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

Overview

Introduction

This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and molecular subtypes.

Summary

Testing the association between copy number variation 82 arm-level events and 8 molecular subtypes across 625 patients, 458 significant findings detected with P value < 0.05 and Q value < 0.25.

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

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 82 arm-level events and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 458 significant findings detected.


		Clinical Features	CN CNMF	METHLYATION CNMF	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
1q gain	167 (27%)	458	1e-05 (3.69e-05)	1e-05 (3.69e-05)	0.0269 (0.0411)	0.00491 (0.00914)	0.00352 (0.00696)	1e-05 (3.69e-05)	0.00061 (0.00144)	0.00151 (0.00326)
2p gain	137 (22%)	488	1e-05 (3.69e-05)	1e-05 (3.69e-05)	9e-05 (0.000273)	3e-05 (9.74e-05)	1e-05 (3.69e-05)	2e-05 (6.94e-05)	1e-05 (3.69e-05)	1e-05 (3.69e-05)
2q gain	111 (18%)	514	1e-05 (3.69e-05)	7e-05 (0.000216)	0.0345 (0.0514)	0.00383 (0.0075)	0.00477 (0.00897)	0.0245 (0.0379)	0.00134 (0.00293)	0.0129 (0.0216)
3q gain	170 (27%)	455	1e-05 (3.69e-05)	1e-05 (3.69e-05)	0.00026 (0.000705)	0.00054 (0.00131)	1e-05 (3.69e-05)	1e-05 (3.69e-05)	1e-05 (3.69e-05)	1e-05 (3.69e-05)
5p gain	177 (28%)	448	1e-05 (3.69e-05)	1e-05 (3.69e-05)	3e-05 (9.74e-05)	1e-05 (3.69e-05)	1e-05 (3.69e-05)	1e-05 (3.69e-05)	1e-05 (3.69e-05)	1e-05 (3.69e-05)
7p gain	306 (49%)	319	1e-05 (3.69e-05)	2e-05 (6.94e-05)	0.00058 (0.00139)	0.00526 (0.00967)	0.00227 (0.00467)	0.0278 (0.0423)	0.00198 (0.00414)	0.00071 (0.00166)
12p gain	148 (24%)	477	1e-05 (3.69e-05)	2e-05 (6.94e-05)	0.00076 (0.00176)	0.00023 (0.000642)	9e-05 (0.000273)	1e-05 (3.69e-05)	0.00151 (0.00326)	0.00015 (0.000424)
14q gain	75 (12%)	550	1e-05 (3.69e-05)	2e-05 (6.94e-05)	1e-05 (3.69e-05)	1e-05 (3.69e-05)	1e-05 (3.69e-05)	1e-05 (3.69e-05)	0.00019 (0.000533)	1e-05 (3.69e-05)
16q gain	86 (14%)	539	1e-05 (3.69e-05)	0.00113 (0.00254)	0.0011 (0.00248)	0.00013 (0.000377)	0.00028 (0.000744)	2e-05 (6.94e-05)	0.00195 (0.0041)	3e-05 (9.74e-05)
17p gain	62 (10%)	563	1e-05 (3.69e-05)	0.0006 (0.00143)	0.00479 (0.00898)	0.00028 (0.000744)	4e-05 (0.000127)	0.00384 (0.0075)	0.00241 (0.00491)	0.00039 (0.000995)
18p gain	137 (22%)	488	1e-05 (3.69e-05)	1e-05 (3.69e-05)	0.00201 (0.00419)	0.00053 (0.0013)	0.00032 (0.000833)	0.00011 (0.000325)	0.00068 (0.0016)	0.00016 (0.00045)
21q gain	36 (6%)	589	1e-05 (3.69e-05)	1e-05 (3.69e-05)	0.03 (0.0452)	0.00124 (0.00274)	0.0179 (0.0285)	4e-05 (0.000127)	0.0239 (0.0371)	0.0329 (0.0491)
22q gain	64 (10%)	561	1e-05 (3.69e-05)	1e-05 (3.69e-05)	6e-05 (0.000187)	1e-05 (3.69e-05)	1e-05 (3.69e-05)	1e-05 (3.69e-05)	1e-05 (3.69e-05)	1e-05 (3.69e-05)
3p loss	187 (30%)	438	1e-05 (3.69e-05)	1e-05 (3.69e-05)	1e-05 (3.69e-05)	1e-05 (3.69e-05)	1e-05 (3.69e-05)	1e-05 (3.69e-05)	1e-05 (3.69e-05)	1e-05 (3.69e-05)
4p loss	271 (43%)	354	1e-05 (3.69e-05)	1e-05 (3.69e-05)	0.00047 (0.00116)	1e-05 (3.69e-05)	1e-05 (3.69e-05)	1e-05 (3.69e-05)	1e-05 (3.69e-05)	1e-05 (3.69e-05)
5q loss	195 (31%)	430	1e-05 (3.69e-05)	1e-05 (3.69e-05)	1e-05 (3.69e-05)	1e-05 (3.69e-05)	1e-05 (3.69e-05)	1e-05 (3.69e-05)	5e-05 (0.000158)	1e-05 (3.69e-05)
6p loss	93 (15%)	532	1e-05 (3.69e-05)	0.00471 (0.0089)	0.00218 (0.0045)	0.00763 (0.0136)	0.0173 (0.0277)	0.00015 (0.000424)	0.01 (0.0173)	0.00427 (0.00817)
8p loss	153 (24%)	472	1e-05 (3.69e-05)	0.00543 (0.00995)	0.00409 (0.00791)	1e-05 (3.69e-05)	0.00014 (0.000399)	3e-05 (9.74e-05)	0.00041 (0.00104)	0.00012 (0.000353)
9p loss	250 (40%)	375	1e-05 (3.69e-05)	0.00024 (0.000662)	0.00115 (0.00257)	3e-05 (9.74e-05)	0.00054 (0.00131)	1e-05 (3.69e-05)	0.00344 (0.00682)	0.00031 (0.000813)
9q loss	175 (28%)	450	1e-05 (3.69e-05)	0.00011 (0.000325)	0.0141 (0.0234)	0.00026 (0.000705)	0.00011 (0.000325)	1e-05 (3.69e-05)	0.00028 (0.000744)	2e-05 (6.94e-05)
10p loss	117 (19%)	508	1e-05 (3.69e-05)	2e-05 (6.94e-05)	3e-05 (9.74e-05)	1e-05 (3.69e-05)	0.00176 (0.00375)	1e-05 (3.69e-05)	0.00031 (0.000813)	1e-05 (3.69e-05)
10q loss	117 (19%)	508	1e-05 (3.69e-05)	1e-05 (3.69e-05)	0.00014 (0.000399)	1e-05 (3.69e-05)	0.00054 (0.00131)	1e-05 (3.69e-05)	0.00097 (0.00222)	1e-05 (3.69e-05)
11p loss	118 (19%)	507	1e-05 (3.69e-05)	3e-05 (9.74e-05)	3e-05 (9.74e-05)	0.00071 (0.00166)	7e-05 (0.000216)	0.00026 (0.000705)	0.00024 (0.000662)	0.0055 (0.01)
11q loss	120 (19%)	505	1e-05 (3.69e-05)	1e-05 (3.69e-05)	1e-05 (3.69e-05)	1e-05 (3.69e-05)	1e-05 (3.69e-05)	1e-05 (3.69e-05)	1e-05 (3.69e-05)	1e-05 (3.69e-05)
13q loss	102 (16%)	523	1e-05 (3.69e-05)	1e-05 (3.69e-05)	1e-05 (3.69e-05)	1e-05 (3.69e-05)	1e-05 (3.69e-05)	1e-05 (3.69e-05)	1e-05 (3.69e-05)	1e-05 (3.69e-05)
19p loss	177 (28%)	448	1e-05 (3.69e-05)	1e-05 (3.69e-05)	1e-05 (3.69e-05)	1e-05 (3.69e-05)	1e-05 (3.69e-05)	1e-05 (3.69e-05)	1e-05 (3.69e-05)	1e-05 (3.69e-05)
19q loss	136 (22%)	489	1e-05 (3.69e-05)	1e-05 (3.69e-05)	3e-05 (9.74e-05)	1e-05 (3.69e-05)	1e-05 (3.69e-05)	1e-05 (3.69e-05)	1e-05 (3.69e-05)	4e-05 (0.000127)
xp loss	122 (20%)	503	1e-05 (3.69e-05)	2e-05 (6.94e-05)	1e-05 (3.69e-05)	5e-05 (0.000158)	1e-05 (3.69e-05)	0.00085 (0.00195)	0.0159 (0.0261)	0.00055 (0.00133)
6p gain	117 (19%)	508	1e-05 (3.69e-05)	3e-05 (9.74e-05)	0.269 (0.308)	0.00013 (0.000377)	0.0024 (0.0049)	1e-05 (3.69e-05)	0.00323 (0.00642)	1e-05 (3.69e-05)
15q gain	67 (11%)	558	1e-05 (3.69e-05)	0.0312 (0.0469)	0.00802 (0.0142)	0.00011 (0.000325)	0.0132 (0.0221)	0.234 (0.272)	0.0158 (0.0259)	0.00033 (0.000852)
18q gain	82 (13%)	543	0.00243 (0.00494)	0.00483 (0.00903)	0.0201 (0.0318)	0.00277 (0.00559)	0.0374 (0.055)	0.0285 (0.0432)	0.0645 (0.0871)	0.0354 (0.0525)
20p gain	349 (56%)	276	1e-05 (3.69e-05)	0.0071 (0.0127)	0.0789 (0.104)	0.00045 (0.00112)	0.0156 (0.0257)	1e-05 (3.69e-05)	0.0417 (0.0609)	1e-05 (3.69e-05)
xq gain	91 (15%)	534	0.00024 (0.000662)	0.00155 (0.00332)	0.00443 (0.00842)	0.00949 (0.0165)	0.00038 (0.000974)	0.00278 (0.00559)	0.104 (0.133)	0.00027 (0.000726)
2q loss	51 (8%)	574	3e-05 (9.74e-05)	0.012 (0.0205)	0.00165 (0.00353)	0.00102 (0.00232)	0.0554 (0.0772)	0.0245 (0.0379)	0.0186 (0.0296)	0.0299 (0.0451)
4q loss	251 (40%)	374	1e-05 (3.69e-05)	6e-05 (0.000187)	0.319 (0.358)	0.0123 (0.0209)	0.00615 (0.0111)	1e-05 (3.69e-05)	0.00076 (0.00176)	0.00014 (0.000399)
5p loss	112 (18%)	513	1e-05 (3.69e-05)	1e-05 (3.69e-05)	0.00118 (0.00263)	1e-05 (3.69e-05)	0.00126 (0.00277)	1e-05 (3.69e-05)	0.0562 (0.078)	1e-05 (3.69e-05)
16p loss	156 (25%)	469	1e-05 (3.69e-05)	0.00305 (0.00612)	0.235 (0.272)	1e-05 (3.69e-05)	0.00872 (0.0153)	3e-05 (9.74e-05)	0.0125 (0.0211)	1e-05 (3.69e-05)
17p loss	236 (38%)	389	1e-05 (3.69e-05)	0.00045 (0.00112)	0.0138 (0.023)	1e-05 (3.69e-05)	0.00547 (0.01)	1e-05 (3.69e-05)	0.233 (0.271)	2e-05 (6.94e-05)
21q loss	289 (46%)	336	1e-05 (3.69e-05)	0.0558 (0.0776)	0.0007 (0.00165)	3e-05 (9.74e-05)	0.00475 (0.00895)	0.00046 (0.00114)	0.0039 (0.00759)	0.0164 (0.0266)
xq loss	96 (15%)	529	1e-05 (3.69e-05)	0.00625 (0.0112)	0.00215 (0.00445)	0.00104 (0.00235)	0.00033 (0.000852)	0.0654 (0.0881)	0.0169 (0.0272)	0.00991 (0.0171)
4p gain	39 (6%)	586	0.0008 (0.00185)	0.425 (0.46)	0.00991 (0.0171)	0.0062 (0.0112)	0.363 (0.4)	0.0251 (0.0387)	0.0433 (0.0627)	0.005 (0.00927)
6q gain	100 (16%)	525	1e-05 (3.69e-05)	0.00029 (0.000767)	0.598 (0.629)	0.00181 (0.00382)	0.0315 (0.0472)	4e-05 (0.000127)	0.0626 (0.0852)	1e-05 (3.69e-05)
11p gain	99 (16%)	526	1e-05 (3.69e-05)	0.011 (0.0188)	0.0637 (0.0865)	0.0258 (0.0396)	0.0533 (0.0748)	0.0265 (0.0405)	0.0169 (0.0271)	0.0425 (0.0619)
11q gain	104 (17%)	521	1e-05 (3.69e-05)	0.0963 (0.124)	0.0219 (0.0341)	0.00435 (0.0083)	0.0623 (0.0851)	0.012 (0.0205)	0.00384 (0.0075)	0.00963 (0.0167)
13q gain	197 (32%)	428	1e-05 (3.69e-05)	0.101 (0.13)	2e-05 (6.94e-05)	1e-05 (3.69e-05)	0.0161 (0.0263)	1e-05 (3.69e-05)	0.266 (0.306)	1e-05 (3.69e-05)
16p gain	99 (16%)	526	1e-05 (3.69e-05)	0.00057 (0.00137)	0.0599 (0.0821)	0.00049 (0.0012)	0.0134 (0.0223)	0.00013 (0.000377)	0.111 (0.139)	0.00011 (0.000325)
17q gain	106 (17%)	519	1e-05 (3.69e-05)	0.00123 (0.00273)	0.0202 (0.0318)	0.0572 (0.079)	0.00321 (0.0064)	0.0518 (0.0732)	0.028 (0.0425)	0.00447 (0.00847)
12p loss	95 (15%)	530	1e-05 (3.69e-05)	0.00588 (0.0107)	0.0775 (0.102)	1e-05 (3.69e-05)	0.0954 (0.123)	1e-05 (3.69e-05)	0.0371 (0.0548)	0.00099 (0.00225)
16q loss	168 (27%)	457	1e-05 (3.69e-05)	0.0468 (0.0673)	0.666 (0.694)	1e-05 (3.69e-05)	0.11 (0.139)	1e-05 (3.69e-05)	0.0142 (0.0235)	1e-05 (3.69e-05)
17q loss	99 (16%)	526	1e-05 (3.69e-05)	0.0213 (0.0334)	0.0701 (0.0933)	0.004 (0.00776)	0.0291 (0.044)	0.00034 (0.000875)	0.399 (0.434)	0.00813 (0.0144)
4q gain	33 (5%)	592	0.00315 (0.0063)	0.432 (0.466)	0.00948 (0.0165)	0.00046 (0.00114)	0.17 (0.205)	0.00132 (0.0029)	0.144 (0.179)	0.00137 (0.00299)
20q gain	395 (63%)	230	1e-05 (3.69e-05)	0.0732 (0.0973)	0.0231 (0.0359)	1e-05 (3.69e-05)	0.217 (0.256)	1e-05 (3.69e-05)	0.355 (0.394)	1e-05 (3.69e-05)
1p loss	95 (15%)	530	1e-05 (3.69e-05)	0.00059 (0.00141)	0.0168 (0.0271)	0.135 (0.167)	0.0163 (0.0265)	0.0319 (0.0477)	0.0573 (0.079)	0.0884 (0.115)
3q loss	90 (14%)	535	1e-05 (3.69e-05)	0.00139 (0.00302)	0.0646 (0.0871)	1e-05 (3.69e-05)	0.0188 (0.0298)	0.00215 (0.00445)	0.06 (0.0821)	0.058 (0.0798)
14q loss	158 (25%)	467	1e-05 (3.69e-05)	0.0125 (0.0211)	0.285 (0.324)	0.00043 (0.00108)	0.588 (0.621)	1e-05 (3.69e-05)	0.514 (0.551)	0.00177 (0.00375)
18q loss	256 (41%)	369	1e-05 (3.69e-05)	0.0252 (0.0387)	0.129 (0.161)	0.0516 (0.0731)	0.0207 (0.0325)	0.00153 (0.00329)	0.0369 (0.0547)	0.0866 (0.113)
22q loss	218 (35%)	407	1e-05 (3.69e-05)	0.0625 (0.0852)	0.28 (0.319)	2e-05 (6.94e-05)	0.00419 (0.00806)	1e-05 (3.69e-05)	0.146 (0.18)	0.00025 (0.000686)
7q gain	257 (41%)	368	1e-05 (3.69e-05)	0.00032 (0.000833)	0.0392 (0.0576)	0.178 (0.213)	0.19 (0.227)	0.209 (0.248)	0.00492 (0.00914)	0.0657 (0.0883)
8q gain	338 (54%)	287	0.634 (0.661)	0.0189 (0.0299)	0.0693 (0.0925)	0.0167 (0.0269)	0.0397 (0.0581)	0.0128 (0.0215)	0.294 (0.333)	0.767 (0.782)
7p loss	33 (5%)	592	0.00084 (0.00193)	0.00044 (0.00111)	0.211 (0.25)	0.331 (0.37)	0.0442 (0.0639)	0.0373 (0.055)	0.153 (0.187)	0.269 (0.308)
1p gain	82 (13%)	543	1e-05 (3.69e-05)	0.00277 (0.00559)	0.157 (0.191)	0.109 (0.138)	0.0538 (0.0751)	0.00866 (0.0152)	0.205 (0.244)	0.105 (0.133)
8p gain	248 (40%)	377	0.00509 (0.00938)	0.051 (0.0726)	0.00883 (0.0154)	0.0162 (0.0264)	0.0942 (0.122)	0.108 (0.137)	0.267 (0.306)	0.693 (0.718)
10p gain	135 (22%)	490	1e-05 (3.69e-05)	0.185 (0.221)	0.205 (0.244)	0.0166 (0.0269)	0.965 (0.968)	0.00756 (0.0135)	0.614 (0.641)	0.199 (0.237)
19q gain	117 (19%)	508	1e-05 (3.69e-05)	0.406 (0.441)	0.323 (0.361)	0.45 (0.485)	0.543 (0.579)	0.00506 (0.00935)	0.0566 (0.0783)	0.00424 (0.00813)
xp gain	71 (11%)	554	0.00363 (0.00715)	0.0101 (0.0173)	0.0501 (0.0716)	0.216 (0.255)	0.0423 (0.0617)	0.233 (0.272)	0.0638 (0.0865)	0.0514 (0.073)
2p loss	38 (6%)	587	6e-05 (0.000187)	0.165 (0.199)	0.229 (0.268)	0.00682 (0.0122)	0.362 (0.399)	0.0735 (0.0974)	0.0829 (0.108)	0.0459 (0.0662)
7q loss	51 (8%)	574	0.00014 (0.000399)	0.00832 (0.0147)	0.0943 (0.122)	0.217 (0.256)	0.00978 (0.0169)	0.0922 (0.12)	0.394 (0.43)	0.347 (0.387)
12q loss	82 (13%)	543	1e-05 (3.69e-05)	0.0668 (0.0896)	0.109 (0.138)	0.00011 (0.000325)	0.0825 (0.108)	0.00027 (0.000726)	0.175 (0.21)	0.0818 (0.107)
10q gain	98 (16%)	527	0.00041 (0.00104)	0.561 (0.595)	0.405 (0.441)	0.0144 (0.0237)	0.516 (0.552)	0.0527 (0.0742)	0.424 (0.459)	0.108 (0.137)
12q gain	115 (18%)	510	0.0012 (0.00267)	0.155 (0.19)	0.3 (0.339)	0.522 (0.557)	0.172 (0.207)	0.149 (0.183)	0.0215 (0.0336)	0.297 (0.336)
1q loss	47 (8%)	578	1e-05 (3.69e-05)	0.0207 (0.0325)	0.396 (0.432)	0.0683 (0.0915)	0.0687 (0.0919)	0.127 (0.159)	0.0983 (0.126)	0.604 (0.634)
6q loss	110 (18%)	515	1e-05 (3.69e-05)	0.0507 (0.0722)	0.049 (0.0703)	0.109 (0.138)	0.259 (0.298)	0.101 (0.129)	0.145 (0.179)	0.211 (0.25)
8q loss	57 (9%)	568	1e-05 (3.69e-05)	0.371 (0.407)	0.357 (0.396)	0.0776 (0.102)	0.24 (0.277)	0.274 (0.312)	0.133 (0.165)	0.0478 (0.0686)
15q loss	149 (24%)	476	1e-05 (3.69e-05)	0.365 (0.402)	0.162 (0.196)	0.134 (0.166)	0.227 (0.267)	0.00198 (0.00414)	0.347 (0.387)	0.231 (0.27)
3p gain	83 (13%)	542	0.00414 (0.00799)	0.0533 (0.0748)	0.249 (0.288)	0.69 (0.716)	0.447 (0.482)	0.678 (0.705)	0.0752 (0.0995)	0.302 (0.34)
5q gain	63 (10%)	562	0.00238 (0.00488)	0.785 (0.798)	0.739 (0.755)	0.585 (0.618)	0.614 (0.641)	0.358 (0.396)	0.537 (0.573)	0.234 (0.272)
9q gain	109 (17%)	516	0.0432 (0.0627)	0.709 (0.73)	0.349 (0.388)	0.719 (0.739)	0.701 (0.725)	0.976 (0.976)	0.553 (0.588)	0.869 (0.88)
19p gain	83 (13%)	542	8e-05 (0.000245)	0.32 (0.359)	0.733 (0.751)	0.737 (0.754)	0.937 (0.946)	0.569 (0.602)	0.392 (0.429)	0.774 (0.788)
18p loss	187 (30%)	438	1e-05 (3.69e-05)	0.122 (0.154)	0.834 (0.845)	0.722 (0.741)	0.567 (0.601)	0.159 (0.193)	0.705 (0.727)	0.699 (0.723)
20p loss	41 (7%)	584	0.00177 (0.00375)	0.125 (0.156)	0.942 (0.949)	0.368 (0.405)	0.976 (0.976)	0.264 (0.304)	0.272 (0.311)	0.607 (0.636)
20q loss	8 (1%)	617	0.164 (0.198)	0.0521 (0.0735)	0.0535 (0.0748)	0.157 (0.191)	0.00566 (0.0103)	0.157 (0.191)	0.13 (0.162)	0.153 (0.188)
9p gain	77 (12%)	548	0.479 (0.515)	0.934 (0.944)	0.811 (0.824)	0.959 (0.964)	0.308 (0.346)	0.458 (0.493)	0.955 (0.961)	0.596 (0.628)

