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

Breast Invasive Carcinoma (Primary solid tumor)

21 April 2013 | analyses__2013_04_21

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): Breast Invasive Carcinoma (Primary solid tumor cohort) - 21 April 2013: Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C16H4FBG

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 10 molecular subtypes across 913 patients, 374 significant findings detected with Q value < 0.25.

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

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 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 374 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
	nCNV (%)	nWild-Type	Chi-square test	Fisher's exact test	Chi-square test	Chi-square test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
2p gain	0 (0%)	865	1.06e-08 (7.28e-06)	3.56e-11 (2.57e-08)	3.7e-10 (2.62e-07)	4.62e-05 (0.0247)	1.97e-08 (1.33e-05)	3.14e-08 (2.1e-05)	7.82e-12 (5.7e-09)	7.35e-14 (5.5e-11)	7.96e-11 (5.7e-08)	3.26e-08 (2.18e-05)
10p gain	0 (0%)	803	7.38e-11 (5.3e-08)	9.62e-08 (6.31e-05)	5.04e-15 (3.85e-12)	3.37e-15 (2.58e-12)	2.39e-05 (0.0133)	1.42e-06 (0.000878)	1.15e-15 (8.85e-13)	2.46e-16 (1.9e-13)	2.44e-12 (1.8e-09)	2.15e-14 (1.62e-11)
4p loss	0 (0%)	728	4.5e-12 (3.29e-09)	1.24e-12 (9.11e-10)	9.98e-28 (7.93e-25)	3.87e-14 (2.91e-11)	0.00014 (0.0692)	7.57e-06 (0.0044)	2.85e-17 (2.21e-14)	9.21e-18 (7.18e-15)	6.76e-14 (5.07e-11)	5.98e-15 (4.56e-12)
5p loss	0 (0%)	840	1.49e-08 (1.01e-05)	4.14e-06 (0.00244)	8.97e-21 (7.04e-18)	4.03e-12 (2.95e-09)	4.28e-05 (0.0229)	6.72e-06 (0.00391)	1.79e-08 (1.21e-05)	3.4e-08 (2.27e-05)	1.86e-14 (1.41e-11)	1.1e-16 (8.48e-14)
5q loss	0 (0%)	789	4.14e-19 (3.24e-16)	9.95e-15 (7.55e-12)	4.59e-45 (3.67e-42)	1.21e-32 (9.64e-30)	1.86e-09 (1.29e-06)	6.93e-11 (4.98e-08)	4.87e-22 (3.83e-19)	9.55e-24 (7.56e-21)	1.06e-27 (8.39e-25)	1.15e-33 (9.17e-31)
14q loss	0 (0%)	777	1.09e-10 (7.8e-08)	8.5e-08 (5.6e-05)	2.6e-22 (2.05e-19)	6.83e-16 (5.27e-13)	0.000185 (0.0897)	8.52e-05 (0.0438)	2.46e-11 (1.78e-08)	1.53e-11 (1.11e-08)	5.57e-13 (4.13e-10)	1.18e-13 (8.81e-11)
16q loss	0 (0%)	523	7.08e-08 (4.68e-05)	1.75e-13 (1.3e-10)	9.63e-12 (7.01e-09)	6.1e-17 (4.73e-14)	8.18e-06 (0.00473)	1.02e-09 (7.12e-07)	1.01e-16 (7.81e-14)	8.02e-20 (6.29e-17)	9.39e-15 (7.14e-12)	4.4e-18 (3.43e-15)
