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

Breast Invasive Carcinoma (Primary solid tumor)

23 September 2013 | analyses__2013_09_23

Maintainer Information

Citation Information

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

Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1WW7FZP

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 985 patients, 455 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', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
1q gain cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_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', and 'MRNASEQ_CNMF'.
4q gain cnv correlated to 'MRNA_CNMF', '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_CHIERARCHICAL'.
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'.
7q gain cnv correlated to 'CN_CNMF'.
8p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
8q gain cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
9p gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_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'.
11q gain cnv correlated to 'CN_CNMF'.
12p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
12q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
14q gain cnv correlated to 'MRNA_CNMF', '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'.
16q gain cnv correlated to 'MRNASEQ_CHIERARCHICAL'.
17q gain cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_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', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
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', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
20q gain cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Xq gain cnv correlated to 'MRNA_CHIERARCHICAL', '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', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
2q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
3p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
3q loss cnv correlated to 'CN_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', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
7p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
7q loss cnv correlated to 'MIRSEQ_CHIERARCHICAL'.
8p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 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', and 'MIRSEQ_MATURE_CNMF'.
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', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
11p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
12q 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'.
13q loss cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_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', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_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', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
19q loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_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', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', '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_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Xq loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_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, 455 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%)	933	4.41e-08 (3.43e-05)	2.44e-10 (2.05e-07)	3.76e-12 (3.3e-09)	1.36e-07 (0.000102)	5.42e-09 (4.37e-06)	1.03e-07 (7.82e-05)	2.32e-12 (2.04e-09)	1.12e-15 (1.02e-12)	7.53e-10 (6.2e-07)	1.63e-09 (1.33e-06)	6.7e-09 (5.38e-06)	2.43e-07 (0.000179)
10p gain	0 (0%)	867	9.81e-11 (8.31e-08)	8.01e-08 (6.13e-05)	3.5e-19 (3.26e-16)	2.51e-15 (2.28e-12)	9.23e-06 (0.00601)	6.71e-07 (0.000478)	8.68e-19 (8.07e-16)	1.37e-14 (1.24e-11)	2.99e-13 (2.66e-10)	1.13e-11 (9.74e-09)	1.63e-11 (1.41e-08)	1e-12 (8.86e-10)
4p loss	0 (0%)	783	2.8e-13 (2.49e-10)	2.1e-12 (1.84e-09)	2.91e-29 (2.78e-26)	2.75e-20 (2.57e-17)	4.26e-05 (0.0255)	1.78e-06 (0.00123)	6.16e-22 (5.81e-19)	6.44e-21 (6.04e-18)	1.71e-18 (1.59e-15)	2.71e-16 (2.49e-13)	1.58e-12 (1.4e-09)	2.05e-11 (1.75e-08)
5p loss	0 (0%)	910	1.88e-08 (1.49e-05)	9.1e-06 (0.00594)	1.91e-20 (1.79e-17)	4e-12 (3.5e-09)	4.28e-05 (0.0256)	6.72e-06 (0.00444)	1.18e-15 (1.07e-12)	2.66e-10 (2.22e-07)	2.32e-12 (2.04e-09)	3.08e-14 (2.77e-11)	1.93e-11 (1.65e-08)	1.56e-08 (1.24e-05)
5q loss	0 (0%)	849	2.06e-18 (1.91e-15)	1.84e-14 (1.66e-11)	4.34e-52 (4.16e-49)	1.01e-32 (9.65e-30)	7.26e-09 (5.81e-06)	1.7e-10 (1.43e-07)	1.36e-36 (1.3e-33)	5.74e-28 (5.46e-25)	4.76e-30 (4.54e-27)	5.17e-35 (4.95e-32)	4.27e-21 (4.01e-18)	1.19e-21 (1.12e-18)
14q loss	0 (0%)	833	2.54e-10 (2.12e-07)	1.32e-08 (1.05e-05)	2.57e-24 (2.44e-21)	4.24e-17 (3.91e-14)	0.000185 (0.101)	8.52e-05 (0.0496)	4.52e-22 (4.26e-19)	2.45e-16 (2.24e-13)	2.8e-17 (2.59e-14)	9.47e-16 (8.66e-13)	2.6e-11 (2.22e-08)	9.94e-10 (8.15e-07)
16q loss	0 (0%)	565	1.13e-08 (8.98e-06)	3e-13 (2.66e-10)	4.47e-12 (3.91e-09)	5.87e-18 (5.44e-15)	2.66e-06 (0.00181)	3.64e-10 (3.02e-07)	4.36e-20 (4.07e-17)	1.46e-22 (1.38e-19)	1.43e-15 (1.3e-12)	1.48e-19 (1.38e-16)	2.05e-12 (1.81e-09)	1.2e-11 (1.04e-08)
1p gain	0 (0%)	881	0.000345 (0.18)	2.81e-06 (0.0019)	5.77e-12 (5.04e-09)	0.00056 (0.281)	1.49e-05 (0.00951)	0.000436 (0.223)	5.42e-08 (4.18e-05)	2.73e-07 (2e-04)	1.25e-07 (9.38e-05)	8.68e-08 (6.63e-05)	0.00122 (0.571)	6.13e-06 (0.00406)
6p gain	0 (0%)	865	0.00017 (0.0938)	0.000252 (0.135)	1.03e-17 (9.54e-15)	3.49e-14 (3.13e-11)	0.00459 (1.00)	0.0486 (1.00)	3.87e-12 (3.39e-09)	1.69e-11 (1.46e-08)	1.55e-10 (1.31e-07)	9.86e-12 (8.56e-09)	1.11e-11 (9.59e-09)	1.38e-08 (1.1e-05)
21q gain	0 (0%)	873	3.09e-05 (0.0189)	0.000302 (0.159)	3.45e-10 (2.87e-07)	1.07e-07 (8.09e-05)	0.0684 (1.00)	0.00554 (1.00)	2.43e-10 (2.03e-07)	5.99e-12 (5.22e-09)	1.52e-09 (1.24e-06)	2.68e-07 (0.000197)	3.68e-08 (2.87e-05)	3.42e-09 (2.76e-06)
4q loss	0 (0%)	816	4.78e-07 (0.000345)	7.12e-08 (5.47e-05)	1.41e-21 (1.33e-18)	4.42e-14 (3.96e-11)	0.0115 (1.00)	0.000976 (0.467)	2.21e-15 (2.01e-12)	1.59e-16 (1.46e-13)	3.23e-13 (2.87e-10)	7.95e-11 (6.74e-08)	1.23e-09 (1.01e-06)	1.18e-07 (8.91e-05)
12q loss	0 (0%)	926	0.000481 (0.244)	0.000108 (0.0619)	7.06e-09 (5.66e-06)	3.4e-13 (3.01e-10)	0.00143 (0.666)	0.00127 (0.596)	2.09e-13 (1.86e-10)	5.1e-09 (4.11e-06)	3e-08 (2.34e-05)	9.86e-10 (8.09e-07)	8.26e-09 (6.6e-06)	7.65e-08 (5.87e-05)
17q loss	0 (0%)	830	1.99e-11 (1.7e-08)	2.63e-06 (0.00179)	6e-12 (5.23e-09)	1.69e-05 (0.0107)	1.1e-09 (9.01e-07)	3.1e-07 (0.000226)	4.01e-14 (3.6e-11)	3.51e-07 (0.000255)	0.00011 (0.0626)	1.83e-05 (0.0115)	0.00702 (1.00)	0.00507 (1.00)
22q loss	0 (0%)	656	0.000201 (0.109)	2.12e-07 (0.000157)	3.65e-14 (3.28e-11)	2.8e-08 (2.2e-05)	0.000476 (0.242)	1.64e-05 (0.0104)	1.08e-06 (0.000761)	6.1e-11 (5.18e-08)	1.66e-06 (0.00115)	1.64e-05 (0.0104)	0.000925 (0.446)	0.000714 (0.354)
6q gain	0 (0%)	911	0.0026 (1.00)	0.0137 (1.00)	7.93e-17 (7.3e-14)	1.97e-07 (0.000146)	0.000273 (0.144)	0.0242 (1.00)	1.85e-07 (0.000137)	4.54e-08 (3.52e-05)	9e-07 (0.000636)	2.41e-08 (1.9e-05)	6.77e-07 (0.000482)	3.64e-06 (0.00245)
9p gain	0 (0%)	913	2.34e-08 (1.84e-05)	1.85e-08 (1.47e-05)	1.22e-10 (1.03e-07)	9.79e-05 (0.0567)	0.00881 (1.00)	0.000106 (0.0611)	3.13e-10 (2.61e-07)	2.69e-08 (2.11e-05)	3.17e-07 (0.000231)	1.96e-06 (0.00135)	0.00316 (1.00)	0.00383 (1.00)
6q loss	0 (0%)	812	2.46e-05 (0.0152)	1.62e-06 (0.00112)	3.76e-18 (3.48e-15)	4.22e-08 (3.29e-05)	0.000956 (0.458)	0.00983 (1.00)	1.7e-10 (1.43e-07)	5.13e-07 (0.000369)	0.000365 (0.19)	1.18e-07 (8.91e-05)	0.00244 (1.00)	7.15e-05 (0.042)
9p loss	0 (0%)	787	3.11e-05 (0.019)	4.42e-05 (0.0263)	5.03e-27 (4.78e-24)	2.1e-13 (1.87e-10)	0.0381 (1.00)	0.858 (1.00)	1.16e-11 (1.01e-08)	1.94e-06 (0.00134)	2.11e-09 (1.72e-06)	2.01e-08 (1.6e-05)	2.73e-05 (0.0168)	0.0473 (1.00)
9q loss	0 (0%)	829	0.00465 (1.00)	2.04e-05 (0.0127)	1.84e-21 (1.73e-18)	1.21e-13 (1.08e-10)	0.00849 (1.00)	0.127 (1.00)	3.19e-11 (2.72e-08)	9.44e-08 (7.21e-05)	5.2e-10 (4.3e-07)	5.42e-10 (4.47e-07)	5.51e-06 (0.00366)	0.000397 (0.204)
15q loss	0 (0%)	808	0.00823 (1.00)	0.000181 (0.0996)	2.12e-23 (2.01e-20)	6.1e-09 (4.9e-06)	0.117 (1.00)	0.00548 (1.00)	7.89e-07 (0.00056)	1.43e-07 (0.000107)	2.29e-06 (0.00156)	8e-07 (0.000566)	8.14e-06 (0.00533)	2.27e-06 (0.00155)
3q gain	0 (0%)	872	0.0141 (1.00)	0.00485 (1.00)	5.88e-11 (5e-08)	2.62e-07 (0.000193)	0.0149 (1.00)	0.11 (1.00)	2.12e-08 (1.67e-05)	6.52e-07 (0.000465)	7.34e-08 (5.63e-05)	1.25e-07 (9.38e-05)	1.24e-06 (0.000869)	1.5e-06 (0.00104)
8q gain	0 (0%)	579	0.000172 (0.0947)	0.00093 (0.448)	1.82e-24 (1.72e-21)	7.37e-12 (6.41e-09)	0.668 (1.00)	0.637 (1.00)	1e-11 (8.7e-09)	1.88e-11 (1.62e-08)	1.37e-09 (1.12e-06)	1.51e-07 (0.000113)	1.22e-07 (9.15e-05)	0.000592 (0.295)
16p gain	0 (0%)	709	1.5e-05 (0.00955)	6.32e-05 (0.0372)	0.00474 (1.00)	8.46e-08 (6.47e-05)	0.000158 (0.088)	0.000183 (0.1)	9.99e-06 (0.00647)	1.84e-06 (0.00127)	0.000725 (0.358)	0.0881 (1.00)	0.000441 (0.225)	0.00663 (1.00)
3p loss	0 (0%)	889	0.000805 (0.393)	0.000576 (0.288)	3.15e-09 (2.55e-06)	3.76e-06 (0.00252)	0.00716 (1.00)	2.44e-05 (0.0151)	5.01e-05 (0.0297)	1.12e-05 (0.00719)	5.28e-07 (0.000379)	0.000258 (0.137)	0.000244 (0.131)	0.00818 (1.00)
13q loss	0 (0%)	698	0.000435 (0.223)	0.00124 (0.582)	3.36e-37 (3.23e-34)	4.46e-11 (3.8e-08)	0.727 (1.00)	0.489 (1.00)	8.71e-05 (0.0506)	1.48e-05 (0.00947)	4.74e-07 (0.000342)	5.09e-05 (0.0301)	0.00021 (0.114)	0.0765 (1.00)
19p loss	0 (0%)	913	0.00022 (0.118)	0.000355 (0.185)	1.78e-14 (1.6e-11)	4.23e-10 (3.5e-07)	0.424 (1.00)	0.0741 (1.00)	4.87e-07 (0.000351)	0.000108 (0.0616)	3.37e-05 (0.0204)	8.81e-07 (0.000623)	0.000774 (0.379)	0.473 (1.00)
19q loss	0 (0%)	929	0.000372 (0.193)	3.92e-05 (0.0235)	1.94e-11 (1.66e-08)	3.35e-06 (0.00226)	0.188 (1.00)	0.135 (1.00)	2.06e-06 (0.00141)	9.99e-05 (0.0575)	9.87e-05 (0.057)	1.26e-06 (0.000882)	0.00118 (0.553)	0.263 (1.00)
20p loss	0 (0%)	927	0.0455 (1.00)	0.0958 (1.00)	9.62e-08 (7.32e-05)	5.31e-08 (4.1e-05)	0.47 (1.00)	0.609 (1.00)	6.93e-06 (0.00456)	1.05e-05 (0.00678)	7.38e-06 (0.00485)	2.37e-07 (0.000175)	1.72e-05 (0.0108)	3.5e-06 (0.00236)
20q loss	0 (0%)	954	0.0886 (1.00)	0.161 (1.00)	2e-05 (0.0125)	5.73e-09 (4.61e-06)	0.374 (1.00)	0.257 (1.00)	1.08e-05 (0.007)	3.21e-05 (0.0195)	8.45e-05 (0.0493)	2.73e-06 (0.00185)	4.5e-07 (0.000326)	2.98e-07 (0.000218)
2q gain	0 (0%)	958	0.00491 (1.00)	3.77e-05 (0.0227)	1.09e-05 (0.00703)	0.00358 (1.00)	1.54e-07 (0.000115)	0.000444 (0.226)	6.41e-05 (0.0377)	1.26e-07 (9.43e-05)	0.00312 (1.00)	0.000125 (0.071)	0.000757 (0.372)	0.00176 (0.797)
18p gain	0 (0%)	893	0.00137 (0.64)	0.00021 (0.114)	2.4e-07 (0.000178)	1.49e-06 (0.00104)	0.0139 (1.00)	0.0126 (1.00)	1.04e-06 (0.000731)	2.19e-10 (1.84e-07)	5.65e-07 (0.000405)	1.25e-05 (0.008)	0.00185 (0.834)	0.00182 (0.821)
20q gain	0 (0%)	690	1.88e-05 (0.0117)	0.0486 (1.00)	5.13e-32 (4.9e-29)	7.28e-12 (6.33e-09)	0.237 (1.00)	0.722 (1.00)	1.46e-09 (1.19e-06)	3.43e-09 (2.77e-06)	1.25e-06 (0.000879)	5.2e-05 (0.0308)	0.0098 (1.00)	0.0628 (1.00)
22q gain	0 (0%)	940	0.0731 (1.00)	0.00146 (0.676)	2.63e-10 (2.19e-07)	0.000907 (0.439)	0.0685 (1.00)	0.153 (1.00)	4.35e-05 (0.0259)	5.13e-08 (3.98e-05)	3.07e-08 (2.4e-05)	1.73e-07 (0.000129)	0.000168 (0.093)	3.98e-05 (0.0239)
2p loss	0 (0%)	909	0.00556 (1.00)	9.96e-05 (0.0575)	1.14e-10 (9.68e-08)	2.9e-07 (0.000212)	0.00858 (1.00)	0.00161 (0.742)	7.62e-06 (0.005)	5.68e-08 (4.38e-05)	1.71e-05 (0.0108)	9.53e-06 (0.00618)	0.0547 (1.00)	0.037 (1.00)
10q loss	0 (0%)	867	0.000204 (0.11)	0.00139 (0.645)	2.15e-13 (1.92e-10)	6.46e-07 (0.000461)	0.0083 (1.00)	0.137 (1.00)	3.48e-07 (0.000254)	7.02e-06 (0.00462)	0.000252 (0.134)	5.29e-05 (0.0312)	0.0026 (1.00)	0.00554 (1.00)
11q loss	0 (0%)	734	3.29e-06 (0.00223)	0.000185 (0.101)	2.99e-29 (2.85e-26)	1.53e-14 (1.38e-11)	0.222 (1.00)	0.3 (1.00)	8.45e-13 (7.47e-10)	0.000208 (0.113)	0.074 (1.00)	3.66e-05 (0.0221)	0.00646 (1.00)	0.0085 (1.00)
16p loss	0 (0%)	927	0.0115 (1.00)	0.0196 (1.00)	5.3e-06 (0.00353)	1.07e-07 (8.13e-05)	0.134 (1.00)	0.238 (1.00)	9.23e-07 (0.000651)	0.000626 (0.311)	2.71e-05 (0.0167)	1.63e-06 (0.00113)	0.000108 (0.0618)	0.000222 (0.119)
17q gain	0 (0%)	853	2.59e-06 (0.00176)	0.00808 (1.00)	1.71e-23 (1.62e-20)	1.08e-05 (0.00695)	0.585 (1.00)	0.0113 (1.00)	2.29e-14 (2.06e-11)	1.17e-07 (8.88e-05)	0.00254 (1.00)	9.08e-06 (0.00593)	0.617 (1.00)	0.0115 (1.00)
20p gain	0 (0%)	729	1.32e-05 (0.00844)	0.0634 (1.00)	8.43e-23 (7.97e-20)	1.69e-06 (0.00117)	0.036 (1.00)	0.173 (1.00)	1.14e-05 (0.00733)	3.26e-06 (0.00221)	0.000387 (0.2)	0.0457 (1.00)	0.147 (1.00)	0.168 (1.00)
7p loss	0 (0%)	934	0.066 (1.00)	0.00287 (1.00)	4.23e-06 (0.00283)	6.32e-06 (0.00418)	0.491 (1.00)	0.592 (1.00)	4.07e-05 (0.0244)	0.000805 (0.393)	2.65e-05 (0.0163)	3.13e-05 (0.0191)	0.00426 (1.00)	0.000194 (0.106)
8p loss	0 (0%)	692	0.00172 (0.782)	0.142 (1.00)	2.99e-17 (2.76e-14)	2.56e-08 (2.02e-05)	0.599 (1.00)	0.86 (1.00)	2.93e-08 (2.3e-05)	0.000985 (0.469)	4.58e-06 (0.00306)	2e-07 (0.000148)	1.93e-05 (0.0121)	0.102 (1.00)
1q gain	0 (0%)	459	0.00033 (0.173)	0.532 (1.00)	5.81e-09 (4.67e-06)	1.07e-15 (9.8e-13)	0.0593 (1.00)	0.102 (1.00)	3.06e-10 (2.55e-07)	0.0146 (1.00)	0.0886 (1.00)	7.33e-05 (0.043)	0.0773 (1.00)	0.0427 (1.00)
12p gain	0 (0%)	862	0.0044 (1.00)	0.00154 (0.711)	6.24e-15 (5.65e-12)	1.3e-06 (0.000906)	0.246 (1.00)	0.0679 (1.00)	1.73e-05 (0.0108)	3.74e-06 (0.00251)	0.000585 (0.292)	0.000636 (0.316)	1.44e-05 (0.00921)	0.0281 (1.00)
14q gain	0 (0%)	903	0.000383 (0.198)	0.00304 (1.00)	5.19e-06 (0.00346)	0.001 (0.476)	0.949 (1.00)	0.316 (1.00)	0.000114 (0.065)	0.000203 (0.11)	0.00029 (0.153)	0.0302 (1.00)	0.1 (1.00)	0.366 (1.00)
Xq gain	0 (0%)	960	0.000854 (0.416)	0.000161 (0.0899)	0.000719 (0.355)	0.00444 (1.00)	0.0754 (1.00)	0.00725 (1.00)	5.39e-06 (0.00359)	3.9e-05 (0.0235)	2.84e-05 (0.0174)	2.36e-05 (0.0147)	0.0286 (1.00)	0.0114 (1.00)
1p loss	0 (0%)	853	0.00166 (0.758)	2.25e-08 (1.78e-05)	4.51e-20 (4.21e-17)	2.09e-08 (1.66e-05)	0.699 (1.00)	0.416 (1.00)	1.21e-07 (9.12e-05)	1.22e-13 (1.09e-10)	0.00105 (0.498)	0.000886 (0.43)	0.481 (1.00)	0.0083 (1.00)
2q loss	0 (0%)	892	0.0741 (1.00)	0.00163 (0.747)	1.21e-10 (1.02e-07)	5.28e-07 (0.000379)	0.0236 (1.00)	0.0219 (1.00)	0.00166 (0.758)	0.000151 (0.0845)	0.000167 (0.0928)	0.000136 (0.0766)	0.0264 (1.00)	0.372 (1.00)
6p loss	0 (0%)	874	0.00996 (1.00)	0.000114 (0.0648)	5.34e-10 (4.41e-07)	0.000137 (0.0773)	0.0191 (1.00)	0.00741 (1.00)	1.53e-06 (0.00107)	1.7e-05 (0.0107)	0.00687 (1.00)	0.00088 (0.428)	0.0495 (1.00)	0.0059 (1.00)
11p loss	0 (0%)	827	0.0236 (1.00)	0.0942 (1.00)	1.64e-16 (1.5e-13)	1.92e-11 (1.65e-08)	0.0663 (1.00)	0.00732 (1.00)	0.000119 (0.0674)	0.00195 (0.872)	0.00014 (0.0789)	2.9e-05 (0.0178)	0.00364 (1.00)	0.00833 (1.00)
12p loss	0 (0%)	911	0.423 (1.00)	0.107 (1.00)	0.000485 (0.246)	1.58e-06 (0.0011)	0.0958 (1.00)	0.251 (1.00)	0.000519 (0.261)	0.000431 (0.221)	0.000216 (0.116)	0.000168 (0.093)	0.0024 (1.00)	0.00189 (0.85)
Xq loss	0 (0%)	954	0.317 (1.00)	0.169 (1.00)	0.000337 (0.176)	0.000166 (0.0925)	0.0326 (1.00)	0.316 (1.00)	0.0171 (1.00)	0.00797 (1.00)	0.000153 (0.0854)	0.00014 (0.0789)	0.00033 (0.173)	0.00655 (1.00)
4p gain	0 (0%)	953	9.4e-06 (0.00611)	9.59e-05 (0.0556)	8.31e-10 (6.83e-07)	0.00102 (0.485)	0.0485 (1.00)	0.0396 (1.00)	2.82e-07 (0.000207)	0.00262 (1.00)	0.00194 (0.869)	0.00292 (1.00)	0.000539 (0.271)	0.0154 (1.00)
4q gain	0 (0%)	955	3.56e-05 (0.0216)	0.000499 (0.252)	1.35e-10 (1.13e-07)	0.0139 (1.00)	0.082 (1.00)	0.0162 (1.00)	4.21e-07 (0.000305)	0.00423 (1.00)	0.00436 (1.00)	0.000282 (0.149)	0.0158 (1.00)	0.00769 (1.00)
18q gain	0 (0%)	904	0.00155 (0.714)	0.00519 (1.00)	7.96e-07 (0.000564)	0.0377 (1.00)	0.311 (1.00)	0.274 (1.00)	1.53e-05 (0.00973)	5.28e-08 (4.08e-05)	0.000149 (0.0837)	0.00305 (1.00)	0.0385 (1.00)	0.0645 (1.00)
17p loss	0 (0%)	579	1.51e-06 (0.00105)	0.676 (1.00)	8.71e-16 (7.97e-13)	2.88e-09 (2.34e-06)	0.00269 (1.00)	0.135 (1.00)	6.17e-07 (0.000442)	0.198 (1.00)	0.0336 (1.00)	0.108 (1.00)	0.0132 (1.00)	0.893 (1.00)
18p loss	0 (0%)	794	0.000176 (0.0967)	0.431 (1.00)	5.96e-08 (4.59e-05)	4.19e-07 (0.000304)	0.892 (1.00)	0.962 (1.00)	3.06e-09 (2.48e-06)	0.114 (1.00)	0.0184 (1.00)	0.00896 (1.00)	0.0469 (1.00)	0.655 (1.00)
5q gain	0 (0%)	868	0.00918 (1.00)	0.00267 (1.00)	3.82e-17 (3.52e-14)	0.0047 (1.00)	0.004 (1.00)	0.00371 (1.00)	0.00132 (0.614)	8.3e-05 (0.0485)	0.0211 (1.00)	0.000102 (0.0589)	0.0556 (1.00)	0.0129 (1.00)
8p gain	0 (0%)	798	0.0512 (1.00)	0.102 (1.00)	4.85e-11 (4.12e-08)	8.21e-05 (0.048)	0.263 (1.00)	0.17 (1.00)	0.00165 (0.754)	8.21e-06 (0.00537)	0.0214 (1.00)	0.507 (1.00)	0.027 (1.00)	0.249 (1.00)
18q loss	0 (0%)	790	0.000762 (0.374)	0.42 (1.00)	3.25e-10 (2.7e-07)	7.33e-10 (6.04e-07)	0.535 (1.00)	0.828 (1.00)	4.95e-08 (3.84e-05)	0.0425 (1.00)	0.0314 (1.00)	0.119 (1.00)	0.00945 (1.00)	0.982 (1.00)
10q gain	0 (0%)	935	0.0162 (1.00)	0.0437 (1.00)	6.26e-07 (0.000448)	0.0636 (1.00)	0.0313 (1.00)	0.0317 (1.00)	2.45e-05 (0.0151)	0.000614 (0.306)	0.00839 (1.00)	0.246 (1.00)	0.0132 (1.00)	0.0435 (1.00)
12q gain	0 (0%)	894	0.0224 (1.00)	0.0149 (1.00)	1.16e-15 (1.06e-12)	2.39e-05 (0.0149)	0.275 (1.00)	0.4 (1.00)	0.0554 (1.00)	0.00169 (0.769)	0.192 (1.00)	0.0464 (1.00)	0.241 (1.00)	0.164 (1.00)
3p gain	0 (0%)	920	0.262 (1.00)	0.16 (1.00)	9.46e-08 (7.21e-05)	0.191 (1.00)	0.444 (1.00)	0.278 (1.00)	0.0162 (1.00)	0.000932 (0.448)	0.00228 (1.00)	0.0248 (1.00)	0.0222 (1.00)	0.0582 (1.00)
5p gain	0 (0%)	801	0.377 (1.00)	0.483 (1.00)	9.73e-14 (8.7e-11)	0.0034 (1.00)	0.622 (1.00)	0.282 (1.00)	0.313 (1.00)	0.0587 (1.00)	0.0781 (1.00)	0.695 (1.00)	0.167 (1.00)	0.553 (1.00)
7q gain	0 (0%)	845	0.00863 (1.00)	0.0127 (1.00)	0.00037 (0.192)	0.00548 (1.00)	0.539 (1.00)	0.374 (1.00)	0.00889 (1.00)	0.00292 (1.00)	0.0159 (1.00)	0.0143 (1.00)	0.0695 (1.00)	0.117 (1.00)
9q gain	0 (0%)	925	0.533 (1.00)	0.0755 (1.00)	3.48e-06 (0.00235)	0.128 (1.00)	1 (1.00)	0.488 (1.00)	0.116 (1.00)	0.0284 (1.00)	0.0724 (1.00)	0.12 (1.00)	0.418 (1.00)	0.95 (1.00)
11q gain	0 (0%)	933	0.517 (1.00)	0.943 (1.00)	0.000257 (0.137)	0.23 (1.00)	0.97 (1.00)	0.881 (1.00)	0.543 (1.00)	0.199 (1.00)	0.172 (1.00)	0.0619 (1.00)	0.6 (1.00)	0.151 (1.00)
16q gain	0 (0%)	921	0.513 (1.00)	0.363 (1.00)	0.00222 (0.987)	0.0755 (1.00)	0.0937 (1.00)	0.631 (1.00)	0.0762 (1.00)	0.000268 (0.142)	0.00753 (1.00)	0.00177 (0.801)	0.00503 (1.00)	0.00764 (1.00)
19p gain	0 (0%)	911	0.12 (1.00)	0.0329 (1.00)	3.62e-05 (0.0219)	0.147 (1.00)	0.0302 (1.00)	0.0902 (1.00)	0.0451 (1.00)	0.00194 (0.868)	0.00365 (1.00)	0.021 (1.00)	0.0816 (1.00)	0.339 (1.00)
19q gain	0 (0%)	891	0.172 (1.00)	0.051 (1.00)	4.9e-05 (0.0291)	0.0343 (1.00)	0.127 (1.00)	0.209 (1.00)	0.0595 (1.00)	0.00542 (1.00)	0.0298 (1.00)	0.0508 (1.00)	0.0388 (1.00)	0.17 (1.00)
3q loss	0 (0%)	939	0.0432 (1.00)	0.0122 (1.00)	3.18e-05 (0.0193)	0.0101 (1.00)	0.356 (1.00)	0.0852 (1.00)	0.014 (1.00)	0.00511 (1.00)	0.0047 (1.00)	0.0265 (1.00)	0.0138 (1.00)	0.482 (1.00)
7q loss	0 (0%)	921	0.59 (1.00)	0.0815 (1.00)	0.016 (1.00)	0.108 (1.00)	0.236 (1.00)	0.421 (1.00)	0.424 (1.00)	0.157 (1.00)	0.00444 (1.00)	0.000414 (0.213)	0.0361 (1.00)	0.155 (1.00)
10p loss	0 (0%)	905	0.00645 (1.00)	0.00276 (1.00)	5.62e-06 (0.00373)	0.00719 (1.00)	0.764 (1.00)	0.408 (1.00)	0.000979 (0.467)	0.00498 (1.00)	0.0601 (1.00)	0.0141 (1.00)	0.134 (1.00)	0.102 (1.00)
21q loss	0 (0%)	896	0.0153 (1.00)	0.197 (1.00)	2.55e-07 (0.000188)	0.151 (1.00)	1 (1.00)	0.812 (1.00)	0.597 (1.00)	0.585 (1.00)	0.169 (1.00)	0.199 (1.00)	0.148 (1.00)	0.893 (1.00)
7p gain	0 (0%)	807	0.234 (1.00)	0.402 (1.00)	0.00766 (1.00)	0.0305 (1.00)	0.947 (1.00)	0.52 (1.00)	0.143 (1.00)	0.0571 (1.00)	0.372 (1.00)	0.361 (1.00)	0.499 (1.00)	0.436 (1.00)
11p gain	0 (0%)	914	0.954 (1.00)	0.843 (1.00)	0.000916 (0.442)	0.135 (1.00)	0.544 (1.00)	0.282 (1.00)	0.201 (1.00)	0.157 (1.00)	0.0298 (1.00)	0.00738 (1.00)	0.495 (1.00)	0.114 (1.00)
13q gain	0 (0%)	936	0.519 (1.00)	0.345 (1.00)	0.0439 (1.00)	0.0793 (1.00)	0.0642 (1.00)	0.258 (1.00)	0.106 (1.00)	0.00115 (0.543)	0.0287 (1.00)	0.0117 (1.00)	0.76 (1.00)	0.245 (1.00)
15q gain	0 (0%)	938	0.711 (1.00)	0.462 (1.00)	0.575 (1.00)	0.457 (1.00)	0.817 (1.00)	0.561 (1.00)	0.536 (1.00)	0.103 (1.00)	0.178 (1.00)	0.266 (1.00)	0.102 (1.00)	0.547 (1.00)
17p gain	0 (0%)	939	0.0114 (1.00)	0.44 (1.00)	0.00197 (0.877)	0.646 (1.00)	0.222 (1.00)	0.235 (1.00)	0.099 (1.00)	0.728 (1.00)	0.261 (1.00)	0.354 (1.00)	0.33 (1.00)	0.578 (1.00)
1q loss	0 (0%)	961	0.654 (1.00)	0.101 (1.00)	0.0106 (1.00)	0.00973 (1.00)	0.438 (1.00)	0.921 (1.00)	0.057 (1.00)	0.0117 (1.00)	0.0676 (1.00)	0.0187 (1.00)	0.602 (1.00)	0.129 (1.00)
8q loss	0 (0%)	933	0.277 (1.00)	0.664 (1.00)	0.00563 (1.00)	0.017 (1.00)	0.823 (1.00)	0.857 (1.00)	0.606 (1.00)	0.132 (1.00)	0.163 (1.00)	0.0653 (1.00)	0.0643 (1.00)	0.651 (1.00)

