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 80 arm-level events and 12 molecular subtypes across 514 patients, 396 significant findings detected with P value < 0.05 and Q value < 0.25.

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

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 80 arm-level events and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 396 significant findings detected.


		Clinical Features	MRNA CNMF	MRNA CHIERARCHICAL	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Chi-square test	Fisher's exact test	Chi-square test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Chi-square test	Fisher's exact test	Fisher's exact test	Fisher's exact test
15q loss	102 (20%)	412	0.000567 (0.282)	4.17e-05 (0.0235)	1.41e-40 (1.26e-37)	9.28e-15 (7.52e-12)	0.00036 (0.183)	0.212 (1.00)	6.18e-24 (5.38e-21)	4.92e-22 (4.25e-19)	2.43e-20 (2.08e-17)	2.31e-15 (1.9e-12)	1.63e-07 (0.000111)	1.44e-09 (1.06e-06)
20q gain	123 (24%)	391	0.00202 (0.938)	0.000218 (0.114)	1.67e-46 (1.5e-43)	5.27e-12 (4.13e-09)	0.0303 (1.00)	0.378 (1.00)	1.36e-17 (1.13e-14)	2.45e-15 (2.01e-12)	3.65e-14 (2.93e-11)	5.6e-09 (4.05e-06)	0.000109 (0.0591)	1.55e-08 (1.1e-05)
4p loss	98 (19%)	416	0.00381 (1.00)	0.000454 (0.229)	8.18e-37 (7.26e-34)	2.53e-16 (2.1e-13)	0.00389 (1.00)	0.346 (1.00)	3.64e-22 (3.15e-19)	1.6e-20 (1.37e-17)	6.47e-20 (5.52e-17)	1.54e-14 (1.24e-11)	2.43e-06 (0.00152)	2.24e-09 (1.63e-06)
9q loss	117 (23%)	397	2.35e-05 (0.0135)	1.13e-06 (0.000721)	1.94e-48 (1.74e-45)	1.2e-11 (9.33e-09)	0.000759 (0.369)	0.205 (1.00)	2.74e-21 (2.36e-18)	1.41e-18 (1.19e-15)	8.69e-22 (7.5e-19)	4.05e-11 (3.11e-08)	0.000758 (0.369)	1.33e-05 (0.00782)
14q loss	59 (11%)	455	0.00202 (0.938)	0.000218 (0.114)	4.69e-23 (4.06e-20)	1.69e-11 (1.31e-08)	0.0273 (1.00)	0.00216 (0.988)	2.3e-16 (1.91e-13)	1.34e-12 (1.06e-09)	5.03e-09 (3.65e-06)	3.66e-13 (2.9e-10)	1.66e-05 (0.00974)	3.64e-06 (0.00223)
16p loss	93 (18%)	421	0.00202 (0.938)	0.000218 (0.114)	8.75e-36 (7.76e-33)	2.55e-13 (2.02e-10)	0.0713 (1.00)	0.157 (1.00)	4.39e-20 (3.76e-17)	7.94e-17 (6.61e-14)	1.98e-14 (1.6e-11)	4.7e-11 (3.6e-08)	2.8e-05 (0.016)	2.3e-07 (0.000155)
16q loss	134 (26%)	380	0.000771 (0.373)	9.8e-05 (0.0533)	1.94e-46 (1.73e-43)	4.2e-14 (3.36e-11)	0.308 (1.00)	1 (1.00)	2.51e-24 (2.19e-21)	3.27e-19 (2.78e-16)	8.72e-19 (7.37e-16)	1.83e-11 (1.42e-08)	1.67e-06 (0.00106)	7.91e-09 (5.69e-06)
2p gain	88 (17%)	426	0.855 (1.00)	0.683 (1.00)	2.04e-33 (1.8e-30)	1.53e-08 (1.09e-05)	0.0545 (1.00)	1 (1.00)	2.06e-07 (0.000139)	1.85e-07 (0.000125)	2.85e-06 (0.00177)	1.43e-06 (0.000905)	0.000264 (0.135)	3e-05 (0.0171)
2q gain	71 (14%)	443	0.343 (1.00)	1 (1.00)	3.48e-30 (3.07e-27)	4.81e-07 (0.000318)	0.0342 (1.00)	0.813 (1.00)	1.24e-05 (0.00733)	2.84e-06 (0.00177)	1.22e-05 (0.00725)	3.2e-06 (0.00198)	0.000267 (0.137)	4.05e-05 (0.0229)
3q gain	76 (15%)	438	0.617 (1.00)	0.847 (1.00)	3.32e-24 (2.9e-21)	5.9e-10 (4.39e-07)	0.163 (1.00)	0.0444 (1.00)	5.83e-13 (4.62e-10)	1.5e-11 (1.17e-08)	3.55e-06 (0.00218)	1.63e-08 (1.16e-05)	0.000235 (0.121)	4.3e-07 (0.000286)
5p gain	49 (10%)	465	0.902 (1.00)	0.312 (1.00)	3.03e-15 (2.48e-12)	2.52e-07 (0.000169)	0.0743 (1.00)	1 (1.00)	1.83e-11 (1.42e-08)	5.13e-08 (3.58e-05)	2.51e-08 (1.77e-05)	2.05e-06 (0.00129)	3.21e-05 (0.0183)	7.64e-07 (0.000494)
18p gain	65 (13%)	449	0.333 (1.00)	0.158 (1.00)	3.67e-24 (3.2e-21)	4.33e-10 (3.23e-07)	0.0184 (1.00)	0.0242 (1.00)	4.15e-15 (3.38e-12)	8.32e-14 (6.65e-11)	4.64e-12 (3.64e-09)	4.24e-11 (3.25e-08)	1.18e-06 (0.000751)	1.94e-11 (1.49e-08)
18q gain	40 (8%)	474	0.253 (1.00)	0.0902 (1.00)	2.87e-12 (2.26e-09)	1.16e-05 (0.00692)	0.292 (1.00)	0.0831 (1.00)	1.94e-08 (1.37e-05)	4.83e-08 (3.37e-05)	4e-08 (2.8e-05)	1.12e-06 (0.000715)	0.000138 (0.074)	5.13e-07 (0.000338)
20p gain	106 (21%)	408	0.00809 (1.00)	0.00105 (0.499)	1.06e-37 (9.42e-35)	7.91e-11 (6.04e-08)	0.143 (1.00)	0.812 (1.00)	8.7e-15 (7.06e-12)	8.55e-14 (6.82e-11)	2.22e-12 (1.75e-09)	5.19e-08 (3.61e-05)	3.21e-05 (0.0183)	3.74e-08 (2.63e-05)
22q gain	31 (6%)	483			8.4e-09 (6.02e-06)	3.96e-09 (2.88e-06)	0.341 (1.00)	0.0519 (1.00)	1.08e-09 (7.95e-07)	5.35e-10 (3.98e-07)	0.000164 (0.0867)	2.78e-05 (0.0159)	6.07e-06 (0.00362)	4.77e-07 (0.000316)
4q loss	97 (19%)	417	0.151 (1.00)	0.0272 (1.00)	4.21e-38 (3.75e-35)	8.96e-17 (7.46e-14)	0.0198 (1.00)	0.346 (1.00)	1.48e-24 (1.29e-21)	3.75e-20 (3.21e-17)	3.04e-15 (2.49e-12)	2.76e-15 (2.26e-12)	1.83e-06 (0.00115)	5.02e-09 (3.64e-06)
5q loss	72 (14%)	442	0.0129 (1.00)	0.00193 (0.899)	4.45e-28 (3.93e-25)	2.47e-14 (1.99e-11)	0.00283 (1.00)	0.0233 (1.00)	3.64e-15 (2.96e-12)	1.48e-14 (1.2e-11)	1.11e-10 (8.46e-08)	9.74e-11 (7.42e-08)	3.56e-05 (0.0201)	5.68e-07 (0.000373)
8p loss	74 (14%)	440	0.00809 (1.00)	0.00105 (0.499)	5.91e-32 (5.23e-29)	1.49e-15 (1.23e-12)	0.04 (1.00)	0.58 (1.00)	4.35e-19 (3.68e-16)	7.42e-17 (6.19e-14)	2.36e-18 (1.99e-15)	9.35e-12 (7.28e-09)	7.31e-08 (5.04e-05)	5.91e-09 (4.26e-06)
9p loss	100 (19%)	414	0.000997 (0.478)	9.8e-05 (0.0533)	3.41e-41 (3.05e-38)	5.04e-11 (3.86e-08)	0.00267 (1.00)	0.113 (1.00)	5.72e-20 (4.88e-17)	1.65e-15 (1.36e-12)	3.22e-15 (2.63e-12)	3.92e-10 (2.93e-07)	0.00339 (1.00)	4.57e-05 (0.0256)
11q loss	68 (13%)	446			1.24e-24 (1.08e-21)	1.81e-09 (1.33e-06)	0.777 (1.00)	1 (1.00)	5.81e-11 (4.44e-08)	8.62e-11 (6.57e-08)	9.12e-12 (7.12e-09)	6.42e-07 (0.000419)	0.000207 (0.109)	2.32e-09 (1.7e-06)
17p loss	120 (23%)	394	0.00324 (1.00)	0.000454 (0.229)	1.49e-58 (1.33e-55)	1.13e-15 (9.35e-13)	0.00274 (1.00)	0.827 (1.00)	3.33e-26 (2.92e-23)	3.04e-19 (2.59e-16)	3.95e-21 (3.4e-18)	1.79e-10 (1.35e-07)	0.000577 (0.287)	3.82e-06 (0.00233)
19p loss	57 (11%)	457			2.35e-19 (2e-16)	1.37e-12 (1.08e-09)	0.0523 (1.00)	0.393 (1.00)	2.09e-09 (1.53e-06)	1.42e-10 (1.08e-07)	1.37e-09 (1.01e-06)	4.38e-07 (0.000291)	1.97e-05 (0.0114)	5.3e-08 (3.68e-05)
21q loss	51 (10%)	463	0.0391 (1.00)	0.00466 (1.00)	3.62e-14 (2.91e-11)	2.12e-06 (0.00133)	0.207 (1.00)	0.243 (1.00)	5.34e-10 (3.98e-07)	1.67e-08 (1.18e-05)	2.59e-08 (1.83e-05)	5.86e-08 (4.05e-05)	1.11e-06 (0.000714)	2.17e-07 (0.000146)
22q loss	105 (20%)	409	0.00202 (0.938)	0.000218 (0.114)	4.41e-44 (3.94e-41)	2.74e-10 (2.06e-07)	0.0443 (1.00)	0.813 (1.00)	3.35e-18 (2.81e-15)	2.18e-16 (1.81e-13)	3.38e-16 (2.8e-13)	8.38e-09 (6.02e-06)	0.0111 (1.00)	2.13e-05 (0.0123)
xq loss	69 (13%)	445	0.00809 (1.00)	0.00105 (0.499)	7.32e-28 (6.46e-25)	2.26e-07 (0.000152)	2.71e-05 (0.0155)	0.059 (1.00)	2.36e-14 (1.9e-11)	2.46e-12 (1.94e-09)	2.78e-11 (2.14e-08)	4.02e-08 (2.81e-05)	0.000527 (0.264)	3.73e-06 (0.00229)
3p loss	49 (10%)	465	0.0391 (1.00)	0.00466 (1.00)	3.72e-19 (3.15e-16)	8.1e-07 (0.000522)	0.00865 (1.00)	0.0444 (1.00)	2.36e-12 (1.86e-09)	9.68e-12 (7.53e-09)	8.46e-08 (5.82e-05)	3.47e-06 (0.00214)	0.00453 (1.00)	5.93e-05 (0.0329)
5p loss	54 (11%)	460	0.151 (1.00)	0.0272 (1.00)	1.64e-18 (1.38e-15)	5.53e-09 (4e-06)	0.0303 (1.00)	0.0242 (1.00)	9.88e-08 (6.78e-05)	1.61e-10 (1.22e-07)	3.22e-06 (0.00199)	6.14e-07 (0.000402)	0.00268 (1.00)	0.000141 (0.0752)
7q loss	40 (8%)	474			2.7e-19 (2.29e-16)	3.17e-08 (2.23e-05)	0.0844 (1.00)	0.000752 (0.366)	8.77e-15 (7.11e-12)	2.53e-10 (1.9e-07)	1.97e-11 (1.51e-08)	1.12e-06 (0.000715)	0.000833 (0.401)	3.91e-06 (0.00238)
10p loss	40 (8%)	474	0.0391 (1.00)	0.00466 (1.00)	6.06e-18 (5.07e-15)	5.26e-07 (0.000346)	0.0823 (1.00)	0.477 (1.00)	3.73e-09 (2.72e-06)	4.66e-08 (3.25e-05)	1.48e-08 (1.06e-05)	3.18e-06 (0.00197)	0.00825 (1.00)	0.000161 (0.0855)
11p loss	71 (14%)	443			1.36e-27 (1.2e-24)	1.53e-10 (1.16e-07)	0.218 (1.00)	0.373 (1.00)	3.26e-12 (2.56e-09)	1.81e-12 (1.43e-09)	1.76e-11 (1.36e-08)	1.89e-07 (0.000128)	0.000728 (0.357)	5.86e-07 (0.000384)
12q loss	35 (7%)	479			6.25e-14 (5e-11)	1.71e-05 (0.01)	0.101 (1.00)	0.0429 (1.00)	4.2e-10 (3.14e-07)	7.73e-07 (0.000499)	6.38e-05 (0.0352)	5.86e-06 (0.00351)	0.000596 (0.296)	0.000198 (0.104)
17q loss	86 (17%)	428	0.00202 (0.938)	0.000218 (0.114)	3.2e-37 (2.85e-34)	1.16e-07 (7.93e-05)	0.0924 (1.00)	0.612 (1.00)	3.33e-15 (2.71e-12)	6.49e-10 (4.81e-07)	1.64e-10 (1.24e-07)	6.47e-06 (0.00386)	0.0175 (1.00)	0.00345 (1.00)
19q loss	52 (10%)	462	0.253 (1.00)	0.0902 (1.00)	4.42e-16 (3.66e-13)	4.89e-07 (0.000323)	0.159 (1.00)	0.56 (1.00)	7.12e-07 (0.000462)	5.76e-08 (3.99e-05)	1.64e-06 (0.00104)	1.8e-05 (0.0105)	0.00247 (1.00)	4.92e-05 (0.0274)
6p gain	74 (14%)	440	0.209 (1.00)	0.173 (1.00)	5.51e-26 (4.83e-23)	6.68e-07 (0.000434)	0.168 (1.00)	0.0935 (1.00)	1.48e-08 (1.06e-05)	8.38e-08 (5.77e-05)	1.35e-06 (0.000859)	2.91e-06 (0.00181)	0.0139 (1.00)	0.00822 (1.00)
13q gain	28 (5%)	486	0.137 (1.00)	0.0194 (1.00)	4.5e-10 (3.35e-07)	0.000149 (0.0797)	0.224 (1.00)	0.477 (1.00)	2.62e-07 (0.000175)	1.75e-06 (0.0011)	3.94e-06 (0.0024)	8.63e-05 (0.0471)	0.0397 (1.00)	0.00425 (1.00)
19q gain	55 (11%)	459			2.75e-23 (2.39e-20)	2.29e-05 (0.0132)	0.331 (1.00)	0.477 (1.00)	1.19e-13 (9.46e-11)	2.86e-14 (2.3e-11)	1.26e-10 (9.58e-08)	3.49e-07 (0.000232)	0.00338 (1.00)	0.000712 (0.35)
8q loss	24 (5%)	490			5.79e-08 (4.01e-05)	2.82e-07 (0.000188)	0.333 (1.00)	1 (1.00)	8.97e-06 (0.00534)	2.67e-05 (0.0154)	1.33e-05 (0.00786)	0.00107 (0.507)	0.000734 (0.359)	6.97e-05 (0.0384)
10q loss	38 (7%)	476	0.137 (1.00)	0.0194 (1.00)	2.2e-15 (1.81e-12)	6.28e-07 (0.00041)	0.0907 (1.00)	0.731 (1.00)	1.62e-07 (0.00011)	1.39e-06 (0.000885)	4.35e-07 (0.000289)	4.09e-05 (0.023)	0.0465 (1.00)	0.00215 (0.988)
12p loss	42 (8%)	472	0.137 (1.00)	0.0194 (1.00)	7.88e-18 (6.59e-15)	0.000111 (0.0596)	0.0355 (1.00)	0.106 (1.00)	2.45e-10 (1.85e-07)	3.51e-06 (0.00216)	2.77e-07 (0.000185)	5.58e-05 (0.031)	0.000608 (0.301)	0.000764 (0.37)
13q loss	86 (17%)	428	0.902 (1.00)	0.667 (1.00)	1.62e-26 (1.42e-23)	2.92e-06 (0.00182)	0.0492 (1.00)	0.142 (1.00)	1.85e-08 (1.31e-05)	6.16e-10 (4.57e-07)	5.15e-08 (3.58e-05)	1.05e-06 (0.000674)	0.0564 (1.00)	0.02 (1.00)
18p loss	52 (10%)	462			6.39e-18 (5.35e-15)	2.39e-07 (0.000161)	0.417 (1.00)	1 (1.00)	1.3e-05 (0.00769)	5.58e-06 (0.00335)	4.56e-06 (0.00276)	7.28e-05 (0.0399)	0.00313 (1.00)	0.00549 (1.00)
18q loss	65 (13%)	449	0.536 (1.00)	0.272 (1.00)	4.66e-24 (4.06e-21)	1.7e-08 (1.2e-05)	0.627 (1.00)	1 (1.00)	1.12e-07 (7.65e-05)	6.55e-10 (4.85e-07)	1.72e-07 (0.000117)	2.09e-07 (0.000141)	0.00244 (1.00)	0.00331 (1.00)
1p gain	43 (8%)	471	0.534 (1.00)	0.312 (1.00)	2.35e-09 (1.72e-06)	0.00149 (0.7)	0.065 (1.00)	0.137 (1.00)	0.000101 (0.0545)	0.00103 (0.494)	4.76e-06 (0.00287)	1.94e-05 (0.0113)	0.000206 (0.108)	0.00401 (1.00)
8q gain	150 (29%)	364	0.0106 (1.00)	0.015 (1.00)	2.42e-23 (2.11e-20)	0.245 (1.00)	0.00029 (0.148)	0.728 (1.00)	0.000261 (0.134)	0.000151 (0.0805)	0.00021 (0.11)	0.00365 (1.00)	0.101 (1.00)	0.144 (1.00)
17q gain	28 (5%)	486			6.68e-08 (4.61e-05)	3.6e-05 (0.0204)	0.062 (1.00)	0.674 (1.00)	6.15e-05 (0.0341)	1.93e-05 (0.0113)	0.000421 (0.214)	0.0125 (1.00)	0.0748 (1.00)	0.0139 (1.00)
19p gain	50 (10%)	464	0.0391 (1.00)	0.00466 (1.00)	7.03e-23 (6.09e-20)	0.00054 (0.27)	0.812 (1.00)	0.155 (1.00)	9.27e-12 (7.23e-09)	6.79e-10 (5.02e-07)	2.23e-08 (1.57e-05)	0.00013 (0.0698)	0.0321 (1.00)	0.0587 (1.00)
21q gain	36 (7%)	478			2.02e-13 (1.61e-10)	0.00355 (1.00)	0.474 (1.00)	0.151 (1.00)	9.34e-07 (0.000601)	5.35e-06 (0.00322)	7.14e-07 (0.000462)	6.59e-05 (0.0363)	0.136 (1.00)	0.00469 (1.00)
1p loss	24 (5%)	490			1.43e-08 (1.03e-05)	5.91e-06 (0.00353)	0.655 (1.00)	0.151 (1.00)	1.6e-05 (0.00942)	2.67e-05 (0.0154)	0.0586 (1.00)	7.92e-05 (0.0433)	0.0769 (1.00)	0.00404 (1.00)
6q loss	23 (4%)	491	0.379 (1.00)	0.0902 (1.00)	8.04e-09 (5.78e-06)	0.00017 (0.0899)	0.423 (1.00)	0.674 (1.00)	5.33e-07 (0.00035)	5.53e-05 (0.0308)	0.00328 (1.00)	2.17e-05 (0.0126)	0.0366 (1.00)	0.00958 (1.00)
12p gain	65 (13%)	449	0.387 (1.00)	1 (1.00)	7.68e-12 (6.01e-09)	4.21e-05 (0.0236)	0.857 (1.00)	0.812 (1.00)	3.38e-05 (0.0192)	4.61e-05 (0.0258)	0.003 (1.00)	0.00332 (1.00)	0.00132 (0.621)	0.000534 (0.267)
14q gain	36 (7%)	478	1 (1.00)	0.769 (1.00)	3.23e-07 (0.000215)	0.00846 (1.00)	0.225 (1.00)	1 (1.00)	6.52e-07 (0.000425)	1.83e-05 (0.0107)	0.000439 (0.223)	0.0268 (1.00)	0.364 (1.00)	0.0492 (1.00)
3q loss	29 (6%)	485	0.0391 (1.00)	0.00466 (1.00)	3.29e-10 (2.47e-07)	0.000525 (0.263)	0.0637 (1.00)	0.201 (1.00)	7.13e-07 (0.000462)	1.75e-06 (0.0011)	0.000484 (0.243)	0.00701 (1.00)	0.14 (1.00)	0.0187 (1.00)
7p loss	42 (8%)	472	0.0391 (1.00)	0.00466 (1.00)	6.17e-15 (5.01e-12)	0.000675 (0.334)	0.0684 (1.00)	0.0546 (1.00)	9.74e-10 (7.19e-07)	5.8e-09 (4.19e-06)	5.11e-06 (0.00308)	0.000784 (0.378)	0.0774 (1.00)	0.00434 (1.00)
6q gain	60 (12%)	454	0.209 (1.00)	0.173 (1.00)	4.42e-19 (3.74e-16)	0.00086 (0.413)	0.0946 (1.00)	0.0444 (1.00)	0.00025 (0.129)	0.000159 (0.0846)	0.00202 (0.938)	0.00108 (0.509)	0.462 (1.00)	0.198 (1.00)
3p gain	42 (8%)	472			3.1e-18 (2.6e-15)	0.00353 (1.00)	0.395 (1.00)	0.713 (1.00)	9.83e-05 (0.0533)	0.00296 (1.00)	0.0362 (1.00)	0.00347 (1.00)	0.0526 (1.00)	0.0241 (1.00)
11p gain	22 (4%)	492	0.0391 (1.00)	0.0902 (1.00)	2.48e-06 (0.00155)	0.0924 (1.00)	0.0383 (1.00)	1 (1.00)	0.000441 (0.223)	0.00232 (1.00)	0.0344 (1.00)	0.0369 (1.00)	0.228 (1.00)	0.25 (1.00)
1q loss	15 (3%)	499			0.000113 (0.0607)	0.00263 (1.00)		0.14 (1.00)	0.000323 (0.165)	0.00123 (0.582)	0.0988 (1.00)	0.00603 (1.00)	0.512 (1.00)	0.112 (1.00)
2q loss	16 (3%)	498			5.25e-06 (0.00316)	0.206 (1.00)		0.14 (1.00)	9.66e-05 (0.0526)	0.00408 (1.00)	0.0457 (1.00)	0.0281 (1.00)	0.828 (1.00)	0.316 (1.00)
6p loss	16 (3%)	498	0.379 (1.00)	0.0902 (1.00)	4.15e-06 (0.00252)	0.0106 (1.00)	0.261 (1.00)	0.367 (1.00)	0.000189 (0.0999)	0.00408 (1.00)	0.0419 (1.00)	0.000743 (0.363)	0.319 (1.00)	0.134 (1.00)
4p gain	12 (2%)	502			0.000165 (0.0873)	0.656 (1.00)	0.451 (1.00)	0.00691 (1.00)	0.0072 (1.00)	0.0343 (1.00)	0.258 (1.00)	0.034 (1.00)	0.336 (1.00)	0.178 (1.00)
5q gain	19 (4%)	495			2.07e-05 (0.012)	0.0528 (1.00)	0.297 (1.00)	1 (1.00)	0.00353 (1.00)	0.00538 (1.00)	0.0105 (1.00)	0.00624 (1.00)	0.0338 (1.00)	0.00124 (0.584)
7p gain	63 (12%)	451	0.855 (1.00)	1 (1.00)	2.2e-20 (1.89e-17)	0.0111 (1.00)	0.811 (1.00)	0.45 (1.00)	0.0154 (1.00)	0.16 (1.00)	0.11 (1.00)	0.0234 (1.00)	0.292 (1.00)	0.52 (1.00)
7q gain	61 (12%)	453	0.855 (1.00)	1 (1.00)	2.43e-20 (2.09e-17)	0.0162 (1.00)	0.842 (1.00)	0.173 (1.00)	0.0943 (1.00)	0.356 (1.00)	0.331 (1.00)	0.132 (1.00)	0.648 (1.00)	0.721 (1.00)
8p gain	114 (22%)	400	0.355 (1.00)	0.468 (1.00)	1.83e-18 (1.54e-15)	0.962 (1.00)	0.0264 (1.00)	0.845 (1.00)	0.0544 (1.00)	0.197 (1.00)	0.0731 (1.00)	0.299 (1.00)	0.589 (1.00)	0.32 (1.00)
10p gain	112 (22%)	402	0.00713 (1.00)	0.0426 (1.00)	3.74e-06 (0.00229)	0.735 (1.00)	0.192 (1.00)	0.219 (1.00)	0.29 (1.00)	0.0127 (1.00)	0.443 (1.00)	0.367 (1.00)	0.136 (1.00)	0.49 (1.00)
10q gain	104 (20%)	410	0.00486 (1.00)	0.0374 (1.00)	1.19e-07 (8.1e-05)	0.707 (1.00)	0.117 (1.00)	0.156 (1.00)	0.0957 (1.00)	0.0333 (1.00)	0.353 (1.00)	0.14 (1.00)	0.14 (1.00)	0.296 (1.00)
11q gain	19 (4%)	495			4.54e-06 (0.00275)	0.102 (1.00)	0.157 (1.00)	0.712 (1.00)	0.00374 (1.00)	0.0117 (1.00)	0.16 (1.00)	0.187 (1.00)	0.735 (1.00)	0.407 (1.00)
12q gain	50 (10%)	464	0.387 (1.00)	1 (1.00)	2.16e-09 (1.58e-06)	0.0112 (1.00)	0.899 (1.00)	0.796 (1.00)	0.0216 (1.00)	0.0134 (1.00)	0.223 (1.00)	0.122 (1.00)	0.0529 (1.00)	0.0401 (1.00)
15q gain	10 (2%)	504			0.000233 (0.121)	1 (1.00)		1 (1.00)	1 (1.00)	0.438 (1.00)	0.568 (1.00)	0.635 (1.00)	0.528 (1.00)	0.834 (1.00)
16p gain	23 (4%)	491			4.55e-06 (0.00276)	0.00778 (1.00)	0.157 (1.00)	0.712 (1.00)	0.0974 (1.00)	0.138 (1.00)	0.0638 (1.00)	0.287 (1.00)	1 (1.00)	0.515 (1.00)
xq gain	61 (12%)	453	0.704 (1.00)	0.847 (1.00)	3.87e-27 (3.41e-24)	0.775 (1.00)	0.917 (1.00)	0.329 (1.00)	0.349 (1.00)	0.842 (1.00)	0.816 (1.00)	1 (1.00)	0.15 (1.00)	0.614 (1.00)
20p loss	18 (4%)	496			6.27e-05 (0.0347)	0.198 (1.00)	0.735 (1.00)	0.0675 (1.00)	0.097 (1.00)	0.0313 (1.00)	0.203 (1.00)	0.0102 (1.00)	0.512 (1.00)	0.232 (1.00)
20q loss	10 (2%)	504			7.61e-05 (0.0417)	0.0368 (1.00)	0.586 (1.00)	0.633 (1.00)	0.0988 (1.00)	0.0637 (1.00)	0.267 (1.00)	0.00342 (1.00)	0.219 (1.00)	0.07 (1.00)
1q gain	173 (34%)	341	0.174 (1.00)	0.201 (1.00)	0.00189 (0.884)	0.148 (1.00)	0.0855 (1.00)	0.014 (1.00)	0.0302 (1.00)	0.0533 (1.00)	0.018 (1.00)	0.28 (1.00)	0.855 (1.00)	0.0592 (1.00)
4q gain	8 (2%)	506			0.0072 (1.00)	0.618 (1.00)		0.14 (1.00)	0.178 (1.00)	0.398 (1.00)	0.286 (1.00)	0.257 (1.00)	0.547 (1.00)	0.117 (1.00)
9p gain	20 (4%)	494			0.000676 (0.334)	0.0119 (1.00)	0.161 (1.00)	0.367 (1.00)	0.0768 (1.00)	0.00944 (1.00)	0.00161 (0.752)	0.0777 (1.00)	0.267 (1.00)	0.312 (1.00)
9q gain	9 (2%)	505			0.155 (1.00)	0.136 (1.00)		0.14 (1.00)	0.483 (1.00)	0.199 (1.00)	0.0253 (1.00)	0.145 (1.00)	0.336 (1.00)	0.289 (1.00)
16q gain	10 (2%)	504			0.00247 (1.00)	0.628 (1.00)	0.858 (1.00)	0.558 (1.00)	0.252 (1.00)	0.438 (1.00)	0.415 (1.00)	0.635 (1.00)	1 (1.00)	0.739 (1.00)
17p gain	12 (2%)	502			0.0227 (1.00)	0.32 (1.00)	0.326 (1.00)	0.558 (1.00)	0.0128 (1.00)	0.00331 (1.00)	0.251 (1.00)	0.131 (1.00)	0.713 (1.00)	0.294 (1.00)
2p loss	10 (2%)	504			0.000679 (0.334)	0.354 (1.00)		0.14 (1.00)	0.0034 (1.00)	0.0405 (1.00)	0.106 (1.00)	0.384 (1.00)	0.91 (1.00)	0.364 (1.00)