'1p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
1P GAIN MUTATED	28	45	9
1P GAIN WILD-TYPE	138	165	240

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

'1p gain' versus 'METHLYATION_CNMF'

P value = 0.00277 (Fisher's exact test), Q value = 0.0056

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
1P GAIN MUTATED	33	31	12
1P GAIN WILD-TYPE	215	126	160

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

'1p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00866 (Fisher's exact test), Q value = 0.015

Table S3. Gene #1: '1p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
1P GAIN MUTATED	26	14	19	17	6
1P GAIN WILD-TYPE	101	91	210	78	61

Figure S3. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'1q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
1Q GAIN MUTATED	64	79	24
1Q GAIN WILD-TYPE	102	131	225

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

'1q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
1Q GAIN MUTATED	65	66	26
1Q GAIN WILD-TYPE	183	91	146

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

'1q gain' versus 'MRNASEQ_CNMF'

P value = 0.0269 (Fisher's exact test), Q value = 0.041

Table S6. Gene #2: '1q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
1Q GAIN MUTATED	67	45	17
1Q GAIN WILD-TYPE	167	84	75

Figure S6. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'1q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00491 (Fisher's exact test), Q value = 0.0091

Table S7. Gene #2: '1q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
1Q GAIN MUTATED	26	41	5	36	21
1Q GAIN WILD-TYPE	49	109	20	53	95

Figure S7. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_CNMF'

P value = 0.00352 (Fisher's exact test), Q value = 0.007

Table S8. Gene #2: '1q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
1Q GAIN MUTATED	59	82	25
1Q GAIN WILD-TYPE	105	246	106

Figure S8. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'1q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S9. Gene #2: '1q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
1Q GAIN MUTATED	48	28	37	37	16
1Q GAIN WILD-TYPE	79	77	192	58	51

Figure S9. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00061 (Fisher's exact test), Q value = 0.0014

Table S10. Gene #2: '1q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
1Q GAIN MUTATED	56	52	34
1Q GAIN WILD-TYPE	88	157	137

Figure S10. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'1q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00151 (Fisher's exact test), Q value = 0.0033

Table S11. Gene #2: '1q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
1Q GAIN MUTATED	18	36	30	22	36
1Q GAIN WILD-TYPE	29	86	132	79	56

Figure S11. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S12. Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
2P GAIN MUTATED	48	73	16
2P GAIN WILD-TYPE	118	137	233

Figure S12. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

'2p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
2P GAIN MUTATED	56	59	16
2P GAIN WILD-TYPE	192	98	156

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

'2p gain' versus 'MRNASEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00027

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
2P GAIN MUTATED	48	45	10
2P GAIN WILD-TYPE	186	84	82

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

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 9.7e-05

Table S15. Gene #3: '2p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
2P GAIN MUTATED	19	26	9	35	14
2P GAIN WILD-TYPE	56	124	16	54	102

Figure S15. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S16. Gene #3: '2p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
2P GAIN MUTATED	59	64	14
2P GAIN WILD-TYPE	105	264	117

Figure S16. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'2p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 6.9e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
2P GAIN MUTATED	35	21	37	37	7
2P GAIN WILD-TYPE	92	84	192	58	60

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

'2p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
2P GAIN MUTATED	53	45	20
2P GAIN WILD-TYPE	91	164	151

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

'2p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
2P GAIN MUTATED	11	40	21	11	35
2P GAIN WILD-TYPE	36	82	141	90	57

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

'2q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S20. Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
2Q GAIN MUTATED	43	54	14
2Q GAIN WILD-TYPE	123	156	235

Figure S20. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

'2q gain' versus 'METHLYATION_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00022

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
2Q GAIN MUTATED	51	40	15
2Q GAIN WILD-TYPE	197	117	157

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

'2q gain' versus 'MRNASEQ_CNMF'

P value = 0.0345 (Fisher's exact test), Q value = 0.051

Table S22. Gene #4: '2q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
2Q GAIN MUTATED	42	33	11
2Q GAIN WILD-TYPE	192	96	81

Figure S22. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'2q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00383 (Fisher's exact test), Q value = 0.0075

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
2Q GAIN MUTATED	20	19	9	22	16
2Q GAIN WILD-TYPE	55	131	16	67	100

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

'2q gain' versus 'MIRSEQ_CNMF'

P value = 0.00477 (Fisher's exact test), Q value = 0.009

Table S24. Gene #4: '2q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
2Q GAIN MUTATED	43	51	17
2Q GAIN WILD-TYPE	121	277	114

Figure S24. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'2q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0245 (Fisher's exact test), Q value = 0.038

Table S25. Gene #4: '2q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
2Q GAIN MUTATED	30	18	32	24	7
2Q GAIN WILD-TYPE	97	87	197	71	60

Figure S25. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00134 (Fisher's exact test), Q value = 0.0029

Table S26. Gene #4: '2q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
2Q GAIN MUTATED	41	37	21
2Q GAIN WILD-TYPE	103	172	150

Figure S26. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'2q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0129 (Fisher's exact test), Q value = 0.022

Table S27. Gene #4: '2q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
2Q GAIN MUTATED	11	30	21	13	24
2Q GAIN WILD-TYPE	36	92	141	88	68

Figure S27. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3p gain' versus 'CN_CNMF'

P value = 0.00414 (Fisher's exact test), Q value = 0.008

Table S28. Gene #5: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
3P GAIN MUTATED	25	38	20
3P GAIN WILD-TYPE	141	172	229

Figure S28. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'

'3q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S29. Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
3Q GAIN MUTATED	37	99	34
3Q GAIN WILD-TYPE	129	111	215

Figure S29. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

'3q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S30. Gene #6: '3q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
3Q GAIN MUTATED	60	69	29
3Q GAIN WILD-TYPE	188	88	143

Figure S30. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3q gain' versus 'MRNASEQ_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 7e-04

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
3Q GAIN MUTATED	60	53	16
3Q GAIN WILD-TYPE	174	76	76

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

'3q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00054 (Fisher's exact test), Q value = 0.0013