17q loss	0 (0%)	770	1.08e-10 (7.74e-08)	1.72e-06 (0.00106)	8.88e-11 (6.35e-08)	7.48e-05 (0.0388)	9.69e-10 (6.78e-07)	6.4e-07 (0.000404)	1.9e-10 (1.35e-07)	4.84e-08 (3.22e-05)	9.64e-07 (0.000605)	2.69e-05 (0.0148)
22q loss	0 (0%)	607	4.25e-05 (0.0228)	1.42e-07 (9.23e-05)	2.97e-06 (0.00179)	5.32e-07 (0.000338)	0.000476 (0.208)	1.64e-05 (0.0092)	2.18e-10 (1.55e-07)	2.62e-11 (1.89e-08)	1.57e-08 (1.07e-05)	0.000171 (0.0839)
1p gain	0 (0%)	818	1.33e-05 (0.00755)	6.2e-07 (0.000392)	3.78e-07 (0.000242)	0.0198 (1.00)	2.11e-05 (0.0118)	0.000125 (0.0622)	1.32e-07 (8.61e-05)	2.53e-06 (0.00154)	3.47e-05 (0.0188)	2.24e-05 (0.0125)
6p gain	0 (0%)	809	0.000185 (0.0897)	4.92e-05 (0.0261)	1e-14 (7.58e-12)	6.04e-11 (4.35e-08)	0.00785 (1.00)	0.0427 (1.00)	1.69e-09 (1.18e-06)	3.84e-09 (2.66e-06)	2.95e-09 (2.04e-06)	3.86e-09 (2.66e-06)
8q gain	0 (0%)	532	2.29e-05 (0.0127)	0.000315 (0.147)	1.33e-23 (1.05e-20)	8.16e-13 (6.03e-10)	0.668 (1.00)	0.503 (1.00)	1.36e-08 (9.29e-06)	1.11e-07 (7.25e-05)	1.05e-09 (7.32e-07)	5.51e-06 (0.00322)
9p gain	0 (0%)	845	1.38e-08 (9.4e-06)	1.6e-08 (1.09e-05)	1.79e-08 (1.21e-05)	0.000842 (0.347)	0.00881 (1.00)	0.000106 (0.0537)	8.46e-08 (5.58e-05)	3.98e-09 (2.74e-06)	1.11e-06 (0.00069)	1.44e-07 (9.34e-05)
21q gain	0 (0%)	809	5.97e-05 (0.0314)	0.00019 (0.0921)	7.1e-10 (4.97e-07)	4.67e-09 (3.21e-06)	0.0684 (1.00)	0.00554 (1.00)	2.05e-11 (1.49e-08)	1.13e-10 (8.03e-08)	3.95e-05 (0.0213)	3.66e-07 (0.000235)
4q loss	0 (0%)	758	1.79e-06 (0.0011)	2.1e-08 (1.42e-05)	7.17e-21 (5.64e-18)	1.19e-10 (8.46e-08)	0.0168 (1.00)	0.00171 (0.651)	4.88e-12 (3.56e-09)	1.13e-12 (8.31e-10)	4.17e-07 (0.000266)	4.61e-10 (3.24e-07)
6q loss	0 (0%)	742	4.71e-05 (0.0252)	9.19e-07 (0.000577)	1.2e-14 (9.07e-12)	6.48e-08 (4.29e-05)	0.00055 (0.236)	0.0052 (1.00)	2.4e-08 (1.62e-05)	5.38e-07 (0.000341)	0.00447 (1.00)	2.54e-06 (0.00154)
2q gain	0 (0%)	888	0.00458 (1.00)	1.99e-05 (0.0111)	0.000123 (0.0611)	0.00625 (1.00)	1.54e-07 (9.95e-05)	0.000444 (0.198)	3.22e-06 (0.00193)	7.38e-07 (0.000465)	0.000367 (0.169)	0.00137 (0.54)
16p gain	0 (0%)	659	1.01e-05 (0.00578)	8.07e-05 (0.0416)	0.0119 (1.00)	5.27e-07 (0.000335)	0.000119 (0.0594)	6.58e-05 (0.0345)	1.2e-05 (0.00684)	2.56e-06 (0.00155)	0.00235 (0.866)	0.0184 (1.00)