'1p gain' versus 'CN_CNMF'

P value = 2.35e-09 (Chi-square test), Q value = 1.7e-06

Table S1. Gene #1: '1p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
1P GAIN MUTATED	6	3	32	1	1	0
1P GAIN WILD-TYPE	294	21	120	21	14	1

Figure S1. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #3: 'CN_CNMF'

'1p gain' versus 'MRNASEQ_CNMF'

P value = 0.000101 (Fisher's exact test), Q value = 0.055

Table S2. Gene #1: '1p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
1P GAIN MUTATED	29	5	4	5
1P GAIN WILD-TYPE	145	81	111	125

Figure S2. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1p gain' versus 'MIRSEQ_CNMF'

P value = 4.76e-06 (Chi-square test), Q value = 0.0029

Table S3. Gene #1: '1p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
1P GAIN MUTATED	27	2	2	5	6
1P GAIN WILD-TYPE	122	136	47	48	110

Figure S3. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.94e-05 (Fisher's exact test), Q value = 0.011

Table S4. Gene #1: '1p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
1P GAIN MUTATED	0	5	37
1P GAIN WILD-TYPE	13	209	241

Figure S4. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000206 (Fisher's exact test), Q value = 0.11

Table S5. Gene #1: '1p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	90	116
1P GAIN MUTATED	29	3	5
1P GAIN WILD-TYPE	147	87	111

Figure S5. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'2p gain' versus 'CN_CNMF'

P value = 2.04e-33 (Chi-square test), Q value = 1.8e-30

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
2P GAIN MUTATED	8	21	52	2	5	0
2P GAIN WILD-TYPE	292	3	100	20	10	1

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

'2p gain' versus 'METHLYATION_CNMF'

