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 subtypes.

Summary

Testing the association between copy number variation 80 arm-level results and 12 molecular subtypes across 934 patients, 414 significant findings detected with Q value < 0.25.

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

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 80 arm-level results and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 414 significant findings detected.


		Molecular subtypes	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	Chi-square test	Fisher's exact test	Chi-square test	Chi-square test	Fisher's exact test	Fisher's exact test	Chi-square test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
2p gain	0 (0%)	887	4.41e-08 (3.53e-05)	2.44e-10 (2.09e-07)	3.47e-11 (3.02e-08)	0.000334 (0.188)	4.99e-08 (3.98e-05)	1.03e-07 (8.13e-05)	8.08e-10 (6.8e-07)	1.05e-12 (9.31e-10)	6.83e-10 (5.75e-07)	2.58e-07 (0.000201)	1.78e-07 (0.000139)	2.92e-05 (0.0192)
10p gain	0 (0%)	822	1.39e-10 (1.19e-07)	8.01e-08 (6.35e-05)	6.71e-17 (6.21e-14)	7.67e-14 (6.92e-11)	2.39e-05 (0.016)	1.42e-06 (0.00105)	1.17e-19 (1.1e-16)	8.93e-15 (8.18e-12)	2.44e-12 (2.16e-09)	2.15e-14 (1.95e-11)	1.57e-10 (1.35e-07)	2.41e-12 (2.13e-09)
4p loss	0 (0%)	742	1.23e-12 (1.09e-09)	1.03e-11 (9.01e-09)	8.07e-29 (7.69e-26)	4.83e-16 (4.46e-13)	9.69e-05 (0.0598)	5.38e-06 (0.00381)	6.59e-19 (6.15e-16)	2.98e-18 (2.77e-15)	1.44e-14 (1.31e-11)	3.12e-15 (2.86e-12)	7.39e-12 (6.48e-09)	3.85e-08 (3.08e-05)
5p loss	0 (0%)	862	1e-08 (8.2e-06)	5.35e-06 (0.0038)	1.98e-18 (1.84e-15)	3.38e-13 (3.03e-10)	0.000104 (0.0633)	2.63e-06 (0.00191)	3.09e-15 (2.84e-12)	1.87e-09 (1.56e-06)	2.97e-14 (2.69e-11)	1.14e-15 (1.04e-12)	3.22e-13 (2.89e-10)	7.02e-14 (6.34e-11)
5q loss	0 (0%)	805	9.89e-19 (9.23e-16)	1.24e-14 (1.13e-11)	7.45e-47 (7.15e-44)	5.59e-36 (5.36e-33)	1.51e-08 (1.24e-05)	6.07e-11 (5.25e-08)	6.02e-35 (5.77e-32)	2.84e-25 (2.7e-22)	1.06e-27 (1.01e-24)	9.11e-33 (8.72e-30)	2.91e-24 (2.75e-21)	1.3e-25 (1.24e-22)
14q loss	0 (0%)	794	8.47e-11 (7.29e-08)	1.1e-08 (8.95e-06)	3.9e-24 (3.69e-21)	8.47e-16 (7.8e-13)	0.000185 (0.109)	8.52e-05 (0.0532)	5.87e-21 (5.53e-18)	4.9e-13 (4.38e-10)	5.57e-13 (4.97e-10)	1.18e-13 (1.07e-10)	5.5e-10 (4.64e-07)	4.79e-08 (3.82e-05)
16q loss	0 (0%)	531	3.67e-08 (2.95e-05)	6.5e-14 (5.87e-11)	6.67e-12 (5.86e-09)	1.16e-17 (1.08e-14)	4.59e-06 (0.00327)	8.65e-10 (7.26e-07)	1.35e-21 (1.28e-18)	9.06e-24 (8.56e-21)	1.26e-15 (1.16e-12)	5.33e-19 (4.99e-16)	1.32e-14 (1.2e-11)	1.45e-10 (1.25e-07)
6p gain	0 (0%)	825	0.00017 (0.101)	0.000252 (0.145)	1.99e-17 (1.84e-14)	4.71e-11 (4.08e-08)	0.00459 (1.00)	0.0486 (1.00)	3.07e-10 (2.61e-07)	2.56e-09 (2.12e-06)	1.86e-09 (1.55e-06)	1.9e-09 (1.58e-06)	2.59e-11 (2.26e-08)	2.37e-09 (1.97e-06)
8q gain	0 (0%)	549	0.000127 (0.0772)	0.000364 (0.203)	3.26e-25 (3.1e-22)	5.69e-11 (4.92e-08)	0.797 (1.00)	0.742 (1.00)	2.79e-11 (2.43e-08)	2.64e-09 (2.18e-06)	1.55e-09 (1.3e-06)	3.65e-06 (0.00262)	2.11e-06 (0.00155)	4.11e-06 (0.00294)
21q gain	0 (0%)	829	3.09e-05 (0.0202)	0.000302 (0.172)	3.34e-10 (2.84e-07)	3.4e-08 (2.74e-05)	0.0684 (1.00)	0.00554 (1.00)	3.06e-10 (2.61e-07)	8.35e-11 (7.19e-08)	3.95e-05 (0.0255)	3.66e-07 (0.000281)	4.19e-08 (3.36e-05)	4.73e-07 (0.000362)
4q loss	0 (0%)	774	1.65e-06 (0.00122)	5.26e-07 (0.000402)	7.93e-21 (7.46e-18)	6.71e-11 (5.79e-08)	0.0256 (1.00)	0.0029 (1.00)	5.65e-12 (4.96e-09)	3.7e-13 (3.31e-10)	1.31e-07 (0.000103)	2.76e-10 (2.36e-07)	5.32e-08 (4.24e-05)	9.91e-06 (0.0069)
9p loss	0 (0%)	741	1.8e-05 (0.0122)	2.89e-05 (0.019)	1.39e-20 (1.3e-17)	1.21e-14 (1.1e-11)	0.0381 (1.00)	0.858 (1.00)	5.1e-11 (4.42e-08)	5.47e-07 (0.000417)	2.64e-05 (0.0175)	3.08e-07 (0.000238)	0.000129 (0.078)	1.11e-06 (0.000832)
17q loss	0 (0%)	787	1.99e-11 (1.74e-08)	2.63e-06 (0.00191)	2.21e-11 (1.93e-08)	1.25e-05 (0.00859)	1.1e-09 (9.21e-07)	3.1e-07 (0.00024)	1.41e-13 (1.27e-10)	1.01e-07 (8e-05)	5.26e-07 (0.000402)	1.59e-05 (0.0109)	0.000925 (0.474)	0.00782 (1.00)
22q loss	0 (0%)	622	0.000201 (0.118)	2.12e-07 (0.000165)	3.51e-09 (2.89e-06)	3.36e-06 (0.00242)	0.000476 (0.258)	1.64e-05 (0.0112)	2.91e-06 (0.00211)	2.79e-12 (2.47e-09)	1.57e-08 (1.28e-05)	0.000171 (0.102)	3.57e-07 (0.000275)	0.00468 (1.00)
1p gain	0 (0%)	834	5.35e-05 (0.0341)	2.34e-06 (0.0017)	6.29e-09 (5.17e-06)	0.0459 (1.00)	4.26e-05 (0.0275)	0.000247 (0.143)	1.62e-07 (0.000127)	8.22e-06 (0.00576)	4.96e-05 (0.0319)	2.94e-05 (0.0193)	0.0074 (1.00)	0.00217 (1.00)
6q gain	0 (0%)	867	0.0026 (1.00)	0.0137 (1.00)	2.7e-18 (2.51e-15)	0.0004 (0.222)	0.000273 (0.156)	0.0242 (1.00)	5.97e-06 (0.00422)	1.29e-06 (0.000956)	2.12e-05 (0.0142)	7.66e-07 (0.00058)	1.29e-06 (0.000957)	9.94e-05 (0.0611)
9q loss	0 (0%)	783	0.00506 (1.00)	1.5e-05 (0.0103)	1.36e-17 (1.27e-14)	4.42e-11 (3.84e-08)	0.00849 (1.00)	0.127 (1.00)	1.07e-08 (8.75e-06)	3.25e-07 (0.000251)	1.72e-05 (0.0117)	3.8e-10 (3.22e-07)	7.03e-06 (0.00495)	2.97e-12 (2.62e-09)
12q loss	0 (0%)	879	0.000874 (0.451)	0.000409 (0.226)	7.14e-05 (0.0449)	1.52e-08 (1.24e-05)	0.00486 (1.00)	0.00265 (1.00)	1.98e-09 (1.64e-06)	1.11e-07 (8.75e-05)	3.21e-06 (0.00231)	1.34e-06 (0.000994)	0.0001 (0.0613)	8.54e-05 (0.0532)
15q loss	0 (0%)	766	0.00499 (1.00)	0.000102 (0.0623)	6.25e-20 (5.85e-17)	2.99e-08 (2.41e-05)	0.117 (1.00)	0.00548 (1.00)	1.74e-05 (0.0118)	3.65e-05 (0.0236)	0.000121 (0.0734)	9.37e-07 (0.000706)	1.17e-06 (0.000879)	0.000319 (0.18)
3q gain	0 (0%)	830	0.0147 (1.00)	0.00507 (1.00)	8.14e-10 (6.84e-07)	5.61e-05 (0.0356)	0.0149 (1.00)	0.11 (1.00)	9.49e-06 (0.00661)	5.16e-05 (0.033)	4.79e-06 (0.00341)	2.53e-06 (0.00184)	8.25e-05 (0.0515)	0.00035 (0.197)
9p gain	0 (0%)	865	2.34e-08 (1.89e-05)	1.85e-08 (1.5e-05)	5.29e-10 (4.47e-07)	0.00164 (0.792)	0.00881 (1.00)	0.000106 (0.0649)	4.31e-10 (3.65e-07)	3.45e-08 (2.77e-05)	1.11e-06 (0.00083)	1.44e-07 (0.000113)	0.00117 (0.588)	0.0089 (1.00)
16p gain	0 (0%)	675	1.65e-06 (0.00122)	0.000291 (0.166)	0.0106 (1.00)	1.71e-06 (0.00126)	5.23e-05 (0.0334)	6.05e-05 (0.0382)	6.28e-07 (0.000477)	3.16e-06 (0.00228)	0.00364 (1.00)	0.0227 (1.00)	8.17e-05 (0.0512)	0.00527 (1.00)
20p loss	0 (0%)	878	0.0446 (1.00)	0.097 (1.00)	1.93e-07 (0.00015)	8.96e-05 (0.0555)	0.362 (1.00)	0.43 (1.00)	0.000398 (0.221)	0.000226 (0.131)	0.000176 (0.105)	0.000223 (0.13)	0.000181 (0.107)	5.24e-05 (0.0334)
18p gain	0 (0%)	846	0.00139 (0.682)	0.000213 (0.125)	1.27e-06 (0.000946)	6.18e-07 (0.000471)	0.00823 (1.00)	0.00735 (1.00)	2.01e-07 (0.000156)	1.99e-09 (1.65e-06)	7.88e-06 (0.00553)	5.01e-05 (0.0321)	0.00378 (1.00)	0.00241 (1.00)
6q loss	0 (0%)	762	5.75e-05 (0.0364)	1.24e-06 (0.000923)	5.44e-16 (5.01e-13)	1.64e-07 (0.000129)	0.00055 (0.296)	0.0052 (1.00)	3.18e-08 (2.57e-05)	9.18e-07 (0.000693)	0.00587 (1.00)	3.61e-06 (0.00259)	0.00887 (1.00)	0.00144 (0.709)
11q loss	0 (0%)	698	7.42e-06 (0.00521)	0.000266 (0.153)	2.34e-32 (2.24e-29)	2.29e-12 (2.03e-09)	0.275 (1.00)	0.318 (1.00)	9.63e-13 (8.57e-10)	1.82e-05 (0.0123)	0.00307 (1.00)	1.09e-05 (0.00759)	0.0062 (1.00)	0.00972 (1.00)
12p gain	0 (0%)	815	0.0044 (1.00)	0.00154 (0.748)	1.69e-14 (1.53e-11)	2.66e-06 (0.00193)	0.246 (1.00)	0.0679 (1.00)	1.44e-05 (0.0099)	2.63e-05 (0.0175)	0.000457 (0.25)	0.00187 (0.885)	0.000154 (0.0925)	0.0762 (1.00)
20q gain	0 (0%)	651	1.88e-05 (0.0127)	0.0486 (1.00)	3.63e-32 (3.46e-29)	2.73e-11 (2.38e-08)	0.199 (1.00)	0.792 (1.00)	2.35e-10 (2.01e-07)	2.78e-05 (0.0184)	4.27e-06 (0.00305)	0.0109 (1.00)	0.00195 (0.913)	0.0715 (1.00)
22q gain	0 (0%)	891	0.0731 (1.00)	0.00146 (0.712)	1.93e-07 (0.000151)	0.00065 (0.345)	0.0685 (1.00)	0.153 (1.00)	3.31e-05 (0.0215)	7.86e-09 (6.45e-06)	0.00134 (0.663)	1.03e-06 (0.000776)	1.92e-05 (0.013)	2.97e-05 (0.0195)
Xq gain	0 (0%)	912	0.000854 (0.442)	0.000161 (0.0967)	1.21e-05 (0.00834)	0.029 (1.00)	0.0754 (1.00)	0.00725 (1.00)	0.000158 (0.0947)	0.000363 (0.203)	4.83e-05 (0.0311)	0.000182 (0.108)	0.0353 (1.00)	0.0232 (1.00)
2p loss	0 (0%)	859	0.0284 (1.00)	9.96e-05 (0.0611)	5.88e-13 (5.25e-10)	1.91e-05 (0.0129)	0.0652 (1.00)	0.00748 (1.00)	0.000387 (0.216)	4.48e-10 (3.79e-07)	0.000438 (0.242)	0.0013 (0.646)	0.0668 (1.00)	0.0274 (1.00)
3p loss	0 (0%)	843	0.00109 (0.55)	0.0016 (0.775)	2.77e-08 (2.24e-05)	0.000494 (0.267)	0.00716 (1.00)	8.6e-05 (0.0535)	6.46e-05 (0.0406)	0.000234 (0.136)	5.88e-06 (0.00416)	0.00085 (0.441)	0.000296 (0.169)	0.0145 (1.00)
13q loss	0 (0%)	660	0.000435 (0.24)	0.00124 (0.621)	8.5e-28 (8.1e-25)	1.7e-09 (1.42e-06)	0.727 (1.00)	0.489 (1.00)	4.31e-05 (0.0278)	2.88e-07 (0.000223)	2.49e-08 (2.01e-05)	0.00278 (1.00)	0.00414 (1.00)	0.0379 (1.00)
16p loss	0 (0%)	876	0.00435 (1.00)	0.0125 (1.00)	1.22e-05 (0.00842)	7.44e-05 (0.0466)	0.0811 (1.00)	0.164 (1.00)	9.88e-05 (0.0609)	0.000125 (0.0759)	0.00044 (0.242)	0.000305 (0.173)	0.00165 (0.796)	0.00131 (0.651)
19p loss	0 (0%)	865	0.00022 (0.129)	0.000355 (0.199)	2.33e-14 (2.11e-11)	8.91e-10 (7.47e-07)	0.424 (1.00)	0.0741 (1.00)	3.44e-07 (0.000265)	0.000252 (0.145)	0.000883 (0.455)	0.000788 (0.411)	0.034 (1.00)	0.0628 (1.00)
19q loss	0 (0%)	881	0.000443 (0.243)	6.38e-05 (0.0402)	2.78e-10 (2.37e-07)	1.27e-05 (0.00872)	0.101 (1.00)	0.0767 (1.00)	2.49e-05 (0.0166)	2.5e-05 (0.0167)	0.00554 (1.00)	0.00046 (0.251)	0.0278 (1.00)	0.0207 (1.00)
20q loss	0 (0%)	904	0.0489 (1.00)	0.167 (1.00)	0.000197 (0.116)	1e-05 (0.00697)	0.496 (1.00)	0.172 (1.00)	0.000608 (0.323)	0.0019 (0.898)	0.000443 (0.243)	3.3e-05 (0.0215)	1.95e-06 (0.00142)	7.92e-07 (0.000599)
4p gain	0 (0%)	904	9.4e-06 (0.00657)	9.59e-05 (0.0594)	1.72e-07 (0.000135)	0.00058 (0.31)	0.0485 (1.00)	0.0396 (1.00)	3.31e-05 (0.0215)	0.00226 (1.00)	0.000222 (0.13)	0.00146 (0.712)	0.00189 (0.895)	0.00165 (0.796)
4q gain	0 (0%)	906	9.4e-06 (0.00657)	9.59e-05 (0.0594)	1.71e-09 (1.42e-06)	0.00153 (0.747)	0.0551 (1.00)	0.0126 (1.00)	6.1e-06 (0.0043)	0.00493 (1.00)	0.00394 (1.00)	0.000218 (0.128)	0.0244 (1.00)	0.0165 (1.00)
17q gain	0 (0%)	809	1.26e-06 (0.000939)	0.00605 (1.00)	3.09e-20 (2.9e-17)	5.81e-06 (0.00412)	0.464 (1.00)	0.00912 (1.00)	4.85e-12 (4.27e-09)	6.88e-07 (0.000521)	0.0126 (1.00)	0.00416 (1.00)	0.165 (1.00)	0.0168 (1.00)
20p gain	0 (0%)	689	2.64e-05 (0.0175)	0.0897 (1.00)	3.97e-25 (3.77e-22)	2.85e-06 (0.00206)	0.0217 (1.00)	0.133 (1.00)	4.63e-06 (0.0033)	0.00101 (0.516)	0.000252 (0.145)	0.499 (1.00)	0.025 (1.00)	0.193 (1.00)
1p loss	0 (0%)	809	0.000703 (0.37)	4.12e-09 (3.39e-06)	2.51e-20 (2.35e-17)	4.27e-07 (0.000327)	0.787 (1.00)	0.329 (1.00)	9.55e-07 (0.000719)	1.43e-14 (1.3e-11)	0.00208 (0.973)	0.000491 (0.266)	0.0535 (1.00)	0.1 (1.00)
6p loss	0 (0%)	824	0.0211 (1.00)	0.000114 (0.0694)	6.45e-10 (5.44e-07)	5.6e-05 (0.0356)	0.0131 (1.00)	0.00604 (1.00)	3.76e-05 (0.0243)	8.87e-06 (0.00621)	0.0268 (1.00)	0.000566 (0.304)	0.0385 (1.00)	0.0672 (1.00)
8p loss	0 (0%)	656	0.000309 (0.175)	0.111 (1.00)	2.11e-16 (1.95e-13)	6.53e-07 (0.000496)	0.509 (1.00)	0.782 (1.00)	2.7e-07 (0.000209)	0.00313 (1.00)	0.00609 (1.00)	0.00496 (1.00)	3.3e-05 (0.0215)	0.0403 (1.00)
10q loss	0 (0%)	817	0.000163 (0.0976)	0.00104 (0.526)	6.04e-13 (5.38e-10)	3.67e-06 (0.00263)	0.00524 (1.00)	0.112 (1.00)	3.82e-07 (0.000294)	0.000313 (0.177)	0.00792 (1.00)	0.00126 (0.629)	0.0032 (1.00)	0.00069 (0.364)
11p loss	0 (0%)	786	0.0386 (1.00)	0.106 (1.00)	1.25e-14 (1.14e-11)	8.73e-08 (6.92e-05)	0.0464 (1.00)	0.00543 (1.00)	0.000128 (0.0774)	0.00053 (0.286)	0.00259 (1.00)	2.02e-05 (0.0136)	0.000234 (0.136)	0.00128 (0.64)
2q gain	0 (0%)	911	0.0194 (1.00)	0.000267 (0.153)	2.82e-05 (0.0186)	0.0155 (1.00)	4.89e-07 (0.000374)	0.000991 (0.505)	0.000601 (0.32)	1.2e-05 (0.00827)	0.00426 (1.00)	0.006 (1.00)	0.00702 (1.00)	0.00919 (1.00)
14q gain	0 (0%)	856	0.000912 (0.469)	0.00194 (0.91)	0.000164 (0.0978)	0.00851 (1.00)	0.949 (1.00)	0.316 (1.00)	5.79e-05 (0.0366)	1.19e-06 (0.000888)	5.08e-05 (0.0325)	0.279 (1.00)	0.368 (1.00)	0.945 (1.00)
2q loss	0 (0%)	843	0.209 (1.00)	0.00163 (0.788)	1.21e-12 (1.08e-09)	3.05e-05 (0.02)	0.0948 (1.00)	0.0429 (1.00)	0.0076 (1.00)	1.26e-07 (9.91e-05)	0.000733 (0.385)	0.000365 (0.203)	0.0568 (1.00)	0.0272 (1.00)
17p loss	0 (0%)	553	1.75e-06 (0.00128)	0.695 (1.00)	3.64e-13 (3.26e-10)	3.39e-09 (2.79e-06)	0.00194 (0.91)	0.0939 (1.00)	1.58e-06 (0.00116)	0.533 (1.00)	0.0261 (1.00)	0.078 (1.00)	0.0145 (1.00)	0.521 (1.00)
18p loss	0 (0%)	753	0.000176 (0.104)	0.431 (1.00)	1.99e-08 (1.61e-05)	1.49e-06 (0.0011)	0.892 (1.00)	0.962 (1.00)	2.01e-10 (1.73e-07)	0.0972 (1.00)	0.0262 (1.00)	0.0095 (1.00)	0.00688 (1.00)	0.061 (1.00)
1q gain	0 (0%)	434	0.000569 (0.305)	0.597 (1.00)	4.05e-10 (3.43e-07)	3.52e-12 (3.1e-09)	0.0678 (1.00)	0.125 (1.00)	5.11e-08 (4.08e-05)	0.00813 (1.00)	0.0392 (1.00)	0.0148 (1.00)	0.0735 (1.00)	0.00211 (0.981)
5q gain	0 (0%)	821	0.0141 (1.00)	0.00547 (1.00)	3.31e-22 (3.12e-19)	0.0153 (1.00)	0.00469 (1.00)	0.00449 (1.00)	0.00145 (0.709)	0.000128 (0.0776)	0.000147 (0.0882)	0.00135 (0.665)	0.000806 (0.419)	0.00607 (1.00)
8p gain	0 (0%)	758	0.0144 (1.00)	0.0244 (1.00)	2.15e-13 (1.93e-10)	8.85e-05 (0.055)	0.139 (1.00)	0.365 (1.00)	0.00169 (0.812)	6.71e-08 (5.33e-05)	0.00289 (1.00)	0.204 (1.00)	0.00761 (1.00)	0.0523 (1.00)
18q gain	0 (0%)	857	0.00105 (0.528)	0.00569 (1.00)	2.62e-05 (0.0175)	0.0297 (1.00)	0.311 (1.00)	0.274 (1.00)	1.29e-05 (0.00888)	5.57e-08 (4.42e-05)	0.00103 (0.522)	0.00782 (1.00)	0.0132 (1.00)	0.00796 (1.00)
18q loss	0 (0%)	750	0.000762 (0.399)	0.42 (1.00)	5.82e-11 (5.04e-08)	7.63e-09 (6.27e-06)	0.535 (1.00)	0.828 (1.00)	1.93e-08 (1.57e-05)	0.0118 (1.00)	0.0377 (1.00)	0.0618 (1.00)	0.0105 (1.00)	0.483 (1.00)
10q gain	0 (0%)	886	0.0133 (1.00)	0.0451 (1.00)	0.000274 (0.157)	0.0433 (1.00)	0.0394 (1.00)	0.0288 (1.00)	0.000354 (0.199)	0.0146 (1.00)	0.00481 (1.00)	0.0284 (1.00)	0.0915 (1.00)	0.176 (1.00)
12q gain	0 (0%)	845	0.0224 (1.00)	0.0149 (1.00)	3.61e-17 (3.34e-14)	9.97e-06 (0.00693)	0.275 (1.00)	0.4 (1.00)	0.00762 (1.00)	0.00117 (0.586)	0.0379 (1.00)	0.191 (1.00)	0.0293 (1.00)	0.34 (1.00)
3p gain	0 (0%)	873	0.273 (1.00)	0.16 (1.00)	1.83e-06 (0.00134)	0.232 (1.00)	0.23 (1.00)	0.113 (1.00)	0.0754 (1.00)	0.0354 (1.00)	0.101 (1.00)	0.0155 (1.00)	0.0331 (1.00)	0.0587 (1.00)
5p gain	0 (0%)	757	0.368 (1.00)	0.367 (1.00)	1.04e-14 (9.56e-12)	0.0546 (1.00)	0.692 (1.00)	0.486 (1.00)	0.381 (1.00)	0.288 (1.00)	0.187 (1.00)	0.903 (1.00)	0.116 (1.00)	0.996 (1.00)
9q gain	0 (0%)	877	0.533 (1.00)	0.0755 (1.00)	2.25e-06 (0.00164)	0.132 (1.00)	1 (1.00)	0.488 (1.00)	0.178 (1.00)	0.0089 (1.00)	0.0115 (1.00)	0.0346 (1.00)	0.0464 (1.00)	0.825 (1.00)
17p gain	0 (0%)	887	0.013 (1.00)	0.371 (1.00)	0.000406 (0.225)	0.825 (1.00)	0.18 (1.00)	0.2 (1.00)	0.0933 (1.00)	0.585 (1.00)	0.89 (1.00)	0.842 (1.00)	0.833 (1.00)	0.671 (1.00)
19p gain	0 (0%)	864	0.12 (1.00)	0.0329 (1.00)	2.85e-05 (0.0188)	0.0734 (1.00)	0.0302 (1.00)	0.0902 (1.00)	0.0238 (1.00)	0.00179 (0.853)	0.00246 (1.00)	0.000742 (0.389)	0.00185 (0.878)	0.0876 (1.00)
19q gain	0 (0%)	844	0.172 (1.00)	0.051 (1.00)	2.46e-05 (0.0165)	0.0504 (1.00)	0.127 (1.00)	0.209 (1.00)	0.107 (1.00)	0.015 (1.00)	0.00609 (1.00)	0.0119 (1.00)	0.0158 (1.00)	0.134 (1.00)
7p loss	0 (0%)	884	0.0804 (1.00)	0.00191 (0.9)	4.63e-06 (0.0033)	0.00228 (1.00)	0.371 (1.00)	0.438 (1.00)	0.000952 (0.486)	0.000673 (0.357)	0.000581 (0.31)	0.000559 (0.301)	0.0276 (1.00)	0.0104 (1.00)
7q loss	0 (0%)	870	0.59 (1.00)	0.0815 (1.00)	0.000927 (0.475)	0.226 (1.00)	0.236 (1.00)	0.421 (1.00)	0.375 (1.00)	0.0669 (1.00)	0.00491 (1.00)	2.08e-05 (0.0139)	0.304 (1.00)	0.39 (1.00)
10p loss	0 (0%)	853	0.0122 (1.00)	0.005 (1.00)	1.41e-05 (0.00965)	0.0236 (1.00)	0.716 (1.00)	0.46 (1.00)	0.00315 (1.00)	0.00988 (1.00)	0.0912 (1.00)	0.0987 (1.00)	0.131 (1.00)	0.0389 (1.00)
12p loss	0 (0%)	865	0.319 (1.00)	0.2 (1.00)	0.0156 (1.00)	1.69e-05 (0.0115)	0.149 (1.00)	0.274 (1.00)	0.00371 (1.00)	0.00174 (0.832)	0.000791 (0.412)	0.000682 (0.361)	0.0189 (1.00)	0.012 (1.00)
21q loss	0 (0%)	846	0.0153 (1.00)	0.197 (1.00)	1.02e-06 (0.000768)	0.264 (1.00)	1 (1.00)	0.812 (1.00)	0.322 (1.00)	0.224 (1.00)	0.0366 (1.00)	0.291 (1.00)	0.204 (1.00)	0.0806 (1.00)
Xq loss	0 (0%)	903	0.317 (1.00)	0.169 (1.00)	3.47e-05 (0.0225)	0.000716 (0.377)	0.0326 (1.00)	0.316 (1.00)	0.0354 (1.00)	0.0141 (1.00)	0.00396 (1.00)	0.000461 (0.251)	0.00209 (0.976)	0.00104 (0.526)
7p gain	0 (0%)	771	0.234 (1.00)	0.402 (1.00)	0.0437 (1.00)	0.0268 (1.00)	0.947 (1.00)	0.52 (1.00)	0.24 (1.00)	0.0325 (1.00)	0.51 (1.00)	0.469 (1.00)	0.401 (1.00)	0.509 (1.00)
7q gain	0 (0%)	810	0.00939 (1.00)	0.00904 (1.00)	0.0133 (1.00)	0.00133 (0.658)	0.522 (1.00)	0.323 (1.00)	0.00696 (1.00)	0.000461 (0.251)	0.0691 (1.00)	0.0254 (1.00)	0.0858 (1.00)	0.184 (1.00)
11p gain	0 (0%)	866	0.89 (1.00)	0.583 (1.00)	0.00495 (1.00)	0.0803 (1.00)	0.318 (1.00)	0.155 (1.00)	0.0823 (1.00)	0.49 (1.00)	0.0487 (1.00)	0.124 (1.00)	0.0946 (1.00)	0.0282 (1.00)
11q gain	0 (0%)	887	0.361 (1.00)	0.787 (1.00)	0.0018 (0.857)	0.355 (1.00)	0.909 (1.00)	0.745 (1.00)	0.291 (1.00)	0.276 (1.00)	0.114 (1.00)	0.0646 (1.00)	0.192 (1.00)	0.0429 (1.00)
13q gain	0 (0%)	886	0.519 (1.00)	0.345 (1.00)	0.0213 (1.00)	0.0831 (1.00)	0.0642 (1.00)	0.258 (1.00)	0.0155 (1.00)	0.0013 (0.646)	0.0529 (1.00)	0.0245 (1.00)	0.197 (1.00)	0.045 (1.00)
15q gain	0 (0%)	887	0.711 (1.00)	0.462 (1.00)	0.574 (1.00)	0.093 (1.00)	0.817 (1.00)	0.561 (1.00)	0.606 (1.00)	0.183 (1.00)	0.391 (1.00)	0.428 (1.00)	0.145 (1.00)	0.567 (1.00)
16q gain	0 (0%)	876	0.584 (1.00)	0.48 (1.00)	0.0136 (1.00)	0.0835 (1.00)	0.333 (1.00)	0.969 (1.00)	0.133 (1.00)	0.124 (1.00)	0.0112 (1.00)	0.000855 (0.442)	0.0041 (1.00)	0.00807 (1.00)
1q loss	0 (0%)	911	0.489 (1.00)	0.0813 (1.00)	0.0067 (1.00)	0.122 (1.00)	0.272 (1.00)	0.739 (1.00)	0.169 (1.00)	0.00166 (0.796)	0.185 (1.00)	0.15 (1.00)	0.281 (1.00)	0.262 (1.00)
3q loss	0 (0%)	889	0.0298 (1.00)	0.0175 (1.00)	0.00215 (0.995)	0.091 (1.00)	0.263 (1.00)	0.126 (1.00)	0.00587 (1.00)	0.00992 (1.00)	0.00255 (1.00)	0.0338 (1.00)	0.272 (1.00)	0.532 (1.00)
8q loss	0 (0%)	887	0.256 (1.00)	0.359 (1.00)	0.102 (1.00)	0.0546 (1.00)	0.688 (1.00)	0.566 (1.00)	0.372 (1.00)	0.347 (1.00)	0.316 (1.00)	0.398 (1.00)	0.121 (1.00)	0.572 (1.00)