1p loss	0 (0%)	790	0.000228 (0.109)	3.98e-10 (2.8e-07)	2.44e-23 (1.93e-20)	1.84e-06 (0.00113)	0.702 (1.00)	0.175 (1.00)	3.92e-11 (2.83e-08)	2.18e-13 (1.62e-10)	0.000899 (0.37)	0.000177 (0.0863)
2p loss	0 (0%)	838	0.0116 (1.00)	3.09e-05 (0.0169)	2.58e-12 (1.89e-09)	1.72e-07 (0.000111)	0.0361 (1.00)	0.00428 (1.00)	2.09e-07 (0.000135)	7.81e-07 (0.000491)	0.000265 (0.125)	0.00057 (0.244)
2q loss	0 (0%)	822	0.112 (1.00)	0.000444 (0.198)	2.48e-12 (1.82e-09)	4.01e-06 (0.00237)	0.0688 (1.00)	0.0281 (1.00)	0.000387 (0.176)	0.000322 (0.15)	0.000495 (0.215)	0.000423 (0.189)
3p loss	0 (0%)	821	0.000694 (0.29)	0.000914 (0.374)	2.58e-09 (1.79e-06)	3.42e-05 (0.0186)	0.00233 (0.864)	5.31e-05 (0.0281)	3.32e-05 (0.018)	0.000279 (0.131)	2.18e-06 (0.00133)	0.000443 (0.198)
9p loss	0 (0%)	723	2.39e-05 (0.0133)	0.00148 (0.574)	5.07e-19 (3.97e-16)	1.08e-13 (8.09e-11)	0.0381 (1.00)	0.858 (1.00)	3.34e-06 (0.00199)	7.71e-06 (0.00447)	5.65e-05 (0.0297)	2.37e-07 (0.000152)
11q loss	0 (0%)	684	2.01e-07 (0.000129)	0.000327 (0.152)	2.04e-31 (1.62e-28)	1.5e-11 (1.09e-08)	0.208 (1.00)	0.191 (1.00)	4.03e-06 (0.00238)	1.26e-05 (0.00716)	0.00368 (1.00)	3.01e-05 (0.0165)
12q loss	0 (0%)	861	0.000708 (0.295)	0.000244 (0.116)	9.88e-05 (0.0504)	4.1e-09 (2.82e-06)	0.00486 (1.00)	0.00265 (0.974)	4.09e-08 (2.72e-05)	1.98e-07 (0.000128)	3.21e-06 (0.00192)	1.34e-06 (0.000833)
15q loss	0 (0%)	751	0.00701 (1.00)	0.000121 (0.0604)	3.85e-17 (2.99e-14)	4.94e-07 (0.000315)	0.117 (1.00)	0.00548 (1.00)	0.000106 (0.0536)	0.000116 (0.058)	7.41e-05 (0.0385)	3.04e-06 (0.00182)
19p loss	0 (0%)	846	1.65e-05 (0.00926)	0.000461 (0.203)	7.77e-13 (5.75e-10)	1.43e-08 (9.72e-06)	0.424 (1.00)	0.0741 (1.00)	0.000554 (0.237)	0.000512 (0.222)	0.000287 (0.135)	0.000754 (0.312)
3q gain	0 (0%)	814	0.0146 (1.00)	0.00685 (1.00)	2.38e-09 (1.65e-06)	0.000321 (0.15)	0.0149 (1.00)	0.11 (1.00)	0.000357 (0.165)	0.000108 (0.0544)	4.79e-06 (0.00282)	2.53e-06 (0.00154)
6q gain	0 (0%)	852	0.00194 (0.73)	0.0048 (1.00)	1.72e-14 (1.3e-11)	0.00131 (0.522)	0.000535 (0.23)	0.0271 (1.00)	4.89e-06 (0.00287)	3.35e-06 (0.00199)	6.69e-05 (0.035)	3.4e-06 (0.00202)
18p gain	0 (0%)	826	0.00268 (0.983)	0.00417 (1.00)	2.57e-07 (0.000165)	1.03e-07 (6.74e-05)	0.0139 (1.00)	0.0126 (1.00)	3.57e-06 (0.00211)	1.42e-07 (9.23e-05)	1.52e-05 (0.00857)	0.000104 (0.0528)