P value = 1.53e-08 (Fisher's exact test), Q value = 1.1e-05

Table S7. Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
2P GAIN MUTATED	47	10	10
2P GAIN WILD-TYPE	105	78	150

Figure S7. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2p gain' versus 'MRNASEQ_CNMF'

P value = 2.06e-07 (Fisher's exact test), Q value = 0.00014

Table S8. Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
2P GAIN MUTATED	53	11	13	9
2P GAIN WILD-TYPE	121	75	102	121

Figure S8. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.85e-07 (Fisher's exact test), Q value = 0.00013

Table S9. Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
2P GAIN MUTATED	64	8	14
2P GAIN WILD-TYPE	175	76	168

Figure S9. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_CNMF'

P value = 2.85e-06 (Chi-square test), Q value = 0.0018

Table S10. Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
2P GAIN MUTATED	43	9	13	9	13
2P GAIN WILD-TYPE	106	129	36	44	103

Figure S10. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.43e-06 (Fisher's exact test), Q value = 0.00091

Table S11. Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
2P GAIN MUTATED	0	18	69
2P GAIN WILD-TYPE	13	196	209

Figure S11. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000264 (Fisher's exact test), Q value = 0.14

Table S12. Gene #3: '2p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	90	116
2P GAIN MUTATED	40	18	7
2P GAIN WILD-TYPE	136	72	109

Figure S12. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'2p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.017

Table S13. Gene #3: '2p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	100	146	35
2P GAIN MUTATED	23	28	10	4
2P GAIN WILD-TYPE	78	72	136	31

Figure S13. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q gain' versus 'CN_CNMF'

P value = 3.48e-30 (Chi-square test), Q value = 3.1e-27

Table S14. Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
2Q GAIN MUTATED	5	19	41	2	4	0
2Q GAIN WILD-TYPE	295	5	111	20	11	1

Figure S14. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

'2q gain' versus 'METHLYATION_CNMF'

P value = 4.81e-07 (Fisher's exact test), Q value = 0.00032

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
2Q GAIN MUTATED	40	8	9
2Q GAIN WILD-TYPE	112	80	151

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

'2q gain' versus 'MRNASEQ_CNMF'

P value = 1.24e-05 (Fisher's exact test), Q value = 0.0073

Table S16. Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
2Q GAIN MUTATED	42	10	10	7
2Q GAIN WILD-TYPE	132	76	105	123

Figure S16. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.84e-06 (Fisher's exact test), Q value = 0.0018

Table S17. Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
2Q GAIN MUTATED	52	6	11
2Q GAIN WILD-TYPE	187	78	171

Figure S17. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_CNMF'

P value = 1.22e-05 (Chi-square test), Q value = 0.0073

Table S18. Gene #4: '2q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
2Q GAIN MUTATED	37	7	10	7	10
2Q GAIN WILD-TYPE	112	131	39	46	106

Figure S18. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.2e-06 (Fisher's exact test), Q value = 0.002

Table S19. Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
2Q GAIN MUTATED	0	13	58
2Q GAIN WILD-TYPE	13	201	220

Figure S19. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000267 (Fisher's exact test), Q value = 0.14

Table S20. Gene #4: '2q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	90	116
2Q GAIN MUTATED	35	15	5
2Q GAIN WILD-TYPE	141	75	111

Figure S20. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'2q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.05e-05 (Fisher's exact test), Q value = 0.023

Table S21. Gene #4: '2q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	100	146	35
2Q GAIN MUTATED	20	24	7	4
2Q GAIN WILD-TYPE	81	76	139	31

Figure S21. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3p gain' versus 'CN_CNMF'

P value = 3.1e-18 (Chi-square test), Q value = 2.6e-15

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
3P GAIN MUTATED	2	3	24	4	9	0
3P GAIN WILD-TYPE	298	21	128	18	6	1

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

'3p gain' versus 'MRNASEQ_CNMF'

P value = 9.83e-05 (Fisher's exact test), Q value = 0.053

Table S23. Gene #5: '3p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
3P GAIN MUTATED	26	6	1	8
3P GAIN WILD-TYPE	148	80	114	122

Figure S23. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3q gain' versus 'CN_CNMF'

P value = 3.32e-24 (Chi-square test), Q value = 2.9e-21

Table S24. Gene #6: '3q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
3Q GAIN MUTATED	5	4	52	5	10	0
3Q GAIN WILD-TYPE	295	20	100	17	5	1

Figure S24. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #3: 'CN_CNMF'

'3q gain' versus 'METHLYATION_CNMF'

P value = 5.9e-10 (Fisher's exact test), Q value = 4.4e-07

Table S25. Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
3Q GAIN MUTATED	48	10	8
3Q GAIN WILD-TYPE	104	78	152

Figure S25. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3q gain' versus 'MRNASEQ_CNMF'

P value = 5.83e-13 (Fisher's exact test), Q value = 4.6e-10

Table S26. Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
3Q GAIN MUTATED	52	13	1	9
3Q GAIN WILD-TYPE	122	73	114	121

Figure S26. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.5e-11 (Fisher's exact test), Q value = 1.2e-08

Table S27. Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
3Q GAIN MUTATED	63	3	9
3Q GAIN WILD-TYPE	176	81	173

Figure S27. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_CNMF'

P value = 3.55e-06 (Chi-square test), Q value = 0.0022

Table S28. Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
3Q GAIN MUTATED	39	9	12	3	13
3Q GAIN WILD-TYPE	110	129	37	50	103

Figure S28. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.63e-08 (Fisher's exact test), Q value = 1.2e-05

Table S29. Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
3Q GAIN MUTATED	3	10	63
3Q GAIN WILD-TYPE	10	204	215

Figure S29. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000235 (Fisher's exact test), Q value = 0.12

Table S30. Gene #6: '3q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	90	116
3Q GAIN MUTATED	41	16	7
3Q GAIN WILD-TYPE	135	74	109

Figure S30. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'3q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.3e-07 (Fisher's exact test), Q value = 0.00029

Table S31. Gene #6: '3q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	100	146	35
3Q GAIN MUTATED	19	33	9	3
3Q GAIN WILD-TYPE	82	67	137	32

Figure S31. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p gain' versus 'CN_CNMF'

P value = 0.000165 (Chi-square test), Q value = 0.087

Table S32. Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
4P GAIN MUTATED	0	0	11	1	0	0
4P GAIN WILD-TYPE	300	24	141	21	15	1

Figure S32. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

'5p gain' versus 'CN_CNMF'

P value = 3.03e-15 (Chi-square test), Q value = 2.5e-12

Table S33. Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
5P GAIN MUTATED	3	3	40	3	0	0
5P GAIN WILD-TYPE	297	21	112	19	15	1

Figure S33. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

'5p gain' versus 'METHLYATION_CNMF'

P value = 2.52e-07 (Fisher's exact test), Q value = 0.00017

Table S34. Gene #9: '5p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
5P GAIN MUTATED	32	4	5
5P GAIN WILD-TYPE	120	84	155

Figure S34. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5p gain' versus 'MRNASEQ_CNMF'

P value = 1.83e-11 (Fisher's exact test), Q value = 1.4e-08

Table S35. Gene #9: '5p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
5P GAIN MUTATED	39	4	6	0
5P GAIN WILD-TYPE	135	82	109	130

Figure S35. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.13e-08 (Fisher's exact test), Q value = 3.6e-05

Table S36. Gene #9: '5p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
5P GAIN MUTATED	42	2	5
5P GAIN WILD-TYPE	197	82	177

Figure S36. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_CNMF'

P value = 2.51e-08 (Chi-square test), Q value = 1.8e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
5P GAIN MUTATED	32	1	4	6	5
5P GAIN WILD-TYPE	117	137	45	47	111

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

'5p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.05e-06 (Fisher's exact test), Q value = 0.0013

Table S38. Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
5P GAIN MUTATED	2	5	41
5P GAIN WILD-TYPE	11	209	237

Figure S38. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.21e-05 (Fisher's exact test), Q value = 0.018

Table S39. Gene #9: '5p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	90	116
5P GAIN MUTATED	30	7	2
5P GAIN WILD-TYPE	146	83	114

Figure S39. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.64e-07 (Fisher's exact test), Q value = 0.00049

Table S40. Gene #9: '5p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	100	146	35
5P GAIN MUTATED	10	24	3	2
5P GAIN WILD-TYPE	91	76	143	33

Figure S40. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q gain' versus 'CN_CNMF'

P value = 2.07e-05 (Chi-square test), Q value = 0.012

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
5Q GAIN MUTATED	1	1	14	3	0	0
5Q GAIN WILD-TYPE	299	23	138	19	15	1

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

'6p gain' versus 'CN_CNMF'

P value = 5.51e-26 (Chi-square test), Q value = 4.8e-23

Table S42. Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
6P GAIN MUTATED	5	2	56	2	9	0
6P GAIN WILD-TYPE	295	22	96	20	6	1

Figure S42. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

'6p gain' versus 'METHLYATION_CNMF'

P value = 6.68e-07 (Fisher's exact test), Q value = 0.00043

Table S43. Gene #11: '6p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
6P GAIN MUTATED	43	13	10
6P GAIN WILD-TYPE	109	75	150

Figure S43. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6p gain' versus 'MRNASEQ_CNMF'

P value = 1.48e-08 (Fisher's exact test), Q value = 1.1e-05

Table S44. Gene #11: '6p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
6P GAIN MUTATED	49	6	5	14
6P GAIN WILD-TYPE	125	80	110	116

Figure S44. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.38e-08 (Fisher's exact test), Q value = 5.8e-05

Table S45. Gene #11: '6p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
6P GAIN MUTATED	57	3	14
6P GAIN WILD-TYPE	182	81	168

Figure S45. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_CNMF'

P value = 1.35e-06 (Chi-square test), Q value = 0.00086

Table S46. Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
6P GAIN MUTATED	40	11	11	4	8
6P GAIN WILD-TYPE	109	127	38	49	108

Figure S46. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.91e-06 (Fisher's exact test), Q value = 0.0018

Table S47. Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
6P GAIN MUTATED	1	13	60
6P GAIN WILD-TYPE	12	201	218

Figure S47. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6q gain' versus 'CN_CNMF'

P value = 4.42e-19 (Chi-square test), Q value = 3.7e-16

Table S48. Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
6Q GAIN MUTATED	5	2	43	2	8	0
6Q GAIN WILD-TYPE	295	22	109	20	7	1

Figure S48. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

'6q gain' versus 'MRNASEQ_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.13

Table S49. Gene #12: '6q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
6Q GAIN MUTATED	35	6	5	14
6Q GAIN WILD-TYPE	139	80	110	116

Figure S49. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000159 (Fisher's exact test), Q value = 0.085

Table S50. Gene #12: '6q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
6Q GAIN MUTATED	43	3	14
6Q GAIN WILD-TYPE	196	81	168

Figure S50. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

P value = 2.2e-20 (Chi-square test), Q value = 1.9e-17

Table S51. Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
7P GAIN MUTATED	8	14	27	7	7	0
7P GAIN WILD-TYPE	292	10	125	15	8	1

Figure S51. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7q gain' versus 'CN_CNMF'

P value = 2.43e-20 (Chi-square test), Q value = 2.1e-17

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
7Q GAIN MUTATED	11	15	22	6	7	0
7Q GAIN WILD-TYPE	289	9	130	16	8	1

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

'8p gain' versus 'CN_CNMF'

P value = 1.83e-18 (Chi-square test), Q value = 1.5e-15

Table S53. Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
8P GAIN MUTATED	38	6	41	14	15	0
8P GAIN WILD-TYPE	262	18	111	8	0	1

Figure S53. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'CN_CNMF'

P value = 2.42e-23 (Chi-square test), Q value = 2.1e-20

Table S54. Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
8Q GAIN MUTATED	40	7	72	15	15	1
8Q GAIN WILD-TYPE	260	17	80	7	0	0

Figure S54. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'RPPA_CNMF'

P value = 0.00029 (Chi-square test), Q value = 0.15

Table S55. Gene #16: '8q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	37	39	12	41	24
8Q GAIN MUTATED	9	12	7	2	2	13
8Q GAIN WILD-TYPE	32	25	32	10	39	11

Figure S55. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 0.000261 (Fisher's exact test), Q value = 0.13

Table S56. Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
8Q GAIN MUTATED	72	17	30	29
8Q GAIN WILD-TYPE	102	69	85	101

Figure S56. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000151 (Fisher's exact test), Q value = 0.081

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
8Q GAIN MUTATED	91	15	42
8Q GAIN WILD-TYPE	148	69	140

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

'8q gain' versus 'MIRSEQ_CNMF'

P value = 0.00021 (Chi-square test), Q value = 0.11

Table S58. Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
8Q GAIN MUTATED	61	33	13	20	20
8Q GAIN WILD-TYPE	88	105	36	33	96

Figure S58. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10p gain' versus 'CN_CNMF'

P value = 3.74e-06 (Chi-square test), Q value = 0.0023

Table S59. Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
10P GAIN MUTATED	47	14	37	7	7	0
10P GAIN WILD-TYPE	253	10	115	15	8	1

Figure S59. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

'10q gain' versus 'CN_CNMF'

P value = 1.19e-07 (Chi-square test), Q value = 8.1e-05

Table S60. Gene #20: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
10Q GAIN MUTATED	46	16	31	5	6	0
10Q GAIN WILD-TYPE	254	8	121	17	9	1

Figure S60. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

'11p gain' versus 'CN_CNMF'

P value = 2.48e-06 (Chi-square test), Q value = 0.0015

Table S61. Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
11P GAIN MUTATED	0	3	15	3	1	0
11P GAIN WILD-TYPE	300	21	137	19	14	1

Figure S61. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

'11p gain' versus 'MRNASEQ_CNMF'

P value = 0.000441 (Fisher's exact test), Q value = 0.22

Table S62. Gene #21: '11p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
11P GAIN MUTATED	17	0	2	3
11P GAIN WILD-TYPE	157	86	113	127

Figure S62. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11q gain' versus 'CN_CNMF'

P value = 4.54e-06 (Chi-square test), Q value = 0.0028

Table S63. Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
11Q GAIN MUTATED	0	4	12	2	1	0
11Q GAIN WILD-TYPE	300	20	140	20	14	1

Figure S63. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 7.68e-12 (Chi-square test), Q value = 6e-09

Table S64. Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
12P GAIN MUTATED	12	8	35	9	1	0
12P GAIN WILD-TYPE	288	16	117	13	14	1

Figure S64. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 4.21e-05 (Fisher's exact test), Q value = 0.024

Table S65. Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
12P GAIN MUTATED	31	13	7
12P GAIN WILD-TYPE	121	75	153

Figure S65. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 3.38e-05 (Fisher's exact test), Q value = 0.019

Table S66. Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
12P GAIN MUTATED	39	10	7	8
12P GAIN WILD-TYPE	135	76	108	122

Figure S66. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.61e-05 (Fisher's exact test), Q value = 0.026

Table S67. Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
12P GAIN MUTATED	47	5	12
12P GAIN WILD-TYPE	192	79	170

Figure S67. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q gain' versus 'CN_CNMF'

P value = 2.16e-09 (Chi-square test), Q value = 1.6e-06

Table S68. Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
12Q GAIN MUTATED	12	7	21	9	1	0
12Q GAIN WILD-TYPE	288	17	131	13	14	1

Figure S68. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

'13q gain' versus 'CN_CNMF'

P value = 4.5e-10 (Chi-square test), Q value = 3.4e-07

Table S69. Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
13Q GAIN MUTATED	1	1	25	0	1	0
13Q GAIN WILD-TYPE	299	23	127	22	14	1

Figure S69. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

'13q gain' versus 'METHLYATION_CNMF'

P value = 0.000149 (Fisher's exact test), Q value = 0.08

Table S70. Gene #25: '13q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
13Q GAIN MUTATED	16	7	1
13Q GAIN WILD-TYPE	136	81	159

Figure S70. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q gain' versus 'MRNASEQ_CNMF'

P value = 2.62e-07 (Fisher's exact test), Q value = 0.00018

Table S71. Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
13Q GAIN MUTATED	24	2	0	2
13Q GAIN WILD-TYPE	150	84	115	128