'1p gain' versus 'MRNA_CNMF'

P value = 5.35e-05 (Chi-square test), Q value = 0.034

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
1P GAIN CNV	1	2	12	27	5	10	4	5
1P GAIN WILD-TYPE	20	34	107	69	104	62	16	35

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

'1p gain' versus 'MRNA_CHIERARCHICAL'

P value = 2.34e-06 (Fisher's exact test), Q value = 0.0017

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
1P GAIN CNV	14	33	19
1P GAIN WILD-TYPE	108	92	247

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

'1p gain' versus 'CN_CNMF'

P value = 6.29e-09 (Chi-square test), Q value = 5.2e-06

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	356	212	71	241	54
1P GAIN CNV	21	16	5	53	5
1P GAIN WILD-TYPE	335	196	66	188	49

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

'1p gain' versus 'RPPA_CNMF'

P value = 4.26e-05 (Fisher's exact test), Q value = 0.027

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
1P GAIN CNV	34	13	6
1P GAIN WILD-TYPE	113	120	111

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

'1p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.000247 (Fisher's exact test), Q value = 0.14

Table S5. Gene #1: '1p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	110	126
1P GAIN CNV	20	5	28
1P GAIN WILD-TYPE	141	105	98

Figure S5. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'1p gain' versus 'MRNASEQ_CNMF'

P value = 1.62e-07 (Chi-square test), Q value = 0.00013

Table S6. Gene #1: '1p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	158	81	228	146	217	53	16
1P GAIN CNV	38	5	18	13	16	1	3
1P GAIN WILD-TYPE	120	76	210	133	201	52	13

Figure S6. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.22e-06 (Fisher's exact test), Q value = 0.0058

Table S7. Gene #1: '1p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	215	458
1P GAIN CNV	44	15	35
1P GAIN WILD-TYPE	182	200	423

Figure S7. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p gain' versus 'MIRSEQ_CNMF'

P value = 4.96e-05 (Fisher's exact test), Q value = 0.032

Table S8. Gene #1: '1p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
1P GAIN CNV	17	28	45
1P GAIN WILD-TYPE	217	364	210

Figure S8. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.94e-05 (Fisher's exact test), Q value = 0.019

Table S9. Gene #1: '1p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
1P GAIN CNV	28	19	43
1P GAIN WILD-TYPE	334	265	192

Figure S9. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1q gain' versus 'CN_CNMF'

P value = 4.05e-10 (Chi-square test), Q value = 3.4e-07

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	356	212	71	241	54
1Q GAIN CNV	172	121	65	117	25
1Q GAIN WILD-TYPE	184	91	6	124	29

Figure S10. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

'1q gain' versus 'METHLYATION_CNMF'

P value = 3.52e-12 (Chi-square test), Q value = 3.1e-09

Table S11. Gene #2: '1q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	151	99	118	38	96
1Q GAIN CNV	46	113	59	51	15	28
1Q GAIN WILD-TYPE	59	38	40	67	23	68

Figure S11. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1q gain' versus 'MRNASEQ_CNMF'

P value = 5.11e-08 (Chi-square test), Q value = 4.1e-05

Table S12. Gene #2: '1q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	158	81	228	146	217	53	16
1Q GAIN CNV	79	37	164	75	93	27	7
1Q GAIN WILD-TYPE	79	44	64	71	124	26	9

Figure S12. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2p gain' versus 'MRNA_CNMF'

P value = 4.41e-08 (Chi-square test), Q value = 3.5e-05

Table S13. Gene #3: '2p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
2P GAIN CNV	0	0	3	17	1	11	0	0
2P GAIN WILD-TYPE	21	36	116	79	108	61	20	40