20q gain	0 (0%)	637	1.44e-05 (0.00815)	0.00883 (1.00)	3.32e-29 (2.65e-26)	2.35e-14 (1.77e-11)	0.199 (1.00)	0.792 (1.00)	3.01e-05 (0.0165)	2.95e-06 (0.00178)	5.37e-06 (0.00314)	0.0136 (1.00)
Xq gain	0 (0%)	892	0.000738 (0.306)	0.000165 (0.0811)	0.000166 (0.0817)	0.0193 (1.00)	0.0754 (1.00)	0.00725 (1.00)	0.000388 (0.176)	1.47e-05 (0.00831)	4.83e-05 (0.0257)	0.000182 (0.0886)
6p loss	0 (0%)	804	0.0142 (1.00)	9.32e-05 (0.0476)	1.09e-09 (7.57e-07)	4.96e-05 (0.0263)	0.0131 (1.00)	0.00604 (1.00)	1.23e-05 (0.00703)	1.85e-05 (0.0104)	0.0197 (1.00)	0.000394 (0.178)
9q loss	0 (0%)	766	0.0075 (1.00)	0.000614 (0.259)	9.61e-16 (7.4e-13)	1.74e-12 (1.28e-09)	0.0135 (1.00)	0.18 (1.00)	9.07e-08 (5.96e-05)	8.3e-06 (0.00479)	4.12e-05 (0.0222)	2.12e-10 (1.51e-07)
13q loss	0 (0%)	646	0.000134 (0.0664)	0.000611 (0.259)	1.62e-27 (1.28e-24)	2.84e-10 (2.01e-07)	0.727 (1.00)	0.489 (1.00)	0.000411 (0.185)	0.000523 (0.226)	2.49e-08 (1.67e-05)	0.00278 (1.00)
4p gain	0 (0%)	884	1.38e-06 (0.000858)	2.66e-05 (0.0147)	1.12e-06 (7e-04)	4.15e-05 (0.0224)	0.0485 (1.00)	0.0396 (1.00)	0.0221 (1.00)	0.00514 (1.00)	0.000222 (0.107)	0.00146 (0.569)
4q gain	0 (0%)	886	1.38e-06 (0.000858)	2.66e-05 (0.0147)	1.27e-08 (8.7e-06)	0.000389 (0.176)	0.0551 (1.00)	0.0126 (1.00)	0.0159 (1.00)	0.00313 (1.00)	0.00394 (1.00)	0.000218 (0.105)
12p gain	0 (0%)	798	0.00691 (1.00)	0.00154 (0.593)	9e-14 (6.72e-11)	4.76e-05 (0.0254)	0.246 (1.00)	0.0679 (1.00)	9.11e-05 (0.0466)	0.000256 (0.121)	0.000371 (0.17)	0.0017 (0.651)
17q gain	0 (0%)	790	4.01e-07 (0.000256)	0.00782 (1.00)	2.64e-18 (2.06e-15)	3.27e-06 (0.00196)	0.464 (1.00)	0.00912 (1.00)	0.000108 (0.0542)	1.19e-06 (0.000741)	0.0126 (1.00)	0.00416 (1.00)
10q loss	0 (0%)	802	0.000512 (0.222)	0.00147 (0.571)	4.34e-14 (3.26e-11)	9.95e-07 (0.000623)	0.00524 (1.00)	0.112 (1.00)	5.36e-05 (0.0283)	0.000363 (0.167)	0.00792 (1.00)	0.00126 (0.502)
19q loss	0 (0%)	860	7.41e-05 (0.0385)	0.00138 (0.544)	3.66e-10 (2.59e-07)	1.62e-05 (0.00912)	0.101 (1.00)	0.0767 (1.00)	0.0017 (0.651)	8.9e-06 (0.00512)	0.00554 (1.00)	0.00046 (0.202)
20p loss	0 (0%)	860	0.0561 (1.00)	0.0463 (1.00)	1.42e-06 (0.000878)	2.42e-05 (0.0134)	0.362 (1.00)	0.43 (1.00)	0.00268 (0.983)	0.000252 (0.12)	0.000176 (0.0863)	0.000223 (0.107)