'1p gain' versus 'MRNA_CNMF'

P value = 0.000345 (Chi-square test), Q value = 0.18

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	25	5	11	4	5
1P GAIN WILD-TYPE	20	34	107	71	104	61	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 = 2.81e-06 (Fisher's exact test), Q value = 0.0019

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	15	32	18
1P GAIN WILD-TYPE	107	93	248

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

'1p gain' versus 'CN_CNMF'

P value = 5.77e-12 (Chi-square test), Q value = 5e-09

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	374	232	79	252	48
1P GAIN CNV	19	17	4	58	6
1P GAIN WILD-TYPE	355	215	75	194	42

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

'1p gain' versus 'RPPA_CNMF'

P value = 1.49e-05 (Fisher's exact test), Q value = 0.0095

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	5
1P GAIN WILD-TYPE	113	120	112

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

'1p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.000436 (Fisher's exact test), Q value = 0.22

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	27
1P GAIN WILD-TYPE	141	105	99

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

'1p gain' versus 'MRNASEQ_CNMF'

P value = 5.42e-08 (Chi-square test), Q value = 4.2e-05

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	175	139	217	154	224	47	15
1P GAIN CNV	42	9	16	13	17	2	3
1P GAIN WILD-TYPE	133	130	201	141	207	45	12

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

'1p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.73e-07 (Fisher's exact test), Q value = 2e-04

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	291	246	434
1P GAIN CNV	22	50	30
1P GAIN WILD-TYPE	269	196	404

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

'1p gain' versus 'MIRSEQ_CNMF'

P value = 1.25e-07 (Fisher's exact test), Q value = 9.4e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	274	413	279
1P GAIN CNV	17	30	55
1P GAIN WILD-TYPE	257	383	224

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

'1p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.68e-08 (Fisher's exact test), Q value = 6.6e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	225	376	365
1P GAIN CNV	48	24	30
1P GAIN WILD-TYPE	177	352	335

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

'1p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.13e-06 (Fisher's exact test), Q value = 0.0041

Table S10. Gene #1: '1p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	311	185
1P GAIN CNV	7	21	35
1P GAIN WILD-TYPE	153	290	150

Figure S10. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1q gain' versus 'MRNA_CNMF'

P value = 0.00033 (Chi-square test), Q value = 0.17

Table S11. Gene #2: '1q 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
1Q GAIN CNV	12	18	52	53	83	37	10	24
1Q GAIN WILD-TYPE	9	18	67	43	26	35	10	16

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

'1q gain' versus 'CN_CNMF'

P value = 5.81e-09 (Chi-square test), Q value = 4.7e-06

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	374	232	79	252	48
1Q GAIN CNV	189	123	70	120	24
1Q GAIN WILD-TYPE	185	109	9	132	24

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

'1q gain' versus 'METHLYATION_CNMF'

P value = 1.07e-15 (Chi-square test), Q value = 9.8e-13

Table S13. Gene #2: '1q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	109	155	106	136	44	113
1Q GAIN CNV	51	119	66	56	23	30
1Q GAIN WILD-TYPE	58	36	40	80	21	83

Figure S13. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1q gain' versus 'MRNASEQ_CNMF'

P value = 3.06e-10 (Chi-square test), Q value = 2.5e-07

Table S14. 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	175	139	217	154	224	47	15
1Q GAIN CNV	87	71	162	75	93	26	6
1Q GAIN WILD-TYPE	88	68	55	79	131	21	9