Figure S13. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'2p gain' versus 'MRNA_CHIERARCHICAL'

P value = 2.44e-10 (Fisher's exact test), Q value = 2.1e-07

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
2P GAIN CNV	0	24	8
2P GAIN WILD-TYPE	122	101	258

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

'2p gain' versus 'CN_CNMF'

P value = 3.47e-11 (Chi-square test), Q value = 3e-08

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	356	212	71	241	54
2P GAIN CNV	2	9	2	33	1
2P GAIN WILD-TYPE	354	203	69	208	53

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

'2p gain' versus 'METHLYATION_CNMF'

P value = 0.000334 (Chi-square test), Q value = 0.19

Table S16. Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	151	99	118	38	96
2P GAIN CNV	13	1	4	5	1	2
2P GAIN WILD-TYPE	92	150	95	113	37	94

Figure S16. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2p gain' versus 'RPPA_CNMF'

P value = 4.99e-08 (Fisher's exact test), Q value = 4e-05

Table S17. Gene #3: '2p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
2P GAIN CNV	23	0	4
2P GAIN WILD-TYPE	124	133	113

Figure S17. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'2p gain' versus 'RPPA_CHIERARCHICAL'

P value = 1.03e-07 (Fisher's exact test), Q value = 8.1e-05

Table S18. Gene #3: '2p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	110	126
2P GAIN CNV	4	1	22
2P GAIN WILD-TYPE	157	109	104

Figure S18. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'2p gain' versus 'MRNASEQ_CNMF'

P value = 8.08e-10 (Chi-square test), Q value = 6.8e-07

Table S19. Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	158	81	228	146	217	53	16
2P GAIN CNV	21	0	2	17	5	0	1
2P GAIN WILD-TYPE	137	81	226	129	212	53	15

Figure S19. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.05e-12 (Fisher's exact test), Q value = 9.3e-10

Table S20. Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	215	458
2P GAIN CNV	33	0	13
2P GAIN WILD-TYPE	193	215	445

Figure S20. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_CNMF'

P value = 6.83e-10 (Fisher's exact test), Q value = 5.8e-07

Table S21. Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
2P GAIN CNV	1	9	30
2P GAIN WILD-TYPE	233	383	225

Figure S21. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.58e-07 (Fisher's exact test), Q value = 2e-04

Table S22. Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
2P GAIN CNV	11	3	26
2P GAIN WILD-TYPE	351	281	209

Figure S22. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.78e-07 (Fisher's exact test), Q value = 0.00014

Table S23. Gene #3: '2p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	213	179	178
2P GAIN CNV	3	1	20
2P GAIN WILD-TYPE	210	178	158

Figure S23. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'2p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.92e-05 (Fisher's exact test), Q value = 0.019

Table S24. Gene #3: '2p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	122	142	185
2P GAIN CNV	4	6	14	0
2P GAIN WILD-TYPE	117	116	128	185

Figure S24. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.000267 (Fisher's exact test), Q value = 0.15

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
2Q GAIN CNV	0	11	6
2Q GAIN WILD-TYPE	122	114	260

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

'2q gain' versus 'CN_CNMF'

P value = 2.82e-05 (Chi-square test), Q value = 0.019

Table S26. Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	356	212	71	241	54
2Q GAIN CNV	1	4	2	16	0
2Q GAIN WILD-TYPE	355	208	69	225	54

Figure S26. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

'2q gain' versus 'RPPA_CNMF'

P value = 4.89e-07 (Fisher's exact test), Q value = 0.00037

Table S27. Gene #4: '2q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
2Q GAIN CNV	15	0	0
2Q GAIN WILD-TYPE	132	133	117

Figure S27. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'2q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.2e-05 (Fisher's exact test), Q value = 0.0083

Table S28. Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	215	458
2Q GAIN CNV	15	0	7
2Q GAIN WILD-TYPE	211	215	451

Figure S28. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3p gain' versus 'CN_CNMF'

P value = 1.83e-06 (Chi-square test), Q value = 0.0013

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	356	212	71	241	54
3P GAIN CNV	5	21	10	17	8
3P GAIN WILD-TYPE	351	191	61	224	46

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

'3q gain' versus 'CN_CNMF'

P value = 8.14e-10 (Chi-square test), Q value = 6.8e-07

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	356	212	71	241	54
3Q GAIN CNV	9	27	12	47	9
3Q GAIN WILD-TYPE	347	185	59	194	45

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

'3q gain' versus 'METHLYATION_CNMF'

P value = 5.61e-05 (Chi-square test), Q value = 0.036

Table S31. Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	151	99	118	38	96
3Q GAIN CNV	19	4	12	12	2	2
3Q GAIN WILD-TYPE	86	147	87	106	36	94

Figure S31. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3q gain' versus 'MRNASEQ_CNMF'

P value = 9.49e-06 (Chi-square test), Q value = 0.0066

Table S32. Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	158	81	228	146	217	53	16
3Q GAIN CNV	33	1	18	21	22	1	3
3Q GAIN WILD-TYPE	125	80	210	125	195	52	13

Figure S32. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.16e-05 (Fisher's exact test), Q value = 0.033

Table S33. Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	215	458
3Q GAIN CNV	40	10	49
3Q GAIN WILD-TYPE	186	205	409

Figure S33. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_CNMF'

P value = 4.79e-06 (Fisher's exact test), Q value = 0.0034

Table S34. Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
3Q GAIN CNV	11	38	47
3Q GAIN WILD-TYPE	223	354	208

Figure S34. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.53e-06 (Fisher's exact test), Q value = 0.0018

Table S35. Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
3Q GAIN CNV	40	13	43
3Q GAIN WILD-TYPE	322	271	192

Figure S35. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 8.25e-05 (Fisher's exact test), Q value = 0.052

Table S36. Gene #6: '3q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	213	179	178
3Q GAIN CNV	18	7	31
3Q GAIN WILD-TYPE	195	172	147

Figure S36. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'3q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00035 (Fisher's exact test), Q value = 0.2

Table S37. Gene #6: '3q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	122	142	185
3Q GAIN CNV	7	14	26	9
3Q GAIN WILD-TYPE	114	108	116	176

Figure S37. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p gain' versus 'MRNA_CNMF'

P value = 9.4e-06 (Chi-square test), Q value = 0.0066

Table S38. Gene #7: '4p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
4P GAIN CNV	0	0	14	0	2	1	0	0
4P GAIN WILD-TYPE	21	36	105	96	107	71	20	40

Figure S38. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'4p gain' versus 'MRNA_CHIERARCHICAL'

P value = 9.59e-05 (Fisher's exact test), Q value = 0.059

Table S39. Gene #7: '4p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
4P GAIN CNV	0	0	17
4P GAIN WILD-TYPE	122	125	249

Figure S39. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'4p gain' versus 'CN_CNMF'

P value = 1.72e-07 (Chi-square test), Q value = 0.00013

Table S40. Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	356	212	71	241	54
4P GAIN CNV	1	18	2	4	5
4P GAIN WILD-TYPE	355	194	69	237	49

Figure S40. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

'4p gain' versus 'MRNASEQ_CNMF'

P value = 3.31e-05 (Chi-square test), Q value = 0.022

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	158	81	228	146	217	53	16
4P GAIN CNV	0	2	5	3	19	0	0
4P GAIN WILD-TYPE	158	79	223	143	198	53	16

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

'4p gain' versus 'MIRSEQ_CNMF'

P value = 0.000222 (Fisher's exact test), Q value = 0.13

Table S42. Gene #7: '4p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
4P GAIN CNV	3	23	2
4P GAIN WILD-TYPE	231	369	253

Figure S42. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4q gain' versus 'MRNA_CNMF'

P value = 9.4e-06 (Chi-square test), Q value = 0.0066

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
4Q GAIN CNV	0	0	14	0	2	1	0	0
4Q GAIN WILD-TYPE	21	36	105	96	107	71	20	40

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

'4q gain' versus 'MRNA_CHIERARCHICAL'

P value = 9.59e-05 (Fisher's exact test), Q value = 0.059

Table S44. Gene #8: '4q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
4Q GAIN CNV	0	0	17
4Q GAIN WILD-TYPE	122	125	249

Figure S44. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'4q gain' versus 'CN_CNMF'

P value = 1.71e-09 (Chi-square test), Q value = 1.4e-06

Table S45. Gene #8: '4q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	356	212	71	241	54
4Q GAIN CNV	1	19	1	2	5
4Q GAIN WILD-TYPE	355	193	70	239	49

Figure S45. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #3: 'CN_CNMF'

'4q gain' versus 'MRNASEQ_CNMF'

P value = 6.1e-06 (Chi-square test), Q value = 0.0043

Table S46. Gene #8: '4q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	158	81	228	146	217	53	16
4Q GAIN CNV	0	1	4	3	19	0	0
4Q GAIN WILD-TYPE	158	80	224	143	198	53	16

Figure S46. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000218 (Fisher's exact test), Q value = 0.13

Table S47. Gene #8: '4q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
4Q GAIN CNV	21	3	2
4Q GAIN WILD-TYPE	341	281	233

Figure S47. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5p gain' versus 'CN_CNMF'

P value = 1.04e-14 (Chi-square test), Q value = 9.6e-12

Table S48. Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	356	212	71	241	54
5P GAIN CNV	26	62	30	47	12
5P GAIN WILD-TYPE	330	150	41	194	42

Figure S48. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

'5q gain' versus 'CN_CNMF'

P value = 3.31e-22 (Chi-square test), Q value = 3.1e-19

Table S49. Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	356	212	71	241	54
5Q GAIN CNV	19	48	28	8	10
5Q GAIN WILD-TYPE	337	164	43	233	44

Figure S49. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'

'5q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000128 (Fisher's exact test), Q value = 0.078

Table S50. Gene #10: '5q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	215	458
5Q GAIN CNV	12	23	73
5Q GAIN WILD-TYPE	214	192	385

Figure S50. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_CNMF'

P value = 0.000147 (Fisher's exact test), Q value = 0.088

Table S51. Gene #10: '5q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
5Q GAIN CNV	22	65	16
5Q GAIN WILD-TYPE	212	327	239

Figure S51. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6p gain' versus 'MRNA_CNMF'

P value = 0.00017 (Chi-square test), Q value = 0.1

Table S52. Gene #11: '6p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
6P GAIN CNV	0	0	11	20	10	13	5	0
6P GAIN WILD-TYPE	21	36	108	76	99	59	15	40

Figure S52. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'6p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.000252 (Fisher's exact test), Q value = 0.15

Table S53. Gene #11: '6p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
6P GAIN CNV	4	24	31
6P GAIN WILD-TYPE	118	101	235

Figure S53. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6p gain' versus 'CN_CNMF'

P value = 1.99e-17 (Chi-square test), Q value = 1.8e-14

Table S54. Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	356	212	71	241	54
6P GAIN CNV	10	13	15	60	11
6P GAIN WILD-TYPE	346	199	56	181	43

Figure S54. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

'6p gain' versus 'METHLYATION_CNMF'

P value = 4.71e-11 (Chi-square test), Q value = 4.1e-08

Table S55. Gene #11: '6p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	151	99	118	38	96
6P GAIN CNV	33	9	13	12	1	2
6P GAIN WILD-TYPE	72	142	86	106	37	94

Figure S55. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6p gain' versus 'MRNASEQ_CNMF'

P value = 3.07e-10 (Chi-square test), Q value = 2.6e-07

Table S56. Gene #11: '6p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	158	81	228	146	217	53	16
6P GAIN CNV	42	2	19	22	16	1	4
6P GAIN WILD-TYPE	116	79	209	124	201	52	12

Figure S56. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.56e-09 (Fisher's exact test), Q value = 2.1e-06

Table S57. Gene #11: '6p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	215	458
6P GAIN CNV	50	7	49
6P GAIN WILD-TYPE	176	208	409

Figure S57. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_CNMF'

P value = 1.86e-09 (Fisher's exact test), Q value = 1.6e-06

Table S58. Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
6P GAIN CNV	9	33	54
6P GAIN WILD-TYPE	225	359	201

Figure S58. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.9e-09 (Fisher's exact test), Q value = 1.6e-06

Table S59. Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
6P GAIN CNV	35	11	50
6P GAIN WILD-TYPE	327	273	185

Figure S59. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.59e-11 (Fisher's exact test), Q value = 2.3e-08

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	213	179	178
6P GAIN CNV	16	3	42
6P GAIN WILD-TYPE	197	176	136

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

'6p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.37e-09 (Fisher's exact test), Q value = 2e-06

Table S61. Gene #11: '6p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	122	142	185
6P GAIN CNV	7	14	35	5
6P GAIN WILD-TYPE	114	108	107	180

Figure S61. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q gain' versus 'CN_CNMF'

P value = 2.7e-18 (Chi-square test), Q value = 2.5e-15

Table S62. Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	356	212	71	241	54
6Q GAIN CNV	3	5	11	46	2
6Q GAIN WILD-TYPE	353	207	60	195	52

Figure S62. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

'6q gain' versus 'METHLYATION_CNMF'

P value = 4e-04 (Chi-square test), Q value = 0.22

Table S63. Gene #12: '6q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	151	99	118	38	96
6Q GAIN CNV	16	3	6	7	1	3
6Q GAIN WILD-TYPE	89	148	93	111	37	93

Figure S63. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6q gain' versus 'RPPA_CNMF'

P value = 0.000273 (Fisher's exact test), Q value = 0.16

Table S64. Gene #12: '6q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
6Q GAIN CNV	21	7	2
6Q GAIN WILD-TYPE	126	126	115

Figure S64. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'6q gain' versus 'MRNASEQ_CNMF'

P value = 5.97e-06 (Chi-square test), Q value = 0.0042

Table S65. Gene #12: '6q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	158	81	228	146	217	53	16
6Q GAIN CNV	26	2	12	12	8	1	3
6Q GAIN WILD-TYPE	132	79	216	134	209	52	13

Figure S65. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.29e-06 (Fisher's exact test), Q value = 0.00096

Table S66. Gene #12: '6q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	215	458
6Q GAIN CNV	31	3	30
6Q GAIN WILD-TYPE	195	212	428

Figure S66. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6q gain' versus 'MIRSEQ_CNMF'

P value = 2.12e-05 (Fisher's exact test), Q value = 0.014

Table S67. Gene #12: '6q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
6Q GAIN CNV	6	19	32
6Q GAIN WILD-TYPE	228	373	223

Figure S67. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.66e-07 (Fisher's exact test), Q value = 0.00058

Table S68. Gene #12: '6q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
6Q GAIN CNV	19	6	32
6Q GAIN WILD-TYPE	343	278	203

Figure S68. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.29e-06 (Fisher's exact test), Q value = 0.00096

Table S69. Gene #12: '6q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	213	179	178
6Q GAIN CNV	9	2	25
6Q GAIN WILD-TYPE	204	177	153

Figure S69. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'6q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9.94e-05 (Fisher's exact test), Q value = 0.061

Table S70. Gene #12: '6q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	122	142	185
6Q GAIN CNV	6	7	20	3
6Q GAIN WILD-TYPE	115	115	122	182

Figure S70. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

P value = 2.15e-13 (Chi-square test), Q value = 1.9e-10

Table S71. Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	356	212	71	241	54
8P GAIN CNV	33	39	28	52	24
8P GAIN WILD-TYPE	323	173	43	189	30

Figure S71. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

'8p gain' versus 'METHLYATION_CNMF'

P value = 8.85e-05 (Chi-square test), Q value = 0.055

Table S72. Gene #15: '8p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	151	99	118	38	96
8P GAIN CNV	30	23	19	28	6	3
8P GAIN WILD-TYPE	75	128	80	90	32	93

Figure S72. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.71e-08 (Fisher's exact test), Q value = 5.3e-05

Table S73. Gene #15: '8p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	215	458
8P GAIN CNV	43	15	112
8P GAIN WILD-TYPE	183	200	346

Figure S73. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'MRNA_CNMF'

P value = 0.000127 (Chi-square test), Q value = 0.077

Table S74. Gene #16: '8q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
8Q GAIN CNV	13	11	68	50	39	35	11	8
8Q GAIN WILD-TYPE	8	25	51	46	70	37	9	32

Figure S74. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'8q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.000364 (Fisher's exact test), Q value = 0.2

Table S75. Gene #16: '8q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
8Q GAIN CNV	37	62	136
8Q GAIN WILD-TYPE	85	63	130

Figure S75. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'8q gain' versus 'CN_CNMF'

P value = 3.26e-25 (Chi-square test), Q value = 3.1e-22

Table S76. Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	356	212	71	241	54
8Q GAIN CNV	70	114	33	128	40
8Q GAIN WILD-TYPE	286	98	38	113	14

Figure S76. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 5.69e-11 (Chi-square test), Q value = 4.9e-08

Table S77. Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	151	99	118	38	96
8Q GAIN CNV	57	37	37	67	9	20
8Q GAIN WILD-TYPE	48	114	62	51	29	76

Figure S77. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 2.79e-11 (Chi-square test), Q value = 2.4e-08

Table S78. Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	158	81	228	146	217	53	16
8Q GAIN CNV	84	21	75	61	119	6	9
8Q GAIN WILD-TYPE	74	60	153	85	98	47	7

Figure S78. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.64e-09 (Fisher's exact test), Q value = 2.2e-06

Table S79. Gene #16: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	215	458
8Q GAIN CNV	109	51	215
8Q GAIN WILD-TYPE	117	164	243

Figure S79. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_CNMF'

P value = 1.55e-09 (Fisher's exact test), Q value = 1.3e-06

Table S80. Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
8Q GAIN CNV	60	170	136
8Q GAIN WILD-TYPE	174	222	119

Figure S80. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.65e-06 (Fisher's exact test), Q value = 0.0026

Table S81. Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
8Q GAIN CNV	160	86	120
8Q GAIN WILD-TYPE	202	198	115