Figure S71. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.75e-06 (Fisher's exact test), Q value = 0.0011

Table S72. Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
13Q GAIN MUTATED	26	0	2
13Q GAIN WILD-TYPE	213	84	180

Figure S72. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q gain' versus 'MIRSEQ_CNMF'

P value = 3.94e-06 (Chi-square test), Q value = 0.0024

Table S73. Gene #25: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
13Q GAIN MUTATED	21	2	2	0	3
13Q GAIN WILD-TYPE	128	136	47	53	113

Figure S73. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'13q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.63e-05 (Fisher's exact test), Q value = 0.047

Table S74. Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
13Q GAIN MUTATED	0	2	26
13Q GAIN WILD-TYPE	13	212	252

Figure S74. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q gain' versus 'CN_CNMF'

P value = 3.23e-07 (Chi-square test), Q value = 0.00022

Table S75. Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
14Q GAIN MUTATED	4	2	24	3	3	0
14Q GAIN WILD-TYPE	296	22	128	19	12	1

Figure S75. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

'14q gain' versus 'MRNASEQ_CNMF'

P value = 6.52e-07 (Fisher's exact test), Q value = 0.00042

Table S76. Gene #26: '14q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
14Q GAIN MUTATED	27	0	2	6
14Q GAIN WILD-TYPE	147	86	113	124

Figure S76. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.83e-05 (Fisher's exact test), Q value = 0.011

Table S77. Gene #26: '14q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
14Q GAIN MUTATED	29	0	6
14Q GAIN WILD-TYPE	210	84	176

Figure S77. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_CNMF'

P value = 0.000439 (Chi-square test), Q value = 0.22

Table S78. Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
14Q GAIN MUTATED	21	7	5	2	1
14Q GAIN WILD-TYPE	128	131	44	51	115

Figure S78. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'15q gain' versus 'CN_CNMF'

P value = 0.000233 (Chi-square test), Q value = 0.12

Table S79. Gene #27: '15q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
15Q GAIN MUTATED	1	0	6	3	0	0
15Q GAIN WILD-TYPE	299	24	146	19	15	1

Figure S79. Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #3: 'CN_CNMF'

'16p gain' versus 'CN_CNMF'

P value = 4.55e-06 (Chi-square test), Q value = 0.0028

Table S80. Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
16P GAIN MUTATED	1	1	17	3	1	0
16P GAIN WILD-TYPE	299	23	135	19	14	1

Figure S80. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'CN_CNMF'

P value = 6.68e-08 (Chi-square test), Q value = 4.6e-05

Table S81. Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
17Q GAIN MUTATED	1	3	22	1	1	0
17Q GAIN WILD-TYPE	299	21	130	21	14	1

Figure S81. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 3.6e-05 (Fisher's exact test), Q value = 0.02

Table S82. Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
17Q GAIN MUTATED	20	3	2
17Q GAIN WILD-TYPE	132	85	158

Figure S82. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 6.15e-05 (Fisher's exact test), Q value = 0.034

Table S83. Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
17Q GAIN MUTATED	21	4	1	2
17Q GAIN WILD-TYPE	153	82	114	128

Figure S83. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.93e-05 (Fisher's exact test), Q value = 0.011

Table S84. Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
17Q GAIN MUTATED	25	1	2
17Q GAIN WILD-TYPE	214	83	180

Figure S84. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_CNMF'

P value = 0.000421 (Chi-square test), Q value = 0.21

Table S85. Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
17Q GAIN MUTATED	18	3	4	1	2
17Q GAIN WILD-TYPE	131	135	45	52	114

Figure S85. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18p gain' versus 'CN_CNMF'

P value = 3.67e-24 (Chi-square test), Q value = 3.2e-21

Table S86. Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
18P GAIN MUTATED	3	4	56	1	1	0
18P GAIN WILD-TYPE	297	20	96	21	14	1

Figure S86. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 4.33e-10 (Fisher's exact test), Q value = 3.2e-07

Table S87. Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
18P GAIN MUTATED	39	13	3
18P GAIN WILD-TYPE	113	75	157

Figure S87. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p gain' versus 'MRNASEQ_CNMF'

P value = 4.15e-15 (Fisher's exact test), Q value = 3.4e-12

Table S88. Gene #32: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
18P GAIN MUTATED	52	6	2	4
18P GAIN WILD-TYPE	122	80	113	126

Figure S88. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.32e-14 (Fisher's exact test), Q value = 6.6e-11

Table S89. Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
18P GAIN MUTATED	58	1	5
18P GAIN WILD-TYPE	181	83	177

Figure S89. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_CNMF'

P value = 4.64e-12 (Chi-square test), Q value = 3.6e-09

Table S90. Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
18P GAIN MUTATED	43	2	9	6	5
18P GAIN WILD-TYPE	106	136	40	47	111

Figure S90. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.24e-11 (Fisher's exact test), Q value = 3.2e-08

Table S91. Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
18P GAIN MUTATED	0	5	60
18P GAIN WILD-TYPE	13	209	218

Figure S91. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.18e-06 (Fisher's exact test), Q value = 0.00075

Table S92. Gene #32: '18p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	90	116
18P GAIN MUTATED	37	14	2
18P GAIN WILD-TYPE	139	76	114

Figure S92. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.94e-11 (Fisher's exact test), Q value = 1.5e-08

Table S93. Gene #32: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	100	146	35
18P GAIN MUTATED	20	30	2	1
18P GAIN WILD-TYPE	81	70	144	34

Figure S93. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q gain' versus 'CN_CNMF'

P value = 2.87e-12 (Chi-square test), Q value = 2.3e-09

Table S94. Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
18Q GAIN MUTATED	3	3	33	0	1	0
18Q GAIN WILD-TYPE	297	21	119	22	14	1

Figure S94. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

'18q gain' versus 'METHLYATION_CNMF'

P value = 1.16e-05 (Fisher's exact test), Q value = 0.0069

Table S95. Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
18Q GAIN MUTATED	22	10	2
18Q GAIN WILD-TYPE	130	78	158

Figure S95. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q gain' versus 'MRNASEQ_CNMF'

P value = 1.94e-08 (Fisher's exact test), Q value = 1.4e-05

Table S96. Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
18Q GAIN MUTATED	32	2	2	3
18Q GAIN WILD-TYPE	142	84	113	127

Figure S96. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.83e-08 (Fisher's exact test), Q value = 3.4e-05

Table S97. Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
18Q GAIN MUTATED	35	0	4
18Q GAIN WILD-TYPE	204	84	178

Figure S97. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_CNMF'

P value = 4e-08 (Chi-square test), Q value = 2.8e-05

Table S98. Gene #33: '18q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
18Q GAIN MUTATED	27	1	5	6	1
18Q GAIN WILD-TYPE	122	137	44	47	115

Figure S98. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.12e-06 (Fisher's exact test), Q value = 0.00072

Table S99. Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
18Q GAIN MUTATED	0	3	37
18Q GAIN WILD-TYPE	13	211	241

Figure S99. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000138 (Fisher's exact test), Q value = 0.074

Table S100. Gene #33: '18q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	90	116
18Q GAIN MUTATED	24	7	1
18Q GAIN WILD-TYPE	152	83	115

Figure S100. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.13e-07 (Fisher's exact test), Q value = 0.00034

Table S101. Gene #33: '18q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	100	146	35
18Q GAIN MUTATED	10	20	1	1
18Q GAIN WILD-TYPE	91	80	145	34

Figure S101. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p gain' versus 'CN_CNMF'

P value = 7.03e-23 (Chi-square test), Q value = 6.1e-20

Table S102. Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
19P GAIN MUTATED	0	1	47	0	2	0
19P GAIN WILD-TYPE	300	23	105	22	13	1

Figure S102. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

'19p gain' versus 'MRNASEQ_CNMF'

P value = 9.27e-12 (Fisher's exact test), Q value = 7.2e-09

Table S103. Gene #34: '19p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
19P GAIN MUTATED	41	2	2	4
19P GAIN WILD-TYPE	133	84	113	126

Figure S103. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.79e-10 (Fisher's exact test), Q value = 5e-07

Table S104. Gene #34: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
19P GAIN MUTATED	44	1	4
19P GAIN WILD-TYPE	195	83	178

Figure S104. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_CNMF'

P value = 2.23e-08 (Chi-square test), Q value = 1.6e-05

Table S105. Gene #34: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
19P GAIN MUTATED	33	5	7	2	3
19P GAIN WILD-TYPE	116	133	42	51	113

Figure S105. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.07

Table S106. Gene #34: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
19P GAIN MUTATED	2	8	40
19P GAIN WILD-TYPE	11	206	238

Figure S106. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q gain' versus 'CN_CNMF'

P value = 2.75e-23 (Chi-square test), Q value = 2.4e-20

Table S107. Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
19Q GAIN MUTATED	0	2	50	1	2	0
19Q GAIN WILD-TYPE	300	22	102	21	13	1

Figure S107. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

'19q gain' versus 'METHLYATION_CNMF'

P value = 2.29e-05 (Fisher's exact test), Q value = 0.013

Table S108. Gene #35: '19q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
19Q GAIN MUTATED	30	13	6
19Q GAIN WILD-TYPE	122	75	154

Figure S108. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 1.19e-13 (Fisher's exact test), Q value = 9.5e-11

Table S109. Gene #35: '19q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
19Q GAIN MUTATED	46	4	2	3
19Q GAIN WILD-TYPE	128	82	113	127

Figure S109. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.86e-14 (Fisher's exact test), Q value = 2.3e-11

Table S110. Gene #35: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
19Q GAIN MUTATED	52	0	3
19Q GAIN WILD-TYPE	187	84	179

Figure S110. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_CNMF'

P value = 1.26e-10 (Chi-square test), Q value = 9.6e-08

Table S111. Gene #35: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
19Q GAIN MUTATED	38	4	7	3	3
19Q GAIN WILD-TYPE	111	134	42	50	113

Figure S111. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.49e-07 (Fisher's exact test), Q value = 0.00023

Table S112. Gene #35: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
19Q GAIN MUTATED	1	6	48
19Q GAIN WILD-TYPE	12	208	230

Figure S112. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 1.06e-37 (Chi-square test), Q value = 9.4e-35

Table S113. Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
20P GAIN MUTATED	6	7	76	16	1	0
20P GAIN WILD-TYPE	294	17	76	6	14	1

Figure S113. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 7.91e-11 (Fisher's exact test), Q value = 6e-08

Table S114. Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
20P GAIN MUTATED	65	15	17
20P GAIN WILD-TYPE	87	73	143

Figure S114. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 8.7e-15 (Fisher's exact test), Q value = 7.1e-12

Table S115. Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
20P GAIN MUTATED	73	11	8	14
20P GAIN WILD-TYPE	101	75	107	116

Figure S115. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.55e-14 (Fisher's exact test), Q value = 6.8e-11

Table S116. Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
20P GAIN MUTATED	84	3	19
20P GAIN WILD-TYPE	155	81	163

Figure S116. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_CNMF'

P value = 2.22e-12 (Chi-square test), Q value = 1.8e-09

Table S117. Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
20P GAIN MUTATED	62	15	11	8	9
20P GAIN WILD-TYPE	87	123	38	45	107

Figure S117. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.19e-08 (Fisher's exact test), Q value = 3.6e-05

Table S118. Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
20P GAIN MUTATED	2	20	83
20P GAIN WILD-TYPE	11	194	195

Figure S118. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.21e-05 (Fisher's exact test), Q value = 0.018

Table S119. Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	90	116
20P GAIN MUTATED	61	16	15
20P GAIN WILD-TYPE	115	74	101

Figure S119. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.74e-08 (Fisher's exact test), Q value = 2.6e-05

Table S120. Gene #36: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	100	146	35
20P GAIN MUTATED	20	47	20	5
20P GAIN WILD-TYPE	81	53	126	30

Figure S120. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.000218 (Fisher's exact test), Q value = 0.11

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	19	19	15
20Q GAIN MUTATED	0	0	6
20Q GAIN WILD-TYPE	19	19	9

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

'20q gain' versus 'CN_CNMF'

P value = 1.67e-46 (Chi-square test), Q value = 1.5e-43

Table S122. Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
20Q GAIN MUTATED	7	7	90	18	1	0
20Q GAIN WILD-TYPE	293	17	62	4	14	1

Figure S122. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 5.27e-12 (Fisher's exact test), Q value = 4.1e-09

Table S123. Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
20Q GAIN MUTATED	73	18	20
20Q GAIN WILD-TYPE	79	70	140

Figure S123. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 1.36e-17 (Fisher's exact test), Q value = 1.1e-14

Table S124. Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
20Q GAIN MUTATED	84	13	9	17
20Q GAIN WILD-TYPE	90	73	106	113

Figure S124. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.45e-15 (Fisher's exact test), Q value = 2e-12

Table S125. Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
20Q GAIN MUTATED	96	4	23
20Q GAIN WILD-TYPE	143	80	159

Figure S125. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 3.65e-14 (Chi-square test), Q value = 2.9e-11

Table S126. Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
20Q GAIN MUTATED	71	18	12	8	12
20Q GAIN WILD-TYPE	78	120	37	45	104

Figure S126. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.6e-09 (Fisher's exact test), Q value = 4e-06

Table S127. Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
20Q GAIN MUTATED	2	24	95
20Q GAIN WILD-TYPE	11	190	183

Figure S127. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000109 (Fisher's exact test), Q value = 0.059

Table S128. Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	90	116
20Q GAIN MUTATED	67	20	19
20Q GAIN WILD-TYPE	109	70	97

Figure S128. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.55e-08 (Fisher's exact test), Q value = 1.1e-05

Table S129. Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	100	146	35
20Q GAIN MUTATED	24	52	24	6
20Q GAIN WILD-TYPE	77	48	122	29

Figure S129. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q gain' versus 'CN_CNMF'

P value = 2.02e-13 (Chi-square test), Q value = 1.6e-10

Table S130. Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
21Q GAIN MUTATED	1	0	32	2	1	0
21Q GAIN WILD-TYPE	299	24	120	20	14	1

Figure S130. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

'21q gain' versus 'MRNASEQ_CNMF'

P value = 9.34e-07 (Fisher's exact test), Q value = 6e-04

Table S131. Gene #38: '21q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
21Q GAIN MUTATED	28	3	1	4
21Q GAIN WILD-TYPE	146	83	114	126

Figure S131. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.35e-06 (Fisher's exact test), Q value = 0.0032

Table S132. Gene #38: '21q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
21Q GAIN MUTATED	31	1	4
21Q GAIN WILD-TYPE	208	83	178

Figure S132. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'21q gain' versus 'MIRSEQ_CNMF'

P value = 7.14e-07 (Chi-square test), Q value = 0.00046

Table S133. Gene #38: '21q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
21Q GAIN MUTATED	25	3	5	1	2
21Q GAIN WILD-TYPE	124	135	44	52	114

Figure S133. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'21q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.59e-05 (Fisher's exact test), Q value = 0.036

Table S134. Gene #38: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
21Q GAIN MUTATED	0	4	32
21Q GAIN WILD-TYPE	13	210	246

Figure S134. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q gain' versus 'CN_CNMF'

P value = 8.4e-09 (Chi-square test), Q value = 6e-06

Table S135. Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
22Q GAIN MUTATED	3	4	24	0	0	0
22Q GAIN WILD-TYPE	297	20	128	22	15	1

Figure S135. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

'22q gain' versus 'METHLYATION_CNMF'

P value = 3.96e-09 (Fisher's exact test), Q value = 2.9e-06

Table S136. Gene #39: '22q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
22Q GAIN MUTATED	26	1	1
22Q GAIN WILD-TYPE	126	87	159

Figure S136. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q gain' versus 'MRNASEQ_CNMF'

P value = 1.08e-09 (Fisher's exact test), Q value = 7.9e-07

Table S137. Gene #39: '22q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
22Q GAIN MUTATED	27	4	0	0
22Q GAIN WILD-TYPE	147	82	115	130