Figure S14. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.33e-05 (Fisher's exact test), Q value = 0.043

Table S15. Gene #2: '1q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	225	376	365
1Q GAIN CNV	108	233	173
1Q GAIN WILD-TYPE	117	143	192

Figure S15. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2p gain' versus 'MRNA_CNMF'

P value = 4.41e-08 (Chi-square test), Q value = 3.4e-05

Table S16. 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 S16. 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 = 2e-07

Table S17. 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 S17. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'2p gain' versus 'CN_CNMF'

P value = 3.76e-12 (Chi-square test), Q value = 3.3e-09

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	374	232	79	252	48
2P GAIN CNV	2	10	2	36	2
2P GAIN WILD-TYPE	372	222	77	216	46

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

'2p gain' versus 'METHLYATION_CNMF'

P value = 1.36e-07 (Chi-square test), Q value = 1e-04

Table S19. Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	109	155	106	136	44	113
2P GAIN CNV	18	2	4	5	1	2
2P GAIN WILD-TYPE	91	153	102	131	43	111

Figure S19. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2p gain' versus 'RPPA_CNMF'

P value = 5.42e-09 (Fisher's exact test), Q value = 4.4e-06

Table S20. Gene #3: '2p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
2P GAIN CNV	24	0	3
2P GAIN WILD-TYPE	123	133	114

Figure S20. 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 = 7.8e-05

Table S21. 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 S21. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'2p gain' versus 'MRNASEQ_CNMF'

P value = 2.32e-12 (Chi-square test), Q value = 2e-09

Table S22. 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	175	139	217	154	224	47	15
2P GAIN CNV	26	0	3	18	4	0	1
2P GAIN WILD-TYPE	149	139	214	136	220	47	14

Figure S22. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.12e-15 (Fisher's exact test), Q value = 1e-12

Table S23. Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	291	246	434
2P GAIN CNV	0	38	14
2P GAIN WILD-TYPE	291	208	420

Figure S23. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_CNMF'

P value = 7.53e-10 (Fisher's exact test), Q value = 6.2e-07

Table S24. Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	274	413	279
2P GAIN CNV	1	13	32
2P GAIN WILD-TYPE	273	400	247

Figure S24. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.63e-09 (Fisher's exact test), Q value = 1.3e-06

Table S25. Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	225	376	365
2P GAIN CNV	26	2	18
2P GAIN WILD-TYPE	199	374	347

Figure S25. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.7e-09 (Fisher's exact test), Q value = 5.4e-06

Table S26. Gene #3: '2p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	210	196
2P GAIN CNV	4	2	25
2P GAIN WILD-TYPE	246	208	171

Figure S26. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'2p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.43e-07 (Fisher's exact test), Q value = 0.00018

Table S27. Gene #3: '2p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	311	185
2P GAIN CNV	3	5	23
2P GAIN WILD-TYPE	157	306	162

Figure S27. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q gain' versus 'MRNA_CHIERARCHICAL'

P value = 3.77e-05 (Fisher's exact test), Q value = 0.023

Table S28. 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	13	6
2Q GAIN WILD-TYPE	122	112	260

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

'2q gain' versus 'CN_CNMF'

P value = 1.09e-05 (Chi-square test), Q value = 0.007

Table S29. Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	374	232	79	252	48
2Q GAIN CNV	1	6	2	18	0
2Q GAIN WILD-TYPE	373	226	77	234	48

Figure S29. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

'2q gain' versus 'RPPA_CNMF'

P value = 1.54e-07 (Fisher's exact test), Q value = 0.00011

Table S30. Gene #4: '2q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
2Q GAIN CNV	16	0	0
2Q GAIN WILD-TYPE	131	133	117

Figure S30. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'2q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.000444 (Fisher's exact test), Q value = 0.23

Table S31. Gene #4: '2q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	110	126
2Q GAIN CNV	4	0	12
2Q GAIN WILD-TYPE	157	110	114

Figure S31. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'2q gain' versus 'MRNASEQ_CNMF'

P value = 6.41e-05 (Chi-square test), Q value = 0.038

Table S32. Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	175	139	217	154	224	47	15
2Q GAIN CNV	12	0	3	10	2	0	0
2Q GAIN WILD-TYPE	163	139	214	144	222	47	15

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

'2q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.26e-07 (Fisher's exact test), Q value = 9.4e-05

Table S33. Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	291	246	434
2Q GAIN CNV	0	19	8
2Q GAIN WILD-TYPE	291	227	426

Figure S33. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000125 (Fisher's exact test), Q value = 0.071

Table S34. Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	225	376	365
2Q GAIN CNV	12	1	9
2Q GAIN WILD-TYPE	213	375	356

Figure S34. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3p gain' versus 'CN_CNMF'

P value = 9.46e-08 (Chi-square test), Q value = 7.2e-05

Table S35. Gene #5: '3p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	374	232	79	252	48
3P GAIN CNV	3	23	10	21	8
3P GAIN WILD-TYPE	371	209	69	231	40

Figure S35. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #3: 'CN_CNMF'

'3q gain' versus 'CN_CNMF'

P value = 5.88e-11 (Chi-square test), Q value = 5e-08

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	374	232	79	252	48
3Q GAIN CNV	9	32	13	51	8
3Q GAIN WILD-TYPE	365	200	66	201	40

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

'3q gain' versus 'METHLYATION_CNMF'

P value = 2.62e-07 (Chi-square test), Q value = 0.00019

Table S37. Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	109	155	106	136	44	113
3Q GAIN CNV	26	7	11	12	5	2
3Q GAIN WILD-TYPE	83	148	95	124	39	111

Figure S37. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3q gain' versus 'MRNASEQ_CNMF'

P value = 2.12e-08 (Chi-square test), Q value = 1.7e-05

Table S38. 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	175	139	217	154	224	47	15
3Q GAIN CNV	42	6	17	22	20	1	4
3Q GAIN WILD-TYPE	133	133	200	132	204	46	11

Figure S38. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.52e-07 (Fisher's exact test), Q value = 0.00046

Table S39. Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	291	246	434
3Q GAIN CNV	15	49	48
3Q GAIN WILD-TYPE	276	197	386

Figure S39. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_CNMF'

P value = 7.34e-08 (Fisher's exact test), Q value = 5.6e-05

Table S40. Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	274	413	279
3Q GAIN CNV	13	42	56
3Q GAIN WILD-TYPE	261	371	223

Figure S40. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.25e-07 (Fisher's exact test), Q value = 9.4e-05

Table S41. Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	225	376	365
3Q GAIN CNV	47	21	43
3Q GAIN WILD-TYPE	178	355	322

Figure S41. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.24e-06 (Fisher's exact test), Q value = 0.00087

Table S42. Gene #6: '3q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	210	196
3Q GAIN CNV	20	11	41
3Q GAIN WILD-TYPE	230	199	155

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

'3q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.5e-06 (Fisher's exact test), Q value = 0.001

Table S43. Gene #6: '3q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	311	185
3Q GAIN CNV	11	21	40
3Q GAIN WILD-TYPE	149	290	145

Figure S43. 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 = 0.0061

Table S44. 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 S44. 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 = 0.056

Table S45. 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 S45. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'4p gain' versus 'CN_CNMF'

P value = 8.31e-10 (Chi-square test), Q value = 6.8e-07

Table S46. Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	374	232	79	252	48
4P GAIN CNV	1	23	2	3	3
4P GAIN WILD-TYPE	373	209	77	249	45

Figure S46. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

'4p gain' versus 'MRNASEQ_CNMF'

P value = 2.82e-07 (Chi-square test), Q value = 0.00021

Table S47. 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	175	139	217	154	224	47	15
4P GAIN CNV	0	2	5	3	22	0	0
4P GAIN WILD-TYPE	175	137	212	151	202	47	15

Figure S47. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q gain' versus 'MRNA_CNMF'

P value = 3.56e-05 (Chi-square test), Q value = 0.022

Table S48. 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	1	14	0	2	1	0	0
4Q GAIN WILD-TYPE	21	35	105	96	107	71	20	40

Figure S48. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'4q gain' versus 'CN_CNMF'

P value = 1.35e-10 (Chi-square test), Q value = 1.1e-07

Table S49. Gene #8: '4q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	374	232	79	252	48
4Q GAIN CNV	1	22	1	2	4
4Q GAIN WILD-TYPE	373	210	78	250	44

Figure S49. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #3: 'CN_CNMF'

'4q gain' versus 'MRNASEQ_CNMF'

P value = 4.21e-07 (Chi-square test), Q value = 0.00031

Table S50. 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	175	139	217	154	224	47	15
4Q GAIN CNV	0	2	4	3	21	0	0
4Q GAIN WILD-TYPE	175	137	213	151	203	47	15

Figure S50. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000282 (Fisher's exact test), Q value = 0.15

Table S51. Gene #8: '4q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	225	376	365
4Q GAIN CNV	1	7	21
4Q GAIN WILD-TYPE	224	369	344

Figure S51. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5p gain' versus 'CN_CNMF'

P value = 9.73e-14 (Chi-square test), Q value = 8.7e-11

Table S52. Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	374	232	79	252	48
5P GAIN CNV	28	69	29	47	11
5P GAIN WILD-TYPE	346	163	50	205	37

Figure S52. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

'5q gain' versus 'CN_CNMF'

P value = 3.82e-17 (Chi-square test), Q value = 3.5e-14

Table S53. Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	374	232	79	252	48
5Q GAIN CNV	21	48	27	12	9
5Q GAIN WILD-TYPE	353	184	52	240	39

Figure S53. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'

'5q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.3e-05 (Fisher's exact test), Q value = 0.048

Table S54. Gene #10: '5q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	291	246	434
5Q GAIN CNV	30	14	71
5Q GAIN WILD-TYPE	261	232	363

Figure S54. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000102 (Fisher's exact test), Q value = 0.059

Table S55. Gene #10: '5q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	225	376	365
5Q GAIN CNV	10	51	54
5Q GAIN WILD-TYPE	215	325	311

Figure S55. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6p gain' versus 'MRNA_CNMF'

P value = 0.00017 (Chi-square test), Q value = 0.094

Table S56. 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 S56. 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 = 0.13

Table S57. 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 S57. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6p gain' versus 'CN_CNMF'

P value = 1.03e-17 (Chi-square test), Q value = 9.5e-15

Table S58. Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	374	232	79	252	48
6P GAIN CNV	10	21	12	66	11
6P GAIN WILD-TYPE	364	211	67	186	37

Figure S58. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

'6p gain' versus 'METHLYATION_CNMF'

P value = 3.49e-14 (Chi-square test), Q value = 3.1e-11

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	109	155	106	136	44	113
6P GAIN CNV	38	8	16	17	1	3
6P GAIN WILD-TYPE	71	147	90	119	43	110

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

'6p gain' versus 'MRNASEQ_CNMF'

P value = 3.87e-12 (Chi-square test), Q value = 3.4e-09

Table S60. 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	175	139	217	154	224	47	15
6P GAIN CNV	49	6	16	24	19	1	4
6P GAIN WILD-TYPE	126	133	201	130	205	46	11

Figure S60. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.69e-11 (Fisher's exact test), Q value = 1.5e-08

Table S61. Gene #11: '6p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	291	246	434
6P GAIN CNV	11	58	50
6P GAIN WILD-TYPE	280	188	384

Figure S61. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_CNMF'

P value = 1.55e-10 (Fisher's exact test), Q value = 1.3e-07

Table S62. Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	274	413	279
6P GAIN CNV	9	46	59
6P GAIN WILD-TYPE	265	367	220

Figure S62. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.86e-12 (Fisher's exact test), Q value = 8.6e-09

Table S63. Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	225	376	365
6P GAIN CNV	53	16	45
6P GAIN WILD-TYPE	172	360	320

Figure S63. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.11e-11 (Fisher's exact test), Q value = 9.6e-09

Table S64. Gene #11: '6p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	210	196
6P GAIN CNV	16	11	52
6P GAIN WILD-TYPE	234	199	144

Figure S64. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'6p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.38e-08 (Fisher's exact test), Q value = 1.1e-05

Table S65. Gene #11: '6p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	311	185
6P GAIN CNV	10	23	46
6P GAIN WILD-TYPE	150	288	139

Figure S65. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q gain' versus 'CN_CNMF'

P value = 7.93e-17 (Chi-square test), Q value = 7.3e-14

Table S66. Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	374	232	79	252	48
6Q GAIN CNV	5	9	8	50	2
6Q GAIN WILD-TYPE	369	223	71	202	46

Figure S66. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

'6q gain' versus 'METHLYATION_CNMF'

P value = 1.97e-07 (Chi-square test), Q value = 0.00015

Table S67. Gene #12: '6q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	109	155	106	136	44	113
6Q GAIN CNV	21	3	8	9	1	2
6Q GAIN WILD-TYPE	88	152	98	127	43	111

Figure S67. 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 = 0.14

Table S68. 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 S68. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'6q gain' versus 'MRNASEQ_CNMF'

P value = 1.85e-07 (Chi-square test), Q value = 0.00014

Table S69. 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	175	139	217	154	224	47	15
6Q GAIN CNV	31	4	10	14	10	1	3
6Q GAIN WILD-TYPE	144	135	207	140	214	46	12

Figure S69. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.54e-08 (Fisher's exact test), Q value = 3.5e-05

Table S70. Gene #12: '6q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	291	246	434
6Q GAIN CNV	5	36	32
6Q GAIN WILD-TYPE	286	210	402

Figure S70. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6q gain' versus 'MIRSEQ_CNMF'

P value = 9e-07 (Fisher's exact test), Q value = 0.00064

Table S71. Gene #12: '6q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	274	413	279
6Q GAIN CNV	6	26	38
6Q GAIN WILD-TYPE	268	387	241

Figure S71. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.41e-08 (Fisher's exact test), Q value = 1.9e-05

Table S72. Gene #12: '6q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	225	376	365
6Q GAIN CNV	36	10	24
6Q GAIN WILD-TYPE	189	366	341

Figure S72. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.77e-07 (Fisher's exact test), Q value = 0.00048

Table S73. Gene #12: '6q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	210	196
6Q GAIN CNV	10	7	32
6Q GAIN WILD-TYPE	240	203	164

Figure S73. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'6q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.64e-06 (Fisher's exact test), Q value = 0.0024

Table S74. Gene #12: '6q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	311	185
6Q GAIN CNV	6	13	30
6Q GAIN WILD-TYPE	154	298	155

Figure S74. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 0.00037 (Chi-square test), Q value = 0.19

Table S75. Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	374	232	79	252	48
7Q GAIN CNV	35	29	20	47	9
7Q GAIN WILD-TYPE	339	203	59	205	39

Figure S75. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

'8p gain' versus 'CN_CNMF'

P value = 4.85e-11 (Chi-square test), Q value = 4.1e-08

Table S76. Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	374	232	79	252	48
8P GAIN CNV	38	48	27	52	22
8P GAIN WILD-TYPE	336	184	52	200	26

Figure S76. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

'8p gain' versus 'METHLYATION_CNMF'

P value = 8.21e-05 (Chi-square test), Q value = 0.048

Table S77. Gene #15: '8p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	109	155	106	136	44	113
8P GAIN CNV	32	25	20	31	7	5
8P GAIN WILD-TYPE	77	130	86	105	37	108

Figure S77. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.21e-06 (Fisher's exact test), Q value = 0.0054

Table S78. Gene #15: '8p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	291	246	434
8P GAIN CNV	30	51	104
8P GAIN WILD-TYPE	261	195	330

Figure S78. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'MRNA_CNMF'

P value = 0.000172 (Chi-square test), Q value = 0.095

Table S79. 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	13	68	51	39	35	12	8
8Q GAIN WILD-TYPE	8	23	51	45	70	37	8	32

Figure S79. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'8q gain' versus 'CN_CNMF'

P value = 1.82e-24 (Chi-square test), Q value = 1.7e-21

Table S80. Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	374	232	79	252	48
8Q GAIN CNV	80	129	30	130	37
8Q GAIN WILD-TYPE	294	103	49	122	11

Figure S80. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 7.37e-12 (Chi-square test), Q value = 6.4e-09

Table S81. Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	109	155	106	136	44	113
8Q GAIN CNV	57	36	40	78	9	27
8Q GAIN WILD-TYPE	52	119	66	58	35	86

Figure S81. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 1e-11 (Chi-square test), Q value = 8.7e-09

Table S82. 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	175	139	217	154	224	47	15
8Q GAIN CNV	92	37	66	64	125	9	9
8Q GAIN WILD-TYPE	83	102	151	90	99	38	6

Figure S82. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.88e-11 (Fisher's exact test), Q value = 1.6e-08

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	291	246	434
8Q GAIN CNV	72	118	212
8Q GAIN WILD-TYPE	219	128	222

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

'8q gain' versus 'MIRSEQ_CNMF'

P value = 1.37e-09 (Fisher's exact test), Q value = 1.1e-06

Table S84. Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	274	413	279
8Q GAIN CNV	70	188	139
8Q GAIN WILD-TYPE	204	225	140

Figure S84. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.51e-07 (Fisher's exact test), Q value = 0.00011

Table S85. Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	225	376	365
8Q GAIN CNV	115	114	168
8Q GAIN WILD-TYPE	110	262	197

Figure S85. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.22e-07 (Fisher's exact test), Q value = 9.2e-05

Table S86. Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	210	196
8Q GAIN CNV	98	50	99
8Q GAIN WILD-TYPE	152	160	97

Figure S86. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9p gain' versus 'MRNA_CNMF'

P value = 2.34e-08 (Chi-square test), Q value = 1.8e-05

Table S87. 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 S87. 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 S88. 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 S88. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9p gain' versus 'CN_CNMF'

P value = 1.22e-10 (Chi-square test), Q value = 1e-07

Table S89. Gene #17: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	374	232	79	252	48
9P GAIN CNV	10	7	15	36	4
9P GAIN WILD-TYPE	364	225	64	216	44

Figure S89. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'

'9p gain' versus 'METHLYATION_CNMF'