Figure S81. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.11e-06 (Fisher's exact test), Q value = 0.0015

Table S82. Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	213	179	178
8Q GAIN CNV	84	44	90
8Q GAIN WILD-TYPE	129	135	88

Figure S82. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.11e-06 (Fisher's exact test), Q value = 0.0029

Table S83. Gene #16: '8q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	122	142	185
8Q GAIN CNV	34	57	74	53
8Q GAIN WILD-TYPE	87	65	68	132

Figure S83. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p gain' versus 'MRNA_CNMF'

P value = 2.34e-08 (Chi-square test), Q value = 1.9e-05

Table S84. Gene #17: '9p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
9P GAIN CNV	0	1	3	24	7	4	0	2
9P GAIN WILD-TYPE	21	35	116	72	102	68	20	38

Figure S84. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'9p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1.85e-08 (Fisher's exact test), Q value = 1.5e-05

Table S85. Gene #17: '9p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
9P GAIN CNV	4	27	10
9P GAIN WILD-TYPE	118	98	256

Figure S85. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9p gain' versus 'CN_CNMF'

P value = 5.29e-10 (Chi-square test), Q value = 4.5e-07

Table S86. Gene #17: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	356	212	71	241	54
9P GAIN CNV	9	9	15	33	3
9P GAIN WILD-TYPE	347	203	56	208	51

Figure S86. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'

'9p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.000106 (Fisher's exact test), Q value = 0.065

Table S87. Gene #17: '9p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	110	126
9P GAIN CNV	5	7	22
9P GAIN WILD-TYPE	156	103	104

Figure S87. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'9p gain' versus 'MRNASEQ_CNMF'

P value = 4.31e-10 (Chi-square test), Q value = 3.7e-07

Table S88. Gene #17: '9p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	158	81	228	146	217	53	16
9P GAIN CNV	33	2	12	8	6	3	2
9P GAIN WILD-TYPE	125	79	216	138	211	50	14

Figure S88. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.45e-08 (Fisher's exact test), Q value = 2.8e-05

Table S89. Gene #17: '9p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	215	458
9P GAIN CNV	38	8	20
9P GAIN WILD-TYPE	188	207	438

Figure S89. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p gain' versus 'MIRSEQ_CNMF'

P value = 1.11e-06 (Fisher's exact test), Q value = 0.00083

Table S90. Gene #17: '9p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
9P GAIN CNV	8	19	38
9P GAIN WILD-TYPE	226	373	217

Figure S90. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.44e-07 (Fisher's exact test), Q value = 0.00011

Table S91. Gene #17: '9p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
9P GAIN CNV	15	12	38
9P GAIN WILD-TYPE	347	272	197

Figure S91. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9q gain' versus 'CN_CNMF'

P value = 2.25e-06 (Chi-square test), Q value = 0.0016

Table S92. Gene #18: '9q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	356	212	71	241	54
9Q GAIN CNV	10	12	14	19	2
9Q GAIN WILD-TYPE	346	200	57	222	52

Figure S92. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #3: 'CN_CNMF'

'10p gain' versus 'MRNA_CNMF'

P value = 1.39e-10 (Chi-square test), Q value = 1.2e-07

Table S93. Gene #19: '10p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
10P GAIN CNV	0	2	10	33	4	18	2	3
10P GAIN WILD-TYPE	21	34	109	63	105	54	18	37

Figure S93. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'10p gain' versus 'MRNA_CHIERARCHICAL'

P value = 8.01e-08 (Fisher's exact test), Q value = 6.3e-05

Table S94. Gene #19: '10p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
10P GAIN CNV	9	38	25
10P GAIN WILD-TYPE	113	87	241

Figure S94. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'10p gain' versus 'CN_CNMF'

P value = 6.71e-17 (Chi-square test), Q value = 6.2e-14

Table S95. Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	356	212	71	241	54
10P GAIN CNV	9	24	9	65	5
10P GAIN WILD-TYPE	347	188	62	176	49

Figure S95. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

'10p gain' versus 'METHLYATION_CNMF'

P value = 7.67e-14 (Chi-square test), Q value = 6.9e-11

Table S96. Gene #19: '10p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	151	99	118	38	96
10P GAIN CNV	34	5	11	12	0	3
10P GAIN WILD-TYPE	71	146	88	106	38	93

Figure S96. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p gain' versus 'RPPA_CNMF'

P value = 2.39e-05 (Fisher's exact test), Q value = 0.016

Table S97. Gene #19: '10p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
10P GAIN CNV	36	8	12
10P GAIN WILD-TYPE	111	125	105

Figure S97. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'10p gain' versus 'RPPA_CHIERARCHICAL'

P value = 1.42e-06 (Fisher's exact test), Q value = 0.0011

Table S98. Gene #19: '10p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	110	126
10P GAIN CNV	11	10	35
10P GAIN WILD-TYPE	150	100	91

Figure S98. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'10p gain' versus 'MRNASEQ_CNMF'

P value = 1.17e-19 (Chi-square test), Q value = 1.1e-16

Table S99. Gene #19: '10p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	158	81	228	146	217	53	16
10P GAIN CNV	53	4	8	25	15	2	1
10P GAIN WILD-TYPE	105	77	220	121	202	51	15

Figure S99. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.93e-15 (Fisher's exact test), Q value = 8.2e-12

Table S100. Gene #19: '10p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	215	458
10P GAIN CNV	63	10	35
10P GAIN WILD-TYPE	163	205	423

Figure S100. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p gain' versus 'MIRSEQ_CNMF'

P value = 2.44e-12 (Fisher's exact test), Q value = 2.2e-09

Table S101. Gene #19: '10p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
10P GAIN CNV	12	30	64
10P GAIN WILD-TYPE	222	362	191

Figure S101. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.15e-14 (Fisher's exact test), Q value = 1.9e-11

Table S102. Gene #19: '10p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
10P GAIN CNV	27	15	64
10P GAIN WILD-TYPE	335	269	171

Figure S102. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.57e-10 (Fisher's exact test), Q value = 1.3e-07

Table S103. Gene #19: '10p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	213	179	178
10P GAIN CNV	10	9	44
10P GAIN WILD-TYPE	203	170	134

Figure S103. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.41e-12 (Fisher's exact test), Q value = 2.1e-09

Table S104. Gene #19: '10p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	122	142	185
10P GAIN CNV	6	7	42	8
10P GAIN WILD-TYPE	115	115	100	177

Figure S104. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q gain' versus 'CN_CNMF'

P value = 0.000274 (Chi-square test), Q value = 0.16

Table S105. Gene #20: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	356	212	71	241	54
10Q GAIN CNV	5	11	7	22	3
10Q GAIN WILD-TYPE	351	201	64	219	51

Figure S105. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

'10q gain' versus 'MRNASEQ_CNMF'

P value = 0.000354 (Chi-square test), Q value = 0.2

Table S106. Gene #20: '10q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	158	81	228	146	217	53	16
10Q GAIN CNV	14	1	7	14	5	2	3
10Q GAIN WILD-TYPE	144	80	221	132	212	51	13

Figure S106. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 1.69e-14 (Chi-square test), Q value = 1.5e-11

Table S107. Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	356	212	71	241	54
12P GAIN CNV	4	44	15	47	9
12P GAIN WILD-TYPE	352	168	56	194	45

Figure S107. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 2.66e-06 (Chi-square test), Q value = 0.0019

Table S108. Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	151	99	118	38	96
12P GAIN CNV	20	9	13	24	0	2
12P GAIN WILD-TYPE	85	142	86	94	38	94

Figure S108. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 1.44e-05 (Chi-square test), Q value = 0.0099

Table S109. Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	158	81	228	146	217	53	16
12P GAIN CNV	34	2	16	24	35	3	1
12P GAIN WILD-TYPE	124	79	212	122	182	50	15

Figure S109. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.63e-05 (Fisher's exact test), Q value = 0.017

Table S110. Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	215	458
12P GAIN CNV	43	11	61
12P GAIN WILD-TYPE	183	204	397

Figure S110. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_CNMF'

P value = 0.000457 (Fisher's exact test), Q value = 0.25

Table S111. Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
12P GAIN CNV	17	44	48
12P GAIN WILD-TYPE	217	348	207

Figure S111. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000154 (Fisher's exact test), Q value = 0.092

Table S112. Gene #23: '12p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	213	179	178
12P GAIN CNV	23	9	34
12P GAIN WILD-TYPE	190	170	144

Figure S112. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12q gain' versus 'CN_CNMF'

P value = 3.61e-17 (Chi-square test), Q value = 3.3e-14

Table S113. Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	356	212	71	241	54
12Q GAIN CNV	5	46	16	14	8
12Q GAIN WILD-TYPE	351	166	55	227	46

Figure S113. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

'12q gain' versus 'METHLYATION_CNMF'

P value = 9.97e-06 (Chi-square test), Q value = 0.0069

Table S114. Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	151	99	118	38	96
12Q GAIN CNV	5	13	12	23	0	1
12Q GAIN WILD-TYPE	100	138	87	95	38	95

Figure S114. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q gain' versus 'CN_CNMF'

P value = 0.000164 (Chi-square test), Q value = 0.098

Table S115. Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	356	212	71	241	54
14Q GAIN CNV	16	29	11	15	7
14Q GAIN WILD-TYPE	340	183	60	226	47

Figure S115. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

'14q gain' versus 'MRNASEQ_CNMF'

P value = 5.79e-05 (Chi-square test), Q value = 0.037

Table S116. Gene #26: '14q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	158	81	228	146	217	53	16
14Q GAIN CNV	4	1	25	22	24	0	2
14Q GAIN WILD-TYPE	154	80	203	124	193	53	14

Figure S116. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.19e-06 (Fisher's exact test), Q value = 0.00089

Table S117. Gene #26: '14q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	215	458
14Q GAIN CNV	11	6	61
14Q GAIN WILD-TYPE	215	209	397

Figure S117. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_CNMF'

P value = 5.08e-05 (Fisher's exact test), Q value = 0.032

Table S118. Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
14Q GAIN CNV	7	50	19
14Q GAIN WILD-TYPE	227	342	236

Figure S118. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16p gain' versus 'MRNA_CNMF'

P value = 1.65e-06 (Chi-square test), Q value = 0.0012

Table S119. Gene #28: '16p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
16P GAIN CNV	6	5	39	18	57	15	5	11
16P GAIN WILD-TYPE	15	31	80	78	52	57	15	29

Figure S119. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'16p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.000291 (Fisher's exact test), Q value = 0.17

Table S120. Gene #28: '16p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
16P GAIN CNV	35	22	99
16P GAIN WILD-TYPE	87	103	167

Figure S120. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'16p gain' versus 'METHLYATION_CNMF'

P value = 1.71e-06 (Chi-square test), Q value = 0.0013

Table S121. Gene #28: '16p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	151	99	118	38	96
16P GAIN CNV	19	58	31	29	5	9
16P GAIN WILD-TYPE	86	93	68	89	33	87

Figure S121. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16p gain' versus 'RPPA_CNMF'

P value = 5.23e-05 (Fisher's exact test), Q value = 0.033

Table S122. Gene #28: '16p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
16P GAIN CNV	30	59	31
16P GAIN WILD-TYPE	117	74	86

Figure S122. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'16p gain' versus 'RPPA_CHIERARCHICAL'

P value = 6.05e-05 (Fisher's exact test), Q value = 0.038

Table S123. Gene #28: '16p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	110	126
16P GAIN CNV	61	39	20
16P GAIN WILD-TYPE	100	71	106

Figure S123. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 6.28e-07 (Chi-square test), Q value = 0.00048

Table S124. Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	158	81	228	146	217	53	16
16P GAIN CNV	25	19	96	34	58	13	2
16P GAIN WILD-TYPE	133	62	132	112	159	40	14

Figure S124. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.16e-06 (Fisher's exact test), Q value = 0.0023

Table S125. Gene #28: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	215	458
16P GAIN CNV	38	52	157
16P GAIN WILD-TYPE	188	163	301

Figure S125. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 8.17e-05 (Fisher's exact test), Q value = 0.051

Table S126. Gene #28: '16p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	213	179	178
16P GAIN CNV	75	42	29
16P GAIN WILD-TYPE	138	137	149

Figure S126. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'17p gain' versus 'CN_CNMF'

P value = 0.000406 (Chi-square test), Q value = 0.23

Table S127. Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	356	212	71	241	54
17P GAIN CNV	12	23	3	6	3
17P GAIN WILD-TYPE	344	189	68	235	51

Figure S127. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'MRNA_CNMF'

P value = 1.26e-06 (Chi-square test), Q value = 0.00094

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
17Q GAIN CNV	2	5	34	6	6	4	2	5
17Q GAIN WILD-TYPE	19	31	85	90	103	68	18	35

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

'17q gain' versus 'CN_CNMF'

P value = 3.09e-20 (Chi-square test), Q value = 2.9e-17

Table S129. Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	356	212	71	241	54
17Q GAIN CNV	23	69	6	15	12
17Q GAIN WILD-TYPE	333	143	65	226	42

Figure S129. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 5.81e-06 (Chi-square test), Q value = 0.0041

Table S130. Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	151	99	118	38	96
17Q GAIN CNV	5	17	15	33	5	7
17Q GAIN WILD-TYPE	100	134	84	85	33	89

Figure S130. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 4.85e-12 (Chi-square test), Q value = 4.3e-09

Table S131. Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	158	81	228	146	217	53	16
17Q GAIN CNV	8	7	19	14	63	7	4
17Q GAIN WILD-TYPE	150	74	209	132	154	46	12

Figure S131. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.88e-07 (Fisher's exact test), Q value = 0.00052

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	215	458
17Q GAIN CNV	11	25	86
17Q GAIN WILD-TYPE	215	190	372

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

'18p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.000213 (Fisher's exact test), Q value = 0.13

Table S133. Gene #32: '18p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
18P GAIN CNV	4	24	28
18P GAIN WILD-TYPE	118	101	238

Figure S133. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18p gain' versus 'CN_CNMF'

P value = 1.27e-06 (Chi-square test), Q value = 0.00095

Table S134. Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	356	212	71	241	54
18P GAIN CNV	11	24	6	37	10
18P GAIN WILD-TYPE	345	188	65	204	44

Figure S134. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 6.18e-07 (Chi-square test), Q value = 0.00047

Table S135. Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	151	99	118	38	96
18P GAIN CNV	22	7	8	9	0	1
18P GAIN WILD-TYPE	83	144	91	109	38	95

Figure S135. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p gain' versus 'MRNASEQ_CNMF'

P value = 2.01e-07 (Chi-square test), Q value = 0.00016

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	158	81	228	146	217	53	16
18P GAIN CNV	34	0	21	9	23	0	1
18P GAIN WILD-TYPE	124	81	207	137	194	53	15

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

'18p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.99e-09 (Fisher's exact test), Q value = 1.7e-06

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	215	458
18P GAIN CNV	38	2	48
18P GAIN WILD-TYPE	188	213	410

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

'18p gain' versus 'MIRSEQ_CNMF'

P value = 7.88e-06 (Fisher's exact test), Q value = 0.0055

Table S138. Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
18P GAIN CNV	11	28	43
18P GAIN WILD-TYPE	223	364	212

Figure S138. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.01e-05 (Fisher's exact test), Q value = 0.032

Table S139. Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
18P GAIN CNV	28	15	39
18P GAIN WILD-TYPE	334	269	196

Figure S139. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18q gain' versus 'CN_CNMF'

P value = 2.62e-05 (Chi-square test), Q value = 0.017

Table S140. Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	356	212	71	241	54
18Q GAIN CNV	10	20	7	31	9
18Q GAIN WILD-TYPE	346	192	64	210	45

Figure S140. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

'18q gain' versus 'MRNASEQ_CNMF'

P value = 1.29e-05 (Chi-square test), Q value = 0.0089

Table S141. Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	158	81	228	146	217	53	16
18Q GAIN CNV	25	0	21	4	25	0	1
18Q GAIN WILD-TYPE	133	81	207	142	192	53	15

Figure S141. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.57e-08 (Fisher's exact test), Q value = 4.4e-05

Table S142. Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	215	458
18Q GAIN CNV	25	1	50
18Q GAIN WILD-TYPE	201	214	408

Figure S142. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'CN_CNMF'

P value = 2.85e-05 (Chi-square test), Q value = 0.019

Table S143. Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	356	212	71	241	54
19P GAIN CNV	12	12	12	29	5
19P GAIN WILD-TYPE	344	200	59	212	49

Figure S143. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

'19q gain' versus 'CN_CNMF'

P value = 2.46e-05 (Chi-square test), Q value = 0.016

Table S144. Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	356	212	71	241	54
19Q GAIN CNV	15	20	14	34	7
19Q GAIN WILD-TYPE	341	192	57	207	47

Figure S144. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'MRNA_CNMF'

P value = 2.64e-05 (Chi-square test), Q value = 0.018

Table S145. Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
20P GAIN CNV	7	7	40	26	22	32	13	5
20P GAIN WILD-TYPE	14	29	79	70	87	40	7	35

Figure S145. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20p gain' versus 'CN_CNMF'

P value = 3.97e-25 (Chi-square test), Q value = 3.8e-22

Table S146. Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	356	212	71	241	54
20P GAIN CNV	28	98	32	72	15
20P GAIN WILD-TYPE	328	114	39	169	39

Figure S146. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 2.85e-06 (Chi-square test), Q value = 0.0021

Table S147. Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	151	99	118	38	96
20P GAIN CNV	23	28	30	47	5	10
20P GAIN WILD-TYPE	82	123	69	71	33	86

Figure S147. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 4.63e-06 (Chi-square test), Q value = 0.0033

Table S148. Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	158	81	228	146	217	53	16
20P GAIN CNV	34	9	54	54	74	6	6
20P GAIN WILD-TYPE	124	72	174	92	143	47	10