Table S32. Gene #6: '3q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
3Q GAIN MUTATED	16	41	5	42	25
3Q GAIN WILD-TYPE	59	109	20	47	91

Figure S32. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S33. Gene #6: '3q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
3Q GAIN MUTATED	67	77	25
3Q GAIN WILD-TYPE	97	251	106

Figure S33. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'3q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S34. Gene #6: '3q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
3Q GAIN MUTATED	37	22	50	46	14
3Q GAIN WILD-TYPE	90	83	179	49	53

Figure S34. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S35. Gene #6: '3q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
3Q GAIN MUTATED	61	49	29
3Q GAIN WILD-TYPE	83	160	142

Figure S35. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'3q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S36. Gene #6: '3q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
3Q GAIN MUTATED	11	39	30	14	45
3Q GAIN WILD-TYPE	36	83	132	87	47

Figure S36. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p gain' versus 'CN_CNMF'

P value = 8e-04 (Fisher's exact test), Q value = 0.0018

Table S37. Gene #7: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
4P GAIN MUTATED	10	23	6
4P GAIN WILD-TYPE	156	187	243

Figure S37. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

'4p gain' versus 'MRNASEQ_CNMF'

P value = 0.00991 (Fisher's exact test), Q value = 0.017

Table S38. Gene #7: '4p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
4P GAIN MUTATED	14	14	1
4P GAIN WILD-TYPE	220	115	91

Figure S38. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'4p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0062 (Fisher's exact test), Q value = 0.011

Table S39. Gene #7: '4p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
4P GAIN MUTATED	5	10	4	9	1
4P GAIN WILD-TYPE	70	140	21	80	115

Figure S39. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'4p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0251 (Fisher's exact test), Q value = 0.039

Table S40. Gene #7: '4p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
4P GAIN MUTATED	4	8	14	12	1
4P GAIN WILD-TYPE	123	97	215	83	66

Figure S40. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'4p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0433 (Fisher's exact test), Q value = 0.063

Table S41. Gene #7: '4p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
4P GAIN MUTATED	12	18	5
4P GAIN WILD-TYPE	132	191	166

Figure S41. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'4p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.005 (Fisher's exact test), Q value = 0.0093

Table S42. Gene #7: '4p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
4P GAIN MUTATED	1	11	10	1	12
4P GAIN WILD-TYPE	46	111	152	100	80

Figure S42. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q gain' versus 'CN_CNMF'

P value = 0.00315 (Fisher's exact test), Q value = 0.0063

Table S43. Gene #8: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
4Q GAIN MUTATED	7	20	6
4Q GAIN WILD-TYPE	159	190	243

Figure S43. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

'4q gain' versus 'MRNASEQ_CNMF'

P value = 0.00948 (Fisher's exact test), Q value = 0.017

Table S44. Gene #8: '4q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
4Q GAIN MUTATED	10	13	1
4Q GAIN WILD-TYPE	224	116	91

Figure S44. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'4q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00046 (Fisher's exact test), Q value = 0.0011

Table S45. Gene #8: '4q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
4Q GAIN MUTATED	2	6	4	11	1
4Q GAIN WILD-TYPE	73	144	21	78	115

Figure S45. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'4q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00132 (Fisher's exact test), Q value = 0.0029

Table S46. Gene #8: '4q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
4Q GAIN MUTATED	2	5	14	12	0
4Q GAIN WILD-TYPE	125	100	215	83	67

Figure S46. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'4q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00137 (Fisher's exact test), Q value = 0.003

Table S47. Gene #8: '4q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
4Q GAIN MUTATED	0	9	7	1	12
4Q GAIN WILD-TYPE	47	113	155	100	80

Figure S47. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S48. Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
5P GAIN MUTATED	64	89	24
5P GAIN WILD-TYPE	102	121	225

Figure S48. 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 = 3.7e-05

Table S49. Gene #9: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
5P GAIN MUTATED	50	81	32
5P GAIN WILD-TYPE	198	76	140

Figure S49. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p gain' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 9.7e-05

Table S50. Gene #9: '5p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
5P GAIN MUTATED	62	58	16
5P GAIN WILD-TYPE	172	71	76

Figure S50. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S51. Gene #9: '5p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
5P GAIN MUTATED	27	37	4	48	20
5P GAIN WILD-TYPE	48	113	21	41	96

Figure S51. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S52. Gene #9: '5p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
5P GAIN MUTATED	75	77	25
5P GAIN WILD-TYPE	89	251	106

Figure S52. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'5p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S53. Gene #9: '5p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
5P GAIN MUTATED	54	17	46	51	9
5P GAIN WILD-TYPE	73	88	183	44	58

Figure S53. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S54. Gene #9: '5p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
5P GAIN MUTATED	69	55	30
5P GAIN WILD-TYPE	75	154	141

Figure S54. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'5p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S55. Gene #9: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
5P GAIN MUTATED	15	36	37	16	50
5P GAIN WILD-TYPE	32	86	125	85	42

Figure S55. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q gain' versus 'CN_CNMF'

P value = 0.00238 (Fisher's exact test), Q value = 0.0049

Table S56. Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
5Q GAIN MUTATED	20	30	13
5Q GAIN WILD-TYPE	146	180	236

Figure S56. 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 = 3.7e-05

Table S57. Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
6P GAIN MUTATED	62	36	19
6P GAIN WILD-TYPE	104	174	230

Figure S57. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

'6p gain' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 9.7e-05

Table S58. Gene #11: '6p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
6P GAIN MUTATED	37	49	19
6P GAIN WILD-TYPE	211	108	153

Figure S58. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.00038

Table S59. Gene #11: '6p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
6P GAIN MUTATED	25	29	7	16	9
6P GAIN WILD-TYPE	50	121	18	73	107

Figure S59. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_CNMF'

P value = 0.0024 (Fisher's exact test), Q value = 0.0049

Table S60. Gene #11: '6p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
6P GAIN MUTATED	43	59	14
6P GAIN WILD-TYPE	121	269	117

Figure S60. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'6p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S61. Gene #11: '6p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
6P GAIN MUTATED	49	21	23	17	6
6P GAIN WILD-TYPE	78	84	206	78	61

Figure S61. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00323 (Fisher's exact test), Q value = 0.0064

Table S62. Gene #11: '6p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
6P GAIN MUTATED	39	36	21
6P GAIN WILD-TYPE	105	173	150

Figure S62. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'6p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S63. Gene #11: '6p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
6P GAIN MUTATED	21	30	20	8	17
6P GAIN WILD-TYPE	26	92	142	93	75

Figure S63. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S64. Gene #12: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
6Q GAIN MUTATED	51	32	17
6Q GAIN WILD-TYPE	115	178	232

Figure S64. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

'6q gain' versus 'METHLYATION_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.00077

Table S65. Gene #12: '6q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
6Q GAIN MUTATED	37	38	14
6Q GAIN WILD-TYPE	211	119	158

Figure S65. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00181 (Fisher's exact test), Q value = 0.0038

Table S66. Gene #12: '6q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
6Q GAIN MUTATED	20	26	7	14	8
6Q GAIN WILD-TYPE	55	124	18	75	108

Figure S66. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'6q gain' versus 'MIRSEQ_CNMF'

P value = 0.0315 (Fisher's exact test), Q value = 0.047

Table S67. Gene #12: '6q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
6Q GAIN MUTATED	33	54	12
6Q GAIN WILD-TYPE	131	274	119

Figure S67. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'6q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00013

Table S68. Gene #12: '6q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
6Q GAIN MUTATED	37	20	22	15	5
6Q GAIN WILD-TYPE	90	85	207	80	62

Figure S68. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'6q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S69. Gene #12: '6q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
6Q GAIN MUTATED	16	33	12	6	15
6Q GAIN WILD-TYPE	31	89	150	95	77

Figure S69. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S70. Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
7P GAIN MUTATED	105	126	75
7P GAIN WILD-TYPE	61	84	174

Figure S70. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 6.9e-05

Table S71. Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
7P GAIN MUTATED	137	90	59
7P GAIN WILD-TYPE	111	67	113

Figure S71. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 0.00058 (Fisher's exact test), Q value = 0.0014

Table S72. Gene #13: '7p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
7P GAIN MUTATED	123	75	30
7P GAIN WILD-TYPE	111	54	62

Figure S72. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00526 (Fisher's exact test), Q value = 0.0097

Table S73. Gene #13: '7p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
7P GAIN MUTATED	45	73	16	51	43
7P GAIN WILD-TYPE	30	77	9	38	73

Figure S73. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_CNMF'

P value = 0.00227 (Fisher's exact test), Q value = 0.0047

Table S74. Gene #13: '7p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
7P GAIN MUTATED	91	166	47
7P GAIN WILD-TYPE	73	162	84

Figure S74. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'7p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0278 (Fisher's exact test), Q value = 0.042

Table S75. Gene #13: '7p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
7P GAIN MUTATED	71	53	107	51	22
7P GAIN WILD-TYPE	56	52	122	44	45

Figure S75. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00198 (Fisher's exact test), Q value = 0.0041

Table S76. Gene #13: '7p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
7P GAIN MUTATED	86	106	68
7P GAIN WILD-TYPE	58	103	103

Figure S76. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'7p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00071 (Fisher's exact test), Q value = 0.0017

Table S77. Gene #13: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
7P GAIN MUTATED	30	73	70	37	50
7P GAIN WILD-TYPE	17	49	92	64	42

Figure S77. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S78. Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
7Q GAIN MUTATED	84	103	70
7Q GAIN WILD-TYPE	82	107	179

Figure S78. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.00083

Table S79. Gene #14: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
7Q GAIN MUTATED	114	73	49
7Q GAIN WILD-TYPE	134	84	123

Figure S79. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 0.0392 (Fisher's exact test), Q value = 0.058

Table S80. Gene #14: '7q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
7Q GAIN MUTATED	96	64	30
7Q GAIN WILD-TYPE	138	65	62

Figure S80. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'7q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00492 (Fisher's exact test), Q value = 0.0091

Table S81. Gene #14: '7q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
7Q GAIN MUTATED	74	82	57
7Q GAIN WILD-TYPE	70	127	114

Figure S81. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'8p gain' versus 'CN_CNMF'

P value = 0.00509 (Fisher's exact test), Q value = 0.0094

Table S82. Gene #15: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
8P GAIN MUTATED	63	68	117
8P GAIN WILD-TYPE	103	142	132

Figure S82. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

'8p gain' versus 'MRNASEQ_CNMF'

P value = 0.00883 (Fisher's exact test), Q value = 0.015

Table S83. Gene #15: '8p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
8P GAIN MUTATED	106	40	29
8P GAIN WILD-TYPE	128	89	63

Figure S83. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'8p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0162 (Fisher's exact test), Q value = 0.026

Table S84. Gene #15: '8p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
8P GAIN MUTATED	28	69	3	31	44
8P GAIN WILD-TYPE	47	81	22	58	72

Figure S84. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'METHLYATION_CNMF'

P value = 0.0189 (Fisher's exact test), Q value = 0.03

Table S85. Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
8Q GAIN MUTATED	141	90	76
8Q GAIN WILD-TYPE	107	67	96

Figure S85. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0167 (Fisher's exact test), Q value = 0.027

Table S86. Gene #16: '8q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
8Q GAIN MUTATED	48	85	8	49	52
8Q GAIN WILD-TYPE	27	65	17	40	64

Figure S86. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_CNMF'

P value = 0.0397 (Fisher's exact test), Q value = 0.058

Table S87. Gene #16: '8q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
8Q GAIN MUTATED	94	185	58
8Q GAIN WILD-TYPE	70	143	73

Figure S87. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'8q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0128 (Fisher's exact test), Q value = 0.022

Table S88. Gene #16: '8q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
8Q GAIN MUTATED	76	68	113	52	28
8Q GAIN WILD-TYPE	51	37	116	43	39

Figure S88. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'9q gain' versus 'CN_CNMF'

P value = 0.0432 (Fisher's exact test), Q value = 0.063

Table S89. Gene #18: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
9Q GAIN MUTATED	33	44	32
9Q GAIN WILD-TYPE	133	166	217

Figure S89. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

'10p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S90. Gene #19: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
10P GAIN MUTATED	55	55	25
10P GAIN WILD-TYPE	111	155	224

Figure S90. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

'10p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0166 (Fisher's exact test), Q value = 0.027

Table S91. Gene #19: '10p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
10P GAIN MUTATED	28	34	6	13	24
10P GAIN WILD-TYPE	47	116	19	76	92

Figure S91. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'10p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00756 (Fisher's exact test), Q value = 0.013

Table S92. Gene #19: '10p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
10P GAIN MUTATED	42	24	41	14	13
10P GAIN WILD-TYPE	85	81	188	81	54

Figure S92. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'10q gain' versus 'CN_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.001

Table S93. Gene #20: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
10Q GAIN MUTATED	33	43	22
10Q GAIN WILD-TYPE	133	167	227

Figure S93. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

'10q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0144 (Fisher's exact test), Q value = 0.024

Table S94. Gene #20: '10q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
10Q GAIN MUTATED	21	25	5	7	18
10Q GAIN WILD-TYPE	54	125	20	82	98

Figure S94. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'11p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S95. Gene #21: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
11P GAIN MUTATED	44	39	16
11P GAIN WILD-TYPE	122	171	233

Figure S95. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

'11p gain' versus 'METHLYATION_CNMF'

P value = 0.011 (Fisher's exact test), Q value = 0.019

Table S96. Gene #21: '11p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
11P GAIN MUTATED	36	37	20
11P GAIN WILD-TYPE	212	120	152

Figure S96. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0258 (Fisher's exact test), Q value = 0.04

Table S97. Gene #21: '11p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
11P GAIN MUTATED	17	14	5	15	11
11P GAIN WILD-TYPE	58	136	20	74	105

Figure S97. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'11p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0265 (Fisher's exact test), Q value = 0.041

Table S98. Gene #21: '11p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
11P GAIN MUTATED	30	15	28	18	6
11P GAIN WILD-TYPE	97	90	201	77	61

Figure S98. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'11p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0169 (Fisher's exact test), Q value = 0.027

Table S99. Gene #21: '11p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
11P GAIN MUTATED	31	34	17
11P GAIN WILD-TYPE	113	175	154

Figure S99. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'11p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0425 (Fisher's exact test), Q value = 0.062

Table S100. Gene #21: '11p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
11P GAIN MUTATED	12	24	18	11	17
11P GAIN WILD-TYPE	35	98	144	90	75