P value = 9.79e-05 (Chi-square test), Q value = 0.057

Table S90. Gene #17: '9p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	109	155	106	136	44	113
9P GAIN CNV	19	11	3	6	1	5
9P GAIN WILD-TYPE	90	144	103	130	43	108

Figure S90. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.000106 (Fisher's exact test), Q value = 0.061

Table S91. 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 S91. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'9p gain' versus 'MRNASEQ_CNMF'

P value = 3.13e-10 (Chi-square test), Q value = 2.6e-07

Table S92. 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	175	139	217	154	224	47	15
9P GAIN CNV	35	3	11	8	8	3	2
9P GAIN WILD-TYPE	140	136	206	146	216	44	13

Figure S92. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.69e-08 (Fisher's exact test), Q value = 2.1e-05

Table S93. Gene #17: '9p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	291	246	434
9P GAIN CNV	11	40	19
9P GAIN WILD-TYPE	280	206	415

Figure S93. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p gain' versus 'MIRSEQ_CNMF'

P value = 3.17e-07 (Fisher's exact test), Q value = 0.00023

Table S94. Gene #17: '9p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	274	413	279
9P GAIN CNV	9	20	41
9P GAIN WILD-TYPE	265	393	238

Figure S94. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.96e-06 (Fisher's exact test), Q value = 0.0013

Table S95. Gene #17: '9p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	225	376	365
9P GAIN CNV	35	16	19
9P GAIN WILD-TYPE	190	360	346

Figure S95. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9q gain' versus 'CN_CNMF'

P value = 3.48e-06 (Chi-square test), Q value = 0.0023

Table S96. Gene #18: '9q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	374	232	79	252	48
9Q GAIN CNV	11	12	15	19	3
9Q GAIN WILD-TYPE	363	220	64	233	45

Figure S96. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #3: 'CN_CNMF'

'10p gain' versus 'MRNA_CNMF'

P value = 9.81e-11 (Chi-square test), Q value = 8.3e-08

Table S97. 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	9	33	4	18	3	3
10P GAIN WILD-TYPE	21	34	110	63	105	54	17	37

Figure S97. 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 = 6.1e-05

Table S98. 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 S98. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'10p gain' versus 'CN_CNMF'

P value = 3.5e-19 (Chi-square test), Q value = 3.3e-16

Table S99. Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	374	232	79	252	48
10P GAIN CNV	6	26	11	68	7
10P GAIN WILD-TYPE	368	206	68	184	41

Figure S99. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

'10p gain' versus 'METHLYATION_CNMF'

P value = 2.51e-15 (Chi-square test), Q value = 2.3e-12

Table S100. Gene #19: '10p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	109	155	106	136	44	113
10P GAIN CNV	37	8	12	13	0	3
10P GAIN WILD-TYPE	72	147	94	123	44	110

Figure S100. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p gain' versus 'RPPA_CNMF'

P value = 9.23e-06 (Fisher's exact test), Q value = 0.006

Table S101. 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	7	12
10P GAIN WILD-TYPE	111	126	105

Figure S101. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'10p gain' versus 'RPPA_CHIERARCHICAL'

P value = 6.71e-07 (Fisher's exact test), Q value = 0.00048

Table S102. Gene #19: '10p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	110	126
10P GAIN CNV	10	10	35
10P GAIN WILD-TYPE	151	100	91

Figure S102. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'10p gain' versus 'MRNASEQ_CNMF'

P value = 8.68e-19 (Chi-square test), Q value = 8.1e-16

Table S103. 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	175	139	217	154	224	47	15
10P GAIN CNV	56	6	9	25	16	2	2
10P GAIN WILD-TYPE	119	133	208	129	208	45	13

Figure S103. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.37e-14 (Fisher's exact test), Q value = 1.2e-11

Table S104. Gene #19: '10p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	291	246	434
10P GAIN CNV	14	66	36
10P GAIN WILD-TYPE	277	180	398

Figure S104. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p gain' versus 'MIRSEQ_CNMF'

P value = 2.99e-13 (Fisher's exact test), Q value = 2.7e-10

Table S105. Gene #19: '10p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	274	413	279
10P GAIN CNV	10	38	67
10P GAIN WILD-TYPE	264	375	212

Figure S105. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.13e-11 (Fisher's exact test), Q value = 9.7e-09

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	225	376	365
10P GAIN CNV	58	22	35
10P GAIN WILD-TYPE	167	354	330

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

'10p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.63e-11 (Fisher's exact test), Q value = 1.4e-08

Table S107. Gene #19: '10p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	210	196
10P GAIN CNV	15	9	49
10P GAIN WILD-TYPE	235	201	147

Figure S107. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-12 (Fisher's exact test), Q value = 8.9e-10

Table S108. Gene #19: '10p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	311	185
10P GAIN CNV	7	17	49
10P GAIN WILD-TYPE	153	294	136

Figure S108. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q gain' versus 'CN_CNMF'

P value = 6.26e-07 (Chi-square test), Q value = 0.00045

Table S109. Gene #20: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	374	232	79	252	48
10Q GAIN CNV	3	10	10	24	3
10Q GAIN WILD-TYPE	371	222	69	228	45

Figure S109. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

'10q gain' versus 'MRNASEQ_CNMF'

P value = 2.45e-05 (Chi-square test), Q value = 0.015

Table S110. 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	175	139	217	154	224	47	15
10Q GAIN CNV	16	4	7	12	4	2	4
10Q GAIN WILD-TYPE	159	135	210	142	220	45	11

Figure S110. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11q gain' versus 'CN_CNMF'

P value = 0.000257 (Chi-square test), Q value = 0.14

Table S111. Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	374	232	79	252	48
11Q GAIN CNV	7	11	5	23	6
11Q GAIN WILD-TYPE	367	221	74	229	42

Figure S111. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 6.24e-15 (Chi-square test), Q value = 5.7e-12

Table S112. Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	374	232	79	252	48
12P GAIN CNV	4	46	14	51	8
12P GAIN WILD-TYPE	370	186	65	201	40

Figure S112. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 1.3e-06 (Chi-square test), Q value = 0.00091

Table S113. Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	109	155	106	136	44	113
12P GAIN CNV	23	11	13	24	0	2
12P GAIN WILD-TYPE	86	144	93	112	44	111

Figure S113. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 1.73e-05 (Chi-square test), Q value = 0.011

Table S114. 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	175	139	217	154	224	47	15
12P GAIN CNV	39	8	15	20	36	3	1
12P GAIN WILD-TYPE	136	131	202	134	188	44	14

Figure S114. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.74e-06 (Fisher's exact test), Q value = 0.0025

Table S115. Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	291	246	434
12P GAIN CNV	16	47	59
12P GAIN WILD-TYPE	275	199	375

Figure S115. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.44e-05 (Fisher's exact test), Q value = 0.0092

Table S116. Gene #23: '12p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	210	196
12P GAIN CNV	23	12	40
12P GAIN WILD-TYPE	227	198	156

Figure S116. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12q gain' versus 'CN_CNMF'

P value = 1.16e-15 (Chi-square test), Q value = 1.1e-12

Table S117. Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	374	232	79	252	48
12Q GAIN CNV	6	48	15	15	7
12Q GAIN WILD-TYPE	368	184	64	237	41

Figure S117. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

'12q gain' versus 'METHLYATION_CNMF'

P value = 2.39e-05 (Chi-square test), Q value = 0.015

Table S118. Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	109	155	106	136	44	113
12Q GAIN CNV	5	15	13	23	0	1
12Q GAIN WILD-TYPE	104	140	93	113	44	112

Figure S118. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q gain' versus 'MRNA_CNMF'

P value = 0.000383 (Chi-square test), Q value = 0.2

Table S119. Gene #26: '14q 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
14Q GAIN CNV	0	0	11	3	14	14	3	0
14Q GAIN WILD-TYPE	21	36	108	93	95	58	17	40

Figure S119. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'14q gain' versus 'CN_CNMF'

P value = 5.19e-06 (Chi-square test), Q value = 0.0035

Table S120. Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	374	232	79	252	48
14Q GAIN CNV	16	31	14	14	7
14Q GAIN WILD-TYPE	358	201	65	238	41

Figure S120. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

'14q gain' versus 'MRNASEQ_CNMF'

P value = 0.000114 (Chi-square test), Q value = 0.065

Table S121. 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	175	139	217	154	224	47	15
14Q GAIN CNV	4	4	24	22	24	1	2
14Q GAIN WILD-TYPE	171	135	193	132	200	46	13

Figure S121. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000203 (Fisher's exact test), Q value = 0.11

Table S122. Gene #26: '14q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	291	246	434
14Q GAIN CNV	16	11	54
14Q GAIN WILD-TYPE	275	235	380

Figure S122. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.15

Table S123. Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	274	413	279
14Q GAIN CNV	13	52	16
14Q GAIN WILD-TYPE	261	361	263

Figure S123. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16p gain' versus 'MRNA_CNMF'

P value = 1.5e-05 (Chi-square test), Q value = 0.0095

Table S124. 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	5	5	41	18	55	17	6	11
16P GAIN WILD-TYPE	16	31	78	78	54	55	14	29

Figure S124. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'16p gain' versus 'MRNA_CHIERARCHICAL'

P value = 6.32e-05 (Fisher's exact test), Q value = 0.037

Table S125. Gene #28: '16p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
16P GAIN CNV	33	22	103
16P GAIN WILD-TYPE	89	103	163

Figure S125. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'16p gain' versus 'METHLYATION_CNMF'

P value = 8.46e-08 (Chi-square test), Q value = 6.5e-05

Table S126. Gene #28: '16p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	109	155	106	136	44	113
16P GAIN CNV	19	63	33	38	7	11
16P GAIN WILD-TYPE	90	92	73	98	37	102

Figure S126. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16p gain' versus 'RPPA_CNMF'

P value = 0.000158 (Fisher's exact test), Q value = 0.088

Table S127. Gene #28: '16p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
16P GAIN CNV	31	58	31
16P GAIN WILD-TYPE	116	75	86

Figure S127. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'16p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.000183 (Fisher's exact test), Q value = 0.1

Table S128. Gene #28: '16p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	110	126
16P GAIN CNV	60	39	21
16P GAIN WILD-TYPE	101	71	105

Figure S128. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 9.99e-06 (Chi-square test), Q value = 0.0065

Table S129. 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	175	139	217	154	224	47	15
16P GAIN CNV	29	34	89	38	64	14	2
16P GAIN WILD-TYPE	146	105	128	116	160	33	13

Figure S129. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.84e-06 (Fisher's exact test), Q value = 0.0013

Table S130. Gene #28: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	291	246	434
16P GAIN CNV	74	43	153
16P GAIN WILD-TYPE	217	203	281

Figure S130. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000441 (Fisher's exact test), Q value = 0.23

Table S131. Gene #28: '16p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	210	196
16P GAIN CNV	84	52	34
16P GAIN WILD-TYPE	166	158	162

Figure S131. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000268 (Fisher's exact test), Q value = 0.14

Table S132. Gene #29: '16q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	291	246	434
16Q GAIN CNV	6	23	34
16Q GAIN WILD-TYPE	285	223	400

Figure S132. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MRNA_CNMF'

P value = 2.59e-06 (Chi-square test), Q value = 0.0018

Table S133. 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	6	33	6	6	4	2	4
17Q GAIN WILD-TYPE	19	30	86	90	103	68	18	36

Figure S133. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'17q gain' versus 'CN_CNMF'

P value = 1.71e-23 (Chi-square test), Q value = 1.6e-20

Table S134. Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	374	232	79	252	48
17Q GAIN CNV	23	78	6	16	9
17Q GAIN WILD-TYPE	351	154	73	236	39

Figure S134. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 1.08e-05 (Chi-square test), Q value = 0.0069

Table S135. Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	109	155	106	136	44	113
17Q GAIN CNV	6	17	21	35	6	8
17Q GAIN WILD-TYPE	103	138	85	101	38	105

Figure S135. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 2.29e-14 (Chi-square test), Q value = 2.1e-11

Table S136. 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	175	139	217	154	224	47	15
17Q GAIN CNV	9	15	15	16	67	4	4
17Q GAIN WILD-TYPE	166	124	202	138	157	43	11

Figure S136. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.17e-07 (Fisher's exact test), Q value = 8.9e-05

Table S137. Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	291	246	434
17Q GAIN CNV	28	15	87
17Q GAIN WILD-TYPE	263	231	347

Figure S137. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.08e-06 (Fisher's exact test), Q value = 0.0059

Table S138. Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	225	376	365
17Q GAIN CNV	20	35	74
17Q GAIN WILD-TYPE	205	341	291

Figure S138. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.11

Table S139. 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	27
18P GAIN WILD-TYPE	118	101	239

Figure S139. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18p gain' versus 'CN_CNMF'

P value = 2.4e-07 (Chi-square test), Q value = 0.00018

Table S140. Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	374	232	79	252	48
18P GAIN CNV	11	28	6	37	10
18P GAIN WILD-TYPE	363	204	73	215	38

Figure S140. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 1.49e-06 (Chi-square test), Q value = 0.001

Table S141. Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	109	155	106	136	44	113
18P GAIN CNV	22	8	7	12	0	2
18P GAIN WILD-TYPE	87	147	99	124	44	111

Figure S141. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p gain' versus 'MRNASEQ_CNMF'

P value = 1.04e-06 (Chi-square test), Q value = 0.00073

Table S142. 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	175	139	217	154	224	47	15
18P GAIN CNV	35	4	18	9	25	0	1
18P GAIN WILD-TYPE	140	135	199	145	199	47	14

Figure S142. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.19e-10 (Fisher's exact test), Q value = 1.8e-07

Table S143. Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	291	246	434
18P GAIN CNV	4	39	49
18P GAIN WILD-TYPE	287	207	385

Figure S143. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_CNMF'

P value = 5.65e-07 (Fisher's exact test), Q value = 0.00041

Table S144. Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	274	413	279
18P GAIN CNV	11	30	47
18P GAIN WILD-TYPE	263	383	232

Figure S144. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.25e-05 (Fisher's exact test), Q value = 0.008

Table S145. Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	225	376	365
18P GAIN CNV	38	19	31
18P GAIN WILD-TYPE	187	357	334

Figure S145. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18q gain' versus 'CN_CNMF'

P value = 7.96e-07 (Chi-square test), Q value = 0.00056

Table S146. Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	374	232	79	252	48
18Q GAIN CNV	9	24	7	31	10
18Q GAIN WILD-TYPE	365	208	72	221	38

Figure S146. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

'18q gain' versus 'MRNASEQ_CNMF'

P value = 1.53e-05 (Chi-square test), Q value = 0.0097

Table S147. 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	175	139	217	154	224	47	15
18Q GAIN CNV	26	4	19	3	27	0	1
18Q GAIN WILD-TYPE	149	135	198	151	197	47	14

Figure S147. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.28e-08 (Fisher's exact test), Q value = 4.1e-05

Table S148. Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	291	246	434
18Q GAIN CNV	4	26	50
18Q GAIN WILD-TYPE	287	220	384

Figure S148. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_CNMF'

P value = 0.000149 (Fisher's exact test), Q value = 0.084

Table S149. Gene #33: '18q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	274	413	279
18Q GAIN CNV	10	30	37
18Q GAIN WILD-TYPE	264	383	242

Figure S149. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19p gain' versus 'CN_CNMF'

P value = 3.62e-05 (Chi-square test), Q value = 0.022

Table S150. Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	374	232	79	252	48
19P GAIN CNV	12	14	11	32	5
19P GAIN WILD-TYPE	362	218	68	220	43

Figure S150. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

'19q gain' versus 'CN_CNMF'

P value = 4.9e-05 (Chi-square test), Q value = 0.029

Table S151. Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	374	232	79	252	48
19Q GAIN CNV	16	22	14	35	7
19Q GAIN WILD-TYPE	358	210	65	217	41

Figure S151. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'MRNA_CNMF'

P value = 1.32e-05 (Chi-square test), Q value = 0.0084

Table S152. 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	41	26	22	33	13	5
20P GAIN WILD-TYPE	14	29	78	70	87	39	7	35

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

'20p gain' versus 'CN_CNMF'

P value = 8.43e-23 (Chi-square test), Q value = 8e-20

Table S153. Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	374	232	79	252	48
20P GAIN CNV	32	103	31	76	14
20P GAIN WILD-TYPE	342	129	48	176	34

Figure S153. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 1.69e-06 (Chi-square test), Q value = 0.0012

Table S154. Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	109	155	106	136	44	113
20P GAIN CNV	22	29	34	52	5	14
20P GAIN WILD-TYPE	87	126	72	84	39	99

Figure S154. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 1.14e-05 (Chi-square test), Q value = 0.0073

Table S155. 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	175	139	217	154	224	47	15
20P GAIN CNV	37	21	50	59	72	7	6
20P GAIN WILD-TYPE	138	118	167	95	152	40	9

Figure S155. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.26e-06 (Fisher's exact test), Q value = 0.0022

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	291	246	434
20P GAIN CNV	49	59	144
20P GAIN WILD-TYPE	242	187	290

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

'20p gain' versus 'MIRSEQ_CNMF'

P value = 0.000387 (Fisher's exact test), Q value = 0.2

Table S157. Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	274	413	279
20P GAIN CNV	49	129	73
20P GAIN WILD-TYPE	225	284	206

Figure S157. 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 = 0.012

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

'20q gain' versus 'CN_CNMF'

P value = 5.13e-32 (Chi-square test), Q value = 4.9e-29

Table S159. Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	374	232	79	252	48
20Q GAIN CNV	36	130	30	82	17
20Q GAIN WILD-TYPE	338	102	49	170	31

Figure S159. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 7.28e-12 (Chi-square test), Q value = 6.3e-09

Table S160. Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	109	155	106	136	44	113
20Q GAIN CNV	25	31	41	66	5	14
20Q GAIN WILD-TYPE	84	124	65	70	39	99

Figure S160. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 1.46e-09 (Chi-square test), Q value = 1.2e-06

Table S161. 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	175	139	217	154	224	47	15
20Q GAIN CNV	42	22	50	58	102	11	5
20Q GAIN WILD-TYPE	133	117	167	96	122	36	10

Figure S161. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.43e-09 (Fisher's exact test), Q value = 2.8e-06

Table S162. Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	291	246	434
20Q GAIN CNV	55	63	172
20Q GAIN WILD-TYPE	236	183	262