Figure S148. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p gain' versus 'MIRSEQ_CNMF'

P value = 0.000252 (Fisher's exact test), Q value = 0.15

Table S149. Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
20P GAIN CNV	39	117	77
20P GAIN WILD-TYPE	195	275	178

Figure S149. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20q gain' versus 'MRNA_CNMF'

P value = 1.88e-05 (Chi-square test), Q value = 0.013

Table S150. Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
20Q GAIN CNV	6	7	54	26	23	33	12	9
20Q GAIN WILD-TYPE	15	29	65	70	86	39	8	31

Figure S150. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20q gain' versus 'CN_CNMF'

P value = 3.63e-32 (Chi-square test), Q value = 3.5e-29

Table S151. Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	356	212	71	241	54
20Q GAIN CNV	31	119	30	83	20
20Q GAIN WILD-TYPE	325	93	41	158	34

Figure S151. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 2.73e-11 (Chi-square test), Q value = 2.4e-08

Table S152. Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	151	99	118	38	96
20Q GAIN CNV	25	30	39	59	6	10
20Q GAIN WILD-TYPE	80	121	60	59	32	86

Figure S152. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 2.35e-10 (Chi-square test), Q value = 2e-07

Table S153. Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	158	81	228	146	217	53	16
20Q GAIN CNV	38	10	54	54	103	10	5
20Q GAIN WILD-TYPE	120	71	174	92	114	43	11

Figure S153. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.78e-05 (Fisher's exact test), Q value = 0.018

Table S154. Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	215	458
20Q GAIN CNV	59	45	170
20Q GAIN WILD-TYPE	167	170	288

Figure S154. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 4.27e-06 (Fisher's exact test), Q value = 0.0031

Table S155. Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
20Q GAIN CNV	43	142	86
20Q GAIN WILD-TYPE	191	250	169

Figure S155. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'21q gain' versus 'MRNA_CNMF'

P value = 3.09e-05 (Chi-square test), Q value = 0.02

Table S156. Gene #38: '21q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
21Q GAIN CNV	1	0	11	18	7	19	5	2
21Q GAIN WILD-TYPE	20	36	108	78	102	53	15	38

Figure S156. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'21q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.000302 (Fisher's exact test), Q value = 0.17

Table S157. Gene #38: '21q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
21Q GAIN CNV	6	27	30
21Q GAIN WILD-TYPE	116	98	236

Figure S157. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'21q gain' versus 'CN_CNMF'

P value = 3.34e-10 (Chi-square test), Q value = 2.8e-07

Table S158. Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	356	212	71	241	54
21Q GAIN CNV	12	21	17	45	10
21Q GAIN WILD-TYPE	344	191	54	196	44

Figure S158. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

'21q gain' versus 'METHLYATION_CNMF'

P value = 3.4e-08 (Chi-square test), Q value = 2.7e-05

Table S159. Gene #38: '21q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	151	99	118	38	96
21Q GAIN CNV	27	8	15	10	1	2
21Q GAIN WILD-TYPE	78	143	84	108	37	94

Figure S159. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'21q gain' versus 'MRNASEQ_CNMF'

P value = 3.06e-10 (Chi-square test), Q value = 2.6e-07

Table S160. Gene #38: '21q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	158	81	228	146	217	53	16
21Q GAIN CNV	35	2	13	32	17	1	3
21Q GAIN WILD-TYPE	123	79	215	114	200	52	13

Figure S160. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.35e-11 (Fisher's exact test), Q value = 7.2e-08

Table S161. Gene #38: '21q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	215	458
21Q GAIN CNV	53	7	43
21Q GAIN WILD-TYPE	173	208	415

Figure S161. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'21q gain' versus 'MIRSEQ_CNMF'

P value = 3.95e-05 (Fisher's exact test), Q value = 0.026

Table S162. Gene #38: '21q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
21Q GAIN CNV	14	37	47
21Q GAIN WILD-TYPE	220	355	208

Figure S162. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'21q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.66e-07 (Fisher's exact test), Q value = 0.00028

Table S163. Gene #38: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
21Q GAIN CNV	35	15	48
21Q GAIN WILD-TYPE	327	269	187

Figure S163. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'21q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.19e-08 (Fisher's exact test), Q value = 3.4e-05

Table S164. Gene #38: '21q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	213	179	178
21Q GAIN CNV	20	7	42
21Q GAIN WILD-TYPE	193	172	136

Figure S164. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'21q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.73e-07 (Fisher's exact test), Q value = 0.00036

Table S165. Gene #38: '21q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	122	142	185
21Q GAIN CNV	11	11	37	10
21Q GAIN WILD-TYPE	110	111	105	175

Figure S165. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q gain' versus 'CN_CNMF'

P value = 1.93e-07 (Chi-square test), Q value = 0.00015

Table S166. Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	356	212	71	241	54
22Q GAIN CNV	2	10	1	26	4
22Q GAIN WILD-TYPE	354	202	70	215	50

Figure S166. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

'22q gain' versus 'MRNASEQ_CNMF'

P value = 3.31e-05 (Chi-square test), Q value = 0.022

Table S167. Gene #39: '22q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	158	81	228	146	217	53	16
22Q GAIN CNV	17	0	3	12	10	0	0
22Q GAIN WILD-TYPE	141	81	225	134	207	53	16

Figure S167. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.86e-09 (Fisher's exact test), Q value = 6.4e-06

Table S168. Gene #39: '22q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	215	458
22Q GAIN CNV	26	0	16
22Q GAIN WILD-TYPE	200	215	442

Figure S168. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.03e-06 (Fisher's exact test), Q value = 0.00078

Table S169. Gene #39: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
22Q GAIN CNV	16	2	24
22Q GAIN WILD-TYPE	346	282	211

Figure S169. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.92e-05 (Fisher's exact test), Q value = 0.013

Table S170. Gene #39: '22q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	213	179	178
22Q GAIN CNV	8	1	19
22Q GAIN WILD-TYPE	205	178	159

Figure S170. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'22q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.97e-05 (Fisher's exact test), Q value = 0.02

Table S171. Gene #39: '22q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	122	142	185
22Q GAIN CNV	1	7	17	3
22Q GAIN WILD-TYPE	120	115	125	182

Figure S171. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Xq gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.000161 (Fisher's exact test), Q value = 0.097

Table S172. Gene #40: 'Xq gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
XQ GAIN CNV	1	11	3
XQ GAIN WILD-TYPE	121	114	263

Figure S172. Get High-res Image Gene #40: 'Xq gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Xq gain' versus 'CN_CNMF'

P value = 1.21e-05 (Chi-square test), Q value = 0.0083

Table S173. Gene #40: 'Xq gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	356	212	71	241	54
XQ GAIN CNV	1	3	2	16	0
XQ GAIN WILD-TYPE	355	209	69	225	54

Figure S173. Get High-res Image Gene #40: 'Xq gain' versus Molecular Subtype #3: 'CN_CNMF'

'Xq gain' versus 'MRNASEQ_CNMF'

P value = 0.000158 (Chi-square test), Q value = 0.095

Table S174. Gene #40: 'Xq gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	158	81	228	146	217	53	16
XQ GAIN CNV	12	0	2	3	2	1	0
XQ GAIN WILD-TYPE	146	81	226	143	215	52	16

Figure S174. Get High-res Image Gene #40: 'Xq gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Xq gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000363 (Fisher's exact test), Q value = 0.2

Table S175. Gene #40: 'Xq gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	215	458
XQ GAIN CNV	13	1	6
XQ GAIN WILD-TYPE	213	214	452

Figure S175. Get High-res Image Gene #40: 'Xq gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Xq gain' versus 'MIRSEQ_CNMF'

P value = 4.83e-05 (Fisher's exact test), Q value = 0.031

Table S176. Gene #40: 'Xq gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
XQ GAIN CNV	0	5	14
XQ GAIN WILD-TYPE	234	387	241

Figure S176. Get High-res Image Gene #40: 'Xq gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Xq gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000182 (Fisher's exact test), Q value = 0.11

Table S177. Gene #40: 'Xq gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
XQ GAIN CNV	5	1	13
XQ GAIN WILD-TYPE	357	283	222

Figure S177. Get High-res Image Gene #40: 'Xq gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1p loss' versus 'MRNA_CHIERARCHICAL'

P value = 4.12e-09 (Fisher's exact test), Q value = 3.4e-06

Table S178. Gene #41: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
1P LOSS CNV	5	5	59
1P LOSS WILD-TYPE	117	120	207

Figure S178. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

P value = 2.51e-20 (Chi-square test), Q value = 2.4e-17

Table S179. Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	356	212	71	241	54
1P LOSS CNV	16	55	27	18	9
1P LOSS WILD-TYPE	340	157	44	223	45

Figure S179. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 4.27e-07 (Chi-square test), Q value = 0.00033

Table S180. Gene #41: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	151	99	118	38	96
1P LOSS CNV	8	14	25	27	4	2
1P LOSS WILD-TYPE	97	137	74	91	34	94

Figure S180. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 9.55e-07 (Chi-square test), Q value = 0.00072

Table S181. Gene #41: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	158	81	228	146	217	53	16
1P LOSS CNV	9	3	30	31	45	1	2
1P LOSS WILD-TYPE	149	78	198	115	172	52	14

Figure S181. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.43e-14 (Fisher's exact test), Q value = 1.3e-11

Table S182. Gene #41: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	215	458
1P LOSS CNV	12	8	101
1P LOSS WILD-TYPE	214	207	357

Figure S182. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p loss' versus 'MRNA_CHIERARCHICAL'

P value = 9.96e-05 (Fisher's exact test), Q value = 0.061

Table S183. Gene #43: '2p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
2P LOSS CNV	5	3	36
2P LOSS WILD-TYPE	117	122	230

Figure S183. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'2p loss' versus 'CN_CNMF'

P value = 5.88e-13 (Chi-square test), Q value = 5.2e-10

Table S184. Gene #43: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	356	212	71	241	54
2P LOSS CNV	5	29	16	14	11
2P LOSS WILD-TYPE	351	183	55	227	43

Figure S184. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

'2p loss' versus 'METHLYATION_CNMF'

P value = 1.91e-05 (Chi-square test), Q value = 0.013

Table S185. Gene #43: '2p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	151	99	118	38	96
2P LOSS CNV	2	9	12	18	1	0
2P LOSS WILD-TYPE	103	142	87	100	37	96

Figure S185. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2p loss' versus 'MRNASEQ_CNMF'

P value = 0.000387 (Chi-square test), Q value = 0.22

Table S186. Gene #43: '2p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	158	81	228	146	217	53	16
2P LOSS CNV	5	2	21	11	32	1	1
2P LOSS WILD-TYPE	153	79	207	135	185	52	15

Figure S186. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.48e-10 (Fisher's exact test), Q value = 3.8e-07

Table S187. Gene #43: '2p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	215	458
2P LOSS CNV	5	5	63
2P LOSS WILD-TYPE	221	210	395

Figure S187. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_CNMF'

P value = 0.000438 (Fisher's exact test), Q value = 0.24

Table S188. Gene #43: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
2P LOSS CNV	10	47	13
2P LOSS WILD-TYPE	224	345	242

Figure S188. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2q loss' versus 'CN_CNMF'

P value = 1.21e-12 (Chi-square test), Q value = 1.1e-09

Table S189. Gene #44: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	356	212	71	241	54
2Q LOSS CNV	5	36	17	23	10
2Q LOSS WILD-TYPE	351	176	54	218	44

Figure S189. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

'2q loss' versus 'METHLYATION_CNMF'

P value = 3.05e-05 (Chi-square test), Q value = 0.02

Table S190. Gene #44: '2q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	151	99	118	38	96
2Q LOSS CNV	9	9	12	22	1	0
2Q LOSS WILD-TYPE	96	142	87	96	37	96

Figure S190. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.26e-07 (Fisher's exact test), Q value = 9.9e-05

Table S191. Gene #44: '2q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	215	458
2Q LOSS CNV	16	5	68
2Q LOSS WILD-TYPE	210	210	390

Figure S191. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000365 (Fisher's exact test), Q value = 0.2

Table S192. Gene #44: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
2Q LOSS CNV	51	14	21
2Q LOSS WILD-TYPE	311	270	214

Figure S192. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'CN_CNMF'

P value = 2.77e-08 (Chi-square test), Q value = 2.2e-05

Table S193. Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	356	212	71	241	54
3P LOSS CNV	10	28	5	43	5
3P LOSS WILD-TYPE	346	184	66	198	49

Figure S193. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

'3p loss' versus 'RPPA_CHIERARCHICAL'

P value = 8.6e-05 (Fisher's exact test), Q value = 0.053

Table S194. Gene #45: '3p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	110	126
3P LOSS CNV	13	4	26
3P LOSS WILD-TYPE	148	106	100

Figure S194. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 6.46e-05 (Chi-square test), Q value = 0.041

Table S195. Gene #45: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	158	81	228	146	217	53	16
3P LOSS CNV	25	4	11	24	21	0	1
3P LOSS WILD-TYPE	133	77	217	122	196	53	15

Figure S195. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000234 (Fisher's exact test), Q value = 0.14

Table S196. Gene #45: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	215	458
3P LOSS CNV	37	11	38
3P LOSS WILD-TYPE	189	204	420

Figure S196. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CNMF'

P value = 5.88e-06 (Fisher's exact test), Q value = 0.0042

Table S197. Gene #45: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
3P LOSS CNV	14	26	45
3P LOSS WILD-TYPE	220	366	210

Figure S197. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000296 (Fisher's exact test), Q value = 0.17

Table S198. Gene #45: '3p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	213	179	178
3P LOSS CNV	18	7	29
3P LOSS WILD-TYPE	195	172	149

Figure S198. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'MRNA_CNMF'

P value = 1.23e-12 (Chi-square test), Q value = 1.1e-09

Table S199. Gene #47: '4p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
4P LOSS CNV	1	5	16	42	14	34	4	3
4P LOSS WILD-TYPE	20	31	103	54	95	38	16	37

Figure S199. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'4p loss' versus 'MRNA_CHIERARCHICAL'

P value = 1.03e-11 (Fisher's exact test), Q value = 9e-09

Table S200. Gene #47: '4p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
4P LOSS CNV	9	56	54
4P LOSS WILD-TYPE	113	69	212

Figure S200. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

P value = 8.07e-29 (Chi-square test), Q value = 7.7e-26

Table S201. Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	356	212	71	241	54
4P LOSS CNV	18	39	24	104	7
4P LOSS WILD-TYPE	338	173	47	137	47

Figure S201. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 4.83e-16 (Chi-square test), Q value = 4.5e-13

Table S202. Gene #47: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	151	99	118	38	96
4P LOSS CNV	46	19	27	10	3	3
4P LOSS WILD-TYPE	59	132	72	108	35	93

Figure S202. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p loss' versus 'RPPA_CNMF'

P value = 9.69e-05 (Fisher's exact test), Q value = 0.06

Table S203. Gene #47: '4p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
4P LOSS CNV	53	26	17
4P LOSS WILD-TYPE	94	107	100

Figure S203. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'4p loss' versus 'RPPA_CHIERARCHICAL'

P value = 5.38e-06 (Fisher's exact test), Q value = 0.0038

Table S204. Gene #47: '4p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	110	126
4P LOSS CNV	31	15	50
4P LOSS WILD-TYPE	130	95	76

Figure S204. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 6.59e-19 (Chi-square test), Q value = 6.2e-16

Table S205. Gene #47: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	158	81	228	146	217	53	16
4P LOSS CNV	67	4	28	51	30	4	2
4P LOSS WILD-TYPE	91	77	200	95	187	49	14

Figure S205. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.98e-18 (Fisher's exact test), Q value = 2.8e-15

Table S206. Gene #47: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	215	458
4P LOSS CNV	91	14	81
4P LOSS WILD-TYPE	135	201	377

Figure S206. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_CNMF'

P value = 1.44e-14 (Fisher's exact test), Q value = 1.3e-11

Table S207. Gene #47: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
4P LOSS CNV	22	66	96
4P LOSS WILD-TYPE	212	326	159

Figure S207. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.12e-15 (Fisher's exact test), Q value = 2.9e-12

Table S208. Gene #47: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
4P LOSS CNV	66	27	91
4P LOSS WILD-TYPE	296	257	144

Figure S208. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 7.39e-12 (Fisher's exact test), Q value = 6.5e-09

Table S209. Gene #47: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	213	179	178
4P LOSS CNV	44	9	60
4P LOSS WILD-TYPE	169	170	118

Figure S209. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.85e-08 (Fisher's exact test), Q value = 3.1e-05

Table S210. Gene #47: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	122	142	185
4P LOSS CNV	9	21	52	31
4P LOSS WILD-TYPE	112	101	90	154

Figure S210. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'MRNA_CNMF'

P value = 1.65e-06 (Chi-square test), Q value = 0.0012

Table S211. Gene #48: '4q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
4Q LOSS CNV	1	5	15	32	13	25	2	3
4Q LOSS WILD-TYPE	20	31	104	64	96	47	18	37

Figure S211. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'4q loss' versus 'MRNA_CHIERARCHICAL'

P value = 5.26e-07 (Fisher's exact test), Q value = 4e-04

Table S212. Gene #48: '4q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
4Q LOSS CNV	8	41	47
4Q LOSS WILD-TYPE	114	84	219

Figure S212. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 7.93e-21 (Chi-square test), Q value = 7.5e-18

Table S213. Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	356	212	71	241	54
4Q LOSS CNV	17	32	25	80	6
4Q LOSS WILD-TYPE	339	180	46	161	48

Figure S213. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 6.71e-11 (Chi-square test), Q value = 5.8e-08