20q loss	0 (0%)	884	0.0579 (1.00)	0.1 (1.00)	6.97e-05 (0.0364)	2.82e-06 (0.00171)	0.496 (1.00)	0.172 (1.00)	0.00416 (1.00)	0.00032 (0.149)	0.000443 (0.198)	3.3e-05 (0.018)
8p gain	0 (0%)	738	0.0334 (1.00)	0.0797 (1.00)	5.71e-15 (4.36e-12)	0.00037 (0.17)	0.197 (1.00)	0.457 (1.00)	0.00026 (0.123)	1.18e-05 (0.00679)	0.00322 (1.00)	0.2 (1.00)
20p gain	0 (0%)	674	3.66e-05 (0.0198)	0.0269 (1.00)	3.08e-23 (2.43e-20)	3.06e-08 (2.05e-05)	0.0217 (1.00)	0.133 (1.00)	0.00296 (1.00)	0.000719 (0.299)	0.000293 (0.138)	0.523 (1.00)
22q gain	0 (0%)	870	0.0749 (1.00)	0.00523 (1.00)	3.75e-08 (2.5e-05)	0.000999 (0.403)	0.0685 (1.00)	0.153 (1.00)	4.84e-06 (0.00285)	1.57e-06 (0.000965)	0.00134 (0.531)	1.03e-06 (0.000646)
16p loss	0 (0%)	858	0.00385 (1.00)	0.0204 (1.00)	1.42e-05 (0.00803)	2.47e-05 (0.0136)	0.184 (1.00)	0.286 (1.00)	0.00334 (1.00)	0.00469 (1.00)	0.000225 (0.108)	0.000233 (0.111)
1q gain	0 (0%)	426	7.04e-05 (0.0367)	0.714 (1.00)	3.02e-08 (2.03e-05)	2.87e-15 (2.2e-12)	0.103 (1.00)	0.186 (1.00)	0.147 (1.00)	0.12 (1.00)	0.0467 (1.00)	0.0154 (1.00)
5q gain	0 (0%)	805	0.00552 (1.00)	0.00581 (1.00)	7.31e-17 (5.67e-14)	0.00965 (1.00)	0.0042 (1.00)	0.00691 (1.00)	0.00152 (0.587)	0.000152 (0.0749)	0.000236 (0.113)	0.00172 (0.653)
14q gain	0 (0%)	836	0.000674 (0.282)	0.012 (1.00)	0.000978 (0.395)	0.00684 (1.00)	0.949 (1.00)	0.316 (1.00)	5.13e-06 (0.00301)	0.000453 (0.2)	8.16e-05 (0.042)	0.335 (1.00)
18q gain	0 (0%)	836	0.00117 (0.469)	0.03 (1.00)	6.69e-06 (0.0039)	0.0127 (1.00)	0.311 (1.00)	0.274 (1.00)	0.000346 (0.16)	9.95e-05 (0.0506)	0.00103 (0.413)	0.00782 (1.00)
7p loss	0 (0%)	865	0.167 (1.00)	0.024 (1.00)	9.93e-06 (0.00571)	0.0017 (0.651)	0.371 (1.00)	0.438 (1.00)	0.00268 (0.983)	0.000451 (0.2)	0.000601 (0.256)	0.000466 (0.204)
8p loss	0 (0%)	643	0.000103 (0.0525)	0.178 (1.00)	2.58e-15 (1.98e-12)	9.84e-08 (6.44e-05)	0.647 (1.00)	0.909 (1.00)	0.00628 (1.00)	0.0232 (1.00)	0.0103 (1.00)	0.00842 (1.00)
11p loss	0 (0%)	769	0.0342 (1.00)	0.156 (1.00)	8.5e-15 (6.47e-12)	8.61e-08 (5.66e-05)	0.0925 (1.00)	0.0151 (1.00)	0.0232 (1.00)	0.0228 (1.00)	0.00593 (1.00)	5.61e-05 (0.0296)
17p loss	0 (0%)	540	8.23e-06 (0.00476)	0.694 (1.00)	6.2e-14 (4.65e-11)	5.8e-08 (3.85e-05)	0.00142 (0.555)	0.123 (1.00)	0.193 (1.00)	0.458 (1.00)	0.0342 (1.00)	0.0753 (1.00)