Figure S100. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S101. Gene #22: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
11Q GAIN MUTATED	51	35	18
11Q GAIN WILD-TYPE	115	175	231

Figure S101. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

'11q gain' versus 'MRNASEQ_CNMF'

P value = 0.0219 (Fisher's exact test), Q value = 0.034

Table S102. Gene #22: '11q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
11Q GAIN MUTATED	37	21	5
11Q GAIN WILD-TYPE	197	108	87

Figure S102. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'11q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00435 (Fisher's exact test), Q value = 0.0083

Table S103. Gene #22: '11q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
11Q GAIN MUTATED	20	16	6	10	11
11Q GAIN WILD-TYPE	55	134	19	79	105

Figure S103. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.012 (Fisher's exact test), Q value = 0.02

Table S104. Gene #22: '11q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
11Q GAIN MUTATED	33	18	34	13	5
11Q GAIN WILD-TYPE	94	87	195	82	62

Figure S104. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00384 (Fisher's exact test), Q value = 0.0075

Table S105. Gene #22: '11q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
11Q GAIN MUTATED	28	42	15
11Q GAIN WILD-TYPE	116	167	156

Figure S105. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'11q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00963 (Fisher's exact test), Q value = 0.017

Table S106. Gene #22: '11q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
11Q GAIN MUTATED	11	31	20	11	12
11Q GAIN WILD-TYPE	36	91	142	90	80

Figure S106. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S107. Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
12P GAIN MUTATED	32	81	35
12P GAIN WILD-TYPE	134	129	214

Figure S107. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 6.9e-05

Table S108. Gene #23: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
12P GAIN MUTATED	48	63	32
12P GAIN WILD-TYPE	200	94	140

Figure S108. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 0.00076 (Fisher's exact test), Q value = 0.0018

Table S109. Gene #23: '12p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
12P GAIN MUTATED	44	47	20
12P GAIN WILD-TYPE	190	82	72

Figure S109. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.00064

Table S110. Gene #23: '12p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
12P GAIN MUTATED	19	31	3	38	20
12P GAIN WILD-TYPE	56	119	22	51	96

Figure S110. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00027

Table S111. Gene #23: '12p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
12P GAIN MUTATED	59	67	21
12P GAIN WILD-TYPE	105	261	110

Figure S111. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'12p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S112. Gene #23: '12p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
12P GAIN MUTATED	27	18	57	39	6
12P GAIN WILD-TYPE	100	87	172	56	61

Figure S112. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00151 (Fisher's exact test), Q value = 0.0033

Table S113. Gene #23: '12p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
12P GAIN MUTATED	50	49	29
12P GAIN WILD-TYPE	94	160	142

Figure S113. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'12p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.00042

Table S114. Gene #23: '12p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
12P GAIN MUTATED	11	29	36	13	39
12P GAIN WILD-TYPE	36	93	126	88	53

Figure S114. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q gain' versus 'CN_CNMF'

P value = 0.0012 (Fisher's exact test), Q value = 0.0027

Table S115. Gene #24: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
12Q GAIN MUTATED	25	56	34
12Q GAIN WILD-TYPE	141	154	215

Figure S115. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

'12q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0215 (Fisher's exact test), Q value = 0.034

Table S116. Gene #24: '12q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
12Q GAIN MUTATED	35	37	21
12Q GAIN WILD-TYPE	109	172	150

Figure S116. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'13q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S117. Gene #25: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
13Q GAIN MUTATED	109	36	52
13Q GAIN WILD-TYPE	57	174	197

Figure S117. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

'13q gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 6.9e-05

Table S118. Gene #25: '13q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
13Q GAIN MUTATED	91	25	18
13Q GAIN WILD-TYPE	143	104	74

Figure S118. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'13q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S119. Gene #25: '13q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
13Q GAIN MUTATED	33	54	11	9	27
13Q GAIN WILD-TYPE	42	96	14	80	89

Figure S119. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'13q gain' versus 'MIRSEQ_CNMF'

P value = 0.0161 (Fisher's exact test), Q value = 0.026

Table S120. Gene #25: '13q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
13Q GAIN MUTATED	43	120	33
13Q GAIN WILD-TYPE	121	208	98

Figure S120. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'13q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S121. Gene #25: '13q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
13Q GAIN MUTATED	64	41	64	10	17
13Q GAIN WILD-TYPE	63	64	165	85	50

Figure S121. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'13q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S122. Gene #25: '13q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
13Q GAIN MUTATED	26	44	47	34	9
13Q GAIN WILD-TYPE	21	78	115	67	83

Figure S122. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S123. Gene #26: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
14Q GAIN MUTATED	19	46	10
14Q GAIN WILD-TYPE	147	164	239

Figure S123. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

'14q gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 6.9e-05

Table S124. Gene #26: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
14Q GAIN MUTATED	22	38	12
14Q GAIN WILD-TYPE	226	119	160

Figure S124. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'14q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S125. Gene #26: '14q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
14Q GAIN MUTATED	14	35	7
14Q GAIN WILD-TYPE	220	94	85

Figure S125. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S126. Gene #26: '14q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
14Q GAIN MUTATED	7	10	2	32	5
14Q GAIN WILD-TYPE	68	140	23	57	111

Figure S126. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S127. Gene #26: '14q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
14Q GAIN MUTATED	41	24	9
14Q GAIN WILD-TYPE	123	304	122

Figure S127. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'14q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S128. Gene #26: '14q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
14Q GAIN MUTATED	11	10	15	33	5
14Q GAIN WILD-TYPE	116	95	214	62	62

Figure S128. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.00053

Table S129. Gene #26: '14q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
14Q GAIN MUTATED	33	16	18
14Q GAIN WILD-TYPE	111	193	153

Figure S129. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'14q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S130. Gene #26: '14q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
14Q GAIN MUTATED	7	14	6	7	33
14Q GAIN WILD-TYPE	40	108	156	94	59

Figure S130. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S131. Gene #27: '15q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
15Q GAIN MUTATED	25	33	9
15Q GAIN WILD-TYPE	141	177	240

Figure S131. Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #1: 'CN_CNMF'

'15q gain' versus 'METHLYATION_CNMF'

P value = 0.0312 (Fisher's exact test), Q value = 0.047

Table S132. Gene #27: '15q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
15Q GAIN MUTATED	28	24	11
15Q GAIN WILD-TYPE	220	133	161

Figure S132. Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'15q gain' versus 'MRNASEQ_CNMF'

P value = 0.00802 (Fisher's exact test), Q value = 0.014

Table S133. Gene #27: '15q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
15Q GAIN MUTATED	22	22	4
15Q GAIN WILD-TYPE	212	107	88

Figure S133. Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'15q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.00033

Table S134. Gene #27: '15q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
15Q GAIN MUTATED	10	17	8	11	2
15Q GAIN WILD-TYPE	65	133	17	78	114

Figure S134. Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'15q gain' versus 'MIRSEQ_CNMF'

P value = 0.0132 (Fisher's exact test), Q value = 0.022

Table S135. Gene #27: '15q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
15Q GAIN MUTATED	26	33	7
15Q GAIN WILD-TYPE	138	295	124

Figure S135. Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'15q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0158 (Fisher's exact test), Q value = 0.026

Table S136. Gene #27: '15q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
15Q GAIN MUTATED	24	23	11
15Q GAIN WILD-TYPE	120	186	160

Figure S136. Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'15q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00033 (Fisher's exact test), Q value = 0.00085

Table S137. Gene #27: '15q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
15Q GAIN MUTATED	4	26	9	6	13
15Q GAIN WILD-TYPE	43	96	153	95	79

Figure S137. Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S138. Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
16P GAIN MUTATED	20	59	20
16P GAIN WILD-TYPE	146	151	229

Figure S138. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

'16p gain' versus 'METHLYATION_CNMF'

P value = 0.00057 (Fisher's exact test), Q value = 0.0014

Table S139. Gene #28: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
16P GAIN MUTATED	25	38	27
16P GAIN WILD-TYPE	223	119	145

Figure S139. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00049 (Fisher's exact test), Q value = 0.0012

Table S140. Gene #28: '16p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
16P GAIN MUTATED	13	22	0	29	17
16P GAIN WILD-TYPE	62	128	25	60	99

Figure S140. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_CNMF'

P value = 0.0134 (Fisher's exact test), Q value = 0.022

Table S141. Gene #28: '16p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
16P GAIN MUTATED	37	40	21
16P GAIN WILD-TYPE	127	288	110

Figure S141. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'16p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.00038

Table S142. Gene #28: '16p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
16P GAIN MUTATED	23	10	25	30	10
16P GAIN WILD-TYPE	104	95	204	65	57

Figure S142. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.00033

Table S143. Gene #28: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
16P GAIN MUTATED	3	14	27	8	28
16P GAIN WILD-TYPE	44	108	135	93	64

Figure S143. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S144. Gene #29: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
16Q GAIN MUTATED	18	50	18
16Q GAIN WILD-TYPE	148	160	231

Figure S144. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16q gain' versus 'METHLYATION_CNMF'

P value = 0.00113 (Fisher's exact test), Q value = 0.0025

Table S145. Gene #29: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
16Q GAIN MUTATED	23	35	21
16Q GAIN WILD-TYPE	225	122	151

Figure S145. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q gain' versus 'MRNASEQ_CNMF'

P value = 0.0011 (Fisher's exact test), Q value = 0.0025

Table S146. Gene #29: '16q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
16Q GAIN MUTATED	30	32	7
16Q GAIN WILD-TYPE	204	97	85

Figure S146. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'16q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.00038

Table S147. Gene #29: '16q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
16Q GAIN MUTATED	9	14	2	29	15
16Q GAIN WILD-TYPE	66	136	23	60	101

Figure S147. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.00074

Table S148. Gene #29: '16q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
16Q GAIN MUTATED	38	31	16
16Q GAIN WILD-TYPE	126	297	115

Figure S148. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'16q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 6.9e-05

Table S149. Gene #29: '16q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
16Q GAIN MUTATED	15	9	23	30	8
16Q GAIN WILD-TYPE	112	96	206	65	59

Figure S149. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00195 (Fisher's exact test), Q value = 0.0041

Table S150. Gene #29: '16q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
16Q GAIN MUTATED	31	18	20
16Q GAIN WILD-TYPE	113	191	151

Figure S150. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'16q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 9.7e-05

Table S151. Gene #29: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
16Q GAIN MUTATED	3	11	21	6	28
16Q GAIN WILD-TYPE	44	111	141	95	64

Figure S151. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S152. Gene #30: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
17P GAIN MUTATED	18	39	5
17P GAIN WILD-TYPE	148	171	244

Figure S152. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

'17p gain' versus 'METHLYATION_CNMF'

P value = 6e-04 (Fisher's exact test), Q value = 0.0014

Table S153. Gene #30: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
17P GAIN MUTATED	21	28	9
17P GAIN WILD-TYPE	227	129	163

Figure S153. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p gain' versus 'MRNASEQ_CNMF'

P value = 0.00479 (Fisher's exact test), Q value = 0.009

Table S154. Gene #30: '17p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
17P GAIN MUTATED	21	24	5
17P GAIN WILD-TYPE	213	105	87

Figure S154. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'17p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 0.00074

Table S155. Gene #30: '17p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
17P GAIN MUTATED	11	14	0	20	5
17P GAIN WILD-TYPE	64	136	25	69	111

Figure S155. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00013

Table S156. Gene #30: '17p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
17P GAIN MUTATED	32	21	8
17P GAIN WILD-TYPE	132	307	123

Figure S156. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'17p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00384 (Fisher's exact test), Q value = 0.0075

Table S157. Gene #30: '17p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
17P GAIN MUTATED	13	6	21	19	2
17P GAIN WILD-TYPE	114	99	208	76	65

Figure S157. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00241 (Fisher's exact test), Q value = 0.0049

Table S158. Gene #30: '17p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
17P GAIN MUTATED	25	17	10
17P GAIN WILD-TYPE	119	192	161

Figure S158. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'17p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00039 (Fisher's exact test), Q value = 0.001

Table S159. Gene #30: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
17P GAIN MUTATED	7	10	11	4	20
17P GAIN WILD-TYPE	40	112	151	97	72

Figure S159. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S160. Gene #31: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
17Q GAIN MUTATED	33	57	16
17Q GAIN WILD-TYPE	133	153	233

Figure S160. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 0.00123 (Fisher's exact test), Q value = 0.0027

Table S161. Gene #31: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
17Q GAIN MUTATED	48	37	16
17Q GAIN WILD-TYPE	200	120	156

Figure S161. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 0.0202 (Fisher's exact test), Q value = 0.032

Table S162. Gene #31: '17q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
17Q GAIN MUTATED	34	32	11
17Q GAIN WILD-TYPE	200	97	81

Figure S162. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'17q gain' versus 'MIRSEQ_CNMF'

P value = 0.00321 (Fisher's exact test), Q value = 0.0064

Table S163. Gene #31: '17q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
17Q GAIN MUTATED	42	46	17
17Q GAIN WILD-TYPE	122	282	114

Figure S163. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'17q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.028 (Fisher's exact test), Q value = 0.043

Table S164. Gene #31: '17q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
17Q GAIN MUTATED	34	33	21
17Q GAIN WILD-TYPE	110	176	150

Figure S164. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'17q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00447 (Fisher's exact test), Q value = 0.0085

Table S165. Gene #31: '17q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
17Q GAIN MUTATED	12	20	26	7	23
17Q GAIN WILD-TYPE	35	102	136	94	69

Figure S165. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S166. Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
18P GAIN MUTATED	46	66	25
18P GAIN WILD-TYPE	120	144	224

Figure S166. 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 = 3.7e-05

Table S167. Gene #32: '18p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
18P GAIN MUTATED	38	65	25
18P GAIN WILD-TYPE	210	92	147

Figure S167. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18p gain' versus 'MRNASEQ_CNMF'

P value = 0.00201 (Fisher's exact test), Q value = 0.0042

Table S168. Gene #32: '18p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
18P GAIN MUTATED	53	37	9
18P GAIN WILD-TYPE	181	92	83

Figure S168. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'18p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00053 (Fisher's exact test), Q value = 0.0013

Table S169. Gene #32: '18p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
18P GAIN MUTATED	24	32	5	27	11
18P GAIN WILD-TYPE	51	118	20	62	105