Figure S137. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.35e-10 (Fisher's exact test), Q value = 4e-07

Table S138. Gene #39: '22q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
22Q GAIN MUTATED	31	0	0
22Q GAIN WILD-TYPE	208	84	182

Figure S138. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_CNMF'

P value = 0.000164 (Chi-square test), Q value = 0.087

Table S139. Gene #39: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
22Q GAIN MUTATED	19	1	3	0	7
22Q GAIN WILD-TYPE	130	137	46	53	109

Figure S139. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'22q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.78e-05 (Fisher's exact test), Q value = 0.016

Table S140. Gene #39: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
22Q GAIN MUTATED	0	2	28
22Q GAIN WILD-TYPE	13	212	250

Figure S140. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.07e-06 (Fisher's exact test), Q value = 0.0036

Table S141. Gene #39: '22q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	90	116
22Q GAIN MUTATED	25	2	1
22Q GAIN WILD-TYPE	151	88	115

Figure S141. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'22q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.77e-07 (Fisher's exact test), Q value = 0.00032

Table S142. Gene #39: '22q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	100	146	35
22Q GAIN MUTATED	6	20	1	1
22Q GAIN WILD-TYPE	95	80	145	34

Figure S142. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq gain' versus 'CN_CNMF'

P value = 3.87e-27 (Chi-square test), Q value = 3.4e-24

Table S143. Gene #40: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
XQ GAIN MUTATED	8	12	22	7	12	0
XQ GAIN WILD-TYPE	292	12	130	15	3	1

Figure S143. Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'CN_CNMF'

P value = 1.43e-08 (Chi-square test), Q value = 1e-05

Table S144. Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
1P LOSS MUTATED	0	5	17	2	0	0
1P LOSS WILD-TYPE	300	19	135	20	15	1

Figure S144. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 5.91e-06 (Fisher's exact test), Q value = 0.0035

Table S145. Gene #41: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
1P LOSS MUTATED	18	1	1
1P LOSS WILD-TYPE	134	87	159

Figure S145. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 1.6e-05 (Fisher's exact test), Q value = 0.0094

Table S146. Gene #41: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
1P LOSS MUTATED	20	2	1	1
1P LOSS WILD-TYPE	154	84	114	129

Figure S146. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.67e-05 (Fisher's exact test), Q value = 0.015

Table S147. Gene #41: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
1P LOSS MUTATED	22	0	2
1P LOSS WILD-TYPE	217	84	180

Figure S147. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.92e-05 (Fisher's exact test), Q value = 0.043

Table S148. Gene #41: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
1P LOSS MUTATED	1	1	22
1P LOSS WILD-TYPE	12	213	256

Figure S148. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1q loss' versus 'CN_CNMF'

P value = 0.000113 (Chi-square test), Q value = 0.061

Table S149. Gene #42: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
1Q LOSS MUTATED	0	2	12	1	0	0
1Q LOSS WILD-TYPE	300	22	140	21	15	1

Figure S149. Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

'1q loss' versus 'MRNASEQ_CNMF'

P value = 0.000323 (Fisher's exact test), Q value = 0.16

Table S150. Gene #42: '1q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
1Q LOSS MUTATED	13	1	0	1
1Q LOSS WILD-TYPE	161	85	115	129

Figure S150. Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2q loss' versus 'CN_CNMF'

P value = 5.25e-06 (Chi-square test), Q value = 0.0032

Table S151. Gene #44: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
2Q LOSS MUTATED	0	0	14	2	0	0
2Q LOSS WILD-TYPE	300	24	138	20	15	1

Figure S151. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

'2q loss' versus 'MRNASEQ_CNMF'

P value = 9.66e-05 (Fisher's exact test), Q value = 0.053

Table S152. Gene #44: '2q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
2Q LOSS MUTATED	14	0	0	2
2Q LOSS WILD-TYPE	160	86	115	128

Figure S152. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3p loss' versus 'CN_CNMF'

P value = 3.72e-19 (Chi-square test), Q value = 3.2e-16

Table S153. Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
3P LOSS MUTATED	0	3	43	3	0	0
3P LOSS WILD-TYPE	300	21	109	19	15	1

Figure S153. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 8.1e-07 (Fisher's exact test), Q value = 0.00052

Table S154. Gene #45: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
3P LOSS MUTATED	29	8	3
3P LOSS WILD-TYPE	123	80	157

Figure S154. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 2.36e-12 (Fisher's exact test), Q value = 1.9e-09

Table S155. Gene #45: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
3P LOSS MUTATED	41	2	3	2
3P LOSS WILD-TYPE	133	84	112	128

Figure S155. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.68e-12 (Fisher's exact test), Q value = 7.5e-09

Table S156. Gene #45: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
3P LOSS MUTATED	45	1	2
3P LOSS WILD-TYPE	194	83	180

Figure S156. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CNMF'

P value = 8.46e-08 (Chi-square test), Q value = 5.8e-05

Table S157. Gene #45: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
3P LOSS MUTATED	32	3	2	4	6
3P LOSS WILD-TYPE	117	135	47	49	110

Figure S157. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.47e-06 (Fisher's exact test), Q value = 0.0021

Table S158. Gene #45: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
3P LOSS MUTATED	2	5	40
3P LOSS WILD-TYPE	11	209	238

Figure S158. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.93e-05 (Fisher's exact test), Q value = 0.033

Table S159. Gene #45: '3p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	100	146	35
3P LOSS MUTATED	10	21	4	3
3P LOSS WILD-TYPE	91	79	142	32

Figure S159. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

P value = 3.29e-10 (Chi-square test), Q value = 2.5e-07

Table S160. Gene #46: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
3Q LOSS MUTATED	0	2	25	2	0	0
3Q LOSS WILD-TYPE	300	22	127	20	15	1

Figure S160. Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

'3q loss' versus 'MRNASEQ_CNMF'

P value = 7.13e-07 (Fisher's exact test), Q value = 0.00046

Table S161. Gene #46: '3q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
3Q LOSS MUTATED	24	1	1	2
3Q LOSS WILD-TYPE	150	85	114	128

Figure S161. Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.75e-06 (Fisher's exact test), Q value = 0.0011

Table S162. Gene #46: '3q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
3Q LOSS MUTATED	26	0	2
3Q LOSS WILD-TYPE	213	84	180

Figure S162. Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_CNMF'

P value = 0.000484 (Chi-square test), Q value = 0.24

Table S163. Gene #46: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
3Q LOSS MUTATED	18	3	2	0	4
3Q LOSS WILD-TYPE	131	135	47	53	112

Figure S163. Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.000454 (Fisher's exact test), Q value = 0.23

Table S164. Gene #47: '4p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	19	19	15
4P LOSS MUTATED	1	0	7
4P LOSS WILD-TYPE	18	19	8

Figure S164. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

P value = 8.18e-37 (Chi-square test), Q value = 7.3e-34

Table S165. Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
4P LOSS MUTATED	4	9	80	4	1	0
4P LOSS WILD-TYPE	296	15	72	18	14	1

Figure S165. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 2.53e-16 (Fisher's exact test), Q value = 2.1e-13

Table S166. Gene #47: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
4P LOSS MUTATED	63	18	6
4P LOSS WILD-TYPE	89	70	154

Figure S166. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 3.64e-22 (Fisher's exact test), Q value = 3.1e-19

Table S167. Gene #47: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
4P LOSS MUTATED	77	9	6	6
4P LOSS WILD-TYPE	97	77	109	124

Figure S167. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.6e-20 (Fisher's exact test), Q value = 1.4e-17

Table S168. Gene #47: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
4P LOSS MUTATED	87	2	9
4P LOSS WILD-TYPE	152	82	173

Figure S168. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_CNMF'

P value = 6.47e-20 (Chi-square test), Q value = 5.5e-17

Table S169. Gene #47: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
4P LOSS MUTATED	66	7	10	8	5
4P LOSS WILD-TYPE	83	131	39	45	111

Figure S169. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.54e-14 (Fisher's exact test), Q value = 1.2e-11

Table S170. Gene #47: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
4P LOSS MUTATED	2	9	85
4P LOSS WILD-TYPE	11	205	193

Figure S170. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.43e-06 (Fisher's exact test), Q value = 0.0015

Table S171. Gene #47: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	90	116
4P LOSS MUTATED	56	22	9
4P LOSS WILD-TYPE	120	68	107

Figure S171. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.24e-09 (Fisher's exact test), Q value = 1.6e-06

Table S172. Gene #47: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	100	146	35
4P LOSS MUTATED	29	41	11	6
4P LOSS WILD-TYPE	72	59	135	29

Figure S172. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 4.21e-38 (Chi-square test), Q value = 3.8e-35

Table S173. Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
4Q LOSS MUTATED	3	8	81	4	1	0
4Q LOSS WILD-TYPE	297	16	71	18	14	1

Figure S173. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 8.96e-17 (Fisher's exact test), Q value = 7.5e-14

Table S174. Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
4Q LOSS MUTATED	62	18	5
4Q LOSS WILD-TYPE	90	70	155

Figure S174. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 1.48e-24 (Fisher's exact test), Q value = 1.3e-21

Table S175. Gene #48: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
4Q LOSS MUTATED	79	7	5	6
4Q LOSS WILD-TYPE	95	79	110	124

Figure S175. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.75e-20 (Fisher's exact test), Q value = 3.2e-17

Table S176. Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
4Q LOSS MUTATED	86	2	9
4Q LOSS WILD-TYPE	153	82	173

Figure S176. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_CNMF'

P value = 3.04e-15 (Chi-square test), Q value = 2.5e-12

Table S177. Gene #48: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
4Q LOSS MUTATED	60	8	12	8	7
4Q LOSS WILD-TYPE	89	130	37	45	109

Figure S177. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.76e-15 (Fisher's exact test), Q value = 2.3e-12

Table S178. Gene #48: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
4Q LOSS MUTATED	2	8	85
4Q LOSS WILD-TYPE	11	206	193

Figure S178. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.83e-06 (Fisher's exact test), Q value = 0.0011

Table S179. Gene #48: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	90	116
4Q LOSS MUTATED	53	24	8
4Q LOSS WILD-TYPE	123	66	108

Figure S179. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.02e-09 (Fisher's exact test), Q value = 3.6e-06

Table S180. Gene #48: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	100	146	35
4Q LOSS MUTATED	33	36	10	6
4Q LOSS WILD-TYPE	68	64	136	29

Figure S180. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p loss' versus 'CN_CNMF'

P value = 1.64e-18 (Chi-square test), Q value = 1.4e-15

Table S181. Gene #49: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
5P LOSS MUTATED	0	5	43	5	1	0
5P LOSS WILD-TYPE	300	19	109	17	14	1

Figure S181. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

'5p loss' versus 'METHLYATION_CNMF'

P value = 5.53e-09 (Fisher's exact test), Q value = 4e-06

Table S182. Gene #49: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
5P LOSS MUTATED	35	7	3
5P LOSS WILD-TYPE	117	81	157

Figure S182. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5p loss' versus 'MRNASEQ_CNMF'

P value = 9.88e-08 (Fisher's exact test), Q value = 6.8e-05

Table S183. Gene #49: '5p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
5P LOSS MUTATED	39	5	5	5
5P LOSS WILD-TYPE	135	81	110	125

Figure S183. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.61e-10 (Fisher's exact test), Q value = 1.2e-07

Table S184. Gene #49: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
5P LOSS MUTATED	48	1	5
5P LOSS WILD-TYPE	191	83	177

Figure S184. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_CNMF'

P value = 3.22e-06 (Chi-square test), Q value = 0.002

Table S185. Gene #49: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
5P LOSS MUTATED	33	5	5	4	7
5P LOSS WILD-TYPE	116	133	44	49	109

Figure S185. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.14e-07 (Fisher's exact test), Q value = 4e-04

Table S186. Gene #49: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
5P LOSS MUTATED	1	6	47
5P LOSS WILD-TYPE	12	208	231

Figure S186. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000141 (Fisher's exact test), Q value = 0.075

Table S187. Gene #49: '5p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	100	146	35
5P LOSS MUTATED	16	20	5	3
5P LOSS WILD-TYPE	85	80	141	32

Figure S187. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q loss' versus 'CN_CNMF'

P value = 4.45e-28 (Chi-square test), Q value = 3.9e-25

Table S188. Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
5Q LOSS MUTATED	0	5	61	5	1	0
5Q LOSS WILD-TYPE	300	19	91	17	14	1

Figure S188. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 2.47e-14 (Fisher's exact test), Q value = 2e-11

Table S189. Gene #50: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
5Q LOSS MUTATED	49	8	3
5Q LOSS WILD-TYPE	103	80	157

Figure S189. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 3.64e-15 (Fisher's exact test), Q value = 3e-12

Table S190. Gene #50: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
5Q LOSS MUTATED	57	5	4	6
5Q LOSS WILD-TYPE	117	81	111	124

Figure S190. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.48e-14 (Fisher's exact test), Q value = 1.2e-11

Table S191. Gene #50: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
5Q LOSS MUTATED	64	1	7
5Q LOSS WILD-TYPE	175	83	175

Figure S191. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CNMF'

P value = 1.11e-10 (Chi-square test), Q value = 8.5e-08

Table S192. Gene #50: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
5Q LOSS MUTATED	45	5	9	5	7
5Q LOSS WILD-TYPE	104	133	40	48	109

Figure S192. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.74e-11 (Fisher's exact test), Q value = 7.4e-08

Table S193. Gene #50: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
5Q LOSS MUTATED	0	7	64
5Q LOSS WILD-TYPE	13	207	214

Figure S193. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.56e-05 (Fisher's exact test), Q value = 0.02

Table S194. Gene #50: '5q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	90	116
5Q LOSS MUTATED	40	13	5
5Q LOSS WILD-TYPE	136	77	111

Figure S194. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.68e-07 (Fisher's exact test), Q value = 0.00037

Table S195. Gene #50: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	100	146	35
5Q LOSS MUTATED	21	26	5	6
5Q LOSS WILD-TYPE	80	74	141	29

Figure S195. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p loss' versus 'CN_CNMF'

P value = 4.15e-06 (Chi-square test), Q value = 0.0025

Table S196. Gene #51: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
6P LOSS MUTATED	0	3	13	0	0	0
6P LOSS WILD-TYPE	300	21	139	22	15	1

Figure S196. Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

'6p loss' versus 'MRNASEQ_CNMF'

P value = 0.000189 (Fisher's exact test), Q value = 0.1

Table S197. Gene #51: '6p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
6P LOSS MUTATED	14	0	1	1
6P LOSS WILD-TYPE	160	86	114	129

Figure S197. Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6q loss' versus 'CN_CNMF'

P value = 8.04e-09 (Chi-square test), Q value = 5.8e-06

Table S198. Gene #52: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
6Q LOSS MUTATED	0	3	20	0	0	0
6Q LOSS WILD-TYPE	300	21	132	22	15	1

Figure S198. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

'6q loss' versus 'METHLYATION_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.09

Table S199. Gene #52: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
6Q LOSS MUTATED	13	4	0
6Q LOSS WILD-TYPE	139	84	160

Figure S199. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6q loss' versus 'MRNASEQ_CNMF'

P value = 5.33e-07 (Fisher's exact test), Q value = 0.00035

Table S200. Gene #52: '6q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
6Q LOSS MUTATED	21	0	1	1
6Q LOSS WILD-TYPE	153	86	114	129

Figure S200. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.53e-05 (Fisher's exact test), Q value = 0.031

Table S201. Gene #52: '6q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
6Q LOSS MUTATED	21	0	2
6Q LOSS WILD-TYPE	218	84	180

Figure S201. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.17e-05 (Fisher's exact test), Q value = 0.013

Table S202. Gene #52: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
6Q LOSS MUTATED	1	0	20
6Q LOSS WILD-TYPE	12	214	258

Figure S202. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7p loss' versus 'CN_CNMF'

P value = 6.17e-15 (Chi-square test), Q value = 5e-12

Table S203. Gene #53: '7p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
7P LOSS MUTATED	3	1	37	1	0	0
7P LOSS WILD-TYPE	297	23	115	21	15	1