Figure S162. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 1.25e-06 (Fisher's exact test), Q value = 0.00088

Table S163. Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	274	413	279
20Q GAIN CNV	52	154	85
20Q GAIN WILD-TYPE	222	259	194

Figure S163. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.2e-05 (Fisher's exact test), Q value = 0.031

Table S164. Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	225	376	365
20Q GAIN CNV	62	89	140
20Q GAIN WILD-TYPE	163	287	225

Figure S164. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'21q gain' versus 'MRNA_CNMF'

P value = 3.09e-05 (Chi-square test), Q value = 0.019

Table S165. 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 S165. 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 = 0.16

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

'21q gain' versus 'CN_CNMF'

P value = 3.45e-10 (Chi-square test), Q value = 2.9e-07

Table S167. Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	374	232	79	252	48
21Q GAIN CNV	13	24	16	50	9
21Q GAIN WILD-TYPE	361	208	63	202	39

Figure S167. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

'21q gain' versus 'METHLYATION_CNMF'

P value = 1.07e-07 (Chi-square test), Q value = 8.1e-05

Table S168. Gene #38: '21q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	109	155	106	136	44	113
21Q GAIN CNV	28	12	15	11	1	3
21Q GAIN WILD-TYPE	81	143	91	125	43	110

Figure S168. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'21q gain' versus 'MRNASEQ_CNMF'

P value = 2.43e-10 (Chi-square test), Q value = 2e-07

Table S169. 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	175	139	217	154	224	47	15
21Q GAIN CNV	38	4	12	33	19	2	3
21Q GAIN WILD-TYPE	137	135	205	121	205	45	12

Figure S169. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.99e-12 (Fisher's exact test), Q value = 5.2e-09

Table S170. Gene #38: '21q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	291	246	434
21Q GAIN CNV	11	58	42
21Q GAIN WILD-TYPE	280	188	392

Figure S170. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'21q gain' versus 'MIRSEQ_CNMF'

P value = 1.52e-09 (Fisher's exact test), Q value = 1.2e-06

Table S171. Gene #38: '21q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	274	413	279
21Q GAIN CNV	11	39	58
21Q GAIN WILD-TYPE	263	374	221

Figure S171. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'21q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.68e-07 (Fisher's exact test), Q value = 2e-04

Table S172. Gene #38: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	225	376	365
21Q GAIN CNV	46	21	41
21Q GAIN WILD-TYPE	179	355	324

Figure S172. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'21q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.68e-08 (Fisher's exact test), Q value = 2.9e-05

Table S173. Gene #38: '21q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	210	196
21Q GAIN CNV	18	14	47
21Q GAIN WILD-TYPE	232	196	149

Figure S173. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'21q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.42e-09 (Fisher's exact test), Q value = 2.8e-06

Table S174. Gene #38: '21q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	311	185
21Q GAIN CNV	10	22	47
21Q GAIN WILD-TYPE	150	289	138

Figure S174. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q gain' versus 'CN_CNMF'

P value = 2.63e-10 (Chi-square test), Q value = 2.2e-07

Table S175. Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	374	232	79	252	48
22Q GAIN CNV	2	9	0	30	4
22Q GAIN WILD-TYPE	372	223	79	222	44

Figure S175. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

'22q gain' versus 'MRNASEQ_CNMF'

P value = 4.35e-05 (Chi-square test), Q value = 0.026

Table S176. 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	175	139	217	154	224	47	15
22Q GAIN CNV	18	1	3	12	10	0	0
22Q GAIN WILD-TYPE	157	138	214	142	214	47	15

Figure S176. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.13e-08 (Fisher's exact test), Q value = 4e-05

Table S177. Gene #39: '22q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	291	246	434
22Q GAIN CNV	2	27	15
22Q GAIN WILD-TYPE	289	219	419

Figure S177. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_CNMF'

P value = 3.07e-08 (Fisher's exact test), Q value = 2.4e-05

Table S178. Gene #39: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	274	413	279
22Q GAIN CNV	0	17	26
22Q GAIN WILD-TYPE	274	396	253

Figure S178. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'22q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.73e-07 (Fisher's exact test), Q value = 0.00013

Table S179. Gene #39: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	225	376	365
22Q GAIN CNV	23	3	17
22Q GAIN WILD-TYPE	202	373	348

Figure S179. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000168 (Fisher's exact test), Q value = 0.093

Table S180. Gene #39: '22q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	210	196
22Q GAIN CNV	7	3	19
22Q GAIN WILD-TYPE	243	207	177

Figure S180. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'22q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.98e-05 (Fisher's exact test), Q value = 0.024

Table S181. Gene #39: '22q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	311	185
22Q GAIN CNV	0	12	17
22Q GAIN WILD-TYPE	160	299	168

Figure S181. 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 = 0.09

Table S182. 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 S182. Get High-res Image Gene #40: 'Xq gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Xq gain' versus 'MRNASEQ_CNMF'

P value = 5.39e-06 (Chi-square test), Q value = 0.0036

Table S183. 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	175	139	217	154	224	47	15
XQ GAIN CNV	15	0	3	3	2	1	0
XQ GAIN WILD-TYPE	160	139	214	151	222	46	15

Figure S183. Get High-res Image Gene #40: 'Xq gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Xq gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.9e-05 (Fisher's exact test), Q value = 0.023

Table S184. Gene #40: 'Xq gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	291	246	434
XQ GAIN CNV	2	16	6
XQ GAIN WILD-TYPE	289	230	428

Figure S184. Get High-res Image Gene #40: 'Xq gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Xq gain' versus 'MIRSEQ_CNMF'

P value = 2.84e-05 (Fisher's exact test), Q value = 0.017

Table S185. Gene #40: 'Xq gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	274	413	279
XQ GAIN CNV	1	6	17
XQ GAIN WILD-TYPE	273	407	262

Figure S185. Get High-res Image Gene #40: 'Xq gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Xq gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.36e-05 (Fisher's exact test), Q value = 0.015

Table S186. Gene #40: 'Xq gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	225	376	365
XQ GAIN CNV	16	4	4
XQ GAIN WILD-TYPE	209	372	361

Figure S186. Get High-res Image Gene #40: 'Xq gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1p loss' versus 'MRNA_CHIERARCHICAL'

P value = 2.25e-08 (Fisher's exact test), Q value = 1.8e-05

Table S187. 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	6	58
1P LOSS WILD-TYPE	117	119	208

Figure S187. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

P value = 4.51e-20 (Chi-square test), Q value = 4.2e-17

Table S188. Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	374	232	79	252	48
1P LOSS CNV	20	56	31	19	6
1P LOSS WILD-TYPE	354	176	48	233	42

Figure S188. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 2.09e-08 (Chi-square test), Q value = 1.7e-05

Table S189. Gene #41: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	109	155	106	136	44	113
1P LOSS CNV	9	15	28	32	3	3
1P LOSS WILD-TYPE	100	140	78	104	41	110

Figure S189. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 1.21e-07 (Chi-square test), Q value = 9.1e-05

Table S190. 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	175	139	217	154	224	47	15
1P LOSS CNV	10	6	30	34	46	2	1
1P LOSS WILD-TYPE	165	133	187	120	178	45	14

Figure S190. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.22e-13 (Fisher's exact test), Q value = 1.1e-10

Table S191. Gene #41: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	291	246	434
1P LOSS CNV	17	14	98
1P LOSS WILD-TYPE	274	232	336

Figure S191. 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 = 0.057

Table S192. 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 S192. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'2p loss' versus 'CN_CNMF'

P value = 1.14e-10 (Chi-square test), Q value = 9.7e-08

Table S193. Gene #43: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	374	232	79	252	48
2P LOSS CNV	8	34	15	12	7
2P LOSS WILD-TYPE	366	198	64	240	41

Figure S193. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

'2p loss' versus 'METHLYATION_CNMF'

P value = 2.9e-07 (Chi-square test), Q value = 0.00021

Table S194. Gene #43: '2p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	109	155	106	136	44	113
2P LOSS CNV	1	7	12	21	1	0
2P LOSS WILD-TYPE	108	148	94	115	43	113

Figure S194. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2p loss' versus 'MRNASEQ_CNMF'

P value = 7.62e-06 (Chi-square test), Q value = 0.005

Table S195. 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	175	139	217	154	224	47	15
2P LOSS CNV	4	4	21	9	34	1	1
2P LOSS WILD-TYPE	171	135	196	145	190	46	14

Figure S195. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.68e-08 (Fisher's exact test), Q value = 4.4e-05

Table S196. Gene #43: '2p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	291	246	434
2P LOSS CNV	13	5	56
2P LOSS WILD-TYPE	278	241	378

Figure S196. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_CNMF'

P value = 1.71e-05 (Fisher's exact test), Q value = 0.011

Table S197. Gene #43: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	274	413	279
2P LOSS CNV	14	50	9
2P LOSS WILD-TYPE	260	363	270

Figure S197. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.53e-06 (Fisher's exact test), Q value = 0.0062

Table S198. Gene #43: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	225	376	365
2P LOSS CNV	6	21	46
2P LOSS WILD-TYPE	219	355	319

Figure S198. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2q loss' versus 'CN_CNMF'

P value = 1.21e-10 (Chi-square test), Q value = 1e-07

Table S199. Gene #44: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	374	232	79	252	48
2Q LOSS CNV	8	40	16	22	7
2Q LOSS WILD-TYPE	366	192	63	230	41

Figure S199. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

'2q loss' versus 'METHLYATION_CNMF'

P value = 5.28e-07 (Chi-square test), Q value = 0.00038

Table S200. Gene #44: '2q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	109	155	106	136	44	113
2Q LOSS CNV	7	7	13	25	1	0
2Q LOSS WILD-TYPE	102	148	93	111	43	113

Figure S200. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000151 (Fisher's exact test), Q value = 0.085

Table S201. Gene #44: '2q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	291	246	434
2Q LOSS CNV	14	18	59
2Q LOSS WILD-TYPE	277	228	375

Figure S201. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_CNMF'

P value = 0.000167 (Fisher's exact test), Q value = 0.093

Table S202. Gene #44: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	274	413	279
2Q LOSS CNV	14	57	19
2Q LOSS WILD-TYPE	260	356	260

Figure S202. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000136 (Fisher's exact test), Q value = 0.077

Table S203. Gene #44: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	225	376	365
2Q LOSS CNV	18	20	52
2Q LOSS WILD-TYPE	207	356	313

Figure S203. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'CN_CNMF'

P value = 3.15e-09 (Chi-square test), Q value = 2.5e-06

Table S204. Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	374	232	79	252	48
3P LOSS CNV	11	29	6	47	3
3P LOSS WILD-TYPE	363	203	73	205	45

Figure S204. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 3.76e-06 (Chi-square test), Q value = 0.0025

Table S205. Gene #45: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	109	155	106	136	44	113
3P LOSS CNV	19	4	16	16	3	1
3P LOSS WILD-TYPE	90	151	90	120	41	112

Figure S205. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3p loss' versus 'RPPA_CHIERARCHICAL'

P value = 2.44e-05 (Fisher's exact test), Q value = 0.015

Table S206. Gene #45: '3p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	110	126
3P LOSS CNV	12	4	27
3P LOSS WILD-TYPE	149	106	99

Figure S206. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 5.01e-05 (Chi-square test), Q value = 0.03

Table S207. 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	175	139	217	154	224	47	15
3P LOSS CNV	29	8	11	24	19	0	1
3P LOSS WILD-TYPE	146	131	206	130	205	47	14

Figure S207. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.12e-05 (Fisher's exact test), Q value = 0.0072

Table S208. Gene #45: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	291	246	434
3P LOSS CNV	13	41	38
3P LOSS WILD-TYPE	278	205	396

Figure S208. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CNMF'

P value = 5.28e-07 (Fisher's exact test), Q value = 0.00038

Table S209. Gene #45: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	274	413	279
3P LOSS CNV	11	33	48
3P LOSS WILD-TYPE	263	380	231

Figure S209. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000258 (Fisher's exact test), Q value = 0.14

Table S210. Gene #45: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	225	376	365
3P LOSS CNV	34	20	38
3P LOSS WILD-TYPE	191	356	327

Figure S210. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000244 (Fisher's exact test), Q value = 0.13

Table S211. Gene #45: '3p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	210	196
3P LOSS CNV	19	10	32
3P LOSS WILD-TYPE	231	200	164

Figure S211. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'3q loss' versus 'CN_CNMF'

P value = 3.18e-05 (Chi-square test), Q value = 0.019

Table S212. Gene #46: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	374	232	79	252	48
3Q LOSS CNV	3	18	3	21	1
3Q LOSS WILD-TYPE	371	214	76	231	47

Figure S212. Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'MRNA_CNMF'

P value = 2.8e-13 (Chi-square test), Q value = 2.5e-10

Table S213. 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	4	15	42	14	34	4	3
4P LOSS WILD-TYPE	20	32	104	54	95	38	16	37

Figure S213. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'4p loss' versus 'MRNA_CHIERARCHICAL'

P value = 2.1e-12 (Fisher's exact test), Q value = 1.8e-09

Table S214. Gene #47: '4p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
4P LOSS CNV	8	56	53
4P LOSS WILD-TYPE	114	69	213

Figure S214. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

P value = 2.91e-29 (Chi-square test), Q value = 2.8e-26

Table S215. Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	374	232	79	252	48
4P LOSS CNV	23	37	23	111	8
4P LOSS WILD-TYPE	351	195	56	141	40

Figure S215. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 2.75e-20 (Chi-square test), Q value = 2.6e-17

Table S216. Gene #47: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	109	155	106	136	44	113
4P LOSS CNV	52	21	28	11	3	4
4P LOSS WILD-TYPE	57	134	78	125	41	109

Figure S216. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p loss' versus 'RPPA_CNMF'

P value = 4.26e-05 (Fisher's exact test), Q value = 0.025

Table S217. 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	25	16
4P LOSS WILD-TYPE	94	108	101

Figure S217. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'4p loss' versus 'RPPA_CHIERARCHICAL'

P value = 1.78e-06 (Fisher's exact test), Q value = 0.0012

Table S218. Gene #47: '4p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	110	126
4P LOSS CNV	30	14	50
4P LOSS WILD-TYPE	131	96	76

Figure S218. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 6.16e-22 (Chi-square test), Q value = 5.8e-19

Table S219. 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	175	139	217	154	224	47	15
4P LOSS CNV	76	5	30	51	31	5	1
4P LOSS WILD-TYPE	99	134	187	103	193	42	14

Figure S219. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.44e-21 (Fisher's exact test), Q value = 6e-18

Table S220. Gene #47: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	291	246	434
4P LOSS CNV	22	101	76
4P LOSS WILD-TYPE	269	145	358

Figure S220. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_CNMF'

P value = 1.71e-18 (Fisher's exact test), Q value = 1.6e-15

Table S221. Gene #47: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	274	413	279
4P LOSS CNV	16	80	100
4P LOSS WILD-TYPE	258	333	179

Figure S221. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.71e-16 (Fisher's exact test), Q value = 2.5e-13

Table S222. Gene #47: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	225	376	365
4P LOSS CNV	87	36	73
4P LOSS WILD-TYPE	138	340	292

Figure S222. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.58e-12 (Fisher's exact test), Q value = 1.4e-09

Table S223. Gene #47: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	210	196
4P LOSS CNV	48	12	66
4P LOSS WILD-TYPE	202	198	130

Figure S223. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.05e-11 (Fisher's exact test), Q value = 1.8e-08

Table S224. Gene #47: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	311	185
4P LOSS CNV	11	49	66
4P LOSS WILD-TYPE	149	262	119

Figure S224. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'MRNA_CNMF'

P value = 4.78e-07 (Chi-square test), Q value = 0.00035

Table S225. 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	4	15	33	13	25	2	3
4Q LOSS WILD-TYPE	20	32	104	63	96	47	18	37

Figure S225. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'4q loss' versus 'MRNA_CHIERARCHICAL'

P value = 7.12e-08 (Fisher's exact test), Q value = 5.5e-05

Table S226. Gene #48: '4q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
4Q LOSS CNV	7	42	47
4Q LOSS WILD-TYPE	115	83	219

Figure S226. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 1.41e-21 (Chi-square test), Q value = 1.3e-18

Table S227. Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	374	232	79	252	48
4Q LOSS CNV	21	29	25	87	7
4Q LOSS WILD-TYPE	353	203	54	165	41

Figure S227. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 4.42e-14 (Chi-square test), Q value = 4e-11

Table S228. Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	109	155	106	136	44	113
4Q LOSS CNV	43	22	20	11	3	3
4Q LOSS WILD-TYPE	66	133	86	125	41	110

Figure S228. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 2.21e-15 (Chi-square test), Q value = 2e-12

Table S229. 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	175	139	217	154	224	47	15
4Q LOSS CNV	61	4	29	41	28	3	0
4Q LOSS WILD-TYPE	114	135	188	113	196	44	15

Figure S229. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.59e-16 (Fisher's exact test), Q value = 1.5e-13

Table S230. Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	291	246	434
4Q LOSS CNV	15	80	71
4Q LOSS WILD-TYPE	276	166	363

Figure S230. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_CNMF'

P value = 3.23e-13 (Fisher's exact test), Q value = 2.9e-10

Table S231. Gene #48: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	274	413	279
4Q LOSS CNV	14	69	79
4Q LOSS WILD-TYPE	260	344	200

Figure S231. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.95e-11 (Fisher's exact test), Q value = 6.7e-08

Table S232. Gene #48: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	225	376	365
4Q LOSS CNV	68	32	62
4Q LOSS WILD-TYPE	157	344	303

Figure S232. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.23e-09 (Fisher's exact test), Q value = 1e-06

Table S233. Gene #48: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	210	196
4Q LOSS CNV	41	9	51
4Q LOSS WILD-TYPE	209	201	145

Figure S233. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.18e-07 (Fisher's exact test), Q value = 8.9e-05

Table S234. Gene #48: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	311	185
4Q LOSS CNV	10	40	51
4Q LOSS WILD-TYPE	150	271	134

Figure S234. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p loss' versus 'MRNA_CNMF'

