	71	105	41	99

Figure S373. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19q loss' versus 'RPPA_CNMF'

P value = 0.0314 (Fisher's exact test), Q value = 0.068

Table S374. Gene #76: '19q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	90	91
19Q LOSS MUTATED	11	9	22
19Q LOSS WILD-TYPE	71	81	69

Figure S374. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'19q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S375. Gene #76: '19q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
19Q LOSS MUTATED	5	2	8	5	23
19Q LOSS WILD-TYPE	60	60	38	32	39

Figure S375. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00022

Table S376. Gene #76: '19q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
19Q LOSS MUTATED	3	1	2	13	8	16	0
19Q LOSS WILD-TYPE	35	20	47	49	33	24	21

Figure S376. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S377. Gene #76: '19q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
19Q LOSS MUTATED	28	10	49
19Q LOSS WILD-TYPE	158	123	72

Figure S377. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'19q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S378. Gene #76: '19q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
19Q LOSS MUTATED	11	20	7	49
19Q LOSS WILD-TYPE	68	155	72	58

Figure S378. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.0011

Table S379. Gene #76: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
19Q LOSS MUTATED	28	12	12	6	5	4
19Q LOSS WILD-TYPE	48	46	48	52	31	54

Figure S379. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'19q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0127 (Fisher's exact test), Q value = 0.032

Table S380. Gene #76: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
19Q LOSS MUTATED	43	6	18
19Q LOSS WILD-TYPE	158	67	54

Figure S380. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p loss' versus 'CN_CNMF'

P value = 0.00246 (Fisher's exact test), Q value = 0.0077

Table S381. Gene #77: '20p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
20P LOSS MUTATED	10	2	2	8	0
20P LOSS WILD-TYPE	113	185	34	68	19

Figure S381. Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #1: 'CN_CNMF'

'20p loss' versus 'METHLYATION_CNMF'

P value = 0.0158 (Fisher's exact test), Q value = 0.039

Table S382. Gene #77: '20p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
20P LOSS MUTATED	13	4	0	3
20P LOSS WILD-TYPE	111	117	42	103

Figure S382. Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20p loss' versus 'MRNASEQ_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.0015

Table S383. Gene #77: '20p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
20P LOSS MUTATED	0	2	8	0	3
20P LOSS WILD-TYPE	65	60	38	37	59

Figure S383. Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S384. Gene #78: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
21Q LOSS MUTATED	68	35	16	50	11
21Q LOSS WILD-TYPE	55	152	20	26	8

Figure S384. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

'21q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S385. Gene #78: '21q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
21Q LOSS MUTATED	68	49	5	41
21Q LOSS WILD-TYPE	56	72	37	65

Figure S385. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'21q loss' versus 'MRNASEQ_CNMF'

P value = 0.0364 (Fisher's exact test), Q value = 0.076

Table S386. Gene #78: '21q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
21Q LOSS MUTATED	19	18	15	10	32
21Q LOSS WILD-TYPE	46	44	31	27	30

Figure S386. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'21q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00173 (Fisher's exact test), Q value = 0.0058

Table S387. Gene #78: '21q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
21Q LOSS MUTATED	16	2	15	19	16	23	3
21Q LOSS WILD-TYPE	22	19	34	43	25	17	18

Figure S387. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_CNMF'

P value = 0.00067 (Fisher's exact test), Q value = 0.0026

Table S388. Gene #78: '21q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
21Q LOSS MUTATED	68	45	67
21Q LOSS WILD-TYPE	118	88	54

Figure S388. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'21q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00442 (Fisher's exact test), Q value = 0.013

Table S389. Gene #78: '21q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
21Q LOSS MUTATED	25	69	27	59
21Q LOSS WILD-TYPE	54	106	52	48

Figure S389. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00161 (Fisher's exact test), Q value = 0.0055

Table S390. Gene #78: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
21Q LOSS MUTATED	41	28	16	21	21	17
21Q LOSS WILD-TYPE	35	30	44	37	15	41

Figure S390. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S391. Gene #79: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
22Q LOSS MUTATED	67	17	11	43	8
22Q LOSS WILD-TYPE	56	170	25	33	11