Figure S203. Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #3: 'CN_CNMF'

'7p loss' versus 'MRNASEQ_CNMF'

P value = 9.74e-10 (Fisher's exact test), Q value = 7.2e-07

Table S204. Gene #53: '7p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
7P LOSS MUTATED	35	1	3	3
7P LOSS WILD-TYPE	139	85	112	127

Figure S204. Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.8e-09 (Fisher's exact test), Q value = 4.2e-06

Table S205. Gene #53: '7p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
7P LOSS MUTATED	38	0	4
7P LOSS WILD-TYPE	201	84	178

Figure S205. Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7p loss' versus 'MIRSEQ_CNMF'

P value = 5.11e-06 (Chi-square test), Q value = 0.0031

Table S206. Gene #53: '7p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
7P LOSS MUTATED	27	6	5	2	2
7P LOSS WILD-TYPE	122	132	44	51	114

Figure S206. Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7q loss' versus 'CN_CNMF'

P value = 2.7e-19 (Chi-square test), Q value = 2.3e-16

Table S207. Gene #54: '7q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
7Q LOSS MUTATED	0	1	39	0	0	0
7Q LOSS WILD-TYPE	300	23	113	22	15	1

Figure S207. Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #3: 'CN_CNMF'

'7q loss' versus 'METHLYATION_CNMF'

P value = 3.17e-08 (Fisher's exact test), Q value = 2.2e-05

Table S208. Gene #54: '7q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
7Q LOSS MUTATED	28	8	1
7Q LOSS WILD-TYPE	124	80	159

Figure S208. Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7q loss' versus 'MRNASEQ_CNMF'

P value = 8.77e-15 (Fisher's exact test), Q value = 7.1e-12

Table S209. Gene #54: '7q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
7Q LOSS MUTATED	38	1	0	1
7Q LOSS WILD-TYPE	136	85	115	129

Figure S209. Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.53e-10 (Fisher's exact test), Q value = 1.9e-07

Table S210. Gene #54: '7q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
7Q LOSS MUTATED	38	0	2
7Q LOSS WILD-TYPE	201	84	180

Figure S210. Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q loss' versus 'MIRSEQ_CNMF'

P value = 1.97e-11 (Chi-square test), Q value = 1.5e-08

Table S211. Gene #54: '7q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
7Q LOSS MUTATED	32	2	4	1	1
7Q LOSS WILD-TYPE	117	136	45	52	115

Figure S211. Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.12e-06 (Fisher's exact test), Q value = 0.00072

Table S212. Gene #54: '7q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
7Q LOSS MUTATED	0	3	37
7Q LOSS WILD-TYPE	13	211	241

Figure S212. Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.91e-06 (Fisher's exact test), Q value = 0.0024

Table S213. Gene #54: '7q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	100	146	35
7Q LOSS MUTATED	13	19	2	1
7Q LOSS WILD-TYPE	88	81	144	34

Figure S213. Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

P value = 5.91e-32 (Chi-square test), Q value = 5.2e-29

Table S214. Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
8P LOSS MUTATED	4	2	66	1	0	1
8P LOSS WILD-TYPE	296	22	86	21	15	0

Figure S214. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 1.49e-15 (Fisher's exact test), Q value = 1.2e-12

Table S215. Gene #55: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
8P LOSS MUTATED	51	12	2
8P LOSS WILD-TYPE	101	76	158

Figure S215. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 4.35e-19 (Fisher's exact test), Q value = 3.7e-16

Table S216. Gene #55: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
8P LOSS MUTATED	60	8	2	3
8P LOSS WILD-TYPE	114	78	113	127

Figure S216. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.42e-17 (Fisher's exact test), Q value = 6.2e-14

Table S217. Gene #55: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
8P LOSS MUTATED	67	2	4
8P LOSS WILD-TYPE	172	82	178

Figure S217. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_CNMF'

P value = 2.36e-18 (Chi-square test), Q value = 2e-15

Table S218. Gene #55: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
8P LOSS MUTATED	54	4	6	2	5
8P LOSS WILD-TYPE	95	134	43	51	111

Figure S218. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.35e-12 (Fisher's exact test), Q value = 7.3e-09

Table S219. Gene #55: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
8P LOSS MUTATED	2	5	64
8P LOSS WILD-TYPE	11	209	214

Figure S219. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 7.31e-08 (Fisher's exact test), Q value = 5e-05

Table S220. Gene #55: '8p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	90	116
8P LOSS MUTATED	41	18	2
8P LOSS WILD-TYPE	135	72	114

Figure S220. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.91e-09 (Fisher's exact test), Q value = 4.3e-06

Table S221. Gene #55: '8p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	100	146	35
8P LOSS MUTATED	22	31	5	3
8P LOSS WILD-TYPE	79	69	141	32

Figure S221. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q loss' versus 'CN_CNMF'

P value = 5.79e-08 (Chi-square test), Q value = 4e-05

Table S222. Gene #56: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
8Q LOSS MUTATED	1	1	21	1	0	0
8Q LOSS WILD-TYPE	299	23	131	21	15	1

Figure S222. Get High-res Image Gene #56: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'

'8q loss' versus 'METHLYATION_CNMF'

P value = 2.82e-07 (Fisher's exact test), Q value = 0.00019

Table S223. Gene #56: '8q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
8Q LOSS MUTATED	20	2	0
8Q LOSS WILD-TYPE	132	86	160

Figure S223. Get High-res Image Gene #56: '8q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8q loss' versus 'MRNASEQ_CNMF'

P value = 8.97e-06 (Fisher's exact test), Q value = 0.0053

Table S224. Gene #56: '8q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
8Q LOSS MUTATED	20	2	0	2
8Q LOSS WILD-TYPE	154	84	115	128

Figure S224. Get High-res Image Gene #56: '8q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.67e-05 (Fisher's exact test), Q value = 0.015

Table S225. Gene #56: '8q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
8Q LOSS MUTATED	22	0	2
8Q LOSS WILD-TYPE	217	84	180

Figure S225. Get High-res Image Gene #56: '8q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8q loss' versus 'MIRSEQ_CNMF'

P value = 1.33e-05 (Chi-square test), Q value = 0.0079

Table S226. Gene #56: '8q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
8Q LOSS MUTATED	18	2	1	0	2
8Q LOSS WILD-TYPE	131	136	48	53	114

Figure S226. Get High-res Image Gene #56: '8q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.97e-05 (Fisher's exact test), Q value = 0.038

Table S227. Gene #56: '8q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	100	146	35
8Q LOSS MUTATED	6	14	1	0
8Q LOSS WILD-TYPE	95	86	145	35

Figure S227. Get High-res Image Gene #56: '8q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p loss' versus 'MRNA_CHIERARCHICAL'

P value = 9.8e-05 (Fisher's exact test), Q value = 0.053

Table S228. Gene #57: '9p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	19	19	15
9P LOSS MUTATED	1	0	8
9P LOSS WILD-TYPE	18	19	7

Figure S228. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

P value = 3.41e-41 (Chi-square test), Q value = 3e-38

Table S229. Gene #57: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
9P LOSS MUTATED	2	8	84	6	0	0
9P LOSS WILD-TYPE	298	16	68	16	15	1

Figure S229. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 5.04e-11 (Fisher's exact test), Q value = 3.9e-08

Table S230. Gene #57: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
9P LOSS MUTATED	54	22	9
9P LOSS WILD-TYPE	98	66	151

Figure S230. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 5.72e-20 (Fisher's exact test), Q value = 4.9e-17

Table S231. Gene #57: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
9P LOSS MUTATED	76	5	6	13
9P LOSS WILD-TYPE	98	81	109	117

Figure S231. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.65e-15 (Fisher's exact test), Q value = 1.4e-12

Table S232. Gene #57: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
9P LOSS MUTATED	83	3	14
9P LOSS WILD-TYPE	156	81	168

Figure S232. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_CNMF'

P value = 3.22e-15 (Chi-square test), Q value = 2.6e-12

Table S233. Gene #57: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
9P LOSS MUTATED	62	12	10	7	6
9P LOSS WILD-TYPE	87	126	39	46	110

Figure S233. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.92e-10 (Fisher's exact test), Q value = 2.9e-07

Table S234. Gene #57: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
9P LOSS MUTATED	3	14	80
9P LOSS WILD-TYPE	10	200	198

Figure S234. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.57e-05 (Fisher's exact test), Q value = 0.026

Table S235. Gene #57: '9p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	100	146	35
9P LOSS MUTATED	24	37	17	6
9P LOSS WILD-TYPE	77	63	129	29

Figure S235. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q loss' versus 'MRNA_CNMF'

P value = 2.35e-05 (Fisher's exact test), Q value = 0.014

Table S236. Gene #58: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
9Q LOSS MUTATED	0	9	0	0
9Q LOSS WILD-TYPE	14	8	12	10

Figure S236. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'9q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1.13e-06 (Fisher's exact test), Q value = 0.00072

Table S237. Gene #58: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	19	19	15
9Q LOSS MUTATED	0	0	9
9Q LOSS WILD-TYPE	19	19	6

Figure S237. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 1.94e-48 (Chi-square test), Q value = 1.7e-45

Table S238. Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
9Q LOSS MUTATED	4	7	97	9	0	0
9Q LOSS WILD-TYPE	296	17	55	13	15	1

Figure S238. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 1.2e-11 (Fisher's exact test), Q value = 9.3e-09

Table S239. Gene #58: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
9Q LOSS MUTATED	63	25	13
9Q LOSS WILD-TYPE	89	63	147

Figure S239. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 2.74e-21 (Fisher's exact test), Q value = 2.4e-18

Table S240. Gene #58: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
9Q LOSS MUTATED	86	7	10	14
9Q LOSS WILD-TYPE	88	79	105	116

Figure S240. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.41e-18 (Fisher's exact test), Q value = 1.2e-15

Table S241. Gene #58: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
9Q LOSS MUTATED	97	4	16
9Q LOSS WILD-TYPE	142	80	166

Figure S241. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_CNMF'

P value = 8.69e-22 (Chi-square test), Q value = 7.5e-19

Table S242. Gene #58: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
9Q LOSS MUTATED	76	14	11	8	5
9Q LOSS WILD-TYPE	73	124	38	45	111

Figure S242. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.05e-11 (Fisher's exact test), Q value = 3.1e-08

Table S243. Gene #58: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
9Q LOSS MUTATED	4	18	92
9Q LOSS WILD-TYPE	9	196	186

Figure S243. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.33e-05 (Fisher's exact test), Q value = 0.0078

Table S244. Gene #58: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	100	146	35
9Q LOSS MUTATED	27	43	21	8
9Q LOSS WILD-TYPE	74	57	125	27

Figure S244. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 6.06e-18 (Chi-square test), Q value = 5.1e-15

Table S245. Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
10P LOSS MUTATED	0	1	38	1	0	0
10P LOSS WILD-TYPE	300	23	114	21	15	1

Figure S245. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 5.26e-07 (Fisher's exact test), Q value = 0.00035

Table S246. Gene #59: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
10P LOSS MUTATED	24	9	1
10P LOSS WILD-TYPE	128	79	159

Figure S246. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 3.73e-09 (Fisher's exact test), Q value = 2.7e-06

Table S247. Gene #59: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
10P LOSS MUTATED	33	3	1	3
10P LOSS WILD-TYPE	141	83	114	127

Figure S247. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.66e-08 (Fisher's exact test), Q value = 3.3e-05

Table S248. Gene #59: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
10P LOSS MUTATED	36	1	3
10P LOSS WILD-TYPE	203	83	179

Figure S248. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_CNMF'

P value = 1.48e-08 (Chi-square test), Q value = 1.1e-05

Table S249. Gene #59: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
10P LOSS MUTATED	28	1	4	3	2
10P LOSS WILD-TYPE	121	137	45	50	114

Figure S249. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.18e-06 (Fisher's exact test), Q value = 0.002

Table S250. Gene #59: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
10P LOSS MUTATED	0	3	35
10P LOSS WILD-TYPE	13	211	243

Figure S250. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000161 (Fisher's exact test), Q value = 0.086

Table S251. Gene #59: '10p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	100	146	35
10P LOSS MUTATED	13	16	3	1
10P LOSS WILD-TYPE	88	84	143	34

Figure S251. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 2.2e-15 (Chi-square test), Q value = 1.8e-12

Table S252. Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
10Q LOSS MUTATED	1	1	35	1	0	0
10Q LOSS WILD-TYPE	299	23	117	21	15	1

Figure S252. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 6.28e-07 (Fisher's exact test), Q value = 0.00041

Table S253. Gene #60: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
10Q LOSS MUTATED	24	8	1
10Q LOSS WILD-TYPE	128	80	159

Figure S253. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 1.62e-07 (Fisher's exact test), Q value = 0.00011

Table S254. Gene #60: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
10Q LOSS MUTATED	30	3	1	4
10Q LOSS WILD-TYPE	144	83	114	126

Figure S254. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.39e-06 (Fisher's exact test), Q value = 0.00088

Table S255. Gene #60: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
10Q LOSS MUTATED	33	1	4
10Q LOSS WILD-TYPE	206	83	178

Figure S255. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_CNMF'

P value = 4.35e-07 (Chi-square test), Q value = 0.00029

Table S256. Gene #60: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
10Q LOSS MUTATED	26	2	4	3	2
10Q LOSS WILD-TYPE	123	136	45	50	114

Figure S256. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.09e-05 (Fisher's exact test), Q value = 0.023

Table S257. Gene #60: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
10Q LOSS MUTATED	0	4	33
10Q LOSS WILD-TYPE	13	210	245

Figure S257. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 1.36e-27 (Chi-square test), Q value = 1.2e-24

Table S258. Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
11P LOSS MUTATED	1	8	59	3	0	0
11P LOSS WILD-TYPE	299	16	93	19	15	1

Figure S258. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 1.53e-10 (Fisher's exact test), Q value = 1.2e-07

Table S259. Gene #61: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
11P LOSS MUTATED	45	16	5
11P LOSS WILD-TYPE	107	72	155

Figure S259. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p loss' versus 'MRNASEQ_CNMF'

P value = 3.26e-12 (Fisher's exact test), Q value = 2.6e-09

Table S260. Gene #61: '11p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
11P LOSS MUTATED	53	7	5	6
11P LOSS WILD-TYPE	121	79	110	124

Figure S260. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.81e-12 (Fisher's exact test), Q value = 1.4e-09

Table S261. Gene #61: '11p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
11P LOSS MUTATED	61	1	9
11P LOSS WILD-TYPE	178	83	173

Figure S261. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_CNMF'

P value = 1.76e-11 (Chi-square test), Q value = 1.4e-08

Table S262. Gene #61: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
11P LOSS MUTATED	46	8	7	6	3
11P LOSS WILD-TYPE	103	130	42	47	113

Figure S262. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.89e-07 (Fisher's exact test), Q value = 0.00013

Table S263. Gene #61: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
11P LOSS MUTATED	1	10	59
11P LOSS WILD-TYPE	12	204	219

Figure S263. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.86e-07 (Fisher's exact test), Q value = 0.00038

Table S264. Gene #61: '11p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	100	146	35
11P LOSS MUTATED	17	35	11	3
11P LOSS WILD-TYPE	84	65	135	32

Figure S264. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

P value = 1.24e-24 (Chi-square test), Q value = 1.1e-21

Table S265. Gene #62: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
11Q LOSS MUTATED	1	8	54	5	0	0
11Q LOSS WILD-TYPE	299	16	98	17	15	1

Figure S265. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

P value = 1.81e-09 (Fisher's exact test), Q value = 1.3e-06

Table S266. Gene #62: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
11Q LOSS MUTATED	44	15	6
11Q LOSS WILD-TYPE	108	73	154

Figure S266. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11q loss' versus 'MRNASEQ_CNMF'

P value = 5.81e-11 (Fisher's exact test), Q value = 4.4e-08

Table S267. Gene #62: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
11Q LOSS MUTATED	50	6	4	8
11Q LOSS WILD-TYPE	124	80	111	122