P value = 1.88e-08 (Chi-square test), Q value = 1.5e-05

Table S235. 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	2	2	3	24	4	9	0	0
5P LOSS WILD-TYPE	19	34	116	72	105	63	20	40

Figure S235. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'5p loss' versus 'MRNA_CHIERARCHICAL'

P value = 9.1e-06 (Fisher's exact test), Q value = 0.0059

Table S236. 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	17
5P LOSS WILD-TYPE	119	101	249

Figure S236. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'5p loss' versus 'CN_CNMF'

P value = 1.91e-20 (Chi-square test), Q value = 1.8e-17

Table S237. Gene #49: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	374	232	79	252	48
5P LOSS CNV	2	12	3	54	4
5P LOSS WILD-TYPE	372	220	76	198	44

Figure S237. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

'5p loss' versus 'METHLYATION_CNMF'

P value = 4e-12 (Chi-square test), Q value = 3.5e-09

Table S238. Gene #49: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	109	155	106	136	44	113
5P LOSS CNV	25	2	6	11	0	1
5P LOSS WILD-TYPE	84	153	100	125	44	112

Figure S238. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5p loss' versus 'RPPA_CNMF'

P value = 4.28e-05 (Fisher's exact test), Q value = 0.026

Table S239. Gene #49: '5p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
5P LOSS CNV	27	5	6
5P LOSS WILD-TYPE	120	128	111

Figure S239. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'5p loss' versus 'RPPA_CHIERARCHICAL'

P value = 6.72e-06 (Fisher's exact test), Q value = 0.0044

Table S240. Gene #49: '5p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	110	126
5P LOSS CNV	7	5	26
5P LOSS WILD-TYPE	154	105	100

Figure S240. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'5p loss' versus 'MRNASEQ_CNMF'

P value = 1.18e-15 (Chi-square test), Q value = 1.1e-12

Table S241. 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	175	139	217	154	224	47	15
5P LOSS CNV	40	1	5	13	11	1	1
5P LOSS WILD-TYPE	135	138	212	141	213	46	14

Figure S241. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.66e-10 (Fisher's exact test), Q value = 2.2e-07

Table S242. Gene #49: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	291	246	434
5P LOSS CNV	5	41	26
5P LOSS WILD-TYPE	286	205	408

Figure S242. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_CNMF'

P value = 2.32e-12 (Fisher's exact test), Q value = 2e-09

Table S243. Gene #49: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	274	413	279
5P LOSS CNV	3	23	47
5P LOSS WILD-TYPE	271	390	232

Figure S243. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.08e-14 (Fisher's exact test), Q value = 2.8e-11

Table S244. Gene #49: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	225	376	365
5P LOSS CNV	45	7	21
5P LOSS WILD-TYPE	180	369	344

Figure S244. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.93e-11 (Fisher's exact test), Q value = 1.7e-08

Table S245. Gene #49: '5p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	210	196
5P LOSS CNV	7	3	35
5P LOSS WILD-TYPE	243	207	161

Figure S245. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.56e-08 (Fisher's exact test), Q value = 1.2e-05

Table S246. Gene #49: '5p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	311	185
5P LOSS CNV	3	11	31
5P LOSS WILD-TYPE	157	300	154

Figure S246. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q loss' versus 'MRNA_CNMF'

P value = 2.06e-18 (Chi-square test), Q value = 1.9e-15

Table S247. 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	3	3	10	44	3	13	0	1
5Q LOSS WILD-TYPE	18	33	109	52	106	59	20	39

Figure S247. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'5q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1.84e-14 (Fisher's exact test), Q value = 1.7e-11

Table S248. 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	26
5Q LOSS WILD-TYPE	118	78	240

Figure S248. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'5q loss' versus 'CN_CNMF'

P value = 4.34e-52 (Chi-square test), Q value = 4.2e-49

Table S249. Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	374	232	79	252	48
5Q LOSS CNV	1	16	4	107	8
5Q LOSS WILD-TYPE	373	216	75	145	40

Figure S249. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 1.01e-32 (Chi-square test), Q value = 9.6e-30

Table S250. Gene #50: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	109	155	106	136	44	113
5Q LOSS CNV	53	3	9	17	1	2
5Q LOSS WILD-TYPE	56	152	97	119	43	111

Figure S250. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5q loss' versus 'RPPA_CNMF'

P value = 7.26e-09 (Fisher's exact test), Q value = 5.8e-06

Table S251. Gene #50: '5q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
5Q LOSS CNV	46	7	13
5Q LOSS WILD-TYPE	101	126	104

Figure S251. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'5q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1.7e-10 (Fisher's exact test), Q value = 1.4e-07

Table S252. Gene #50: '5q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	110	126
5Q LOSS CNV	12	9	45
5Q LOSS WILD-TYPE	149	101	81

Figure S252. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 1.36e-36 (Chi-square test), Q value = 1.3e-33

Table S253. 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	175	139	217	154	224	47	15
5Q LOSS CNV	77	3	5	22	23	2	1
5Q LOSS WILD-TYPE	98	136	212	132	201	45	14

Figure S253. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.74e-28 (Fisher's exact test), Q value = 5.5e-25

Table S254. Gene #50: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	291	246	434
5Q LOSS CNV	8	87	38
5Q LOSS WILD-TYPE	283	159	396

Figure S254. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CNMF'

P value = 4.76e-30 (Fisher's exact test), Q value = 4.5e-27

Table S255. Gene #50: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	274	413	279
5Q LOSS CNV	6	31	95
5Q LOSS WILD-TYPE	268	382	184

Figure S255. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.17e-35 (Fisher's exact test), Q value = 5e-32

Table S256. Gene #50: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	225	376	365
5Q LOSS CNV	88	8	36
5Q LOSS WILD-TYPE	137	368	329

Figure S256. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.27e-21 (Fisher's exact test), Q value = 4e-18

Table S257. Gene #50: '5q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	210	196
5Q LOSS CNV	13	7	65
5Q LOSS WILD-TYPE	237	203	131

Figure S257. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.19e-21 (Fisher's exact test), Q value = 1.1e-18

Table S258. Gene #50: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	311	185
5Q LOSS CNV	6	15	64
5Q LOSS WILD-TYPE	154	296	121

Figure S258. 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 = 0.065

Table S259. 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 S259. Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6p loss' versus 'CN_CNMF'

P value = 5.34e-10 (Chi-square test), Q value = 4.4e-07

Table S260. Gene #51: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	374	232	79	252	48
6P LOSS CNV	23	50	12	15	11
6P LOSS WILD-TYPE	351	182	67	237	37

Figure S260. Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

'6p loss' versus 'METHLYATION_CNMF'

P value = 0.000137 (Chi-square test), Q value = 0.077

Table S261. Gene #51: '6p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	109	155	106	136	44	113
6P LOSS CNV	5	13	13	27	2	5
6P LOSS WILD-TYPE	104	142	93	109	42	108

Figure S261. Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6p loss' versus 'MRNASEQ_CNMF'

P value = 1.53e-06 (Chi-square test), Q value = 0.0011

Table S262. 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	175	139	217	154	224	47	15
6P LOSS CNV	9	11	28	11	48	3	0
6P LOSS WILD-TYPE	166	128	189	143	176	44	15

Figure S262. Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.7e-05 (Fisher's exact test), Q value = 0.011

Table S263. Gene #51: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	291	246	434
6P LOSS CNV	26	13	71
6P LOSS WILD-TYPE	265	233	363

Figure S263. Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'MRNA_CNMF'

P value = 2.46e-05 (Chi-square test), Q value = 0.015

Table S264. 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	39	6	21	8	1	10
6Q LOSS WILD-TYPE	18	26	80	90	88	64	19	30

Figure S264. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'6q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1.62e-06 (Fisher's exact test), Q value = 0.0011

Table S265. Gene #52: '6q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
6Q LOSS CNV	27	6	65
6Q LOSS WILD-TYPE	95	119	201

Figure S265. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6q loss' versus 'CN_CNMF'

P value = 3.76e-18 (Chi-square test), Q value = 3.5e-15

Table S266. Gene #52: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	374	232	79	252	48
6Q LOSS CNV	44	81	14	17	17
6Q LOSS WILD-TYPE	330	151	65	235	31

Figure S266. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

'6q loss' versus 'METHLYATION_CNMF'

P value = 4.22e-08 (Chi-square test), Q value = 3.3e-05

Table S267. Gene #52: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	109	155	106	136	44	113
6Q LOSS CNV	6	31	20	42	5	6
6Q LOSS WILD-TYPE	103	124	86	94	39	107

Figure S267. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6q loss' versus 'MRNASEQ_CNMF'

P value = 1.7e-10 (Chi-square test), Q value = 1.4e-07

Table S268. 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	175	139	217	154	224	47	15
6Q LOSS CNV	11	22	43	15	72	7	1
6Q LOSS WILD-TYPE	164	117	174	139	152	40	14

Figure S268. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.13e-07 (Fisher's exact test), Q value = 0.00037

Table S269. Gene #52: '6q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	291	246	434
6Q LOSS CNV	55	18	98
6Q LOSS WILD-TYPE	236	228	336

Figure S269. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_CNMF'

P value = 0.000365 (Fisher's exact test), Q value = 0.19

Table S270. Gene #52: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	274	413	279
6Q LOSS CNV	49	92	30
6Q LOSS WILD-TYPE	225	321	249

Figure S270. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.18e-07 (Fisher's exact test), Q value = 8.9e-05

Table S271. Gene #52: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	225	376	365
6Q LOSS CNV	15	69	87
6Q LOSS WILD-TYPE	210	307	278

Figure S271. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.15e-05 (Fisher's exact test), Q value = 0.042

Table S272. Gene #52: '6q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	311	185
6Q LOSS CNV	27	66	13
6Q LOSS WILD-TYPE	133	245	172

Figure S272. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7p loss' versus 'CN_CNMF'

P value = 4.23e-06 (Chi-square test), Q value = 0.0028

Table S273. Gene #53: '7p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	374	232	79	252	48
7P LOSS CNV	4	15	4	27	1
7P LOSS WILD-TYPE	370	217	75	225	47

Figure S273. Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #3: 'CN_CNMF'

'7p loss' versus 'METHLYATION_CNMF'

P value = 6.32e-06 (Chi-square test), Q value = 0.0042

Table S274. Gene #53: '7p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	109	155	106	136	44	113
7P LOSS CNV	17	3	6	7	1	1
7P LOSS WILD-TYPE	92	152	100	129	43	112

Figure S274. Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p loss' versus 'MRNASEQ_CNMF'

P value = 4.07e-05 (Chi-square test), Q value = 0.024

Table S275. Gene #53: '7p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	175	139	217	154	224	47	15
7P LOSS CNV	21	2	4	6	17	1	0
7P LOSS WILD-TYPE	154	137	213	148	207	46	15

Figure S275. Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7p loss' versus 'MIRSEQ_CNMF'

P value = 2.65e-05 (Fisher's exact test), Q value = 0.016

Table S276. Gene #53: '7p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	274	413	279
7P LOSS CNV	3	21	26
7P LOSS WILD-TYPE	271	392	253

Figure S276. Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.13e-05 (Fisher's exact test), Q value = 0.019

Table S277. Gene #53: '7p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	225	376	365
7P LOSS CNV	21	6	23
7P LOSS WILD-TYPE	204	370	342

Figure S277. Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000194 (Fisher's exact test), Q value = 0.11

Table S278. Gene #53: '7p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	311	185
7P LOSS CNV	3	8	19
7P LOSS WILD-TYPE	157	303	166

Figure S278. Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000414 (Fisher's exact test), Q value = 0.21

Table S279. Gene #54: '7q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	225	376	365
7Q LOSS CNV	15	11	36
7Q LOSS WILD-TYPE	210	365	329

Figure S279. Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

P value = 2.99e-17 (Chi-square test), Q value = 2.8e-14

Table S280. Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	374	232	79	252	48
8P LOSS CNV	58	105	13	102	15
8P LOSS WILD-TYPE	316	127	66	150	33

Figure S280. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 2.56e-08 (Chi-square test), Q value = 2e-05

Table S281. Gene #55: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	109	155	106	136	44	113
8P LOSS CNV	39	28	38	59	7	16
8P LOSS WILD-TYPE	70	127	68	77	37	97

Figure S281. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 2.93e-08 (Chi-square test), Q value = 2.3e-05

Table S282. 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	175	139	217	154	224	47	15
8P LOSS CNV	54	26	39	63	91	11	6
8P LOSS WILD-TYPE	121	113	178	91	133	36	9

Figure S282. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p loss' versus 'MIRSEQ_CNMF'

P value = 4.58e-06 (Fisher's exact test), Q value = 0.0031

Table S283. Gene #55: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	274	413	279
8P LOSS CNV	51	141	97
8P LOSS WILD-TYPE	223	272	182

Figure S283. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-07 (Fisher's exact test), Q value = 0.00015

Table S284. Gene #55: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	225	376	365
8P LOSS CNV	77	75	137
8P LOSS WILD-TYPE	148	301	228

Figure S284. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.93e-05 (Fisher's exact test), Q value = 0.012

Table S285. Gene #55: '8p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	210	196
8P LOSS CNV	85	36	68
8P LOSS WILD-TYPE	165	174	128

Figure S285. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9p loss' versus 'MRNA_CNMF'

P value = 3.11e-05 (Chi-square test), Q value = 0.019

Table S286. 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	25	5	2
9P LOSS WILD-TYPE	15	28	79	78	98	47	15	38

Figure S286. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'9p loss' versus 'MRNA_CHIERARCHICAL'

P value = 4.42e-05 (Fisher's exact test), Q value = 0.026

Table S287. 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	78
9P LOSS WILD-TYPE	110	100	188

Figure S287. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

P value = 5.03e-27 (Chi-square test), Q value = 4.8e-24

Table S288. Gene #57: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	374	232	79	252	48
9P LOSS CNV	19	96	7	65	11
9P LOSS WILD-TYPE	355	136	72	187	37

Figure S288. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 2.1e-13 (Chi-square test), Q value = 1.9e-10

Table S289. Gene #57: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	109	155	106	136	44	113
9P LOSS CNV	22	8	32	49	5	7
9P LOSS WILD-TYPE	87	147	74	87	39	106

Figure S289. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 1.16e-11 (Chi-square test), Q value = 1e-08

Table S290. 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	175	139	217	154	224	47	15
9P LOSS CNV	30	12	23	47	74	4	4
9P LOSS WILD-TYPE	145	127	194	107	150	43	11

Figure S290. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.94e-06 (Fisher's exact test), Q value = 0.0013

Table S291. Gene #57: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	291	246	434
9P LOSS CNV	31	52	111
9P LOSS WILD-TYPE	260	194	323

Figure S291. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_CNMF'

P value = 2.11e-09 (Fisher's exact test), Q value = 1.7e-06

Table S292. Gene #57: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	274	413	279
9P LOSS CNV	22	107	65
9P LOSS WILD-TYPE	252	306	214

Figure S292. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.01e-08 (Fisher's exact test), Q value = 1.6e-05

Table S293. Gene #57: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	225	376	365
9P LOSS CNV	49	42	103
9P LOSS WILD-TYPE	176	334	262

Figure S293. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.73e-05 (Fisher's exact test), Q value = 0.017

Table S294. Gene #57: '9p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	210	196
9P LOSS CNV	51	19	50
9P LOSS WILD-TYPE	199	191	146

Figure S294. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9q loss' versus 'MRNA_CHIERARCHICAL'

P value = 2.04e-05 (Fisher's exact test), Q value = 0.013

Table S295. 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	60
9Q LOSS WILD-TYPE	116	101	206

Figure S295. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 1.84e-21 (Chi-square test), Q value = 1.7e-18

Table S296. Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	374	232	79	252	48
9Q LOSS CNV	7	66	8	62	13
9Q LOSS WILD-TYPE	367	166	71	190	35

Figure S296. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 1.21e-13 (Chi-square test), Q value = 1.1e-10

Table S297. Gene #58: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	109	155	106	136	44	113
9Q LOSS CNV	34	6	20	36	3	2
9Q LOSS WILD-TYPE	75	149	86	100	41	111

Figure S297. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 3.19e-11 (Chi-square test), Q value = 2.7e-08

Table S298. 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	175	139	217	154	224	47	15
9Q LOSS CNV	43	4	20	20	59	2	4
9Q LOSS WILD-TYPE	132	135	197	134	165	45	11

Figure S298. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.44e-08 (Fisher's exact test), Q value = 7.2e-05

Table S299. Gene #58: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	291	246	434
9Q LOSS CNV	18	50	84
9Q LOSS WILD-TYPE	273	196	350

Figure S299. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_CNMF'

P value = 5.2e-10 (Fisher's exact test), Q value = 4.3e-07

Table S300. Gene #58: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	274	413	279
9Q LOSS CNV	14	68	67
9Q LOSS WILD-TYPE	260	345	212

Figure S300. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.42e-10 (Fisher's exact test), Q value = 4.5e-07

Table S301. Gene #58: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	225	376	365
9Q LOSS CNV	55	25	69
9Q LOSS WILD-TYPE	170	351	296

Figure S301. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 5.51e-06 (Fisher's exact test), Q value = 0.0037

Table S302. Gene #58: '9q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	210	196
9Q LOSS CNV	27	16	47
9Q LOSS WILD-TYPE	223	194	149

Figure S302. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000397 (Fisher's exact test), Q value = 0.2

Table S303. Gene #58: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	311	185
9Q LOSS CNV	13	36	41
9Q LOSS WILD-TYPE	147	275	144

Figure S303. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 5.62e-06 (Chi-square test), Q value = 0.0037

Table S304. Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	374	232	79	252	48
10P LOSS CNV	8	28	11	28	5
10P LOSS WILD-TYPE	366	204	68	224	43

Figure S304. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

'10q loss' versus 'MRNA_CNMF'

P value = 0.000204 (Chi-square test), Q value = 0.11

Table S305. 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	17	6	9	2	0
10Q LOSS WILD-TYPE	14	34	95	79	103	63	18	40

Figure S305. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'10q loss' versus 'CN_CNMF'

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

Table S306. Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	374	232	79	252	48
10Q LOSS CNV	7	37	11	56	7
10Q LOSS WILD-TYPE	367	195	68	196	41