Figure S169. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.00083

Table S170. Gene #32: '18p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
18P GAIN MUTATED	52	67	17
18P GAIN WILD-TYPE	112	261	114

Figure S170. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'18p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.00033

Table S171. Gene #32: '18p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
18P GAIN MUTATED	41	22	37	30	6
18P GAIN WILD-TYPE	86	83	192	65	61

Figure S171. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00068 (Fisher's exact test), Q value = 0.0016

Table S172. Gene #32: '18p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
18P GAIN MUTATED	41	55	22
18P GAIN WILD-TYPE	103	154	149

Figure S172. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'18p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.00045

Table S173. Gene #32: '18p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
18P GAIN MUTATED	17	35	26	12	28
18P GAIN WILD-TYPE	30	87	136	89	64

Figure S173. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q gain' versus 'CN_CNMF'

P value = 0.00243 (Fisher's exact test), Q value = 0.0049

Table S174. Gene #33: '18q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
18Q GAIN MUTATED	30	33	19
18Q GAIN WILD-TYPE	136	177	230

Figure S174. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #1: 'CN_CNMF'

'18q gain' versus 'METHLYATION_CNMF'

P value = 0.00483 (Fisher's exact test), Q value = 0.009

Table S175. Gene #33: '18q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
18Q GAIN MUTATED	26	33	17
18Q GAIN WILD-TYPE	222	124	155

Figure S175. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18q gain' versus 'MRNASEQ_CNMF'

P value = 0.0201 (Fisher's exact test), Q value = 0.032

Table S176. Gene #33: '18q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
18Q GAIN MUTATED	39	18	5
18Q GAIN WILD-TYPE	195	111	87

Figure S176. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'18q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00277 (Fisher's exact test), Q value = 0.0056

Table S177. Gene #33: '18q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
18Q GAIN MUTATED	15	27	2	13	5
18Q GAIN WILD-TYPE	60	123	23	76	111

Figure S177. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_CNMF'

P value = 0.0374 (Fisher's exact test), Q value = 0.055

Table S178. Gene #33: '18q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
18Q GAIN MUTATED	29	43	10
18Q GAIN WILD-TYPE	135	285	121

Figure S178. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'18q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0285 (Fisher's exact test), Q value = 0.043

Table S179. Gene #33: '18q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
18Q GAIN MUTATED	25	16	21	15	5
18Q GAIN WILD-TYPE	102	89	208	80	62

Figure S179. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0354 (Fisher's exact test), Q value = 0.053

Table S180. Gene #33: '18q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
18Q GAIN MUTATED	7	25	14	9	13
18Q GAIN WILD-TYPE	40	97	148	92	79

Figure S180. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p gain' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00025

Table S181. Gene #34: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
19P GAIN MUTATED	25	42	16
19P GAIN WILD-TYPE	141	168	233

Figure S181. 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 = 3.7e-05

Table S182. Gene #35: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
19Q GAIN MUTATED	41	55	21
19Q GAIN WILD-TYPE	125	155	228

Figure S182. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

'19q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00506 (Fisher's exact test), Q value = 0.0094

Table S183. Gene #35: '19q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
19Q GAIN MUTATED	39	18	36	15	8
19Q GAIN WILD-TYPE	88	87	193	80	59

Figure S183. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00424 (Fisher's exact test), Q value = 0.0081

Table S184. Gene #35: '19q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
19Q GAIN MUTATED	18	26	27	12	14
19Q GAIN WILD-TYPE	29	96	135	89	78

Figure S184. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S185. Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
20P GAIN MUTATED	131	124	94
20P GAIN WILD-TYPE	35	86	155

Figure S185. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 0.0071 (Fisher's exact test), Q value = 0.013

Table S186. Gene #36: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
20P GAIN MUTATED	138	102	82
20P GAIN WILD-TYPE	110	55	90

Figure S186. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00045 (Fisher's exact test), Q value = 0.0011

Table S187. Gene #36: '20p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
20P GAIN MUTATED	57	68	16	48	61
20P GAIN WILD-TYPE	18	82	9	41	55

Figure S187. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_CNMF'

P value = 0.0156 (Fisher's exact test), Q value = 0.026

Table S188. Gene #36: '20p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
20P GAIN MUTATED	105	181	62
20P GAIN WILD-TYPE	59	147	69

Figure S188. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S189. Gene #36: '20p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
20P GAIN MUTATED	98	51	116	51	32
20P GAIN WILD-TYPE	29	54	113	44	35

Figure S189. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0417 (Fisher's exact test), Q value = 0.061

Table S190. Gene #36: '20p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
20P GAIN MUTATED	92	112	86
20P GAIN WILD-TYPE	52	97	85

Figure S190. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'20p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S191. Gene #36: '20p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
20P GAIN MUTATED	42	73	75	50	50
20P GAIN WILD-TYPE	5	49	87	51	42

Figure S191. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S192. Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
20Q GAIN MUTATED	147	144	104
20Q GAIN WILD-TYPE	19	66	145

Figure S192. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 0.0231 (Fisher's exact test), Q value = 0.036

Table S193. Gene #37: '20q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
20Q GAIN MUTATED	160	74	50
20Q GAIN WILD-TYPE	74	55	42

Figure S193. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S194. Gene #37: '20q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
20Q GAIN MUTATED	66	89	17	45	67
20Q GAIN WILD-TYPE	9	61	8	44	49

Figure S194. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S195. Gene #37: '20q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
20Q GAIN MUTATED	114	59	135	49	36
20Q GAIN WILD-TYPE	13	46	94	46	31

Figure S195. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S196. Gene #37: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
20Q GAIN MUTATED	44	91	87	61	48
20Q GAIN WILD-TYPE	3	31	75	40	44

Figure S196. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S197. Gene #38: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
21Q GAIN MUTATED	18	17	1
21Q GAIN WILD-TYPE	148	193	248

Figure S197. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

'21q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S198. Gene #38: '21q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
21Q GAIN MUTATED	9	25	1
21Q GAIN WILD-TYPE	239	132	171

Figure S198. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'21q gain' versus 'MRNASEQ_CNMF'

P value = 0.03 (Fisher's exact test), Q value = 0.045

Table S199. Gene #38: '21q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
21Q GAIN MUTATED	18	11	1
21Q GAIN WILD-TYPE	216	118	91

Figure S199. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'21q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00124 (Fisher's exact test), Q value = 0.0027

Table S200. Gene #38: '21q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
21Q GAIN MUTATED	8	11	2	9	0
21Q GAIN WILD-TYPE	67	139	23	80	116

Figure S200. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'21q gain' versus 'MIRSEQ_CNMF'

P value = 0.0179 (Fisher's exact test), Q value = 0.029

Table S201. Gene #38: '21q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
21Q GAIN MUTATED	16	16	3
21Q GAIN WILD-TYPE	148	312	128

Figure S201. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'21q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00013

Table S202. Gene #38: '21q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
21Q GAIN MUTATED	14	7	4	10	0
21Q GAIN WILD-TYPE	113	98	225	85	67

Figure S202. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'21q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0239 (Fisher's exact test), Q value = 0.037

Table S203. Gene #38: '21q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
21Q GAIN MUTATED	13	15	4
21Q GAIN WILD-TYPE	131	194	167

Figure S203. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'21q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0329 (Fisher's exact test), Q value = 0.049

Table S204. Gene #38: '21q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
21Q GAIN MUTATED	5	9	5	3	10
21Q GAIN WILD-TYPE	42	113	157	98	82

Figure S204. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S205. Gene #39: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
22Q GAIN MUTATED	15	41	8
22Q GAIN WILD-TYPE	151	169	241

Figure S205. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

'22q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S206. Gene #39: '22q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
22Q GAIN MUTATED	15	38	9
22Q GAIN WILD-TYPE	233	119	163

Figure S206. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q gain' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00019

Table S207. Gene #39: '22q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
22Q GAIN MUTATED	17	30	7
22Q GAIN WILD-TYPE	217	99	85

Figure S207. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'22q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S208. Gene #39: '22q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
22Q GAIN MUTATED	5	12	0	29	8
22Q GAIN WILD-TYPE	70	138	25	60	108

Figure S208. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S209. Gene #39: '22q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
22Q GAIN MUTATED	37	19	8
22Q GAIN WILD-TYPE	127	309	123

Figure S209. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'22q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S210. Gene #39: '22q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
22Q GAIN MUTATED	11	10	10	29	4
22Q GAIN WILD-TYPE	116	95	219	66	63

Figure S210. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S211. Gene #39: '22q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
22Q GAIN MUTATED	33	13	13
22Q GAIN WILD-TYPE	111	196	158

Figure S211. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'22q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S212. Gene #39: '22q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
22Q GAIN MUTATED	5	9	12	4	29
22Q GAIN WILD-TYPE	42	113	150	97	63

Figure S212. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xp gain' versus 'CN_CNMF'

P value = 0.00363 (Fisher's exact test), Q value = 0.0072

Table S213. Gene #40: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
XP GAIN MUTATED	29	25	17
XP GAIN WILD-TYPE	137	185	232

Figure S213. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'

'xp gain' versus 'METHLYATION_CNMF'

P value = 0.0101 (Fisher's exact test), Q value = 0.017

Table S214. Gene #40: 'xp gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
XP GAIN MUTATED	30	25	10
XP GAIN WILD-TYPE	218	132	162

Figure S214. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xp gain' versus 'MIRSEQ_CNMF'

P value = 0.0423 (Fisher's exact test), Q value = 0.062

Table S215. Gene #40: 'xp gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
XP GAIN MUTATED	25	36	8
XP GAIN WILD-TYPE	139	292	123

Figure S215. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'xq gain' versus 'CN_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.00066

Table S216. Gene #41: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
XQ GAIN MUTATED	36	35	20
XQ GAIN WILD-TYPE	130	175	229

Figure S216. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

'xq gain' versus 'METHLYATION_CNMF'

P value = 0.00155 (Fisher's exact test), Q value = 0.0033

Table S217. Gene #41: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
XQ GAIN MUTATED	37	35	14
XQ GAIN WILD-TYPE	211	122	158

Figure S217. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq gain' versus 'MRNASEQ_CNMF'

P value = 0.00443 (Fisher's exact test), Q value = 0.0084

Table S218. Gene #41: 'xq gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
XQ GAIN MUTATED	38	29	6
XQ GAIN WILD-TYPE	196	100	86

Figure S218. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'xq gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00949 (Fisher's exact test), Q value = 0.017

Table S219. Gene #41: 'xq gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
XQ GAIN MUTATED	14	21	4	24	10
XQ GAIN WILD-TYPE	61	129	21	65	106

Figure S219. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'xq gain' versus 'MIRSEQ_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.00097

Table S220. Gene #41: 'xq gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
XQ GAIN MUTATED	35	47	7
XQ GAIN WILD-TYPE	129	281	124

Figure S220. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'xq gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00278 (Fisher's exact test), Q value = 0.0056

Table S221. Gene #41: 'xq gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
XQ GAIN MUTATED	19	19	21	24	6
XQ GAIN WILD-TYPE	108	86	208	71	61

Figure S221. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'xq gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 0.00073

Table S222. Gene #41: 'xq gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
XQ GAIN MUTATED	4	25	11	12	23
XQ GAIN WILD-TYPE	43	97	151	89	69

Figure S222. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S223. Gene #42: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
1P LOSS MUTATED	47	44	4
1P LOSS WILD-TYPE	119	166	245

Figure S223. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 0.00059 (Fisher's exact test), Q value = 0.0014

Table S224. Gene #42: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
1P LOSS MUTATED	43	35	13
1P LOSS WILD-TYPE	205	122	159

Figure S224. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 0.0168 (Fisher's exact test), Q value = 0.027

Table S225. Gene #42: '1p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
1P LOSS MUTATED	39	21	5
1P LOSS WILD-TYPE	195	108	87

Figure S225. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'1p loss' versus 'MIRSEQ_CNMF'

P value = 0.0163 (Fisher's exact test), Q value = 0.026

Table S226. Gene #42: '1p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
1P LOSS MUTATED	30	54	10
1P LOSS WILD-TYPE	134	274	121

Figure S226. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'1p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0319 (Fisher's exact test), Q value = 0.048

Table S227. Gene #42: '1p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
1P LOSS MUTATED	29	14	34	13	4
1P LOSS WILD-TYPE	98	91	195	82	63

Figure S227. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'1q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S228. Gene #43: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
1Q LOSS MUTATED	21	25	1
1Q LOSS WILD-TYPE	145	185	248

Figure S228. Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

'1q loss' versus 'METHLYATION_CNMF'

P value = 0.0207 (Fisher's exact test), Q value = 0.033

Table S229. Gene #43: '1q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
1Q LOSS MUTATED	23	17	6
1Q LOSS WILD-TYPE	225	140	166

Figure S229. Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2p loss' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00019

Table S230. Gene #44: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
2P LOSS MUTATED	16	19	3
2P LOSS WILD-TYPE	150	191	246

Figure S230. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

'2p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00682 (Fisher's exact test), Q value = 0.012

Table S231. Gene #44: '2p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
2P LOSS MUTATED	10	8	1	6	1
2P LOSS WILD-TYPE	65	142	24	83	115

Figure S231. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0459 (Fisher's exact test), Q value = 0.066

Table S232. Gene #44: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
2P LOSS MUTATED	6	9	5	4	9
2P LOSS WILD-TYPE	41	113	157	97	83

Figure S232. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q loss' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 9.7e-05

Table S233. Gene #45: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
2Q LOSS MUTATED	20	26	5
2Q LOSS WILD-TYPE	146	184	244

Figure S233. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

'2q loss' versus 'METHLYATION_CNMF'

P value = 0.012 (Fisher's exact test), Q value = 0.02

Table S234. Gene #45: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
2Q LOSS MUTATED	17	22	9
2Q LOSS WILD-TYPE	231	135	163

Figure S234. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2q loss' versus 'MRNASEQ_CNMF'

P value = 0.00165 (Fisher's exact test), Q value = 0.0035

Table S235. Gene #45: '2q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
2Q LOSS MUTATED	15	17	1
2Q LOSS WILD-TYPE	219	112	91

Figure S235. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'2q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00102 (Fisher's exact test), Q value = 0.0023

Table S236. Gene #45: '2q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
2Q LOSS MUTATED	10	9	2	11	1
2Q LOSS WILD-TYPE	65	141	23	78	115