Figure S267. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.62e-11 (Fisher's exact test), Q value = 6.6e-08

Table S268. Gene #62: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
11Q LOSS MUTATED	57	1	10
11Q LOSS WILD-TYPE	182	83	172

Figure S268. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_CNMF'

P value = 9.12e-12 (Chi-square test), Q value = 7.1e-09

Table S269. Gene #62: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
11Q LOSS MUTATED	46	9	4	6	3
11Q LOSS WILD-TYPE	103	129	45	47	113

Figure S269. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.42e-07 (Fisher's exact test), Q value = 0.00042

Table S270. Gene #62: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
11Q LOSS MUTATED	1	10	57
11Q LOSS WILD-TYPE	12	204	221

Figure S270. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000207 (Fisher's exact test), Q value = 0.11

Table S271. Gene #62: '11q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	90	116
11Q LOSS MUTATED	45	10	10
11Q LOSS WILD-TYPE	131	80	106

Figure S271. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.32e-09 (Fisher's exact test), Q value = 1.7e-06

Table S272. Gene #62: '11q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	100	146	35
11Q LOSS MUTATED	13	39	11	2
11Q LOSS WILD-TYPE	88	61	135	33

Figure S272. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12p loss' versus 'CN_CNMF'

P value = 7.88e-18 (Chi-square test), Q value = 6.6e-15

Table S273. Gene #63: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
12P LOSS MUTATED	0	1	39	1	1	0
12P LOSS WILD-TYPE	300	23	113	21	14	1

Figure S273. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

'12p loss' versus 'METHLYATION_CNMF'

P value = 0.000111 (Fisher's exact test), Q value = 0.06

Table S274. Gene #63: '12p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
12P LOSS MUTATED	24	7	4
12P LOSS WILD-TYPE	128	81	156

Figure S274. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p loss' versus 'MRNASEQ_CNMF'

P value = 2.45e-10 (Fisher's exact test), Q value = 1.8e-07

Table S275. Gene #63: '12p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
12P LOSS MUTATED	35	0	2	5
12P LOSS WILD-TYPE	139	86	113	125

Figure S275. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.51e-06 (Fisher's exact test), Q value = 0.0022

Table S276. Gene #63: '12p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
12P LOSS MUTATED	35	1	6
12P LOSS WILD-TYPE	204	83	176

Figure S276. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p loss' versus 'MIRSEQ_CNMF'

P value = 2.77e-07 (Chi-square test), Q value = 0.00019

Table S277. Gene #63: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
12P LOSS MUTATED	28	4	4	1	3
12P LOSS WILD-TYPE	121	134	45	52	113

Figure S277. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.58e-05 (Fisher's exact test), Q value = 0.031

Table S278. Gene #63: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
12P LOSS MUTATED	0	5	35
12P LOSS WILD-TYPE	13	209	243

Figure S278. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12q loss' versus 'CN_CNMF'

P value = 6.25e-14 (Chi-square test), Q value = 5e-11

Table S279. Gene #64: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
12Q LOSS MUTATED	0	1	32	1	1	0
12Q LOSS WILD-TYPE	300	23	120	21	14	1

Figure S279. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

'12q loss' versus 'METHLYATION_CNMF'

P value = 1.71e-05 (Fisher's exact test), Q value = 0.01

Table S280. Gene #64: '12q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
12Q LOSS MUTATED	22	5	2
12Q LOSS WILD-TYPE	130	83	158

Figure S280. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12q loss' versus 'MRNASEQ_CNMF'

P value = 4.2e-10 (Fisher's exact test), Q value = 3.1e-07

Table S281. Gene #64: '12q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
12Q LOSS MUTATED	31	0	1	3
12Q LOSS WILD-TYPE	143	86	114	127

Figure S281. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.73e-07 (Fisher's exact test), Q value = 5e-04

Table S282. Gene #64: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
12Q LOSS MUTATED	31	0	4
12Q LOSS WILD-TYPE	208	84	178

Figure S282. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q loss' versus 'MIRSEQ_CNMF'

P value = 6.38e-05 (Chi-square test), Q value = 0.035

Table S283. Gene #64: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
12Q LOSS MUTATED	21	2	5	2	3
12Q LOSS WILD-TYPE	128	136	44	51	113

Figure S283. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.86e-06 (Fisher's exact test), Q value = 0.0035

Table S284. Gene #64: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
12Q LOSS MUTATED	0	2	31
12Q LOSS WILD-TYPE	13	212	247

Figure S284. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000198 (Fisher's exact test), Q value = 0.1

Table S285. Gene #64: '12q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	100	146	35
12Q LOSS MUTATED	8	16	2	3
12Q LOSS WILD-TYPE	93	84	144	32

Figure S285. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 1.62e-26 (Chi-square test), Q value = 1.4e-23

Table S286. Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
13Q LOSS MUTATED	5	8	63	9	1	0
13Q LOSS WILD-TYPE	295	16	89	13	14	1

Figure S286. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 2.92e-06 (Fisher's exact test), Q value = 0.0018

Table S287. Gene #65: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
13Q LOSS MUTATED	44	18	12
13Q LOSS WILD-TYPE	108	70	148

Figure S287. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 1.85e-08 (Fisher's exact test), Q value = 1.3e-05

Table S288. Gene #65: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
13Q LOSS MUTATED	55	5	12	14
13Q LOSS WILD-TYPE	119	81	103	116

Figure S288. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.16e-10 (Fisher's exact test), Q value = 4.6e-07

Table S289. Gene #65: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
13Q LOSS MUTATED	65	1	20
13Q LOSS WILD-TYPE	174	83	162

Figure S289. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_CNMF'

P value = 5.15e-08 (Chi-square test), Q value = 3.6e-05

Table S290. Gene #65: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
13Q LOSS MUTATED	46	14	6	13	6
13Q LOSS WILD-TYPE	103	124	43	40	110

Figure S290. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'13q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.05e-06 (Fisher's exact test), Q value = 0.00067

Table S291. Gene #65: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
13Q LOSS MUTATED	5	16	64
13Q LOSS WILD-TYPE	8	198	214

Figure S291. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.000218 (Fisher's exact test), Q value = 0.11

Table S292. Gene #66: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	19	19	15
14Q LOSS MUTATED	0	0	6
14Q LOSS WILD-TYPE	19	19	9

Figure S292. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 4.69e-23 (Chi-square test), Q value = 4.1e-20

Table S293. Gene #66: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
14Q LOSS MUTATED	0	5	51	2	1	0
14Q LOSS WILD-TYPE	300	19	101	20	14	1

Figure S293. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 1.69e-11 (Fisher's exact test), Q value = 1.3e-08

Table S294. Gene #66: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
14Q LOSS MUTATED	37	8	1
14Q LOSS WILD-TYPE	115	80	159

Figure S294. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 2.3e-16 (Fisher's exact test), Q value = 1.9e-13

Table S295. Gene #66: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
14Q LOSS MUTATED	51	2	2	4
14Q LOSS WILD-TYPE	123	84	113	126

Figure S295. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.34e-12 (Fisher's exact test), Q value = 1.1e-09

Table S296. Gene #66: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
14Q LOSS MUTATED	53	0	6
14Q LOSS WILD-TYPE	186	84	176

Figure S296. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_CNMF'

P value = 5.03e-09 (Chi-square test), Q value = 3.6e-06

Table S297. Gene #66: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
14Q LOSS MUTATED	37	2	4	7	7
14Q LOSS WILD-TYPE	112	136	45	46	109

Figure S297. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'14q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.66e-13 (Fisher's exact test), Q value = 2.9e-10

Table S298. Gene #66: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
14Q LOSS MUTATED	1	1	55
14Q LOSS WILD-TYPE	12	213	223

Figure S298. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.66e-05 (Fisher's exact test), Q value = 0.0097

Table S299. Gene #66: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	90	116
14Q LOSS MUTATED	35	9	3
14Q LOSS WILD-TYPE	141	81	113

Figure S299. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'14q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.64e-06 (Fisher's exact test), Q value = 0.0022

Table S300. Gene #66: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	100	146	35
14Q LOSS MUTATED	14	24	4	5
14Q LOSS WILD-TYPE	87	76	142	30

Figure S300. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q loss' versus 'MRNA_CHIERARCHICAL'

P value = 4.17e-05 (Fisher's exact test), Q value = 0.023

Table S301. Gene #67: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	19	19	15
15Q LOSS MUTATED	0	0	7
15Q LOSS WILD-TYPE	19	19	8

Figure S301. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 1.41e-40 (Chi-square test), Q value = 1.3e-37

Table S302. Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
15Q LOSS MUTATED	4	5	85	8	0	0
15Q LOSS WILD-TYPE	296	19	67	14	15	1

Figure S302. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 9.28e-15 (Fisher's exact test), Q value = 7.5e-12

Table S303. Gene #67: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
15Q LOSS MUTATED	61	21	7
15Q LOSS WILD-TYPE	91	67	153

Figure S303. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'15q loss' versus 'RPPA_CNMF'

P value = 0.00036 (Chi-square test), Q value = 0.18

Table S304. Gene #67: '15q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	37	39	12	41	24
15Q LOSS MUTATED	1	11	2	1	1	3
15Q LOSS WILD-TYPE	40	26	37	11	40	21

Figure S304. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 6.18e-24 (Fisher's exact test), Q value = 5.4e-21

Table S305. Gene #67: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
15Q LOSS MUTATED	81	5	10	6
15Q LOSS WILD-TYPE	93	81	105	124

Figure S305. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.92e-22 (Fisher's exact test), Q value = 4.2e-19

Table S306. Gene #67: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
15Q LOSS MUTATED	91	2	9
15Q LOSS WILD-TYPE	148	82	173

Figure S306. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_CNMF'

P value = 2.43e-20 (Chi-square test), Q value = 2.1e-17

Table S307. Gene #67: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
15Q LOSS MUTATED	68	8	11	8	5
15Q LOSS WILD-TYPE	81	130	38	45	111

Figure S307. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.31e-15 (Fisher's exact test), Q value = 1.9e-12

Table S308. Gene #67: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
15Q LOSS MUTATED	4	9	87
15Q LOSS WILD-TYPE	9	205	191

Figure S308. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.63e-07 (Fisher's exact test), Q value = 0.00011

Table S309. Gene #67: '15q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	90	116
15Q LOSS MUTATED	61	18	9
15Q LOSS WILD-TYPE	115	72	107

Figure S309. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.44e-09 (Fisher's exact test), Q value = 1.1e-06

Table S310. Gene #67: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	100	146	35
15Q LOSS MUTATED	24	45	13	6
15Q LOSS WILD-TYPE	77	55	133	29

Figure S310. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.000218 (Fisher's exact test), Q value = 0.11

Table S311. Gene #68: '16p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	19	19	15
16P LOSS MUTATED	0	0	6
16P LOSS WILD-TYPE	19	19	9

Figure S311. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'16p loss' versus 'CN_CNMF'

P value = 8.75e-36 (Chi-square test), Q value = 7.8e-33

Table S312. Gene #68: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
16P LOSS MUTATED	5	5	79	3	1	0
16P LOSS WILD-TYPE	295	19	73	19	14	1

Figure S312. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

'16p loss' versus 'METHLYATION_CNMF'

P value = 2.55e-13 (Fisher's exact test), Q value = 2e-10

Table S313. Gene #68: '16p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
16P LOSS MUTATED	54	23	6
16P LOSS WILD-TYPE	98	65	154

Figure S313. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16p loss' versus 'MRNASEQ_CNMF'

P value = 4.39e-20 (Fisher's exact test), Q value = 3.8e-17

Table S314. Gene #68: '16p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
16P LOSS MUTATED	73	5	8	7
16P LOSS WILD-TYPE	101	81	107	123

Figure S314. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.94e-17 (Fisher's exact test), Q value = 6.6e-14

Table S315. Gene #68: '16p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
16P LOSS MUTATED	80	2	11
16P LOSS WILD-TYPE	159	82	171

Figure S315. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_CNMF'

P value = 1.98e-14 (Chi-square test), Q value = 1.6e-11

Table S316. Gene #68: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
16P LOSS MUTATED	58	10	10	6	6
16P LOSS WILD-TYPE	91	128	39	47	110

Figure S316. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.7e-11 (Fisher's exact test), Q value = 3.6e-08

Table S317. Gene #68: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
16P LOSS MUTATED	2	11	77
16P LOSS WILD-TYPE	11	203	201

Figure S317. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.8e-05 (Fisher's exact test), Q value = 0.016

Table S318. Gene #68: '16p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	90	116
16P LOSS MUTATED	49	24	9
16P LOSS WILD-TYPE	127	66	107

Figure S318. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.3e-07 (Fisher's exact test), Q value = 0.00015

Table S319. Gene #68: '16p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	100	146	35
16P LOSS MUTATED	29	35	11	7
16P LOSS WILD-TYPE	72	65	135	28

Figure S319. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q loss' versus 'MRNA_CHIERARCHICAL'

P value = 9.8e-05 (Fisher's exact test), Q value = 0.053

Table S320. Gene #69: '16q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	19	19	15
16Q LOSS MUTATED	0	1	8
16Q LOSS WILD-TYPE	19	18	7

Figure S320. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'16q loss' versus 'CN_CNMF'

P value = 1.94e-46 (Chi-square test), Q value = 1.7e-43

Table S321. Gene #69: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
16Q LOSS MUTATED	15	8	106	4	1	0
16Q LOSS WILD-TYPE	285	16	46	18	14	1

Figure S321. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 4.2e-14 (Fisher's exact test), Q value = 3.4e-11

Table S322. Gene #69: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
16Q LOSS MUTATED	73	29	15
16Q LOSS WILD-TYPE	79	59	145

Figure S322. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 2.51e-24 (Fisher's exact test), Q value = 2.2e-21

Table S323. Gene #69: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
16Q LOSS MUTATED	97	9	15	13
16Q LOSS WILD-TYPE	77	77	100	117

Figure S323. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.27e-19 (Fisher's exact test), Q value = 2.8e-16

Table S324. Gene #69: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
16Q LOSS MUTATED	108	6	20
16Q LOSS WILD-TYPE	131	78	162

Figure S324. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_CNMF'

P value = 8.72e-19 (Chi-square test), Q value = 7.4e-16

Table S325. Gene #69: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
16Q LOSS MUTATED	79	14	14	11	12
16Q LOSS WILD-TYPE	70	124	35	42	104

Figure S325. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.83e-11 (Fisher's exact test), Q value = 1.4e-08

Table S326. Gene #69: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
16Q LOSS MUTATED	3	23	104
16Q LOSS WILD-TYPE	10	191	174

Figure S326. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.67e-06 (Fisher's exact test), Q value = 0.0011

Table S327. Gene #69: '16q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	90	116
16Q LOSS MUTATED	70	30	15
16Q LOSS WILD-TYPE	106	60	101

Figure S327. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.91e-09 (Fisher's exact test), Q value = 5.7e-06

Table S328. Gene #69: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	100	146	35
16Q LOSS MUTATED	37	50	21	7
16Q LOSS WILD-TYPE	64	50	125	28

Figure S328. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.000454 (Fisher's exact test), Q value = 0.23

Table S329. Gene #70: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	19	19	15
17P LOSS MUTATED	1	0	7
17P LOSS WILD-TYPE	18	19	8

Figure S329. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 1.49e-58 (Chi-square test), Q value = 1.3e-55

Table S330. Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
17P LOSS MUTATED	2	4	107	7	0	0
17P LOSS WILD-TYPE	298	20	45	15	15	1

Figure S330. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 1.13e-15 (Fisher's exact test), Q value = 9.3e-13

Table S331. Gene #70: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
17P LOSS MUTATED	71	23	11
17P LOSS WILD-TYPE	81	65	149

Figure S331. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 3.33e-26 (Fisher's exact test), Q value = 2.9e-23

Table S332. Gene #70: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
17P LOSS MUTATED	91	8	6	13
17P LOSS WILD-TYPE	83	78	109	117