Figure S306. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 6.46e-07 (Chi-square test), Q value = 0.00046

Table S307. Gene #60: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	109	155	106	136	44	113
10Q LOSS CNV	25	9	16	24	4	1
10Q LOSS WILD-TYPE	84	146	90	112	40	112

Figure S307. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 3.48e-07 (Chi-square test), Q value = 0.00025

Table S308. 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	175	139	217	154	224	47	15
10Q LOSS CNV	31	4	15	23	43	0	1
10Q LOSS WILD-TYPE	144	135	202	131	181	47	14

Figure S308. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.02e-06 (Fisher's exact test), Q value = 0.0046

Table S309. Gene #60: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	291	246	434
10Q LOSS CNV	14	39	64
10Q LOSS WILD-TYPE	277	207	370

Figure S309. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_CNMF'

P value = 0.000252 (Fisher's exact test), Q value = 0.13

Table S310. Gene #60: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	274	413	279
10Q LOSS CNV	17	49	48
10Q LOSS WILD-TYPE	257	364	231

Figure S310. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.29e-05 (Fisher's exact test), Q value = 0.031

Table S311. Gene #60: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	225	376	365
10Q LOSS CNV	41	25	48
10Q LOSS WILD-TYPE	184	351	317

Figure S311. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 1.64e-16 (Chi-square test), Q value = 1.5e-13

Table S312. Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	374	232	79	252	48
11P LOSS CNV	14	67	15	57	5
11P LOSS WILD-TYPE	360	165	64	195	43

Figure S312. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 1.92e-11 (Chi-square test), Q value = 1.7e-08

Table S313. Gene #61: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	109	155	106	136	44	113
11P LOSS CNV	22	7	28	36	3	2
11P LOSS WILD-TYPE	87	148	78	100	41	111

Figure S313. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p loss' versus 'MRNASEQ_CNMF'

P value = 0.000119 (Chi-square test), Q value = 0.067

Table S314. 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	175	139	217	154	224	47	15
11P LOSS CNV	33	14	18	36	48	5	1
11P LOSS WILD-TYPE	142	125	199	118	176	42	14

Figure S314. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11p loss' versus 'MIRSEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.079

Table S315. Gene #61: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	274	413	279
11P LOSS CNV	25	70	61
11P LOSS WILD-TYPE	249	343	218

Figure S315. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.9e-05 (Fisher's exact test), Q value = 0.018

Table S316. Gene #61: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	225	376	365
11P LOSS CNV	46	36	74
11P LOSS WILD-TYPE	179	340	291

Figure S316. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11q loss' versus 'MRNA_CNMF'

P value = 3.29e-06 (Chi-square test), Q value = 0.0022

Table S317. 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	58	16	22	19	3	9
11Q LOSS WILD-TYPE	16	24	61	80	87	53	17	31

Figure S317. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'11q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.000185 (Fisher's exact test), Q value = 0.1

Table S318. 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	94
11Q LOSS WILD-TYPE	92	105	172

Figure S318. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

P value = 2.99e-29 (Chi-square test), Q value = 2.9e-26

Table S319. Gene #62: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	374	232	79	252	48
11Q LOSS CNV	41	123	25	54	8
11Q LOSS WILD-TYPE	333	109	54	198	40

Figure S319. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

P value = 1.53e-14 (Chi-square test), Q value = 1.4e-11

Table S320. Gene #62: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	109	155	106	136	44	113
11Q LOSS CNV	20	27	38	63	9	5
11Q LOSS WILD-TYPE	89	128	68	73	35	108

Figure S320. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11q loss' versus 'MRNASEQ_CNMF'

P value = 8.45e-13 (Chi-square test), Q value = 7.5e-10

Table S321. 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	175	139	217	154	224	47	15
11Q LOSS CNV	29	35	41	34	102	7	0
11Q LOSS WILD-TYPE	146	104	176	120	122	40	15

Figure S321. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000208 (Fisher's exact test), Q value = 0.11

Table S322. Gene #62: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	291	246	434
11Q LOSS CNV	77	40	131
11Q LOSS WILD-TYPE	214	206	303

Figure S322. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.66e-05 (Fisher's exact test), Q value = 0.022

Table S323. Gene #62: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	225	376	365
11Q LOSS CNV	43	81	123
11Q LOSS WILD-TYPE	182	295	242

Figure S323. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12p loss' versus 'CN_CNMF'

P value = 0.000485 (Chi-square test), Q value = 0.25

Table S324. Gene #63: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	374	232	79	252	48
12P LOSS CNV	16	20	4	33	1
12P LOSS WILD-TYPE	358	212	75	219	47

Figure S324. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

'12p loss' versus 'METHLYATION_CNMF'

P value = 1.58e-06 (Chi-square test), Q value = 0.0011

Table S325. Gene #63: '12p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	109	155	106	136	44	113
12P LOSS CNV	22	7	4	11	5	2
12P LOSS WILD-TYPE	87	148	102	125	39	111

Figure S325. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000431 (Fisher's exact test), Q value = 0.22

Table S326. Gene #63: '12p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	291	246	434
12P LOSS CNV	16	33	23
12P LOSS WILD-TYPE	275	213	411

Figure S326. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p loss' versus 'MIRSEQ_CNMF'

P value = 0.000216 (Fisher's exact test), Q value = 0.12

Table S327. Gene #63: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	274	413	279
12P LOSS CNV	8	31	33
12P LOSS WILD-TYPE	266	382	246

Figure S327. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000168 (Fisher's exact test), Q value = 0.093

Table S328. Gene #63: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	225	376	365
12P LOSS CNV	27	13	32
12P LOSS WILD-TYPE	198	363	333

Figure S328. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12q loss' versus 'MRNA_CNMF'

P value = 0.000481 (Chi-square test), Q value = 0.24

Table S329. Gene #64: '12q 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
12Q LOSS CNV	1	1	4	16	4	6	0	0
12Q LOSS WILD-TYPE	20	35	115	80	105	66	20	40

Figure S329. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'12q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.000108 (Fisher's exact test), Q value = 0.062

Table S330. Gene #64: '12q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
12Q LOSS CNV	2	18	12
12Q LOSS WILD-TYPE	120	107	254

Figure S330. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'12q loss' versus 'CN_CNMF'

P value = 7.06e-09 (Chi-square test), Q value = 5.7e-06

Table S331. Gene #64: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	374	232	79	252	48
12Q LOSS CNV	8	9	5	36	1
12Q LOSS WILD-TYPE	366	223	74	216	47

Figure S331. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

'12q loss' versus 'METHLYATION_CNMF'

P value = 3.4e-13 (Chi-square test), Q value = 3e-10

Table S332. Gene #64: '12q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	109	155	106	136	44	113
12Q LOSS CNV	25	2	2	9	1	2
12Q LOSS WILD-TYPE	84	153	104	127	43	111

Figure S332. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12q loss' versus 'MRNASEQ_CNMF'

P value = 2.09e-13 (Chi-square test), Q value = 1.9e-10

Table S333. 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	175	139	217	154	224	47	15
12Q LOSS CNV	33	1	5	9	7	1	0
12Q LOSS WILD-TYPE	142	138	212	145	217	46	15

Figure S333. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.1e-09 (Fisher's exact test), Q value = 4.1e-06

Table S334. Gene #64: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	291	246	434
12Q LOSS CNV	6	35	15
12Q LOSS WILD-TYPE	285	211	419

Figure S334. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q loss' versus 'MIRSEQ_CNMF'

P value = 3e-08 (Fisher's exact test), Q value = 2.3e-05

Table S335. Gene #64: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	274	413	279
12Q LOSS CNV	6	14	37
12Q LOSS WILD-TYPE	268	399	242

Figure S335. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.86e-10 (Fisher's exact test), Q value = 8.1e-07

Table S336. Gene #64: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	225	376	365
12Q LOSS CNV	34	7	16
12Q LOSS WILD-TYPE	191	369	349

Figure S336. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 8.26e-09 (Fisher's exact test), Q value = 6.6e-06

Table S337. Gene #64: '12q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	210	196
12Q LOSS CNV	5	5	30
12Q LOSS WILD-TYPE	245	205	166

Figure S337. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.65e-08 (Fisher's exact test), Q value = 5.9e-05

Table S338. Gene #64: '12q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	311	185
12Q LOSS CNV	3	9	28
12Q LOSS WILD-TYPE	157	302	157

Figure S338. 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 = 0.22

Table S339. 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 S339. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'13q loss' versus 'CN_CNMF'

P value = 3.36e-37 (Chi-square test), Q value = 3.2e-34

Table S340. Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	374	232	79	252	48
13Q LOSS CNV	21	107	43	90	26
13Q LOSS WILD-TYPE	353	125	36	162	22

Figure S340. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 4.46e-11 (Chi-square test), Q value = 3.8e-08

Table S341. Gene #65: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	109	155	106	136	44	113
13Q LOSS CNV	39	32	51	48	3	13
13Q LOSS WILD-TYPE	70	123	55	88	41	100

Figure S341. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 8.71e-05 (Chi-square test), Q value = 0.051

Table S342. 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	175	139	217	154	224	47	15
13Q LOSS CNV	59	23	52	48	87	9	5
13Q LOSS WILD-TYPE	116	116	165	106	137	38	10

Figure S342. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.48e-05 (Fisher's exact test), Q value = 0.0095

Table S343. Gene #65: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	291	246	434
13Q LOSS CNV	55	81	147
13Q LOSS WILD-TYPE	236	165	287

Figure S343. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_CNMF'

P value = 4.74e-07 (Fisher's exact test), Q value = 0.00034

Table S344. Gene #65: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	274	413	279
13Q LOSS CNV	47	145	90
13Q LOSS WILD-TYPE	227	268	189

Figure S344. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'13q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.09e-05 (Fisher's exact test), Q value = 0.03

Table S345. Gene #65: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	225	376	365
13Q LOSS CNV	69	81	132
13Q LOSS WILD-TYPE	156	295	233

Figure S345. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.11

Table S346. Gene #65: '13q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	210	196
13Q LOSS CNV	70	34	65
13Q LOSS WILD-TYPE	180	176	131

Figure S346. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'14q loss' versus 'MRNA_CNMF'

P value = 2.54e-10 (Chi-square test), Q value = 2.1e-07

Table S347. 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	3	1	25	36	5	9	3	0
14Q LOSS WILD-TYPE	18	35	94	60	104	63	17	40

Figure S347. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'14q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1.32e-08 (Fisher's exact test), Q value = 1e-05

Table S348. 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	40
14Q LOSS WILD-TYPE	118	87	226

Figure S348. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 2.57e-24 (Chi-square test), Q value = 2.4e-21

Table S349. Gene #66: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	374	232	79	252	48
14Q LOSS CNV	9	35	11	85	12
14Q LOSS WILD-TYPE	365	197	68	167	36

Figure S349. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 4.24e-17 (Chi-square test), Q value = 3.9e-14

Table S350. Gene #66: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	109	155	106	136	44	113
14Q LOSS CNV	43	9	18	18	0	4
14Q LOSS WILD-TYPE	66	146	88	118	44	109

Figure S350. 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 = 0.1

Table S351. 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 S351. 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 = 0.05

Table S352. 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 S352. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 4.52e-22 (Chi-square test), Q value = 4.3e-19

Table S353. 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	175	139	217	154	224	47	15
14Q LOSS CNV	68	6	12	21	43	0	2
14Q LOSS WILD-TYPE	107	133	205	133	181	47	13

Figure S353. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.45e-16 (Fisher's exact test), Q value = 2.2e-13

Table S354. Gene #66: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	291	246	434
14Q LOSS CNV	14	77	61
14Q LOSS WILD-TYPE	277	169	373

Figure S354. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_CNMF'

P value = 2.8e-17 (Fisher's exact test), Q value = 2.6e-14

Table S355. Gene #66: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	274	413	279
14Q LOSS CNV	19	39	88
14Q LOSS WILD-TYPE	255	374	191

Figure S355. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'14q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.47e-16 (Fisher's exact test), Q value = 8.7e-13

Table S356. Gene #66: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	225	376	365
14Q LOSS CNV	75	29	42
14Q LOSS WILD-TYPE	150	347	323

Figure S356. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.6e-11 (Fisher's exact test), Q value = 2.2e-08

Table S357. Gene #66: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	210	196
14Q LOSS CNV	23	17	61
14Q LOSS WILD-TYPE	227	193	135

Figure S357. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'14q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9.94e-10 (Fisher's exact test), Q value = 8.2e-07

Table S358. Gene #66: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	311	185
14Q LOSS CNV	19	26	56
14Q LOSS WILD-TYPE	141	285	129

Figure S358. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.000181 (Fisher's exact test), Q value = 0.1

Table S359. 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	37	51
15Q LOSS WILD-TYPE	111	88	215

Figure S359. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 2.12e-23 (Chi-square test), Q value = 2e-20

Table S360. Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	374	232	79	252	48
15Q LOSS CNV	17	37	34	80	9
15Q LOSS WILD-TYPE	357	195	45	172	39

Figure S360. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 6.1e-09 (Chi-square test), Q value = 4.9e-06

Table S361. Gene #67: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	109	155	106	136	44	113
15Q LOSS CNV	41	16	22	23	5	8
15Q LOSS WILD-TYPE	68	139	84	113	39	105

Figure S361. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 7.89e-07 (Chi-square test), Q value = 0.00056

Table S362. 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	175	139	217	154	224	47	15
15Q LOSS CNV	54	13	32	32	36	1	4
15Q LOSS WILD-TYPE	121	126	185	122	188	46	11

Figure S362. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.43e-07 (Fisher's exact test), Q value = 0.00011

Table S363. Gene #67: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	291	246	434
15Q LOSS CNV	25	65	82
15Q LOSS WILD-TYPE	266	181	352

Figure S363. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_CNMF'

P value = 2.29e-06 (Fisher's exact test), Q value = 0.0016

Table S364. Gene #67: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	274	413	279
15Q LOSS CNV	26	73	72
15Q LOSS WILD-TYPE	248	340	207

Figure S364. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8e-07 (Fisher's exact test), Q value = 0.00057

Table S365. Gene #67: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	225	376	365
15Q LOSS CNV	64	42	65
15Q LOSS WILD-TYPE	161	334	300

Figure S365. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 8.14e-06 (Fisher's exact test), Q value = 0.0053

Table S366. Gene #67: '15q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	210	196
15Q LOSS CNV	42	16	49
15Q LOSS WILD-TYPE	208	194	147

Figure S366. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.27e-06 (Fisher's exact test), Q value = 0.0016

Table S367. Gene #67: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	311	185
15Q LOSS CNV	14	41	52
15Q LOSS WILD-TYPE	146	270	133

Figure S367. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p loss' versus 'CN_CNMF'

P value = 5.3e-06 (Chi-square test), Q value = 0.0035

Table S368. Gene #68: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	374	232	79	252	48
16P LOSS CNV	6	18	2	29	3
16P LOSS WILD-TYPE	368	214	77	223	45

Figure S368. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

'16p loss' versus 'METHLYATION_CNMF'

P value = 1.07e-07 (Chi-square test), Q value = 8.1e-05

Table S369. Gene #68: '16p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	109	155	106	136	44	113
16P LOSS CNV	17	1	8	4	0	2
16P LOSS WILD-TYPE	92	154	98	132	44	111

Figure S369. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16p loss' versus 'MRNASEQ_CNMF'

P value = 9.23e-07 (Chi-square test), Q value = 0.00065

Table S370. 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	175	139	217	154	224	47	15
16P LOSS CNV	25	3	3	10	16	0	0
16P LOSS WILD-TYPE	150	136	214	144	208	47	15

Figure S370. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16p loss' versus 'MIRSEQ_CNMF'

P value = 2.71e-05 (Fisher's exact test), Q value = 0.017

Table S371. Gene #68: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	274	413	279
16P LOSS CNV	6	19	31
16P LOSS WILD-TYPE	268	394	248

Figure S371. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.63e-06 (Fisher's exact test), Q value = 0.0011

Table S372. Gene #68: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	225	376	365
16P LOSS CNV	27	7	22
16P LOSS WILD-TYPE	198	369	343

Figure S372. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000108 (Fisher's exact test), Q value = 0.062

Table S373. Gene #68: '16p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	210	196
16P LOSS CNV	8	3	20
16P LOSS WILD-TYPE	242	207	176

Figure S373. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000222 (Fisher's exact test), Q value = 0.12

Table S374. Gene #68: '16p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	311	185
16P LOSS CNV	2	10	19
16P LOSS WILD-TYPE	158	301	166

Figure S374. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q loss' versus 'MRNA_CNMF'

P value = 1.13e-08 (Chi-square test), Q value = 9e-06

Table S375. 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	54	17	69	31	6	24
16Q LOSS WILD-TYPE	10	17	65	79	40	41	14	16

Figure S375. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'16q loss' versus 'MRNA_CHIERARCHICAL'

P value = 3e-13 (Fisher's exact test), Q value = 2.7e-10

Table S376. Gene #69: '16q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
16Q LOSS CNV	63	21	147
16Q LOSS WILD-TYPE	59	104	119

Figure S376. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'16q loss' versus 'CN_CNMF'

P value = 4.47e-12 (Chi-square test), Q value = 3.9e-09

Table S377. Gene #69: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	374	232	79	252	48
16Q LOSS CNV	177	106	53	61	23
16Q LOSS WILD-TYPE	197	126	26	191	25

Figure S377. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 5.87e-18 (Chi-square test), Q value = 5.4e-15

Table S378. Gene #69: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	109	155	106	136	44	113
16Q LOSS CNV	23	106	52	58	16	22
16Q LOSS WILD-TYPE	86	49	54	78	28	91

Figure S378. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16q loss' versus 'RPPA_CNMF'

P value = 2.66e-06 (Fisher's exact test), Q value = 0.0018

Table S379. Gene #69: '16q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
16Q LOSS CNV	39	74	53
16Q LOSS WILD-TYPE	108	59	64

Figure S379. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'16q loss' versus 'RPPA_CHIERARCHICAL'

P value = 3.64e-10 (Fisher's exact test), Q value = 3e-07

Table S380. 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	52	24
16Q LOSS WILD-TYPE	71	58	102