Table S214. Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	151	99	118	38	96
4Q LOSS CNV	38	20	19	9	4	2
4Q LOSS WILD-TYPE	67	131	80	109	34	94

Figure S214. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 5.65e-12 (Chi-square test), Q value = 5e-09

Table S215. Gene #48: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	158	81	228	146	217	53	16
4Q LOSS CNV	52	4	26	41	26	3	1
4Q LOSS WILD-TYPE	106	77	202	105	191	50	15

Figure S215. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.7e-13 (Fisher's exact test), Q value = 3.3e-10

Table S216. Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	215	458
4Q LOSS CNV	70	10	73
4Q LOSS WILD-TYPE	156	205	385

Figure S216. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_CNMF'

P value = 1.31e-07 (Fisher's exact test), Q value = 1e-04

Table S217. Gene #48: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
4Q LOSS CNV	20	61	70
4Q LOSS WILD-TYPE	214	331	185

Figure S217. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.76e-10 (Fisher's exact test), Q value = 2.4e-07

Table S218. Gene #48: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
4Q LOSS CNV	52	26	73
4Q LOSS WILD-TYPE	310	258	162

Figure S218. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 5.32e-08 (Fisher's exact test), Q value = 4.2e-05

Table S219. Gene #48: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	213	179	178
4Q LOSS CNV	37	8	45
4Q LOSS WILD-TYPE	176	171	133

Figure S219. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9.91e-06 (Fisher's exact test), Q value = 0.0069

Table S220. Gene #48: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	122	142	185
4Q LOSS CNV	7	16	40	27
4Q LOSS WILD-TYPE	114	106	102	158

Figure S220. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p loss' versus 'MRNA_CNMF'

P value = 1e-08 (Chi-square test), Q value = 8.2e-06

Table S221. Gene #49: '5p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
5P LOSS CNV	1	2	3	24	4	9	0	0
5P LOSS WILD-TYPE	20	34	116	72	105	63	20	40

Figure S221. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'5p loss' versus 'MRNA_CHIERARCHICAL'

P value = 5.35e-06 (Fisher's exact test), Q value = 0.0038

Table S222. Gene #49: '5p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
5P LOSS CNV	3	24	16
5P LOSS WILD-TYPE	119	101	250

Figure S222. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'5p loss' versus 'CN_CNMF'

P value = 1.98e-18 (Chi-square test), Q value = 1.8e-15

Table S223. Gene #49: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	356	212	71	241	54
5P LOSS CNV	2	13	3	51	3
5P LOSS WILD-TYPE	354	199	68	190	51

Figure S223. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

'5p loss' versus 'METHLYATION_CNMF'

P value = 3.38e-13 (Chi-square test), Q value = 3e-10

Table S224. Gene #49: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	151	99	118	38	96
5P LOSS CNV	26	2	6	7	0	1
5P LOSS WILD-TYPE	79	149	93	111	38	95

Figure S224. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5p loss' versus 'RPPA_CNMF'

P value = 0.000104 (Fisher's exact test), Q value = 0.063

Table S225. Gene #49: '5p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
5P LOSS CNV	26	5	6
5P LOSS WILD-TYPE	121	128	111

Figure S225. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'5p loss' versus 'RPPA_CHIERARCHICAL'

P value = 2.63e-06 (Fisher's exact test), Q value = 0.0019

Table S226. Gene #49: '5p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	110	126
5P LOSS CNV	6	5	26
5P LOSS WILD-TYPE	155	105	100

Figure S226. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'5p loss' versus 'MRNASEQ_CNMF'

P value = 3.09e-15 (Chi-square test), Q value = 2.8e-12

Table S227. Gene #49: '5p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	158	81	228	146	217	53	16
5P LOSS CNV	38	1	6	11	11	0	1
5P LOSS WILD-TYPE	120	80	222	135	206	53	15

Figure S227. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.87e-09 (Fisher's exact test), Q value = 1.6e-06

Table S228. Gene #49: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	215	458
5P LOSS CNV	39	4	25
5P LOSS WILD-TYPE	187	211	433

Figure S228. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_CNMF'

P value = 2.97e-14 (Fisher's exact test), Q value = 2.7e-11

Table S229. Gene #49: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
5P LOSS CNV	4	16	50
5P LOSS WILD-TYPE	230	376	205

Figure S229. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.14e-15 (Fisher's exact test), Q value = 1e-12

Table S230. Gene #49: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
5P LOSS CNV	19	3	48
5P LOSS WILD-TYPE	343	281	187

Figure S230. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.22e-13 (Fisher's exact test), Q value = 2.9e-10

Table S231. Gene #49: '5p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	213	179	178
5P LOSS CNV	5	2	36
5P LOSS WILD-TYPE	208	177	142

Figure S231. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.02e-14 (Fisher's exact test), Q value = 6.3e-11

Table S232. Gene #49: '5p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	122	142	185
5P LOSS CNV	3	6	33	1
5P LOSS WILD-TYPE	118	116	109	184

Figure S232. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q loss' versus 'MRNA_CNMF'

P value = 9.89e-19 (Chi-square test), Q value = 9.2e-16

Table S233. Gene #50: '5q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
5Q LOSS CNV	2	3	10	44	3	13	0	1
5Q LOSS WILD-TYPE	19	33	109	52	106	59	20	39

Figure S233. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'5q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1.24e-14 (Fisher's exact test), Q value = 1.1e-11

Table S234. Gene #50: '5q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
5Q LOSS CNV	4	47	25
5Q LOSS WILD-TYPE	118	78	241

Figure S234. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'5q loss' versus 'CN_CNMF'

P value = 7.45e-47 (Chi-square test), Q value = 7.1e-44

Table S235. Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	356	212	71	241	54
5Q LOSS CNV	4	15	3	101	6
5Q LOSS WILD-TYPE	352	197	68	140	48

Figure S235. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 5.59e-36 (Chi-square test), Q value = 5.4e-33

Table S236. Gene #50: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	151	99	118	38	96
5Q LOSS CNV	53	3	6	11	0	2
5Q LOSS WILD-TYPE	52	148	93	107	38	94

Figure S236. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5q loss' versus 'RPPA_CNMF'

P value = 1.51e-08 (Fisher's exact test), Q value = 1.2e-05

Table S237. Gene #50: '5q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
5Q LOSS CNV	45	7	13
5Q LOSS WILD-TYPE	102	126	104

Figure S237. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'5q loss' versus 'RPPA_CHIERARCHICAL'

P value = 6.07e-11 (Fisher's exact test), Q value = 5.2e-08

Table S238. Gene #50: '5q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	110	126
5Q LOSS CNV	11	9	45
5Q LOSS WILD-TYPE	150	101	81

Figure S238. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 6.02e-35 (Chi-square test), Q value = 5.8e-32

Table S239. Gene #50: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	158	81	228	146	217	53	16
5Q LOSS CNV	71	2	7	19	20	1	1
5Q LOSS WILD-TYPE	87	79	221	127	197	52	15

Figure S239. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.84e-25 (Fisher's exact test), Q value = 2.7e-22

Table S240. Gene #50: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	215	458
5Q LOSS CNV	80	7	34
5Q LOSS WILD-TYPE	146	208	424

Figure S240. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CNMF'

P value = 1.06e-27 (Fisher's exact test), Q value = 1e-24

Table S241. Gene #50: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
5Q LOSS CNV	9	23	89
5Q LOSS WILD-TYPE	225	369	166

Figure S241. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.11e-33 (Fisher's exact test), Q value = 8.7e-30

Table S242. Gene #50: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
5Q LOSS CNV	28	5	88
5Q LOSS WILD-TYPE	334	279	147

Figure S242. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.91e-24 (Fisher's exact test), Q value = 2.8e-21

Table S243. Gene #50: '5q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	213	179	178
5Q LOSS CNV	9	3	63
5Q LOSS WILD-TYPE	204	176	115

Figure S243. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.3e-25 (Fisher's exact test), Q value = 1.2e-22

Table S244. Gene #50: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	122	142	185
5Q LOSS CNV	4	10	58	3
5Q LOSS WILD-TYPE	117	112	84	182

Figure S244. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.000114 (Fisher's exact test), Q value = 0.069

Table S245. Gene #51: '6p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
6P LOSS CNV	18	4	46
6P LOSS WILD-TYPE	104	121	220

Figure S245. Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6p loss' versus 'CN_CNMF'

P value = 6.45e-10 (Chi-square test), Q value = 5.4e-07

Table S246. Gene #51: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	356	212	71	241	54
6P LOSS CNV	21	50	10	18	11
6P LOSS WILD-TYPE	335	162	61	223	43

Figure S246. Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

'6p loss' versus 'METHLYATION_CNMF'

P value = 5.6e-05 (Chi-square test), Q value = 0.036

Table S247. Gene #51: '6p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	151	99	118	38	96
6P LOSS CNV	5	13	12	26	2	4
6P LOSS WILD-TYPE	100	138	87	92	36	92

Figure S247. Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6p loss' versus 'MRNASEQ_CNMF'

P value = 3.76e-05 (Chi-square test), Q value = 0.024

Table S248. Gene #51: '6p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	158	81	228	146	217	53	16
6P LOSS CNV	9	7	26	13	47	5	0
6P LOSS WILD-TYPE	149	74	202	133	170	48	16

Figure S248. Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.87e-06 (Fisher's exact test), Q value = 0.0062

Table S249. Gene #51: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	215	458
6P LOSS CNV	12	18	77
6P LOSS WILD-TYPE	214	197	381

Figure S249. Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'MRNA_CNMF'

P value = 5.75e-05 (Chi-square test), Q value = 0.036

Table S250. Gene #52: '6q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
6Q LOSS CNV	3	10	38	6	21	9	1	11
6Q LOSS WILD-TYPE	18	26	81	90	88	63	19	29

Figure S250. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'6q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1.24e-06 (Fisher's exact test), Q value = 0.00092

Table S251. Gene #52: '6q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
6Q LOSS CNV	28	6	65
6Q LOSS WILD-TYPE	94	119	201

Figure S251. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6q loss' versus 'CN_CNMF'

P value = 5.44e-16 (Chi-square test), Q value = 5e-13

Table S252. Gene #52: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	356	212	71	241	54
6Q LOSS CNV	45	77	12	20	18
6Q LOSS WILD-TYPE	311	135	59	221	36

Figure S252. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

'6q loss' versus 'METHLYATION_CNMF'

P value = 1.64e-07 (Chi-square test), Q value = 0.00013

Table S253. Gene #52: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	151	99	118	38	96
6Q LOSS CNV	7	32	20	38	6	4
6Q LOSS WILD-TYPE	98	119	79	80	32	92

Figure S253. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6q loss' versus 'MRNASEQ_CNMF'

P value = 3.18e-08 (Chi-square test), Q value = 2.6e-05

Table S254. Gene #52: '6q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	158	81	228	146	217	53	16
6Q LOSS CNV	11	13	43	19	70	11	1
6Q LOSS WILD-TYPE	147	68	185	127	147	42	15

Figure S254. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.18e-07 (Fisher's exact test), Q value = 0.00069

Table S255. Gene #52: '6q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	215	458
6Q LOSS CNV	18	41	109
6Q LOSS WILD-TYPE	208	174	349

Figure S255. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.61e-06 (Fisher's exact test), Q value = 0.0026

Table S256. Gene #52: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
6Q LOSS CNV	89	56	21
6Q LOSS WILD-TYPE	273	228	214

Figure S256. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7p loss' versus 'CN_CNMF'

P value = 4.63e-06 (Chi-square test), Q value = 0.0033

Table S257. Gene #53: '7p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	356	212	71	241	54
7P LOSS CNV	4	16	3	26	1
7P LOSS WILD-TYPE	352	196	68	215	53

Figure S257. Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #3: 'CN_CNMF'

'7q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.08e-05 (Fisher's exact test), Q value = 0.014

Table S258. Gene #54: '7q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
7Q LOSS CNV	37	5	18
7Q LOSS WILD-TYPE	325	279	217

Figure S258. Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8p loss' versus 'MRNA_CNMF'

P value = 0.000309 (Chi-square test), Q value = 0.18

Table S259. Gene #55: '8p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
8P LOSS CNV	4	9	54	27	19	28	4	15
8P LOSS WILD-TYPE	17	27	65	69	90	44	16	25

Figure S259. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'8p loss' versus 'CN_CNMF'

P value = 2.11e-16 (Chi-square test), Q value = 2e-13

Table S260. Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	356	212	71	241	54
8P LOSS CNV	57	96	9	96	20
8P LOSS WILD-TYPE	299	116	62	145	34

Figure S260. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 6.53e-07 (Chi-square test), Q value = 5e-04

Table S261. Gene #55: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	151	99	118	38	96
8P LOSS CNV	34	29	33	54	7	14
8P LOSS WILD-TYPE	71	122	66	64	31	82

Figure S261. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 2.7e-07 (Chi-square test), Q value = 0.00021

Table S262. Gene #55: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	158	81	228	146	217	53	16
8P LOSS CNV	47	14	43	54	92	13	7
8P LOSS WILD-TYPE	111	67	185	92	125	40	9

Figure S262. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.3e-05 (Fisher's exact test), Q value = 0.022

Table S263. Gene #55: '8p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	213	179	178
8P LOSS CNV	80	31	56
8P LOSS WILD-TYPE	133	148	122

Figure S263. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9p loss' versus 'MRNA_CNMF'

P value = 1.8e-05 (Chi-square test), Q value = 0.012

Table S264. Gene #57: '9p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
9P LOSS CNV	6	8	40	18	11	26	5	2
9P LOSS WILD-TYPE	15	28	79	78	98	46	15	38

Figure S264. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'9p loss' versus 'MRNA_CHIERARCHICAL'

P value = 2.89e-05 (Fisher's exact test), Q value = 0.019

Table S265. Gene #57: '9p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
9P LOSS CNV	12	25	79
9P LOSS WILD-TYPE	110	100	187

Figure S265. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

P value = 1.39e-20 (Chi-square test), Q value = 1.3e-17

Table S266. Gene #57: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	356	212	71	241	54
9P LOSS CNV	22	80	7	69	15
9P LOSS WILD-TYPE	334	132	64	172	39

Figure S266. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 1.21e-14 (Chi-square test), Q value = 1.1e-11

Table S267. Gene #57: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	151	99	118	38	96
9P LOSS CNV	24	6	31	44	7	3
9P LOSS WILD-TYPE	81	145	68	74	31	93

Figure S267. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 5.1e-11 (Chi-square test), Q value = 4.4e-08

Table S268. Gene #57: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	158	81	228	146	217	53	16
9P LOSS CNV	29	6	26	46	72	3	4
9P LOSS WILD-TYPE	129	75	202	100	145	50	12

Figure S268. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.47e-07 (Fisher's exact test), Q value = 0.00042

Table S269. Gene #57: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	215	458
9P LOSS CNV	49	19	118
9P LOSS WILD-TYPE	177	196	340

Figure S269. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_CNMF'

P value = 2.64e-05 (Fisher's exact test), Q value = 0.018

Table S270. Gene #57: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
9P LOSS CNV	25	92	64
9P LOSS WILD-TYPE	209	300	191

Figure S270. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.08e-07 (Fisher's exact test), Q value = 0.00024

Table S271. Gene #57: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
9P LOSS CNV	92	29	60
9P LOSS WILD-TYPE	270	255	175

Figure S271. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000129 (Fisher's exact test), Q value = 0.078

Table S272. Gene #57: '9p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	213	179	178
9P LOSS CNV	47	16	43
9P LOSS WILD-TYPE	166	163	135

Figure S272. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.11e-06 (Fisher's exact test), Q value = 0.00083

Table S273. Gene #57: '9p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	122	142	185
9P LOSS CNV	17	38	35	16
9P LOSS WILD-TYPE	104	84	107	169

Figure S273. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1.5e-05 (Fisher's exact test), Q value = 0.01

Table S274. Gene #58: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
9Q LOSS CNV	6	24	61
9Q LOSS WILD-TYPE	116	101	205

Figure S274. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 1.36e-17 (Chi-square test), Q value = 1.3e-14

Table S275. Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	356	212	71	241	54
9Q LOSS CNV	11	57	7	61	15
9Q LOSS WILD-TYPE	345	155	64	180	39

Figure S275. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 4.42e-11 (Chi-square test), Q value = 3.8e-08

Table S276. Gene #58: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	151	99	118	38	96
9Q LOSS CNV	31	6	19	30	3	2
9Q LOSS WILD-TYPE	74	145	80	88	35	94

Figure S276. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 1.07e-08 (Chi-square test), Q value = 8.7e-06

Table S277. Gene #58: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	158	81	228	146	217	53	16
9Q LOSS CNV	40	2	22	20	54	2	4
9Q LOSS WILD-TYPE	118	79	206	126	163	51	12

Figure S277. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.25e-07 (Fisher's exact test), Q value = 0.00025

Table S278. Gene #58: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	215	458
9Q LOSS CNV	45	11	88
9Q LOSS WILD-TYPE	181	204	370

Figure S278. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_CNMF'

P value = 1.72e-05 (Fisher's exact test), Q value = 0.012

Table S279. Gene #58: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
9Q LOSS CNV	17	64	56
9Q LOSS WILD-TYPE	217	328	199

Figure S279. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.8e-10 (Fisher's exact test), Q value = 3.2e-07

Table S280. Gene #58: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
9Q LOSS CNV	64	15	58
9Q LOSS WILD-TYPE	298	269	177

Figure S280. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 7.03e-06 (Fisher's exact test), Q value = 0.005

Table S281. Gene #58: '9q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	213	179	178
9Q LOSS CNV	26	10	41
9Q LOSS WILD-TYPE	187	169	137

Figure S281. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.97e-12 (Fisher's exact test), Q value = 2.6e-09