Figure S332. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.04e-19 (Fisher's exact test), Q value = 2.6e-16

Table S333. Gene #70: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
17P LOSS MUTATED	98	3	17
17P LOSS WILD-TYPE	141	81	165

Figure S333. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CNMF'

P value = 3.95e-21 (Chi-square test), Q value = 3.4e-18

Table S334. Gene #70: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
17P LOSS MUTATED	77	15	11	7	7
17P LOSS WILD-TYPE	72	123	38	46	109

Figure S334. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.79e-10 (Fisher's exact test), Q value = 1.3e-07

Table S335. Gene #70: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
17P LOSS MUTATED	3	20	94
17P LOSS WILD-TYPE	10	194	184

Figure S335. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.82e-06 (Fisher's exact test), Q value = 0.0023

Table S336. Gene #70: '17p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	100	146	35
17P LOSS MUTATED	30	44	21	7
17P LOSS WILD-TYPE	71	56	125	28

Figure S336. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.000218 (Fisher's exact test), Q value = 0.11

Table S337. Gene #71: '17q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	19	19	15
17Q LOSS MUTATED	0	0	6
17Q LOSS WILD-TYPE	19	19	9

Figure S337. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

P value = 3.2e-37 (Chi-square test), Q value = 2.8e-34

Table S338. Gene #71: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
17Q LOSS MUTATED	1	3	75	7	0	0
17Q LOSS WILD-TYPE	299	21	77	15	15	1

Figure S338. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

'17q loss' versus 'METHLYATION_CNMF'

P value = 1.16e-07 (Fisher's exact test), Q value = 7.9e-05

Table S339. Gene #71: '17q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
17Q LOSS MUTATED	45	20	10
17Q LOSS WILD-TYPE	107	68	150

Figure S339. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q loss' versus 'MRNASEQ_CNMF'

P value = 3.33e-15 (Fisher's exact test), Q value = 2.7e-12

Table S340. Gene #71: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
17Q LOSS MUTATED	63	5	5	11
17Q LOSS WILD-TYPE	111	81	110	119

Figure S340. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.49e-10 (Fisher's exact test), Q value = 4.8e-07

Table S341. Gene #71: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
17Q LOSS MUTATED	66	3	15
17Q LOSS WILD-TYPE	173	81	167

Figure S341. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_CNMF'

P value = 1.64e-10 (Chi-square test), Q value = 1.2e-07

Table S342. Gene #71: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
17Q LOSS MUTATED	51	12	7	7	6
17Q LOSS WILD-TYPE	98	126	42	46	110

Figure S342. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.47e-06 (Fisher's exact test), Q value = 0.0039

Table S343. Gene #71: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
17Q LOSS MUTATED	3	16	64
17Q LOSS WILD-TYPE	10	198	214

Figure S343. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 6.39e-18 (Chi-square test), Q value = 5.3e-15

Table S344. Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
18P LOSS MUTATED	1	5	38	8	0	0
18P LOSS WILD-TYPE	299	19	114	14	15	1

Figure S344. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

P value = 2.39e-07 (Fisher's exact test), Q value = 0.00016

Table S345. Gene #72: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
18P LOSS MUTATED	33	9	4
18P LOSS WILD-TYPE	119	79	156

Figure S345. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p loss' versus 'MRNASEQ_CNMF'

P value = 1.3e-05 (Fisher's exact test), Q value = 0.0077

Table S346. Gene #72: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
18P LOSS MUTATED	35	5	6	6
18P LOSS WILD-TYPE	139	81	109	124

Figure S346. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.58e-06 (Fisher's exact test), Q value = 0.0034

Table S347. Gene #72: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
18P LOSS MUTATED	41	2	9
18P LOSS WILD-TYPE	198	82	173

Figure S347. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_CNMF'

P value = 4.56e-06 (Chi-square test), Q value = 0.0028

Table S348. Gene #72: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
18P LOSS MUTATED	31	7	4	6	3
18P LOSS WILD-TYPE	118	131	45	47	113

Figure S348. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.28e-05 (Fisher's exact test), Q value = 0.04

Table S349. Gene #72: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
18P LOSS MUTATED	1	8	42
18P LOSS WILD-TYPE	12	206	236

Figure S349. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18q loss' versus 'CN_CNMF'

P value = 4.66e-24 (Chi-square test), Q value = 4.1e-21

Table S350. Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
18Q LOSS MUTATED	1	5	49	10	0	0
18Q LOSS WILD-TYPE	299	19	103	12	15	1

Figure S350. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 1.7e-08 (Fisher's exact test), Q value = 1.2e-05

Table S351. Gene #73: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
18Q LOSS MUTATED	41	12	6
18Q LOSS WILD-TYPE	111	76	154

Figure S351. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 1.12e-07 (Fisher's exact test), Q value = 7.7e-05

Table S352. Gene #73: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
18Q LOSS MUTATED	44	8	6	7
18Q LOSS WILD-TYPE	130	78	109	123

Figure S352. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.55e-10 (Fisher's exact test), Q value = 4.8e-07

Table S353. Gene #73: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
18Q LOSS MUTATED	54	1	10
18Q LOSS WILD-TYPE	185	83	172

Figure S353. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_CNMF'

P value = 1.72e-07 (Chi-square test), Q value = 0.00012

Table S354. Gene #73: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
18Q LOSS MUTATED	39	9	6	5	5
18Q LOSS WILD-TYPE	110	129	43	48	111

Figure S354. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.09e-07 (Fisher's exact test), Q value = 0.00014

Table S355. Gene #73: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
18Q LOSS MUTATED	2	8	54
18Q LOSS WILD-TYPE	11	206	224

Figure S355. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

P value = 2.35e-19 (Chi-square test), Q value = 2e-16

Table S356. Gene #74: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
19P LOSS MUTATED	1	7	42	7	0	0
19P LOSS WILD-TYPE	299	17	110	15	15	1

Figure S356. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

P value = 1.37e-12 (Fisher's exact test), Q value = 1.1e-09

Table S357. Gene #74: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
19P LOSS MUTATED	42	7	2
19P LOSS WILD-TYPE	110	81	158

Figure S357. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p loss' versus 'MRNASEQ_CNMF'

P value = 2.09e-09 (Fisher's exact test), Q value = 1.5e-06

Table S358. Gene #74: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
19P LOSS MUTATED	42	7	4	4
19P LOSS WILD-TYPE	132	79	111	126

Figure S358. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.42e-10 (Fisher's exact test), Q value = 1.1e-07

Table S359. Gene #74: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
19P LOSS MUTATED	50	1	6
19P LOSS WILD-TYPE	189	83	176

Figure S359. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_CNMF'

P value = 1.37e-09 (Chi-square test), Q value = 1e-06

Table S360. Gene #74: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
19P LOSS MUTATED	38	5	3	4	5
19P LOSS WILD-TYPE	111	133	46	49	111

Figure S360. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.38e-07 (Fisher's exact test), Q value = 0.00029

Table S361. Gene #74: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
19P LOSS MUTATED	2	6	47
19P LOSS WILD-TYPE	11	208	231

Figure S361. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.97e-05 (Fisher's exact test), Q value = 0.011

Table S362. Gene #74: '19p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	90	116
19P LOSS MUTATED	38	7	5
19P LOSS WILD-TYPE	138	83	111

Figure S362. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.3e-08 (Fisher's exact test), Q value = 3.7e-05

Table S363. Gene #74: '19p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	100	146	35
19P LOSS MUTATED	10	30	5	5
19P LOSS WILD-TYPE	91	70	141	30

Figure S363. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 4.42e-16 (Chi-square test), Q value = 3.7e-13

Table S364. Gene #75: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
19Q LOSS MUTATED	2	6	39	5	0	0
19Q LOSS WILD-TYPE	298	18	113	17	15	1

Figure S364. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

P value = 4.89e-07 (Fisher's exact test), Q value = 0.00032

Table S365. Gene #75: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
19Q LOSS MUTATED	32	9	4
19Q LOSS WILD-TYPE	120	79	156

Figure S365. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q loss' versus 'MRNASEQ_CNMF'

P value = 7.12e-07 (Fisher's exact test), Q value = 0.00046

Table S366. Gene #75: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
19Q LOSS MUTATED	36	6	4	5
19Q LOSS WILD-TYPE	138	80	111	125

Figure S366. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.76e-08 (Fisher's exact test), Q value = 4e-05

Table S367. Gene #75: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
19Q LOSS MUTATED	43	1	7
19Q LOSS WILD-TYPE	196	83	175

Figure S367. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_CNMF'

P value = 1.64e-06 (Chi-square test), Q value = 0.001

Table S368. Gene #75: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
19Q LOSS MUTATED	32	6	3	4	5
19Q LOSS WILD-TYPE	117	132	46	49	111

Figure S368. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.8e-05 (Fisher's exact test), Q value = 0.011

Table S369. Gene #75: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
19Q LOSS MUTATED	3	7	40
19Q LOSS WILD-TYPE	10	207	238

Figure S369. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.92e-05 (Fisher's exact test), Q value = 0.027

Table S370. Gene #75: '19q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	100	146	35
19Q LOSS MUTATED	10	24	6	4
19Q LOSS WILD-TYPE	91	76	140	31

Figure S370. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p loss' versus 'CN_CNMF'

P value = 6.27e-05 (Chi-square test), Q value = 0.035

Table S371. Gene #76: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
20P LOSS MUTATED	1	3	13	1	0	0
20P LOSS WILD-TYPE	299	21	139	21	15	1

Figure S371. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

'20q loss' versus 'CN_CNMF'

P value = 7.61e-05 (Chi-square test), Q value = 0.042

Table S372. Gene #77: '20q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
20Q LOSS MUTATED	0	3	7	0	0	0
20Q LOSS WILD-TYPE	300	21	145	22	15	1

Figure S372. Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #3: 'CN_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 3.62e-14 (Chi-square test), Q value = 2.9e-11

Table S373. Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
21Q LOSS MUTATED	4	5	39	3	0	0
21Q LOSS WILD-TYPE	296	19	113	19	15	1

Figure S373. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

'21q loss' versus 'METHLYATION_CNMF'

P value = 2.12e-06 (Fisher's exact test), Q value = 0.0013

Table S374. Gene #78: '21q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
21Q LOSS MUTATED	30	9	4
21Q LOSS WILD-TYPE	122	79	156

Figure S374. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'21q loss' versus 'MRNASEQ_CNMF'

P value = 5.34e-10 (Fisher's exact test), Q value = 4e-07

Table S375. Gene #78: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
21Q LOSS MUTATED	38	8	4	1
21Q LOSS WILD-TYPE	136	78	111	129

Figure S375. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.67e-08 (Fisher's exact test), Q value = 1.2e-05

Table S376. Gene #78: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
21Q LOSS MUTATED	43	5	3
21Q LOSS WILD-TYPE	196	79	179

Figure S376. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_CNMF'

P value = 2.59e-08 (Chi-square test), Q value = 1.8e-05

Table S377. Gene #78: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
21Q LOSS MUTATED	33	1	3	4	8
21Q LOSS WILD-TYPE	116	137	46	49	108

Figure S377. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'21q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.86e-08 (Fisher's exact test), Q value = 4.1e-05

Table S378. Gene #78: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
21Q LOSS MUTATED	0	4	45
21Q LOSS WILD-TYPE	13	210	233

Figure S378. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.11e-06 (Fisher's exact test), Q value = 0.00071

Table S379. Gene #78: '21q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	90	116
21Q LOSS MUTATED	33	9	1
21Q LOSS WILD-TYPE	143	81	115

Figure S379. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'21q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.17e-07 (Fisher's exact test), Q value = 0.00015

Table S380. Gene #78: '21q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	100	146	35
21Q LOSS MUTATED	15	23	2	3
21Q LOSS WILD-TYPE	86	77	144	32

Figure S380. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.000218 (Fisher's exact test), Q value = 0.11

Table S381. Gene #79: '22q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	19	19	15
22Q LOSS MUTATED	0	0	6
22Q LOSS WILD-TYPE	19	19	9

Figure S381. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 4.41e-44 (Chi-square test), Q value = 3.9e-41

Table S382. Gene #79: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
22Q LOSS MUTATED	3	5	89	8	0	0
22Q LOSS WILD-TYPE	297	19	63	14	15	1

Figure S382. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 2.74e-10 (Fisher's exact test), Q value = 2.1e-07

Table S383. Gene #79: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
22Q LOSS MUTATED	59	24	13
22Q LOSS WILD-TYPE	93	64	147

Figure S383. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 3.35e-18 (Fisher's exact test), Q value = 2.8e-15

Table S384. Gene #79: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
22Q LOSS MUTATED	76	5	8	15
22Q LOSS WILD-TYPE	98	81	107	115

Figure S384. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.18e-16 (Fisher's exact test), Q value = 1.8e-13

Table S385. Gene #79: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
22Q LOSS MUTATED	85	1	18
22Q LOSS WILD-TYPE	154	83	164

Figure S385. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CNMF'

P value = 3.38e-16 (Chi-square test), Q value = 2.8e-13

Table S386. Gene #79: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
22Q LOSS MUTATED	65	17	10	8	3
22Q LOSS WILD-TYPE	84	121	39	45	113

Figure S386. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.38e-09 (Fisher's exact test), Q value = 6e-06

Table S387. Gene #79: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
22Q LOSS MUTATED	5	18	80
22Q LOSS WILD-TYPE	8	196	198

Figure S387. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.13e-05 (Fisher's exact test), Q value = 0.012

Table S388. Gene #79: '22q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	100	146	35
22Q LOSS MUTATED	27	40	20	5
22Q LOSS WILD-TYPE	74	60	126	30

Figure S388. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq loss' versus 'CN_CNMF'

P value = 7.32e-28 (Chi-square test), Q value = 6.5e-25

Table S389. Gene #80: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
XQ LOSS MUTATED	1	3	60	5	0	0
XQ LOSS WILD-TYPE	299	21	92	17	15	1

Figure S389. Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 2.26e-07 (Fisher's exact test), Q value = 0.00015

Table S390. Gene #80: 'xq loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
XQ LOSS MUTATED	37	15	6
XQ LOSS WILD-TYPE	115	73	154

Figure S390. Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xq loss' versus 'RPPA_CNMF'

P value = 2.71e-05 (Chi-square test), Q value = 0.016

Table S391. Gene #80: 'xq loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	37	39	12	41	24
XQ LOSS MUTATED	3	13	2	1	1	1
XQ LOSS WILD-TYPE	38	24	37	11	40	23

Figure S391. Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'xq loss' versus 'MRNASEQ_CNMF'

P value = 2.36e-14 (Fisher's exact test), Q value = 1.9e-11

Table S392. Gene #80: 'xq loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
XQ LOSS MUTATED	54	4	6	4
XQ LOSS WILD-TYPE	120	82	109	126

Figure S392. Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'xq loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.46e-12 (Fisher's exact test), Q value = 1.9e-09

Table S393. Gene #80: 'xq loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
XQ LOSS MUTATED	59	1	8
XQ LOSS WILD-TYPE	180	83	174

Figure S393. Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_CNMF'

P value = 2.78e-11 (Chi-square test), Q value = 2.1e-08

Table S394. Gene #80: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
XQ LOSS MUTATED	45	7	3	5	6
XQ LOSS WILD-TYPE	104	131	46	48	110

Figure S394. Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xq loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.02e-08 (Fisher's exact test), Q value = 2.8e-05

Table S395. Gene #80: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
XQ LOSS MUTATED	4	8	54
XQ LOSS WILD-TYPE	9	206	224

Figure S395. Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.73e-06 (Fisher's exact test), Q value = 0.0023

Table S396. Gene #80: 'xq loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	100	146	35
XQ LOSS MUTATED	14	30	8	6
XQ LOSS WILD-TYPE	87	70	138	29

Figure S396. Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtypes file = UCEC-TP.transferedmergedcluster.txt
Number of patients = 514
Number of significantly arm-level cnvs = 80
Number of molecular subtypes = 12
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

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.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] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)

[3] 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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