Figure S236. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0245 (Fisher's exact test), Q value = 0.038

Table S237. Gene #45: '2q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
2Q LOSS MUTATED	15	5	14	14	3
2Q LOSS WILD-TYPE	112	100	215	81	64

Figure S237. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0186 (Fisher's exact test), Q value = 0.03

Table S238. Gene #45: '2q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
2Q LOSS MUTATED	19	14	8
2Q LOSS WILD-TYPE	125	195	163

Figure S238. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'2q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0299 (Fisher's exact test), Q value = 0.045

Table S239. Gene #45: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
2Q LOSS MUTATED	4	11	8	4	14
2Q LOSS WILD-TYPE	43	111	154	97	78

Figure S239. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S240. Gene #46: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
3P LOSS MUTATED	69	96	22
3P LOSS WILD-TYPE	97	114	227

Figure S240. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S241. Gene #46: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
3P LOSS MUTATED	69	81	30
3P LOSS WILD-TYPE	179	76	142

Figure S241. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S242. Gene #46: '3p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
3P LOSS MUTATED	55	74	13
3P LOSS WILD-TYPE	179	55	79

Figure S242. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S243. Gene #46: '3p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
3P LOSS MUTATED	25	33	11	62	11
3P LOSS WILD-TYPE	50	117	14	27	105

Figure S243. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S244. Gene #46: '3p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
3P LOSS MUTATED	80	83	24
3P LOSS WILD-TYPE	84	245	107

Figure S244. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S245. Gene #46: '3p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
3P LOSS MUTATED	42	24	48	66	7
3P LOSS WILD-TYPE	85	81	181	29	60

Figure S245. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S246. Gene #46: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
3P LOSS MUTATED	72	48	43
3P LOSS WILD-TYPE	72	161	128

Figure S246. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'3p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S247. Gene #46: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
3P LOSS MUTATED	13	37	30	18	65
3P LOSS WILD-TYPE	34	85	132	83	27

Figure S247. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S248. Gene #47: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
3Q LOSS MUTATED	49	31	10
3Q LOSS WILD-TYPE	117	179	239

Figure S248. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

'3q loss' versus 'METHLYATION_CNMF'

P value = 0.00139 (Fisher's exact test), Q value = 0.003

Table S249. Gene #47: '3q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
3Q LOSS MUTATED	40	33	13
3Q LOSS WILD-TYPE	208	124	159

Figure S249. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S250. Gene #47: '3q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
3Q LOSS MUTATED	20	17	5	18	3
3Q LOSS WILD-TYPE	55	133	20	71	113

Figure S250. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_CNMF'

P value = 0.0188 (Fisher's exact test), Q value = 0.03

Table S251. Gene #47: '3q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
3Q LOSS MUTATED	31	49	10
3Q LOSS WILD-TYPE	133	279	121

Figure S251. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'3q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00215 (Fisher's exact test), Q value = 0.0044

Table S252. Gene #47: '3q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
3Q LOSS MUTATED	27	14	28	19	2
3Q LOSS WILD-TYPE	100	91	201	76	65

Figure S252. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S253. Gene #48: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
4P LOSS MUTATED	100	131	40
4P LOSS WILD-TYPE	66	79	209

Figure S253. 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 = 3.7e-05

Table S254. Gene #48: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
4P LOSS MUTATED	95	102	55
4P LOSS WILD-TYPE	153	55	117

Figure S254. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.0012

Table S255. Gene #48: '4p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
4P LOSS MUTATED	91	74	31
4P LOSS WILD-TYPE	143	55	61

Figure S255. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S256. Gene #48: '4p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
4P LOSS MUTATED	42	50	10	56	38
4P LOSS WILD-TYPE	33	100	15	33	78

Figure S256. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S257. Gene #48: '4p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
4P LOSS MUTATED	101	132	38
4P LOSS WILD-TYPE	63	196	93

Figure S257. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'4p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S258. Gene #48: '4p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
4P LOSS MUTATED	80	39	71	57	24
4P LOSS WILD-TYPE	47	66	158	38	43

Figure S258. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S259. Gene #48: '4p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
4P LOSS MUTATED	95	77	61
4P LOSS WILD-TYPE	49	132	110

Figure S259. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S260. Gene #48: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
4P LOSS MUTATED	34	61	45	36	57
4P LOSS WILD-TYPE	13	61	117	65	35

Figure S260. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S261. Gene #49: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
4Q LOSS MUTATED	97	115	39
4Q LOSS WILD-TYPE	69	95	210

Figure S261. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00019

Table S262. Gene #49: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
4Q LOSS MUTATED	98	85	52
4Q LOSS WILD-TYPE	150	72	120

Figure S262. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0123 (Fisher's exact test), Q value = 0.021

Table S263. Gene #49: '4q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
4Q LOSS MUTATED	42	49	10	37	40
4Q LOSS WILD-TYPE	33	101	15	52	76

Figure S263. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_CNMF'

P value = 0.00615 (Fisher's exact test), Q value = 0.011

Table S264. Gene #49: '4q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
4Q LOSS MUTATED	80	131	40
4Q LOSS WILD-TYPE	84	197	91

Figure S264. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'4q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S265. Gene #49: '4q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
4Q LOSS MUTATED	78	39	72	39	23
4Q LOSS WILD-TYPE	49	66	157	56	44

Figure S265. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00076 (Fisher's exact test), Q value = 0.0018

Table S266. Gene #49: '4q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
4Q LOSS MUTATED	79	77	62
4Q LOSS WILD-TYPE	65	132	109

Figure S266. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'4q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 4e-04

Table S267. Gene #49: '4q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
4Q LOSS MUTATED	32	58	50	39	39
4Q LOSS WILD-TYPE	15	64	112	62	53

Figure S267. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S268. Gene #50: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
5P LOSS MUTATED	53	41	18
5P LOSS WILD-TYPE	113	169	231

Figure S268. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'

'5p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S269. Gene #50: '5p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
5P LOSS MUTATED	58	36	13
5P LOSS WILD-TYPE	190	121	159

Figure S269. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p loss' versus 'MRNASEQ_CNMF'

P value = 0.00118 (Fisher's exact test), Q value = 0.0026

Table S270. Gene #50: '5p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
5P LOSS MUTATED	49	25	5
5P LOSS WILD-TYPE	185	104	87

Figure S270. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S271. Gene #50: '5p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
5P LOSS MUTATED	23	25	13	10	8
5P LOSS WILD-TYPE	52	125	12	79	108

Figure S271. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_CNMF'

P value = 0.00126 (Fisher's exact test), Q value = 0.0028

Table S272. Gene #50: '5p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
5P LOSS MUTATED	35	66	10
5P LOSS WILD-TYPE	129	262	121

Figure S272. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'5p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S273. Gene #50: '5p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
5P LOSS MUTATED	41	25	30	11	4
5P LOSS WILD-TYPE	86	80	199	84	63

Figure S273. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S274. Gene #50: '5p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
5P LOSS MUTATED	21	30	25	12	11
5P LOSS WILD-TYPE	26	92	137	89	81

Figure S274. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S275. Gene #51: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
5Q LOSS MUTATED	84	89	22
5Q LOSS WILD-TYPE	82	121	227

Figure S275. 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 = 3.7e-05

Table S276. Gene #51: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
5Q LOSS MUTATED	80	80	27
5Q LOSS WILD-TYPE	168	77	145

Figure S276. 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 = 3.7e-05

Table S277. Gene #51: '5q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
5Q LOSS MUTATED	78	53	11
5Q LOSS WILD-TYPE	156	76	81

Figure S277. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S278. Gene #51: '5q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
5Q LOSS MUTATED	35	43	15	34	15
5Q LOSS WILD-TYPE	40	107	10	55	101

Figure S278. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S279. Gene #51: '5q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
5Q LOSS MUTATED	71	102	22
5Q LOSS WILD-TYPE	93	226	109

Figure S279. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S280. Gene #51: '5q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
5Q LOSS MUTATED	68	29	53	37	8
5Q LOSS WILD-TYPE	59	76	176	58	59

Figure S280. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00016

Table S281. Gene #51: '5q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
5Q LOSS MUTATED	68	68	41
5Q LOSS WILD-TYPE	76	141	130

Figure S281. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'5q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S282. Gene #51: '5q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
5Q LOSS MUTATED	31	47	41	21	37
5Q LOSS WILD-TYPE	16	75	121	80	55

Figure S282. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S283. Gene #52: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
6P LOSS MUTATED	28	57	8
6P LOSS WILD-TYPE	138	153	241

Figure S283. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

'6p loss' versus 'METHLYATION_CNMF'

P value = 0.00471 (Fisher's exact test), Q value = 0.0089

Table S284. Gene #52: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
6P LOSS MUTATED	36	36	17
6P LOSS WILD-TYPE	212	121	155

Figure S284. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p loss' versus 'MRNASEQ_CNMF'

P value = 0.00218 (Fisher's exact test), Q value = 0.0045

Table S285. Gene #52: '6p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
6P LOSS MUTATED	32	30	6
6P LOSS WILD-TYPE	202	99	86

Figure S285. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00763 (Fisher's exact test), Q value = 0.014

Table S286. Gene #52: '6p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
6P LOSS MUTATED	13	19	4	23	9
6P LOSS WILD-TYPE	62	131	21	66	107

Figure S286. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_CNMF'

P value = 0.0173 (Fisher's exact test), Q value = 0.028

Table S287. Gene #52: '6p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
6P LOSS MUTATED	33	49	11
6P LOSS WILD-TYPE	131	279	120

Figure S287. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'6p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.00042

Table S288. Gene #52: '6p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
6P LOSS MUTATED	22	17	29	24	1
6P LOSS WILD-TYPE	105	88	200	71	66

Figure S288. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.01 (Fisher's exact test), Q value = 0.017

Table S289. Gene #52: '6p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
6P LOSS MUTATED	32	30	17
6P LOSS WILD-TYPE	112	179	154

Figure S289. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'6p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00427 (Fisher's exact test), Q value = 0.0082

Table S290. Gene #52: '6p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
6P LOSS MUTATED	6	23	16	10	24
6P LOSS WILD-TYPE	41	99	146	91	68

Figure S290. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S291. Gene #53: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
6Q LOSS MUTATED	34	63	13
6Q LOSS WILD-TYPE	132	147	236

Figure S291. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

'6q loss' versus 'MRNASEQ_CNMF'

P value = 0.049 (Fisher's exact test), Q value = 0.07

Table S292. Gene #53: '6q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
6Q LOSS MUTATED	37	30	10
6Q LOSS WILD-TYPE	197	99	82

Figure S292. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'7p loss' versus 'CN_CNMF'

P value = 0.00084 (Fisher's exact test), Q value = 0.0019

Table S293. Gene #54: '7p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
7P LOSS MUTATED	15	14	4
7P LOSS WILD-TYPE	151	196	245

Figure S293. Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #1: 'CN_CNMF'

'7p loss' versus 'METHLYATION_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.0011

Table S294. Gene #54: '7p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
7P LOSS MUTATED	8	18	4
7P LOSS WILD-TYPE	240	139	168

Figure S294. Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p loss' versus 'MIRSEQ_CNMF'

P value = 0.0442 (Fisher's exact test), Q value = 0.064

Table S295. Gene #54: '7p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
7P LOSS MUTATED	15	14	4
7P LOSS WILD-TYPE	149	314	127

Figure S295. Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'7p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0373 (Fisher's exact test), Q value = 0.055

Table S296. Gene #54: '7p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
7P LOSS MUTATED	12	4	6	8	3
7P LOSS WILD-TYPE	115	101	223	87	64

Figure S296. Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'7q loss' versus 'CN_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 4e-04

Table S297. Gene #55: '7q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
7Q LOSS MUTATED	21	23	7
7Q LOSS WILD-TYPE	145	187	242

Figure S297. Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #1: 'CN_CNMF'

'7q loss' versus 'METHLYATION_CNMF'

P value = 0.00832 (Fisher's exact test), Q value = 0.015

Table S298. Gene #55: '7q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
7Q LOSS MUTATED	18	22	8
7Q LOSS WILD-TYPE	230	135	164

Figure S298. Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q loss' versus 'MIRSEQ_CNMF'

P value = 0.00978 (Fisher's exact test), Q value = 0.017

Table S299. Gene #55: '7q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
7Q LOSS MUTATED	22	24	5
7Q LOSS WILD-TYPE	142	304	126

Figure S299. Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'8p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S300. Gene #56: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
8P LOSS MUTATED	54	81	18
8P LOSS WILD-TYPE	112	129	231

Figure S300. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 0.00543 (Fisher's exact test), Q value = 0.0099

Table S301. Gene #56: '8p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
8P LOSS MUTATED	58	54	33
8P LOSS WILD-TYPE	190	103	139

Figure S301. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 0.00409 (Fisher's exact test), Q value = 0.0079

Table S302. Gene #56: '8p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
8P LOSS MUTATED	47	44	16
8P LOSS WILD-TYPE	187	85	76

Figure S302. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S303. Gene #56: '8p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
8P LOSS MUTATED	31	26	6	33	11
8P LOSS WILD-TYPE	44	124	19	56	105

Figure S303. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 4e-04

Table S304. Gene #56: '8p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
8P LOSS MUTATED	56	79	17
8P LOSS WILD-TYPE	108	249	114

Figure S304. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'8p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 9.7e-05

Table S305. Gene #56: '8p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
8P LOSS MUTATED	40	25	44	37	6
8P LOSS WILD-TYPE	87	80	185	58	61

Figure S305. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.001

Table S306. Gene #56: '8p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
8P LOSS MUTATED	54	49	31
8P LOSS WILD-TYPE	90	160	140

Figure S306. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'8p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.00035

Table S307. Gene #56: '8p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
8P LOSS MUTATED	17	30	37	13	37
8P LOSS WILD-TYPE	30	92	125	88	55

Figure S307. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S308. Gene #57: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
8Q LOSS MUTATED	23	28	6
8Q LOSS WILD-TYPE	143	182	243

Figure S308. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

'8q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0478 (Fisher's exact test), Q value = 0.069

Table S309. Gene #57: '8q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
8Q LOSS MUTATED	5	16	14	3	12
8Q LOSS WILD-TYPE	42	106	148	98	80

Figure S309. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S310. Gene #58: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
9P LOSS MUTATED	98	115	37
9P LOSS WILD-TYPE	68	95	212