Table S282. Gene #58: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	122	142	185
9Q LOSS CNV	8	24	40	5
9Q LOSS WILD-TYPE	113	98	102	180

Figure S282. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 1.41e-05 (Chi-square test), Q value = 0.0097

Table S283. Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	356	212	71	241	54
10P LOSS CNV	9	27	8	31	6
10P LOSS WILD-TYPE	347	185	63	210	48

Figure S283. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

'10q loss' versus 'MRNA_CNMF'

P value = 0.000163 (Chi-square test), Q value = 0.098

Table S284. Gene #60: '10q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
10Q LOSS CNV	7	2	24	18	6	9	2	0
10Q LOSS WILD-TYPE	14	34	95	78	103	63	18	40

Figure S284. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'10q loss' versus 'CN_CNMF'

P value = 6.04e-13 (Chi-square test), Q value = 5.4e-10

Table S285. Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	356	212	71	241	54
10Q LOSS CNV	10	35	8	58	6
10Q LOSS WILD-TYPE	346	177	63	183	48

Figure S285. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 3.67e-06 (Chi-square test), Q value = 0.0026

Table S286. Gene #60: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	151	99	118	38	96
10Q LOSS CNV	23	8	15	21	3	1
10Q LOSS WILD-TYPE	82	143	84	97	35	95

Figure S286. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 3.82e-07 (Chi-square test), Q value = 0.00029

Table S287. Gene #60: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	158	81	228	146	217	53	16
10Q LOSS CNV	29	1	15	24	41	0	1
10Q LOSS WILD-TYPE	129	80	213	122	176	53	15

Figure S287. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000313 (Fisher's exact test), Q value = 0.18

Table S288. Gene #60: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	215	458
10Q LOSS CNV	36	11	64
10Q LOSS WILD-TYPE	190	204	394

Figure S288. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 1.25e-14 (Chi-square test), Q value = 1.1e-11

Table S289. Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	356	212	71	241	54
11P LOSS CNV	15	58	12	58	5
11P LOSS WILD-TYPE	341	154	59	183	49

Figure S289. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 8.73e-08 (Chi-square test), Q value = 6.9e-05

Table S290. Gene #61: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	151	99	118	38	96
11P LOSS CNV	22	11	24	27	2	1
11P LOSS WILD-TYPE	83	140	75	91	36	95

Figure S290. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p loss' versus 'MRNASEQ_CNMF'

P value = 0.000128 (Chi-square test), Q value = 0.077

Table S291. Gene #61: '11p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	158	81	228	146	217	53	16
11P LOSS CNV	30	5	21	34	45	5	1
11P LOSS WILD-TYPE	128	76	207	112	172	48	15

Figure S291. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.02e-05 (Fisher's exact test), Q value = 0.014

Table S292. Gene #61: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
11P LOSS CNV	74	23	44
11P LOSS WILD-TYPE	288	261	191

Figure S292. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000234 (Fisher's exact test), Q value = 0.14

Table S293. Gene #61: '11p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	213	179	178
11P LOSS CNV	35	10	33
11P LOSS WILD-TYPE	178	169	145

Figure S293. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11q loss' versus 'MRNA_CNMF'

P value = 7.42e-06 (Chi-square test), Q value = 0.0052

Table S294. Gene #62: '11q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
11Q LOSS CNV	5	12	57	16	22	19	3	9
11Q LOSS WILD-TYPE	16	24	62	80	87	53	17	31

Figure S294. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'11q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.000266 (Fisher's exact test), Q value = 0.15

Table S295. Gene #62: '11q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
11Q LOSS CNV	30	20	93
11Q LOSS WILD-TYPE	92	105	173

Figure S295. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

P value = 2.34e-32 (Chi-square test), Q value = 2.2e-29

Table S296. Gene #62: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	356	212	71	241	54
11Q LOSS CNV	40	120	19	50	7
11Q LOSS WILD-TYPE	316	92	52	191	47

Figure S296. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

P value = 2.29e-12 (Chi-square test), Q value = 2e-09

Table S297. Gene #62: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	151	99	118	38	96
11Q LOSS CNV	17	30	35	54	7	4
11Q LOSS WILD-TYPE	88	121	64	64	31	92

Figure S297. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11q loss' versus 'MRNASEQ_CNMF'

P value = 9.63e-13 (Chi-square test), Q value = 8.6e-10

Table S298. Gene #62: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	158	81	228	146	217	53	16
11Q LOSS CNV	23	17	46	32	99	8	1
11Q LOSS WILD-TYPE	135	64	182	114	118	45	15

Figure S298. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.82e-05 (Fisher's exact test), Q value = 0.012

Table S299. Gene #62: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	215	458
11Q LOSS CNV	34	50	142
11Q LOSS WILD-TYPE	192	165	316

Figure S299. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.09e-05 (Fisher's exact test), Q value = 0.0076

Table S300. Gene #62: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
11Q LOSS CNV	123	58	44
11Q LOSS WILD-TYPE	239	226	191

Figure S300. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12p loss' versus 'METHLYATION_CNMF'

P value = 1.69e-05 (Chi-square test), Q value = 0.011

Table S301. Gene #63: '12p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	151	99	118	38	96
12P LOSS CNV	18	7	3	8	6	1
12P LOSS WILD-TYPE	87	144	96	110	32	95

Figure S301. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.000409 (Fisher's exact test), Q value = 0.23

Table S302. Gene #64: '12q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
12Q LOSS CNV	3	18	12
12Q LOSS WILD-TYPE	119	107	254

Figure S302. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'12q loss' versus 'CN_CNMF'

P value = 7.14e-05 (Chi-square test), Q value = 0.045

Table S303. Gene #64: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	356	212	71	241	54
12Q LOSS CNV	11	9	5	29	1
12Q LOSS WILD-TYPE	345	203	66	212	53

Figure S303. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

'12q loss' versus 'METHLYATION_CNMF'

P value = 1.52e-08 (Chi-square test), Q value = 1.2e-05

Table S304. Gene #64: '12q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	151	99	118	38	96
12Q LOSS CNV	20	2	3	7	2	1
12Q LOSS WILD-TYPE	85	149	96	111	36	95

Figure S304. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12q loss' versus 'MRNASEQ_CNMF'

P value = 1.98e-09 (Chi-square test), Q value = 1.6e-06

Table S305. Gene #64: '12q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	158	81	228	146	217	53	16
12Q LOSS CNV	27	1	7	8	7	0	0
12Q LOSS WILD-TYPE	131	80	221	138	210	53	16

Figure S305. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.11e-07 (Fisher's exact test), Q value = 8.8e-05

Table S306. Gene #64: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	215	458
12Q LOSS CNV	30	3	17
12Q LOSS WILD-TYPE	196	212	441

Figure S306. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q loss' versus 'MIRSEQ_CNMF'

P value = 3.21e-06 (Fisher's exact test), Q value = 0.0023

Table S307. Gene #64: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
12Q LOSS CNV	6	13	31
12Q LOSS WILD-TYPE	228	379	224

Figure S307. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.34e-06 (Fisher's exact test), Q value = 0.00099

Table S308. Gene #64: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
12Q LOSS CNV	13	7	30
12Q LOSS WILD-TYPE	349	277	205

Figure S308. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.061

Table S309. Gene #64: '12q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	213	179	178
12Q LOSS CNV	6	5	22
12Q LOSS WILD-TYPE	207	174	156

Figure S309. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8.54e-05 (Fisher's exact test), Q value = 0.053

Table S310. Gene #64: '12q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	122	142	185
12Q LOSS CNV	4	5	20	4
12Q LOSS WILD-TYPE	117	117	122	181

Figure S310. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q loss' versus 'MRNA_CNMF'

P value = 0.000435 (Chi-square test), Q value = 0.24

Table S311. Gene #65: '13q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
13Q LOSS CNV	5	9	55	32	24	25	4	5
13Q LOSS WILD-TYPE	16	27	64	64	85	47	16	35

Figure S311. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'13q loss' versus 'CN_CNMF'

P value = 8.5e-28 (Chi-square test), Q value = 8.1e-25

Table S312. Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	356	212	71	241	54
13Q LOSS CNV	30	92	32	88	32
13Q LOSS WILD-TYPE	326	120	39	153	22

Figure S312. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 1.7e-09 (Chi-square test), Q value = 1.4e-06

Table S313. Gene #65: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	151	99	118	38	96
13Q LOSS CNV	38	33	47	40	2	11
13Q LOSS WILD-TYPE	67	118	52	78	36	85

Figure S313. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 4.31e-05 (Chi-square test), Q value = 0.028

Table S314. Gene #65: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	158	81	228	146	217	53	16
13Q LOSS CNV	55	13	51	46	86	9	5
13Q LOSS WILD-TYPE	103	68	177	100	131	44	11

Figure S314. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.88e-07 (Fisher's exact test), Q value = 0.00022

Table S315. Gene #65: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	215	458
13Q LOSS CNV	72	33	160
13Q LOSS WILD-TYPE	154	182	298

Figure S315. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_CNMF'

P value = 2.49e-08 (Fisher's exact test), Q value = 2e-05

Table S316. Gene #65: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
13Q LOSS CNV	36	131	95
13Q LOSS WILD-TYPE	198	261	160

Figure S316. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'14q loss' versus 'MRNA_CNMF'

P value = 8.47e-11 (Chi-square test), Q value = 7.3e-08

Table S317. Gene #66: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
14Q LOSS CNV	2	1	25	36	5	8	3	0
14Q LOSS WILD-TYPE	19	35	94	60	104	64	17	40

Figure S317. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'14q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1.1e-08 (Fisher's exact test), Q value = 9e-06

Table S318. Gene #66: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
14Q LOSS CNV	4	38	38
14Q LOSS WILD-TYPE	118	87	228

Figure S318. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 3.9e-24 (Chi-square test), Q value = 3.7e-21

Table S319. Gene #66: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	356	212	71	241	54
14Q LOSS CNV	10	25	9	81	15
14Q LOSS WILD-TYPE	346	187	62	160	39

Figure S319. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 8.47e-16 (Chi-square test), Q value = 7.8e-13

Table S320. Gene #66: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	151	99	118	38	96
14Q LOSS CNV	40	6	17	15	1	3
14Q LOSS WILD-TYPE	65	145	82	103	37	93

Figure S320. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q loss' versus 'RPPA_CNMF'

P value = 0.000185 (Fisher's exact test), Q value = 0.11

Table S321. Gene #66: '14q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
14Q LOSS CNV	39	12	14
14Q LOSS WILD-TYPE	108	121	103

Figure S321. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'14q loss' versus 'RPPA_CHIERARCHICAL'

P value = 8.52e-05 (Fisher's exact test), Q value = 0.053

Table S322. Gene #66: '14q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	110	126
14Q LOSS CNV	18	11	36
14Q LOSS WILD-TYPE	143	99	90

Figure S322. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 5.87e-21 (Chi-square test), Q value = 5.5e-18

Table S323. Gene #66: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	158	81	228	146	217	53	16
14Q LOSS CNV	61	2	13	16	40	0	3
14Q LOSS WILD-TYPE	97	79	215	130	177	53	13

Figure S323. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.9e-13 (Fisher's exact test), Q value = 4.4e-10

Table S324. Gene #66: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	215	458
14Q LOSS CNV	66	9	60
14Q LOSS WILD-TYPE	160	206	398

Figure S324. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_CNMF'

P value = 5.57e-13 (Fisher's exact test), Q value = 5e-10

Table S325. Gene #66: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
14Q LOSS CNV	19	34	74
14Q LOSS WILD-TYPE	215	358	181

Figure S325. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'14q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.18e-13 (Fisher's exact test), Q value = 1.1e-10

Table S326. Gene #66: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
14Q LOSS CNV	36	20	71
14Q LOSS WILD-TYPE	326	264	164

Figure S326. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 5.5e-10 (Fisher's exact test), Q value = 4.6e-07

Table S327. Gene #66: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	213	179	178
14Q LOSS CNV	22	10	52
14Q LOSS WILD-TYPE	191	169	126

Figure S327. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'14q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.79e-08 (Fisher's exact test), Q value = 3.8e-05

Table S328. Gene #66: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	122	142	185
14Q LOSS CNV	12	19	42	11
14Q LOSS WILD-TYPE	109	103	100	174

Figure S328. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.000102 (Fisher's exact test), Q value = 0.062

Table S329. Gene #67: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
15Q LOSS CNV	11	38	51
15Q LOSS WILD-TYPE	111	87	215

Figure S329. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 6.25e-20 (Chi-square test), Q value = 5.9e-17

Table S330. Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	356	212	71	241	54
15Q LOSS CNV	19	34	29	77	9
15Q LOSS WILD-TYPE	337	178	42	164	45

Figure S330. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 2.99e-08 (Chi-square test), Q value = 2.4e-05

Table S331. Gene #67: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	151	99	118	38	96
15Q LOSS CNV	39	16	21	17	3	8
15Q LOSS WILD-TYPE	66	135	78	101	35	88

Figure S331. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 1.74e-05 (Chi-square test), Q value = 0.012

Table S332. Gene #67: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	158	81	228	146	217	53	16
15Q LOSS CNV	48	9	34	29	34	1	4
15Q LOSS WILD-TYPE	110	72	194	117	183	52	12

Figure S332. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.65e-05 (Fisher's exact test), Q value = 0.024

Table S333. Gene #67: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	215	458
15Q LOSS CNV	60	22	77
15Q LOSS WILD-TYPE	166	193	381

Figure S333. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_CNMF'

P value = 0.000121 (Fisher's exact test), Q value = 0.073

Table S334. Gene #67: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
15Q LOSS CNV	28	63	67
15Q LOSS WILD-TYPE	206	329	188

Figure S334. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.37e-07 (Fisher's exact test), Q value = 0.00071

Table S335. Gene #67: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
15Q LOSS CNV	63	29	66
15Q LOSS WILD-TYPE	299	255	169

Figure S335. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.17e-06 (Fisher's exact test), Q value = 0.00088

Table S336. Gene #67: '15q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	213	179	178
15Q LOSS CNV	36	11	46
15Q LOSS WILD-TYPE	177	168	132

Figure S336. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000319 (Fisher's exact test), Q value = 0.18

Table S337. Gene #67: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	122	142	185
15Q LOSS CNV	10	17	39	27
15Q LOSS WILD-TYPE	111	105	103	158

Figure S337. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p loss' versus 'CN_CNMF'

P value = 1.22e-05 (Chi-square test), Q value = 0.0084

Table S338. Gene #68: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	356	212	71	241	54
16P LOSS CNV	6	18	2	28	4
16P LOSS WILD-TYPE	350	194	69	213	50

Figure S338. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

'16p loss' versus 'METHLYATION_CNMF'

P value = 7.44e-05 (Chi-square test), Q value = 0.047

Table S339. Gene #68: '16p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	151	99	118	38	96
16P LOSS CNV	14	1	8	4	1	2
16P LOSS WILD-TYPE	91	150	91	114	37	94

Figure S339. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16p loss' versus 'MRNASEQ_CNMF'

P value = 9.88e-05 (Chi-square test), Q value = 0.061

Table S340. Gene #68: '16p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	158	81	228	146	217	53	16
16P LOSS CNV	22	1	6	10	16	1	0
16P LOSS WILD-TYPE	136	80	222	136	201	52	16

Figure S340. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000125 (Fisher's exact test), Q value = 0.076

Table S341. Gene #68: '16p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	215	458
16P LOSS CNV	24	3	29
16P LOSS WILD-TYPE	202	212	429

Figure S341. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.24

Table S342. Gene #68: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
16P LOSS CNV	5	23	27
16P LOSS WILD-TYPE	229	369	228

Figure S342. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000305 (Fisher's exact test), Q value = 0.17

Table S343. Gene #68: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
16P LOSS CNV	20	8	27
16P LOSS WILD-TYPE	342	276	208

Figure S343. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'MRNA_CNMF'

P value = 3.67e-08 (Chi-square test), Q value = 2.9e-05

Table S344. Gene #69: '16q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
16Q LOSS CNV	11	19	56	17	68	33	7	24
16Q LOSS WILD-TYPE	10	17	63	79	41	39	13	16

Figure S344. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'16q loss' versus 'MRNA_CHIERARCHICAL'

P value = 6.5e-14 (Fisher's exact test), Q value = 5.9e-11

Table S345. Gene #69: '16q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
16Q LOSS CNV	64	21	150
16Q LOSS WILD-TYPE	58	104	116

Figure S345. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'16q loss' versus 'CN_CNMF'

P value = 6.67e-12 (Chi-square test), Q value = 5.9e-09

Table S346. Gene #69: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	356	212	71	241	54
16Q LOSS CNV	167	103	45	57	31
16Q LOSS WILD-TYPE	189	109	26	184	23

Figure S346. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 1.16e-17 (Chi-square test), Q value = 1.1e-14

Table S347. Gene #69: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	151	99	118	38	96
16Q LOSS CNV	20	103	50	48	13	19
16Q LOSS WILD-TYPE	85	48	49	70	25	77

Figure S347. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16q loss' versus 'RPPA_CNMF'

P value = 4.59e-06 (Fisher's exact test), Q value = 0.0033

Table S348. Gene #69: '16q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
16Q LOSS CNV	40	74	54
16Q LOSS WILD-TYPE	107	59	63

Figure S348. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'16q loss' versus 'RPPA_CHIERARCHICAL'

P value = 8.65e-10 (Fisher's exact test), Q value = 7.3e-07

Table S349. Gene #69: '16q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	110	126
16Q LOSS CNV	90	53	25
16Q LOSS WILD-TYPE	71	57	101

Figure S349. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 1.35e-21 (Chi-square test), Q value = 1.3e-18