Figure S380. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 4.36e-20 (Chi-square test), Q value = 4.1e-17

Table S381. 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	175	139	217	154	224	47	15
16Q LOSS CNV	32	67	143	53	95	25	2
16Q LOSS WILD-TYPE	143	72	74	101	129	22	13

Figure S381. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.46e-22 (Fisher's exact test), Q value = 1.4e-19

Table S382. Gene #69: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	291	246	434
16Q LOSS CNV	152	41	224
16Q LOSS WILD-TYPE	139	205	210

Figure S382. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_CNMF'

P value = 1.43e-15 (Fisher's exact test), Q value = 1.3e-12

Table S383. Gene #69: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	274	413	279
16Q LOSS CNV	139	211	63
16Q LOSS WILD-TYPE	135	202	216

Figure S383. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.48e-19 (Fisher's exact test), Q value = 1.4e-16

Table S384. Gene #69: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	225	376	365
16Q LOSS CNV	46	219	148
16Q LOSS WILD-TYPE	179	157	217

Figure S384. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.05e-12 (Fisher's exact test), Q value = 1.8e-09

Table S385. Gene #69: '16q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	210	196
16Q LOSS CNV	126	103	39
16Q LOSS WILD-TYPE	124	107	157

Figure S385. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.2e-11 (Fisher's exact test), Q value = 1e-08

Table S386. Gene #69: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	311	185
16Q LOSS CNV	84	147	37
16Q LOSS WILD-TYPE	76	164	148

Figure S386. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'MRNA_CNMF'

P value = 1.51e-06 (Chi-square test), Q value = 0.0011

Table S387. 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	12	19	59	42	27	46	3	15
17P LOSS WILD-TYPE	9	17	60	54	82	26	17	25

Figure S387. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17p loss' versus 'CN_CNMF'

P value = 8.71e-16 (Chi-square test), Q value = 8e-13

Table S388. Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	374	232	79	252	48
17P LOSS CNV	91	128	33	133	21
17P LOSS WILD-TYPE	283	104	46	119	27

Figure S388. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 2.88e-09 (Chi-square test), Q value = 2.3e-06

Table S389. Gene #70: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	109	155	106	136	44	113
17P LOSS CNV	42	54	55	74	14	18
17P LOSS WILD-TYPE	67	101	51	62	30	95

Figure S389. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 6.17e-07 (Chi-square test), Q value = 0.00044

Table S390. 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	175	139	217	154	224	47	15
17P LOSS CNV	65	49	64	88	112	18	5
17P LOSS WILD-TYPE	110	90	153	66	112	29	10

Figure S390. 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 S391. 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 S391. 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 = 0.0018

Table S392. 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 S392. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

P value = 6e-12 (Chi-square test), Q value = 5.2e-09

Table S393. Gene #71: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	374	232	79	252	48
17Q LOSS CNV	25	36	13	74	7
17Q LOSS WILD-TYPE	349	196	66	178	41

Figure S393. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

'17q loss' versus 'METHLYATION_CNMF'

P value = 1.69e-05 (Chi-square test), Q value = 0.011

Table S394. Gene #71: '17q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	109	155	106	136	44	113
17Q LOSS CNV	28	10	15	23	2	8
17Q LOSS WILD-TYPE	81	145	91	113	42	105

Figure S394. 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 = 9e-07

Table S395. 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 S395. 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 = 0.00023

Table S396. 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 S396. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'17q loss' versus 'MRNASEQ_CNMF'

P value = 4.01e-14 (Chi-square test), Q value = 3.6e-11

Table S397. 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	175	139	217	154	224	47	15
17Q LOSS CNV	43	8	14	52	27	7	2
17Q LOSS WILD-TYPE	132	131	203	102	197	40	13

Figure S397. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.51e-07 (Fisher's exact test), Q value = 0.00026

Table S398. Gene #71: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	291	246	434
17Q LOSS CNV	29	66	58
17Q LOSS WILD-TYPE	262	180	376

Figure S398. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.063

Table S399. Gene #71: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	274	413	279
17Q LOSS CNV	26	61	63
17Q LOSS WILD-TYPE	248	352	216

Figure S399. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.83e-05 (Fisher's exact test), Q value = 0.012

Table S400. Gene #71: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	225	376	365
17Q LOSS CNV	53	36	61
17Q LOSS WILD-TYPE	172	340	304

Figure S400. 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 = 0.097

Table S401. 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 S401. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'18p loss' versus 'CN_CNMF'

P value = 5.96e-08 (Chi-square test), Q value = 4.6e-05

Table S402. Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	374	232	79	252	48
18P LOSS CNV	36	62	23	61	9
18P LOSS WILD-TYPE	338	170	56	191	39

Figure S402. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

P value = 4.19e-07 (Chi-square test), Q value = 3e-04

Table S403. Gene #72: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	109	155	106	136	44	113
18P LOSS CNV	16	17	37	32	3	12
18P LOSS WILD-TYPE	93	138	69	104	41	101

Figure S403. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p loss' versus 'MRNASEQ_CNMF'

P value = 3.06e-09 (Chi-square test), Q value = 2.5e-06

Table S404. 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	175	139	217	154	224	47	15
18P LOSS CNV	24	12	31	56	48	10	6
18P LOSS WILD-TYPE	151	127	186	98	176	37	9

Figure S404. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 3.25e-10 (Chi-square test), Q value = 2.7e-07

Table S405. Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	374	232	79	252	48
18Q LOSS CNV	33	64	25	65	8
18Q LOSS WILD-TYPE	341	168	54	187	40

Figure S405. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 7.33e-10 (Chi-square test), Q value = 6e-07

Table S406. Gene #73: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	109	155	106	136	44	113
18Q LOSS CNV	25	17	40	34	2	8
18Q LOSS WILD-TYPE	84	138	66	102	42	105

Figure S406. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 4.95e-08 (Chi-square test), Q value = 3.8e-05

Table S407. 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	175	139	217	154	224	47	15
18Q LOSS CNV	30	12	31	56	50	7	4
18Q LOSS WILD-TYPE	145	127	186	98	174	40	11

Figure S407. 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 = 0.12

Table S408. 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 S408. 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 = 0.18

Table S409. 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 S409. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

P value = 1.78e-14 (Chi-square test), Q value = 1.6e-11

Table S410. Gene #74: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	374	232	79	252	48
19P LOSS CNV	2	41	1	21	7
19P LOSS WILD-TYPE	372	191	78	231	41

Figure S410. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

P value = 4.23e-10 (Chi-square test), Q value = 3.5e-07

Table S411. Gene #74: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	109	155	106	136	44	113
19P LOSS CNV	9	0	8	24	0	0
19P LOSS WILD-TYPE	100	155	98	112	44	113

Figure S411. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p loss' versus 'MRNASEQ_CNMF'

P value = 4.87e-07 (Chi-square test), Q value = 0.00035

Table S412. 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	175	139	217	154	224	47	15
19P LOSS CNV	13	5	3	20	31	0	0
19P LOSS WILD-TYPE	162	134	214	134	193	47	15

Figure S412. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000108 (Fisher's exact test), Q value = 0.062

Table S413. Gene #74: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	291	246	434
19P LOSS CNV	7	22	43
19P LOSS WILD-TYPE	284	224	391

Figure S413. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_CNMF'

P value = 3.37e-05 (Fisher's exact test), Q value = 0.02

Table S414. Gene #74: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	274	413	279
19P LOSS CNV	5	38	27
19P LOSS WILD-TYPE	269	375	252

Figure S414. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.81e-07 (Fisher's exact test), Q value = 0.00062

Table S415. Gene #74: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	225	376	365
19P LOSS CNV	17	9	44
19P LOSS WILD-TYPE	208	367	321

Figure S415. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q loss' versus 'MRNA_CNMF'

P value = 0.000372 (Chi-square test), Q value = 0.19

Table S416. 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	13	4	2	13	1	0
19Q LOSS WILD-TYPE	21	33	106	92	107	59	19	40

Figure S416. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'19q loss' versus 'MRNA_CHIERARCHICAL'

P value = 3.92e-05 (Fisher's exact test), Q value = 0.024

Table S417. 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	29
19Q LOSS WILD-TYPE	122	118	237

Figure S417. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 1.94e-11 (Chi-square test), Q value = 1.7e-08

Table S418. Gene #75: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	374	232	79	252	48
19Q LOSS CNV	2	32	0	16	6
19Q LOSS WILD-TYPE	372	200	79	236	42

Figure S418. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

P value = 3.35e-06 (Chi-square test), Q value = 0.0023

Table S419. Gene #75: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	109	155	106	136	44	113
19Q LOSS CNV	7	0	7	16	0	0
19Q LOSS WILD-TYPE	102	155	99	120	44	113

Figure S419. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q loss' versus 'MRNASEQ_CNMF'

P value = 2.06e-06 (Chi-square test), Q value = 0.0014

Table S420. 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	175	139	217	154	224	47	15
19Q LOSS CNV	9	3	2	18	24	0	0
19Q LOSS WILD-TYPE	166	136	215	136	200	47	15

Figure S420. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.99e-05 (Fisher's exact test), Q value = 0.058

Table S421. Gene #75: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	291	246	434
19Q LOSS CNV	4	17	35
19Q LOSS WILD-TYPE	287	229	399

Figure S421. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_CNMF'

P value = 9.87e-05 (Fisher's exact test), Q value = 0.057

Table S422. Gene #75: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	274	413	279
19Q LOSS CNV	3	31	20
19Q LOSS WILD-TYPE	271	382	259

Figure S422. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.26e-06 (Fisher's exact test), Q value = 0.00088

Table S423. Gene #75: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	225	376	365
19Q LOSS CNV	11	6	37
19Q LOSS WILD-TYPE	214	370	328

Figure S423. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p loss' versus 'CN_CNMF'

P value = 9.62e-08 (Chi-square test), Q value = 7.3e-05

Table S424. Gene #76: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	374	232	79	252	48
20P LOSS CNV	2	19	3	29	5
20P LOSS WILD-TYPE	372	213	76	223	43

Figure S424. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

'20p loss' versus 'METHLYATION_CNMF'

P value = 5.31e-08 (Chi-square test), Q value = 4.1e-05

Table S425. Gene #76: '20p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	109	155	106	136	44	113
20P LOSS CNV	20	3	6	7	1	1
20P LOSS WILD-TYPE	89	152	100	129	43	112

Figure S425. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p loss' versus 'MRNASEQ_CNMF'

P value = 6.93e-06 (Chi-square test), Q value = 0.0046

Table S426. 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	175	139	217	154	224	47	15
20P LOSS CNV	23	2	4	10	18	0	0
20P LOSS WILD-TYPE	152	137	213	144	206	47	15

Figure S426. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.05e-05 (Fisher's exact test), Q value = 0.0068

Table S427. Gene #76: '20p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	291	246	434
20P LOSS CNV	5	28	24
20P LOSS WILD-TYPE	286	218	410

Figure S427. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p loss' versus 'MIRSEQ_CNMF'

P value = 7.38e-06 (Fisher's exact test), Q value = 0.0048

Table S428. Gene #76: '20p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	274	413	279
20P LOSS CNV	4	20	30
20P LOSS WILD-TYPE	270	393	249

Figure S428. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.37e-07 (Fisher's exact test), Q value = 0.00018

Table S429. Gene #76: '20p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	225	376	365
20P LOSS CNV	26	5	23
20P LOSS WILD-TYPE	199	371	342

Figure S429. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.72e-05 (Fisher's exact test), Q value = 0.011

Table S430. Gene #76: '20p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	210	196
20P LOSS CNV	7	5	24
20P LOSS WILD-TYPE	243	205	172

Figure S430. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.5e-06 (Fisher's exact test), Q value = 0.0024

Table S431. Gene #76: '20p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	311	185
20P LOSS CNV	3	9	24
20P LOSS WILD-TYPE	157	302	161

Figure S431. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q loss' versus 'CN_CNMF'

P value = 2e-05 (Chi-square test), Q value = 0.012

Table S432. Gene #77: '20q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	374	232	79	252	48
20Q LOSS CNV	0	7	3	18	3
20Q LOSS WILD-TYPE	374	225	76	234	45

Figure S432. Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #3: 'CN_CNMF'

'20q loss' versus 'METHLYATION_CNMF'

P value = 5.73e-09 (Chi-square test), Q value = 4.6e-06

Table S433. Gene #77: '20q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	109	155	106	136	44	113
20Q LOSS CNV	14	1	1	2	0	1
20Q LOSS WILD-TYPE	95	154	105	134	44	112

Figure S433. Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q loss' versus 'MRNASEQ_CNMF'

P value = 1.08e-05 (Chi-square test), Q value = 0.007

Table S434. Gene #77: '20q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	175	139	217	154	224	47	15
20Q LOSS CNV	16	1	1	6	5	0	0
20Q LOSS WILD-TYPE	159	138	216	148	219	47	15

Figure S434. Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.21e-05 (Fisher's exact test), Q value = 0.02

Table S435. Gene #77: '20q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	291	246	434
20Q LOSS CNV	1	17	11
20Q LOSS WILD-TYPE	290	229	423

Figure S435. Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q loss' versus 'MIRSEQ_CNMF'

P value = 8.45e-05 (Fisher's exact test), Q value = 0.049

Table S436. Gene #77: '20q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	274	413	279
20Q LOSS CNV	2	8	19
20Q LOSS WILD-TYPE	272	405	260

Figure S436. Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.73e-06 (Fisher's exact test), Q value = 0.0019

Table S437. Gene #77: '20q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	225	376	365
20Q LOSS CNV	18	2	9
20Q LOSS WILD-TYPE	207	374	356

Figure S437. Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.5e-07 (Fisher's exact test), Q value = 0.00033

Table S438. Gene #77: '20q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	210	196
20Q LOSS CNV	1	2	17
20Q LOSS WILD-TYPE	249	208	179

Figure S438. Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.98e-07 (Fisher's exact test), Q value = 0.00022

Table S439. Gene #77: '20q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	311	185
20Q LOSS CNV	1	2	17
20Q LOSS WILD-TYPE	159	309	168

Figure S439. Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q loss' versus 'CN_CNMF'

P value = 2.55e-07 (Chi-square test), Q value = 0.00019

Table S440. Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	374	232	79	252	48
21Q LOSS CNV	9	33	11	27	9
21Q LOSS WILD-TYPE	365	199	68	225	39

Figure S440. 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 = 0.11

Table S441. 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 S441. 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 S442. 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 S442. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 3.65e-14 (Chi-square test), Q value = 3.3e-11

Table S443. Gene #79: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	374	232	79	252	48
22Q LOSS CNV	84	105	47	69	24
22Q LOSS WILD-TYPE	290	127	32	183	24

Figure S443. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 2.8e-08 (Chi-square test), Q value = 2.2e-05

Table S444. Gene #79: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	109	155	106	136	44	113
22Q LOSS CNV	28	52	44	68	9	17
22Q LOSS WILD-TYPE	81	103	62	68	35	96

Figure S444. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q loss' versus 'RPPA_CNMF'

P value = 0.000476 (Fisher's exact test), Q value = 0.24

Table S445. Gene #79: '22q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
22Q LOSS CNV	37	63	39
22Q LOSS WILD-TYPE	110	70	78

Figure S445. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'22q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1.64e-05 (Fisher's exact test), Q value = 0.01

Table S446. 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 S446. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 1.08e-06 (Chi-square test), Q value = 0.00076

Table S447. 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	175	139	217	154	224	47	15
22Q LOSS CNV	35	48	82	42	104	11	4
22Q LOSS WILD-TYPE	140	91	135	112	120	36	11

Figure S447. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.1e-11 (Fisher's exact test), Q value = 5.2e-08

Table S448. Gene #79: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	291	246	434
22Q LOSS CNV	98	43	185
22Q LOSS WILD-TYPE	193	203	249

Figure S448. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CNMF'

P value = 1.66e-06 (Fisher's exact test), Q value = 0.0011

Table S449. Gene #79: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	274	413	279
22Q LOSS CNV	88	170	63
22Q LOSS WILD-TYPE	186	243	216

Figure S449. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.64e-05 (Fisher's exact test), Q value = 0.01

Table S450. Gene #79: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	225	376	365
22Q LOSS CNV	47	133	141
22Q LOSS WILD-TYPE	178	243	224

Figure S450. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Xq loss' versus 'CN_CNMF'

P value = 0.000337 (Chi-square test), Q value = 0.18

Table S451. Gene #80: 'Xq loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	374	232	79	252	48
XQ LOSS CNV	0	11	3	15	2
XQ LOSS WILD-TYPE	374	221	76	237	46

Figure S451. Get High-res Image Gene #80: 'Xq loss' versus Molecular Subtype #3: 'CN_CNMF'

'Xq loss' versus 'METHLYATION_CNMF'

P value = 0.000166 (Chi-square test), Q value = 0.093

Table S452. Gene #80: 'Xq loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	109	155	106	136	44	113
XQ LOSS CNV	9	0	7	4	0	0
XQ LOSS WILD-TYPE	100	155	99	132	44	113

Figure S452. Get High-res Image Gene #80: 'Xq loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Xq loss' versus 'MIRSEQ_CNMF'

P value = 0.000153 (Fisher's exact test), Q value = 0.085

Table S453. Gene #80: 'Xq loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	274	413	279
XQ LOSS CNV	0	17	13
XQ LOSS WILD-TYPE	274	396	266

Figure S453. Get High-res Image Gene #80: 'Xq loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Xq loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.079

Table S454. Gene #80: 'Xq loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	225	376	365
XQ LOSS CNV	13	2	15
XQ LOSS WILD-TYPE	212	374	350

Figure S454. Get High-res Image Gene #80: 'Xq loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Xq loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.17

Table S455. Gene #80: 'Xq loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	210	196
XQ LOSS CNV	7	0	12
XQ LOSS WILD-TYPE	243	210	184

Figure S455. Get High-res Image Gene #80: 'Xq loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

Methods & Data

Input

Mutation data file = broad_values_by_arm.mutsig.cluster.txt
Molecular subtypes file = BRCA-TP.transferedmergedcluster.txt
Number of patients = 985
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.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References

[1] 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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