Figure S391. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S392. Gene #79: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
22Q LOSS MUTATED	70	35	2	26
22Q LOSS WILD-TYPE	54	86	40	80

Figure S392. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q loss' versus 'RPPA_CNMF'

P value = 0.0154 (Fisher's exact test), Q value = 0.038

Table S393. Gene #79: '22q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	90	91
22Q LOSS MUTATED	16	26	36
22Q LOSS WILD-TYPE	66	64	55

Figure S393. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'22q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00708 (Fisher's exact test), Q value = 0.02

Table S394. Gene #79: '22q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	83	55	91
22Q LOSS MUTATED	8	34	8	28
22Q LOSS WILD-TYPE	26	49	47	63

Figure S394. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 0.00104 (Fisher's exact test), Q value = 0.0038

Table S395. Gene #79: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
22Q LOSS MUTATED	10	15	15	9	30
22Q LOSS WILD-TYPE	55	47	31	28	32

Figure S395. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0043 (Fisher's exact test), Q value = 0.012

Table S396. Gene #79: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
22Q LOSS MUTATED	12	2	10	21	12	20	2
22Q LOSS WILD-TYPE	26	19	39	41	29	20	19

Figure S396. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

Table S397. Gene #79: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
22Q LOSS MUTATED	48	34	63
22Q LOSS WILD-TYPE	138	99	58

Figure S397. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S398. Gene #79: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
22Q LOSS MUTATED	20	47	18	60
22Q LOSS WILD-TYPE	59	128	61	47

Figure S398. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0014 (Fisher's exact test), Q value = 0.0049

Table S399. Gene #79: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
22Q LOSS MUTATED	37	21	16	12	17	13
22Q LOSS WILD-TYPE	39	37	44	46	19	45

Figure S399. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xp loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S400. Gene #80: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
XP LOSS MUTATED	31	6	4	17	1
XP LOSS WILD-TYPE	92	181	32	59	18

Figure S400. Get High-res Image Gene #80: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'

'xp loss' versus 'METHLYATION_CNMF'

P value = 0.0036 (Fisher's exact test), Q value = 0.011

Table S401. Gene #80: 'xp loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
XP LOSS MUTATED	22	22	2	6
XP LOSS WILD-TYPE	102	99	40	100

Figure S401. Get High-res Image Gene #80: 'xp loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S402. Gene #81: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
XQ LOSS MUTATED	22	4	2	20	2
XQ LOSS WILD-TYPE	101	183	34	56	17

Figure S402. Get High-res Image Gene #81: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 0.00426 (Fisher's exact test), Q value = 0.012

Table S403. Gene #81: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
XQ LOSS MUTATED	21	16	2	4
XQ LOSS WILD-TYPE	103	105	40	102

Figure S403. Get High-res Image Gene #81: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq loss' versus 'MRNASEQ_CNMF'

P value = 0.032 (Fisher's exact test), Q value = 0.068

Table S404. Gene #81: 'xq loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
XQ LOSS MUTATED	4	2	6	4	12
XQ LOSS WILD-TYPE	61	60	40	33	50

Figure S404. Get High-res Image Gene #81: 'xq loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xq loss' versus 'MIRSEQ_CNMF'

P value = 0.0273 (Fisher's exact test), Q value = 0.06

Table S405. Gene #81: 'xq loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
XQ LOSS MUTATED	22	8	20
XQ LOSS WILD-TYPE	164	125	101

Figure S405. Get High-res Image Gene #81: 'xq loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'xq loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0185 (Fisher's exact test), Q value = 0.044

Table S406. Gene #81: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
XQ LOSS MUTATED	17	6	4	6	5	2
XQ LOSS WILD-TYPE	59	52	56	52	31	56

Figure S406. Get High-res Image Gene #81: '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/STAD-TP/15098845/transformed.cor.cli.txt
Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/STAD-TP/15114286/STAD-TP.transferedmergedcluster.txt
Number of patients = 441
Number of significantly arm-level cnvs = 81
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)

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