Table S350. Gene #69: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	158	81	228	146	217	53	16
16Q LOSS CNV	26	40	154	51	92	26	3
16Q LOSS WILD-TYPE	132	41	74	95	125	27	13

Figure S350. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.06e-24 (Fisher's exact test), Q value = 8.6e-21

Table S351. Gene #69: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	215	458
16Q LOSS CNV	37	97	258
16Q LOSS WILD-TYPE	189	118	200

Figure S351. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_CNMF'

P value = 1.26e-15 (Fisher's exact test), Q value = 1.2e-12

Table S352. Gene #69: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
16Q LOSS CNV	107	217	59
16Q LOSS WILD-TYPE	127	175	196

Figure S352. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.33e-19 (Fisher's exact test), Q value = 5e-16

Table S353. Gene #69: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
16Q LOSS CNV	164	170	49
16Q LOSS WILD-TYPE	198	114	186

Figure S353. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.32e-14 (Fisher's exact test), Q value = 1.2e-11

Table S354. Gene #69: '16q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	213	179	178
16Q LOSS CNV	107	93	30
16Q LOSS WILD-TYPE	106	86	148

Figure S354. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.45e-10 (Fisher's exact test), Q value = 1.2e-07

Table S355. Gene #69: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	122	142	185
16Q LOSS CNV	61	43	27	99
16Q LOSS WILD-TYPE	60	79	115	86

Figure S355. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'MRNA_CNMF'

P value = 1.75e-06 (Chi-square test), Q value = 0.0013

Table S356. Gene #70: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
17P LOSS CNV	11	19	56	42	27	47	3	15
17P LOSS WILD-TYPE	10	17	63	54	82	25	17	25

Figure S356. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17p loss' versus 'CN_CNMF'

P value = 3.64e-13 (Chi-square test), Q value = 3.3e-10

Table S357. Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	356	212	71	241	54
17P LOSS CNV	91	113	25	128	24
17P LOSS WILD-TYPE	265	99	46	113	30

Figure S357. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 3.39e-09 (Chi-square test), Q value = 2.8e-06

Table S358. Gene #70: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	151	99	118	38	96
17P LOSS CNV	40	49	56	64	12	16
17P LOSS WILD-TYPE	65	102	43	54	26	80

Figure S358. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 1.58e-06 (Chi-square test), Q value = 0.0012

Table S359. Gene #70: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	158	81	228	146	217	53	16
17P LOSS CNV	60	28	67	83	107	19	5
17P LOSS WILD-TYPE	98	53	161	63	110	34	11

Figure S359. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q loss' versus 'MRNA_CNMF'

P value = 1.99e-11 (Chi-square test), Q value = 1.7e-08

Table S360. Gene #71: '17q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
17Q LOSS CNV	2	2	16	31	5	30	0	7
17Q LOSS WILD-TYPE	19	34	103	65	104	42	20	33

Figure S360. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17q loss' versus 'MRNA_CHIERARCHICAL'

P value = 2.63e-06 (Fisher's exact test), Q value = 0.0019

Table S361. Gene #71: '17q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
17Q LOSS CNV	12	42	39
17Q LOSS WILD-TYPE	110	83	227

Figure S361. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

P value = 2.21e-11 (Chi-square test), Q value = 1.9e-08

Table S362. Gene #71: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	356	212	71	241	54
17Q LOSS CNV	26	31	10	72	8
17Q LOSS WILD-TYPE	330	181	61	169	46

Figure S362. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

'17q loss' versus 'METHLYATION_CNMF'

P value = 1.25e-05 (Chi-square test), Q value = 0.0086

Table S363. Gene #71: '17q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	151	99	118	38	96
17Q LOSS CNV	26	6	16	20	2	8
17Q LOSS WILD-TYPE	79	145	83	98	36	88

Figure S363. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q loss' versus 'RPPA_CNMF'

P value = 1.1e-09 (Fisher's exact test), Q value = 9.2e-07

Table S364. Gene #71: '17q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
17Q LOSS CNV	51	7	20
17Q LOSS WILD-TYPE	96	126	97

Figure S364. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'17q loss' versus 'RPPA_CHIERARCHICAL'

P value = 3.1e-07 (Fisher's exact test), Q value = 0.00024

Table S365. Gene #71: '17q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	110	126
17Q LOSS CNV	16	17	45
17Q LOSS WILD-TYPE	145	93	81

Figure S365. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'17q loss' versus 'MRNASEQ_CNMF'

P value = 1.41e-13 (Chi-square test), Q value = 1.3e-10

Table S366. Gene #71: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	158	81	228	146	217	53	16
17Q LOSS CNV	41	3	13	48	27	9	2
17Q LOSS WILD-TYPE	117	78	215	98	190	44	14

Figure S366. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.01e-07 (Fisher's exact test), Q value = 8e-05

Table S367. Gene #71: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	215	458
17Q LOSS CNV	64	22	57
17Q LOSS WILD-TYPE	162	193	401

Figure S367. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_CNMF'

P value = 5.26e-07 (Fisher's exact test), Q value = 4e-04

Table S368. Gene #71: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
17Q LOSS CNV	26	46	68
17Q LOSS WILD-TYPE	208	346	187

Figure S368. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.59e-05 (Fisher's exact test), Q value = 0.011

Table S369. Gene #71: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
17Q LOSS CNV	50	30	60
17Q LOSS WILD-TYPE	312	254	175

Figure S369. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p loss' versus 'MRNA_CNMF'

P value = 0.000176 (Chi-square test), Q value = 0.1

Table S370. Gene #72: '18p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
18P LOSS CNV	6	5	25	14	13	30	5	9
18P LOSS WILD-TYPE	15	31	94	82	96	42	15	31

Figure S370. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'18p loss' versus 'CN_CNMF'

P value = 1.99e-08 (Chi-square test), Q value = 1.6e-05

Table S371. Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	356	212	71	241	54
18P LOSS CNV	32	58	21	58	12
18P LOSS WILD-TYPE	324	154	50	183	42

Figure S371. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

P value = 1.49e-06 (Chi-square test), Q value = 0.0011

Table S372. Gene #72: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	151	99	118	38	96
18P LOSS CNV	13	16	33	31	3	11
18P LOSS WILD-TYPE	92	135	66	87	35	85

Figure S372. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p loss' versus 'MRNASEQ_CNMF'

P value = 2.01e-10 (Chi-square test), Q value = 1.7e-07

Table S373. Gene #72: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	158	81	228	146	217	53	16
18P LOSS CNV	21	4	30	54	48	9	7
18P LOSS WILD-TYPE	137	77	198	92	169	44	9

Figure S373. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 5.82e-11 (Chi-square test), Q value = 5e-08

Table S374. Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	356	212	71	241	54
18Q LOSS CNV	28	58	23	64	11
18Q LOSS WILD-TYPE	328	154	48	177	43

Figure S374. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 7.63e-09 (Chi-square test), Q value = 6.3e-06

Table S375. Gene #73: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	151	99	118	38	96
18Q LOSS CNV	21	16	37	31	2	7
18Q LOSS WILD-TYPE	84	135	62	87	36	89

Figure S375. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 1.93e-08 (Chi-square test), Q value = 1.6e-05

Table S376. Gene #73: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	158	81	228	146	217	53	16
18Q LOSS CNV	25	5	30	53	49	7	5
18Q LOSS WILD-TYPE	133	76	198	93	168	46	11

Figure S376. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p loss' versus 'MRNA_CNMF'

P value = 0.00022 (Chi-square test), Q value = 0.13

Table S377. Gene #74: '19p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
19P LOSS CNV	1	4	15	6	2	15	1	0
19P LOSS WILD-TYPE	20	32	104	90	107	57	19	40

Figure S377. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'19p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.000355 (Fisher's exact test), Q value = 0.2

Table S378. Gene #74: '19p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
19P LOSS CNV	2	8	34
19P LOSS WILD-TYPE	120	117	232

Figure S378. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

P value = 2.33e-14 (Chi-square test), Q value = 2.1e-11

Table S379. Gene #74: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	356	212	71	241	54
19P LOSS CNV	2	39	1	19	8
19P LOSS WILD-TYPE	354	173	70	222	46

Figure S379. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

P value = 8.91e-10 (Chi-square test), Q value = 7.5e-07

Table S380. Gene #74: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	151	99	118	38	96
19P LOSS CNV	9	0	7	22	0	0
19P LOSS WILD-TYPE	96	151	92	96	38	96

Figure S380. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p loss' versus 'MRNASEQ_CNMF'

P value = 3.44e-07 (Chi-square test), Q value = 0.00027

Table S381. Gene #74: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	158	81	228	146	217	53	16
19P LOSS CNV	10	2	5	19	32	0	0
19P LOSS WILD-TYPE	148	79	223	127	185	53	16

Figure S381. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000252 (Fisher's exact test), Q value = 0.15

Table S382. Gene #74: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	215	458
19P LOSS CNV	19	4	45
19P LOSS WILD-TYPE	207	211	413

Figure S382. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q loss' versus 'MRNA_CNMF'

P value = 0.000443 (Chi-square test), Q value = 0.24

Table S383. Gene #75: '19q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
19Q LOSS CNV	0	3	12	4	2	13	1	0
19Q LOSS WILD-TYPE	21	33	107	92	107	59	19	40

Figure S383. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'19q loss' versus 'MRNA_CHIERARCHICAL'

P value = 6.38e-05 (Fisher's exact test), Q value = 0.04

Table S384. Gene #75: '19q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
19Q LOSS CNV	0	7	28
19Q LOSS WILD-TYPE	122	118	238

Figure S384. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 2.78e-10 (Chi-square test), Q value = 2.4e-07

Table S385. Gene #75: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	356	212	71	241	54
19Q LOSS CNV	3	29	0	14	7
19Q LOSS WILD-TYPE	353	183	71	227	47

Figure S385. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

P value = 1.27e-05 (Chi-square test), Q value = 0.0087

Table S386. Gene #75: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	151	99	118	38	96
19Q LOSS CNV	8	0	7	14	0	0
19Q LOSS WILD-TYPE	97	151	92	104	38	96

Figure S386. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q loss' versus 'MRNASEQ_CNMF'

P value = 2.49e-05 (Chi-square test), Q value = 0.017

Table S387. Gene #75: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	158	81	228	146	217	53	16
19Q LOSS CNV	7	2	4	17	23	0	0
19Q LOSS WILD-TYPE	151	79	224	129	194	53	16

Figure S387. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.5e-05 (Fisher's exact test), Q value = 0.017

Table S388. Gene #75: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	215	458
19Q LOSS CNV	15	1	37
19Q LOSS WILD-TYPE	211	214	421

Figure S388. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p loss' versus 'CN_CNMF'

P value = 1.93e-07 (Chi-square test), Q value = 0.00015

Table S389. Gene #76: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	356	212	71	241	54
20P LOSS CNV	3	17	2	26	8
20P LOSS WILD-TYPE	353	195	69	215	46

Figure S389. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

'20p loss' versus 'METHLYATION_CNMF'

P value = 8.96e-05 (Chi-square test), Q value = 0.056

Table S390. Gene #76: '20p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	151	99	118	38	96
20P LOSS CNV	15	2	6	7	1	1
20P LOSS WILD-TYPE	90	149	93	111	37	95

Figure S390. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p loss' versus 'MRNASEQ_CNMF'

P value = 0.000398 (Chi-square test), Q value = 0.22

Table S391. Gene #76: '20p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	158	81	228	146	217	53	16
20P LOSS CNV	18	1	5	10	18	0	0
20P LOSS WILD-TYPE	140	80	223	136	199	53	16

Figure S391. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000226 (Fisher's exact test), Q value = 0.13

Table S392. Gene #76: '20p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	215	458
20P LOSS CNV	23	3	26
20P LOSS WILD-TYPE	203	212	432

Figure S392. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p loss' versus 'MIRSEQ_CNMF'

P value = 0.000176 (Fisher's exact test), Q value = 0.1

Table S393. Gene #76: '20p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
20P LOSS CNV	7	15	28
20P LOSS WILD-TYPE	227	377	227

Figure S393. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000223 (Fisher's exact test), Q value = 0.13

Table S394. Gene #76: '20p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
20P LOSS CNV	22	5	23
20P LOSS WILD-TYPE	340	279	212

Figure S394. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000181 (Fisher's exact test), Q value = 0.11

Table S395. Gene #76: '20p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	213	179	178
20P LOSS CNV	7	4	21
20P LOSS WILD-TYPE	206	175	157

Figure S395. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.24e-05 (Fisher's exact test), Q value = 0.033

Table S396. Gene #76: '20p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	122	142	185
20P LOSS CNV	4	8	18	2
20P LOSS WILD-TYPE	117	114	124	183

Figure S396. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q loss' versus 'CN_CNMF'

P value = 0.000197 (Chi-square test), Q value = 0.12

Table S397. Gene #77: '20q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	356	212	71	241	54
20Q LOSS CNV	1	7	2	16	4
20Q LOSS WILD-TYPE	355	205	69	225	50

Figure S397. Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #3: 'CN_CNMF'

'20q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Chi-square test), Q value = 0.007

Table S398. Gene #77: '20q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	151	99	118	38	96
20Q LOSS CNV	11	1	1	2	0	1
20Q LOSS WILD-TYPE	94	150	98	116	38	95

Figure S398. Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q loss' versus 'MIRSEQ_CNMF'

P value = 0.000443 (Fisher's exact test), Q value = 0.24

Table S399. Gene #77: '20q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
20Q LOSS CNV	3	7	18
20Q LOSS WILD-TYPE	231	385	237

Figure S399. Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.3e-05 (Fisher's exact test), Q value = 0.022

Table S400. Gene #77: '20q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
20Q LOSS CNV	8	2	18
20Q LOSS WILD-TYPE	354	282	217

Figure S400. Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.95e-06 (Fisher's exact test), Q value = 0.0014

Table S401. Gene #77: '20q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	213	179	178
20Q LOSS CNV	1	2	16
20Q LOSS WILD-TYPE	212	177	162

Figure S401. Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.92e-07 (Fisher's exact test), Q value = 6e-04

Table S402. Gene #77: '20q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	122	142	185
20Q LOSS CNV	2	2	15	0
20Q LOSS WILD-TYPE	119	120	127	185

Figure S402. Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q loss' versus 'CN_CNMF'

P value = 1.02e-06 (Chi-square test), Q value = 0.00077

Table S403. Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	356	212	71	241	54
21Q LOSS CNV	9	31	9	30	9
21Q LOSS WILD-TYPE	347	181	62	211	45

Figure S403. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'MRNA_CNMF'

P value = 0.000201 (Chi-square test), Q value = 0.12

Table S404. Gene #79: '22q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
22Q LOSS CNV	7	17	59	18	40	19	5	13
22Q LOSS WILD-TYPE	14	19	60	78	69	53	15	27

Figure S404. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'22q loss' versus 'MRNA_CHIERARCHICAL'

P value = 2.12e-07 (Fisher's exact test), Q value = 0.00016

Table S405. Gene #79: '22q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
22Q LOSS CNV	47	19	112
22Q LOSS WILD-TYPE	75	106	154

Figure S405. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 3.51e-09 (Chi-square test), Q value = 2.9e-06

Table S406. Gene #79: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	356	212	71	241	54
22Q LOSS CNV	87	89	38	69	29
22Q LOSS WILD-TYPE	269	123	33	172	25

Figure S406. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 3.36e-06 (Chi-square test), Q value = 0.0024

Table S407. Gene #79: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	105	151	99	118	38	96
22Q LOSS CNV	28	52	40	57	9	14
22Q LOSS WILD-TYPE	77	99	59	61	29	82

Figure S407. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1.64e-05 (Fisher's exact test), Q value = 0.011

Table S408. Gene #79: '22q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	110	126
22Q LOSS CNV	74	40	25
22Q LOSS WILD-TYPE	87	70	101

Figure S408. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 2.91e-06 (Chi-square test), Q value = 0.0021

Table S409. Gene #79: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	158	81	228	146	217	53	16
22Q LOSS CNV	31	24	89	39	100	16	5
22Q LOSS WILD-TYPE	127	57	139	107	117	37	11

Figure S409. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.79e-12 (Fisher's exact test), Q value = 2.5e-09

Table S410. Gene #79: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	215	458
22Q LOSS CNV	36	71	197
22Q LOSS WILD-TYPE	190	144	261

Figure S410. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CNMF'

P value = 1.57e-08 (Fisher's exact test), Q value = 1.3e-05

Table S411. Gene #79: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
22Q LOSS CNV	68	170	55
22Q LOSS WILD-TYPE	166	222	200

Figure S411. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000171 (Fisher's exact test), Q value = 0.1

Table S412. Gene #79: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
22Q LOSS CNV	137	103	53
22Q LOSS WILD-TYPE	225	181	182

Figure S412. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.57e-07 (Fisher's exact test), Q value = 0.00028

Table S413. Gene #79: '22q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	213	179	178
22Q LOSS CNV	97	49	37
22Q LOSS WILD-TYPE	116	130	141

Figure S413. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Xq loss' versus 'CN_CNMF'

P value = 3.47e-05 (Chi-square test), Q value = 0.023

Table S414. Gene #80: 'Xq loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	356	212	71	241	54
XQ LOSS CNV	0	9	2	18	2
XQ LOSS WILD-TYPE	356	203	69	223	52

Figure S414. Get High-res Image Gene #80: 'Xq loss' versus Molecular Subtype #3: 'CN_CNMF'

Methods & Data

Input

Mutation data file = broad_values_by_arm.mutsig.cluster.txt
Molecular subtypes file = BRCA-TP.transferedmergedcluster.txt
Number of patients = 934
Number of significantly arm-level cnvs = 80
Number of molecular subtypes = 12
Exclude genes that fewer than K tumors have mutations, K = 3

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

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

References

[1] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)

[2] 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)

[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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