Figure S310. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.00066

Table S311. Gene #58: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
9P LOSS MUTATED	93	86	58
9P LOSS WILD-TYPE	155	71	114

Figure S311. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 0.00115 (Fisher's exact test), Q value = 0.0026

Table S312. Gene #58: '9p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
9P LOSS MUTATED	98	61	22
9P LOSS WILD-TYPE	136	68	70

Figure S312. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 9.7e-05

Table S313. Gene #58: '9p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
9P LOSS MUTATED	40	56	10	47	28
9P LOSS WILD-TYPE	35	94	15	42	88

Figure S313. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_CNMF'

P value = 0.00054 (Fisher's exact test), Q value = 0.0013

Table S314. Gene #58: '9p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
9P LOSS MUTATED	85	125	39
9P LOSS WILD-TYPE	79	203	92

Figure S314. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'9p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S315. Gene #58: '9p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
9P LOSS MUTATED	73	37	68	51	20
9P LOSS WILD-TYPE	54	68	161	44	47

Figure S315. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00344 (Fisher's exact test), Q value = 0.0068

Table S316. Gene #58: '9p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
9P LOSS MUTATED	78	78	66
9P LOSS WILD-TYPE	66	131	105

Figure S316. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'9p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.00081

Table S317. Gene #58: '9p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
9P LOSS MUTATED	26	58	50	37	51
9P LOSS WILD-TYPE	21	64	112	64	41

Figure S317. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S318. Gene #59: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
9Q LOSS MUTATED	65	85	25
9Q LOSS WILD-TYPE	101	125	224

Figure S318. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00033

Table S319. Gene #59: '9q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
9Q LOSS MUTATED	57	66	43
9Q LOSS WILD-TYPE	191	91	129

Figure S319. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 0.0141 (Fisher's exact test), Q value = 0.023

Table S320. Gene #59: '9q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
9Q LOSS MUTATED	66	47	17
9Q LOSS WILD-TYPE	168	82	75

Figure S320. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 7e-04

Table S321. Gene #59: '9q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
9Q LOSS MUTATED	32	35	5	36	22
9Q LOSS WILD-TYPE	43	115	20	53	94

Figure S321. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00033

Table S322. Gene #59: '9q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
9Q LOSS MUTATED	68	79	28
9Q LOSS WILD-TYPE	96	249	103

Figure S322. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'9q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S323. Gene #59: '9q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
9Q LOSS MUTATED	57	22	45	38	13
9Q LOSS WILD-TYPE	70	83	184	57	54

Figure S323. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.00074

Table S324. Gene #59: '9q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
9Q LOSS MUTATED	61	48	45
9Q LOSS WILD-TYPE	83	161	126

Figure S324. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'9q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 6.9e-05

Table S325. Gene #59: '9q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
9Q LOSS MUTATED	25	35	30	26	38
9Q LOSS WILD-TYPE	22	87	132	75	54

Figure S325. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S326. Gene #60: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
10P LOSS MUTATED	35	69	13
10P LOSS WILD-TYPE	131	141	236

Figure S326. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 6.9e-05

Table S327. Gene #60: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
10P LOSS MUTATED	32	52	26
10P LOSS WILD-TYPE	216	105	146

Figure S327. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 9.7e-05

Table S328. Gene #60: '10p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
10P LOSS MUTATED	32	40	9
10P LOSS WILD-TYPE	202	89	83

Figure S328. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S329. Gene #60: '10p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
10P LOSS MUTATED	11	22	4	35	9
10P LOSS WILD-TYPE	64	128	21	54	107

Figure S329. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_CNMF'

P value = 0.00176 (Fisher's exact test), Q value = 0.0037

Table S330. Gene #60: '10p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
10P LOSS MUTATED	46	54	17
10P LOSS WILD-TYPE	118	274	114

Figure S330. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'10p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S331. Gene #60: '10p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
10P LOSS MUTATED	31	13	34	36	3
10P LOSS WILD-TYPE	96	92	195	59	64

Figure S331. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.00081

Table S332. Gene #60: '10p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
10P LOSS MUTATED	44	33	23
10P LOSS WILD-TYPE	100	176	148

Figure S332. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'10p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S333. Gene #60: '10p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
10P LOSS MUTATED	11	20	20	13	36
10P LOSS WILD-TYPE	36	102	142	88	56

Figure S333. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S334. Gene #61: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
10Q LOSS MUTATED	42	65	10
10Q LOSS WILD-TYPE	124	145	239

Figure S334. 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 = 3.7e-05

Table S335. Gene #61: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
10Q LOSS MUTATED	31	56	21
10Q LOSS WILD-TYPE	217	101	151

Figure S335. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 4e-04

Table S336. Gene #61: '10q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
10Q LOSS MUTATED	34	39	9
10Q LOSS WILD-TYPE	200	90	83

Figure S336. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S337. Gene #61: '10q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
10Q LOSS MUTATED	13	22	3	36	8
10Q LOSS WILD-TYPE	62	128	22	53	108

Figure S337. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_CNMF'

P value = 0.00054 (Fisher's exact test), Q value = 0.0013

Table S338. Gene #61: '10q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
10Q LOSS MUTATED	45	59	13
10Q LOSS WILD-TYPE	119	269	118

Figure S338. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S339. Gene #61: '10q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
10Q LOSS MUTATED	34	15	29	36	3
10Q LOSS WILD-TYPE	93	90	200	59	64

Figure S339. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00097 (Fisher's exact test), Q value = 0.0022

Table S340. Gene #61: '10q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
10Q LOSS MUTATED	42	31	24
10Q LOSS WILD-TYPE	102	178	147

Figure S340. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'10q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S341. Gene #61: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
10Q LOSS MUTATED	10	20	17	14	36
10Q LOSS WILD-TYPE	37	102	145	87	56

Figure S341. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S342. Gene #62: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
11P LOSS MUTATED	39	66	13
11P LOSS WILD-TYPE	127	144	236

Figure S342. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 9.7e-05

Table S343. Gene #62: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
11P LOSS MUTATED	43	49	18
11P LOSS WILD-TYPE	205	108	154

Figure S343. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11p loss' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 9.7e-05

Table S344. Gene #62: '11p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
11P LOSS MUTATED	34	41	10
11P LOSS WILD-TYPE	200	88	82

Figure S344. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'11p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00071 (Fisher's exact test), Q value = 0.0017

Table S345. Gene #62: '11p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
11P LOSS MUTATED	17	24	8	26	10
11P LOSS WILD-TYPE	58	126	17	63	106

Figure S345. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00022

Table S346. Gene #62: '11p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
11P LOSS MUTATED	50	53	15
11P LOSS WILD-TYPE	114	275	116

Figure S346. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'11p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 7e-04

Table S347. Gene #62: '11p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
11P LOSS MUTATED	33	15	38	28	4
11P LOSS WILD-TYPE	94	90	191	67	63

Figure S347. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.00066

Table S348. Gene #62: '11p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
11P LOSS MUTATED	44	34	22
11P LOSS WILD-TYPE	100	175	149

Figure S348. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'11p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0055 (Fisher's exact test), Q value = 0.01

Table S349. Gene #62: '11p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
11P LOSS MUTATED	11	28	22	12	27
11P LOSS WILD-TYPE	36	94	140	89	65

Figure S349. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S350. Gene #63: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
11Q LOSS MUTATED	37	70	13
11Q LOSS WILD-TYPE	129	140	236

Figure S350. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S351. Gene #63: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
11Q LOSS MUTATED	37	57	20
11Q LOSS WILD-TYPE	211	100	152

Figure S351. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S352. Gene #63: '11q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
11Q LOSS MUTATED	27	46	12
11Q LOSS WILD-TYPE	207	83	80

Figure S352. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'11q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S353. Gene #63: '11q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
11Q LOSS MUTATED	16	19	6	34	10
11Q LOSS WILD-TYPE	59	131	19	55	106

Figure S353. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S354. Gene #63: '11q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
11Q LOSS MUTATED	59	47	13
11Q LOSS WILD-TYPE	105	281	118

Figure S354. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'11q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S355. Gene #63: '11q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
11Q LOSS MUTATED	29	13	34	37	6
11Q LOSS WILD-TYPE	98	92	195	58	61

Figure S355. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S356. Gene #63: '11q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
11Q LOSS MUTATED	53	24	25
11Q LOSS WILD-TYPE	91	185	146

Figure S356. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'11q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S357. Gene #63: '11q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
11Q LOSS MUTATED	11	22	22	11	36
11Q LOSS WILD-TYPE	36	100	140	90	56

Figure S357. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S358. Gene #64: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
12P LOSS MUTATED	56	32	7
12P LOSS WILD-TYPE	110	178	242

Figure S358. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

'12p loss' versus 'METHLYATION_CNMF'

P value = 0.00588 (Fisher's exact test), Q value = 0.011

Table S359. Gene #64: '12p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
12P LOSS MUTATED	37	33	15
12P LOSS WILD-TYPE	211	124	157

Figure S359. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S360. Gene #64: '12p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
12P LOSS MUTATED	24	21	9	8	5
12P LOSS WILD-TYPE	51	129	16	81	111

Figure S360. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'12p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S361. Gene #64: '12p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
12P LOSS MUTATED	44	10	29	8	4
12P LOSS WILD-TYPE	83	95	200	87	63

Figure S361. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'12p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0371 (Fisher's exact test), Q value = 0.055

Table S362. Gene #64: '12p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
12P LOSS MUTATED	26	39	17
12P LOSS WILD-TYPE	118	170	154

Figure S362. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'12p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00099 (Fisher's exact test), Q value = 0.0023

Table S363. Gene #64: '12p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
12P LOSS MUTATED	17	23	21	13	8
12P LOSS WILD-TYPE	30	99	141	88	84

Figure S363. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S364. Gene #65: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
12Q LOSS MUTATED	44	32	6
12Q LOSS WILD-TYPE	122	178	243

Figure S364. Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'

'12q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.00033

Table S365. Gene #65: '12q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
12Q LOSS MUTATED	14	23	8	9	4
12Q LOSS WILD-TYPE	61	127	17	80	112

Figure S365. Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'12q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 0.00073

Table S366. Gene #65: '12q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
12Q LOSS MUTATED	32	10	29	8	3
12Q LOSS WILD-TYPE	95	95	200	87	64

Figure S366. Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S367. Gene #66: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
13Q LOSS MUTATED	11	77	14
13Q LOSS WILD-TYPE	155	133	235

Figure S367. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S368. Gene #66: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
13Q LOSS MUTATED	32	46	17
13Q LOSS WILD-TYPE	216	111	155

Figure S368. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S369. Gene #66: '13q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
13Q LOSS MUTATED	32	46	13
13Q LOSS WILD-TYPE	202	83	79

Figure S369. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S370. Gene #66: '13q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
13Q LOSS MUTATED	20	19	3	38	11
13Q LOSS WILD-TYPE	55	131	22	51	105

Figure S370. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S371. Gene #66: '13q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
13Q LOSS MUTATED	53	34	15
13Q LOSS WILD-TYPE	111	294	116

Figure S371. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'13q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S372. Gene #66: '13q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
13Q LOSS MUTATED	19	8	26	42	7
13Q LOSS WILD-TYPE	108	97	203	53	60

Figure S372. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S373. Gene #66: '13q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
13Q LOSS MUTATED	45	20	24
13Q LOSS WILD-TYPE	99	189	147

Figure S373. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'13q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S374. Gene #66: '13q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
13Q LOSS MUTATED	8	17	13	10	41
13Q LOSS WILD-TYPE	39	105	149	91	51

Figure S374. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S375. Gene #67: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
14Q LOSS MUTATED	68	62	28
14Q LOSS WILD-TYPE	98	148	221

Figure S375. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 0.0125 (Fisher's exact test), Q value = 0.021

Table S376. Gene #67: '14q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
14Q LOSS MUTATED	66	50	31
14Q LOSS WILD-TYPE	182	107	141

Figure S376. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00043 (Fisher's exact test), Q value = 0.0011

Table S377. Gene #67: '14q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
14Q LOSS MUTATED	33	36	7	13	23
14Q LOSS WILD-TYPE	42	114	18	76	93

Figure S377. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S378. Gene #67: '14q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
14Q LOSS MUTATED	59	23	46	16	14
14Q LOSS WILD-TYPE	68	82	183	79	53

Figure S378. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00177 (Fisher's exact test), Q value = 0.0037

Table S379. Gene #67: '14q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
14Q LOSS MUTATED	21	39	37	19	16
14Q LOSS WILD-TYPE	26	83	125	82	76

Figure S379. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S380. Gene #68: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
15Q LOSS MUTATED	61	64	24
15Q LOSS WILD-TYPE	105	146	225

Figure S380. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00198 (Fisher's exact test), Q value = 0.0041

Table S381. Gene #68: '15q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
15Q LOSS MUTATED	47	23	47	23	9
15Q LOSS WILD-TYPE	80	82	182	72	58

Figure S381. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'16p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S382. Gene #69: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
16P LOSS MUTATED	74	61	21
16P LOSS WILD-TYPE	92	149	228

Figure S382. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

'16p loss' versus 'METHLYATION_CNMF'

P value = 0.00305 (Fisher's exact test), Q value = 0.0061

Table S383. Gene #69: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
16P LOSS MUTATED	63	53	30
16P LOSS WILD-TYPE	185	104	142

Figure S383. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S384. Gene #69: '16p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
16P LOSS MUTATED	35	31	12	13	16
16P LOSS WILD-TYPE	40	119	13	76	100

Figure S384. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_CNMF'

P value = 0.00872 (Fisher's exact test), Q value = 0.015

Table S385. Gene #69: '16p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
16P LOSS MUTATED	49	86	20
16P LOSS WILD-TYPE	115	242	111

Figure S385. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'16p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 9.7e-05

Table S386. Gene #69: '16p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
16P LOSS MUTATED	55	24	52	15	9
16P LOSS WILD-TYPE	72	81	177	80	58

Figure S386. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0125 (Fisher's exact test), Q value = 0.021

Table S387. Gene #69: '16p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
16P LOSS MUTATED	44	59	30
16P LOSS WILD-TYPE	100	150	141

Figure S387. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'16p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S388. Gene #69: '16p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
16P LOSS MUTATED	26	43	29	20	15
16P LOSS WILD-TYPE	21	79	133	81	77

Figure S388. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S389. Gene #70: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
16Q LOSS MUTATED	79	64	25
16Q LOSS WILD-TYPE	87	146	224

Figure S389. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 0.0468 (Fisher's exact test), Q value = 0.067

Table S390. Gene #70: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
16Q LOSS MUTATED	63	54	39
16Q LOSS WILD-TYPE	185	103	133

Figure S390. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S391. Gene #70: '16q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
16Q LOSS MUTATED	38	39	11	11	17
16Q LOSS WILD-TYPE	37	111	14	78	99

Figure S391. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S392. Gene #70: '16q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
16Q LOSS MUTATED	64	24	55	12	12
16Q LOSS WILD-TYPE	63	81	174	83	55

Figure S392. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0142 (Fisher's exact test), Q value = 0.023

Table S393. Gene #70: '16q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
16Q LOSS MUTATED	46	64	33
16Q LOSS WILD-TYPE	98	145	138

Figure S393. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S394. Gene #70: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
16Q LOSS MUTATED	28	46	32	25	12
16Q LOSS WILD-TYPE	19	76	130	76	80

Figure S394. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S395. Gene #71: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
17P LOSS MUTATED	105	88	43
17P LOSS WILD-TYPE	61	122	206

Figure S395. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 0.00045 (Fisher's exact test), Q value = 0.0011

Table S396. Gene #71: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
17P LOSS MUTATED	107	68	45
17P LOSS WILD-TYPE	141	89	127

Figure S396. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 0.0138 (Fisher's exact test), Q value = 0.023

Table S397. Gene #71: '17p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
17P LOSS MUTATED	95	43	22
17P LOSS WILD-TYPE	139	86	70

Figure S397. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S398. Gene #71: '17p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
17P LOSS MUTATED	46	51	14	22	27
17P LOSS WILD-TYPE	29	99	11	67	89

Figure S398. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CNMF'

P value = 0.00547 (Fisher's exact test), Q value = 0.01

Table S399. Gene #71: '17p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
17P LOSS MUTATED	60	140	35
17P LOSS WILD-TYPE	104	188	96

Figure S399. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S400. Gene #71: '17p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
17P LOSS MUTATED	76	40	83	24	12
17P LOSS WILD-TYPE	51	65	146	71	55

Figure S400. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 6.9e-05

Table S401. Gene #71: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
17P LOSS MUTATED	28	61	59	28	23
17P LOSS WILD-TYPE	19	61	103	73	69

Figure S401. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S402. Gene #72: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
17Q LOSS MUTATED	50	31	18
17Q LOSS WILD-TYPE	116	179	231

Figure S402. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

'17q loss' versus 'METHLYATION_CNMF'

P value = 0.0213 (Fisher's exact test), Q value = 0.033

Table S403. Gene #72: '17q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
17Q LOSS MUTATED	30	35	24
17Q LOSS WILD-TYPE	218	122	148

Figure S403. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.004 (Fisher's exact test), Q value = 0.0078

Table S404. Gene #72: '17q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
17Q LOSS MUTATED	21	18	4	9	10
17Q LOSS WILD-TYPE	54	132	21	80	106

Figure S404. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_CNMF'

P value = 0.0291 (Fisher's exact test), Q value = 0.044

Table S405. Gene #72: '17q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
17Q LOSS MUTATED	24	62	12
17Q LOSS WILD-TYPE	140	266	119

Figure S405. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'17q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00034 (Fisher's exact test), Q value = 0.00087

Table S406. Gene #72: '17q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
17Q LOSS MUTATED	37	16	28	11	6
17Q LOSS WILD-TYPE	90	89	201	84	61

Figure S406. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00813 (Fisher's exact test), Q value = 0.014

Table S407. Gene #72: '17q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
17Q LOSS MUTATED	17	19	22	14	11
17Q LOSS WILD-TYPE	30	103	140	87	81

Figure S407. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S408. Gene #73: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
18P LOSS MUTATED	71	72	44
18P LOSS WILD-TYPE	95	138	205

Figure S408. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S409. Gene #74: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
18Q LOSS MUTATED	90	116	50
18Q LOSS WILD-TYPE	76	94	199

Figure S409. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 0.0252 (Fisher's exact test), Q value = 0.039

Table S410. Gene #74: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
18Q LOSS MUTATED	104	76	58
18Q LOSS WILD-TYPE	144	81	114

Figure S410. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18q loss' versus 'MIRSEQ_CNMF'

P value = 0.0207 (Fisher's exact test), Q value = 0.033

Table S411. Gene #74: '18q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
18Q LOSS MUTATED	80	133	43
18Q LOSS WILD-TYPE	84	195	88

Figure S411. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'18q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00153 (Fisher's exact test), Q value = 0.0033

Table S412. Gene #74: '18q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
18Q LOSS MUTATED	68	34	88	46	20
18Q LOSS WILD-TYPE	59	71	141	49	47

Figure S412. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0369 (Fisher's exact test), Q value = 0.055

Table S413. Gene #74: '18q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
18Q LOSS MUTATED	72	80	63
18Q LOSS WILD-TYPE	72	129	108

Figure S413. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'19p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S414. Gene #75: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
19P LOSS MUTATED	85	79	13
19P LOSS WILD-TYPE	81	131	236

Figure S414. 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 = 3.7e-05

Table S415. Gene #75: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
19P LOSS MUTATED	55	83	29
19P LOSS WILD-TYPE	193	74	143

Figure S415. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S416. Gene #75: '19p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
19P LOSS MUTATED	62	48	8
19P LOSS WILD-TYPE	172	81	84

Figure S416. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S417. Gene #75: '19p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
19P LOSS MUTATED	44	31	5	30	8
19P LOSS WILD-TYPE	31	119	20	59	108

Figure S417. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S418. Gene #75: '19p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
19P LOSS MUTATED	73	85	18
19P LOSS WILD-TYPE	91	243	113

Figure S418. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'19p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S419. Gene #75: '19p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
19P LOSS MUTATED	71	25	41	34	5
19P LOSS WILD-TYPE	56	80	188	61	62

Figure S419. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S420. Gene #75: '19p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
19P LOSS MUTATED	67	55	30
19P LOSS WILD-TYPE	77	154	141

Figure S420. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'19p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S421. Gene #75: '19p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
19P LOSS MUTATED	28	38	34	19	33
19P LOSS WILD-TYPE	19	84	128	82	59

Figure S421. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S422. Gene #76: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
19Q LOSS MUTATED	66	58	12
19Q LOSS WILD-TYPE	100	152	237

Figure S422. 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 = 3.7e-05

Table S423. Gene #76: '19q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
19Q LOSS MUTATED	36	71	19
19Q LOSS WILD-TYPE	212	86	153

Figure S423. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19q loss' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 9.7e-05

Table S424. Gene #76: '19q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
19Q LOSS MUTATED	46	40	6
19Q LOSS WILD-TYPE	188	89	86

Figure S424. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'19q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S425. Gene #76: '19q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
19Q LOSS MUTATED	31	27	1	27	6
19Q LOSS WILD-TYPE	44	123	24	62	110

Figure S425. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S426. Gene #76: '19q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
19Q LOSS MUTATED	61	63	12
19Q LOSS WILD-TYPE	103	265	119

Figure S426. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'19q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S427. Gene #76: '19q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
19Q LOSS MUTATED	54	20	27	31	4
19Q LOSS WILD-TYPE	73	85	202	64	63

Figure S427. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S428. Gene #76: '19q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
19Q LOSS MUTATED	54	41	20
19Q LOSS WILD-TYPE	90	168	151

Figure S428. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'19q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00013

Table S429. Gene #76: '19q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
19Q LOSS MUTATED	19	28	24	13	31
19Q LOSS WILD-TYPE	28	94	138	88	61

Figure S429. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p loss' versus 'CN_CNMF'

P value = 0.00177 (Fisher's exact test), Q value = 0.0037

Table S430. Gene #77: '20p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
20P LOSS MUTATED	11	23	7
20P LOSS WILD-TYPE	155	187	242

Figure S430. Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #1: 'CN_CNMF'

'20q loss' versus 'MIRSEQ_CNMF'

P value = 0.00566 (Fisher's exact test), Q value = 0.01

Table S431. Gene #78: '20q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
20Q LOSS MUTATED	6	1	1
20Q LOSS WILD-TYPE	158	327	130

Figure S431. Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S432. Gene #79: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
21Q LOSS MUTATED	96	131	62
21Q LOSS WILD-TYPE	70	79	187

Figure S432. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

'21q loss' versus 'MRNASEQ_CNMF'

P value = 7e-04 (Fisher's exact test), Q value = 0.0016

Table S433. Gene #79: '21q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
21Q LOSS MUTATED	96	74	31
21Q LOSS WILD-TYPE	138	55	61

Figure S433. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'21q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 9.7e-05

Table S434. Gene #79: '21q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
21Q LOSS MUTATED	45	57	18	47	34
21Q LOSS WILD-TYPE	30	93	7	42	82

Figure S434. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_CNMF'

P value = 0.00475 (Fisher's exact test), Q value = 0.009

Table S435. Gene #79: '21q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
21Q LOSS MUTATED	89	154	46
21Q LOSS WILD-TYPE	75	174	85

Figure S435. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'21q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00046 (Fisher's exact test), Q value = 0.0011

Table S436. Gene #79: '21q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
21Q LOSS MUTATED	73	36	109	50	21
21Q LOSS WILD-TYPE	54	69	120	45	46

Figure S436. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0039 (Fisher's exact test), Q value = 0.0076

Table S437. Gene #79: '21q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
21Q LOSS MUTATED	84	97	68
21Q LOSS WILD-TYPE	60	112	103

Figure S437. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'21q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0164 (Fisher's exact test), Q value = 0.027

Table S438. Gene #79: '21q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
21Q LOSS MUTATED	29	65	65	41	49
21Q LOSS WILD-TYPE	18	57	97	60	43

Figure S438. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S439. Gene #80: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
22Q LOSS MUTATED	92	97	29
22Q LOSS WILD-TYPE	74	113	220

Figure S439. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 6.9e-05

Table S440. Gene #80: '22q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
22Q LOSS MUTATED	41	52	11	22	26
22Q LOSS WILD-TYPE	34	98	14	67	90

Figure S440. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CNMF'

P value = 0.00419 (Fisher's exact test), Q value = 0.0081

Table S441. Gene #80: '22q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
22Q LOSS MUTATED	60	127	30
22Q LOSS WILD-TYPE	104	201	101

Figure S441. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S442. Gene #80: '22q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
22Q LOSS MUTATED	73	33	72	24	15
22Q LOSS WILD-TYPE	54	72	157	71	52

Figure S442. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00025 (Fisher's exact test), Q value = 0.00069

Table S443. Gene #80: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
22Q LOSS MUTATED	25	59	48	32	23
22Q LOSS WILD-TYPE	22	63	114	69	69

Figure S443. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xp loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S444. Gene #81: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
XP LOSS MUTATED	40	70	12
XP LOSS WILD-TYPE	126	140	237

Figure S444. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'

'xp loss' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 6.9e-05

Table S445. Gene #81: 'xp loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
XP LOSS MUTATED	53	45	16
XP LOSS WILD-TYPE	195	112	156

Figure S445. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xp loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S446. Gene #81: 'xp loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
XP LOSS MUTATED	44	42	6
XP LOSS WILD-TYPE	190	87	86

Figure S446. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'xp loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00016

Table S447. Gene #81: 'xp loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
XP LOSS MUTATED	21	26	7	29	9
XP LOSS WILD-TYPE	54	124	18	60	107

Figure S447. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S448. Gene #81: 'xp loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
XP LOSS MUTATED	49	65	8
XP LOSS WILD-TYPE	115	263	123

Figure S448. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'xp loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00085 (Fisher's exact test), Q value = 0.0019

Table S449. Gene #81: 'xp loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
XP LOSS MUTATED	29	19	38	31	5
XP LOSS WILD-TYPE	98	86	191	64	62

Figure S449. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0159 (Fisher's exact test), Q value = 0.026

Table S450. Gene #81: 'xp loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
XP LOSS MUTATED	41	43	26
XP LOSS WILD-TYPE	103	166	145

Figure S450. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'xp loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00055 (Fisher's exact test), Q value = 0.0013

Table S451. Gene #81: 'xp loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
XP LOSS MUTATED	11	31	26	11	31
XP LOSS WILD-TYPE	36	91	136	90	61

Figure S451. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S452. Gene #82: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
XQ LOSS MUTATED	32	54	10
XQ LOSS WILD-TYPE	134	156	239

Figure S452. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 0.00625 (Fisher's exact test), Q value = 0.011

Table S453. Gene #82: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
XQ LOSS MUTATED	43	30	14
XQ LOSS WILD-TYPE	205	127	158

Figure S453. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq loss' versus 'MRNASEQ_CNMF'

P value = 0.00215 (Fisher's exact test), Q value = 0.0044

Table S454. Gene #82: 'xq loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
XQ LOSS MUTATED	40	28	5
XQ LOSS WILD-TYPE	194	101	87

Figure S454. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'xq loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00104 (Fisher's exact test), Q value = 0.0024

Table S455. Gene #82: 'xq loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
XQ LOSS MUTATED	21	26	5	14	7
XQ LOSS WILD-TYPE	54	124	20	75	109

Figure S455. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.00085

Table S456. Gene #82: 'xq loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
XQ LOSS MUTATED	34	55	7
XQ LOSS WILD-TYPE	130	273	124

Figure S456. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'xq loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0169 (Fisher's exact test), Q value = 0.027

Table S457. Gene #82: 'xq loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
XQ LOSS MUTATED	31	34	17
XQ LOSS WILD-TYPE	113	175	154

Figure S457. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'xq loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00991 (Fisher's exact test), Q value = 0.017

Table S458. Gene #82: 'xq loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
XQ LOSS MUTATED	11	25	24	6	16
XQ LOSS WILD-TYPE	36	97	138	95	76

Figure S458. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data

Input

Copy number data file = broad_values_by_arm.txt from GISTIC pipeline
Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/STES-TP/15101919/transformed.cor.cli.txt
Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/STES-TP/15125163/STES-TP.transferedmergedcluster.txt
Number of patients = 625
Number of significantly arm-level cnvs = 82
Number of molecular subtypes = 8
Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

References

[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)

[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)

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