18p loss	0 (0%)	738	0.000377 (0.172)	0.645 (1.00)	6.18e-10 (4.34e-07)	3.32e-06 (0.00198)	0.892 (1.00)	0.962 (1.00)	0.0193 (1.00)	0.267 (1.00)	0.0262 (1.00)	0.0095 (1.00)
12q gain	0 (0%)	826	0.0372 (1.00)	0.0631 (1.00)	1.81e-15 (1.39e-12)	8.74e-05 (0.0448)	0.275 (1.00)	0.4 (1.00)	0.00218 (0.813)	0.0257 (1.00)	0.0379 (1.00)	0.191 (1.00)
7q loss	0 (0%)	849	0.327 (1.00)	0.0996 (1.00)	0.000443 (0.198)	0.206 (1.00)	0.236 (1.00)	0.421 (1.00)	0.0227 (1.00)	0.00459 (1.00)	0.00423 (1.00)	1.37e-05 (0.00778)
12p loss	0 (0%)	846	0.305 (1.00)	0.0978 (1.00)	0.0158 (1.00)	1.57e-06 (0.000965)	0.149 (1.00)	0.274 (1.00)	7.88e-05 (0.0407)	0.000909 (0.373)	0.000958 (0.388)	0.000669 (0.281)
18q loss	0 (0%)	736	0.00133 (0.527)	0.644 (1.00)	6.11e-13 (4.52e-10)	7.01e-08 (4.64e-05)	0.535 (1.00)	0.828 (1.00)	0.00179 (0.679)	0.166 (1.00)	0.0377 (1.00)	0.0618 (1.00)
3p gain	0 (0%)	856	0.346 (1.00)	0.153 (1.00)	6.6e-07 (0.000417)	0.532 (1.00)	0.315 (1.00)	0.151 (1.00)	0.277 (1.00)	0.0321 (1.00)	0.132 (1.00)	0.0196 (1.00)
5p gain	0 (0%)	741	0.156 (1.00)	0.421 (1.00)	4.56e-10 (3.21e-07)	0.153 (1.00)	0.593 (1.00)	0.459 (1.00)	0.837 (1.00)	0.123 (1.00)	0.185 (1.00)	0.853 (1.00)
7q gain	0 (0%)	795	0.00273 (0.994)	0.0094 (1.00)	0.00892 (1.00)	0.00182 (0.689)	0.404 (1.00)	0.271 (1.00)	0.0199 (1.00)	0.000482 (0.21)	0.0577 (1.00)	0.02 (1.00)
9q gain	0 (0%)	857	0.455 (1.00)	0.0805 (1.00)	0.000148 (0.0732)	0.161 (1.00)	1 (1.00)	0.488 (1.00)	0.0493 (1.00)	0.0033 (1.00)	0.0115 (1.00)	0.0346 (1.00)
10q gain	0 (0%)	868	0.0114 (1.00)	0.0144 (1.00)	0.000533 (0.23)	0.0159 (1.00)	0.073 (1.00)	0.0476 (1.00)	0.00418 (1.00)	0.00196 (0.736)	0.0125 (1.00)	0.0113 (1.00)
11q gain	0 (0%)	867	0.537 (1.00)	0.77 (1.00)	0.000131 (0.0649)	0.153 (1.00)	0.909 (1.00)	0.745 (1.00)	0.316 (1.00)	0.539 (1.00)	0.0417 (1.00)	0.0232 (1.00)
19p gain	0 (0%)	844	0.125 (1.00)	0.0293 (1.00)	0.000382 (0.174)	0.141 (1.00)	0.0373 (1.00)	0.114 (1.00)	0.00646 (1.00)	0.000944 (0.383)	0.00148 (0.576)	0.000918 (0.374)
19q gain	0 (0%)	827	0.142 (1.00)	0.0376 (1.00)	0.000415 (0.186)	0.111 (1.00)	0.154 (1.00)	0.251 (1.00)	0.0256 (1.00)	0.0021 (0.783)	0.00371 (1.00)	0.0145 (1.00)
10p loss	0 (0%)	838	0.025 (1.00)	0.0119 (1.00)	2.55e-06 (0.00154)	0.0213 (1.00)	0.716 (1.00)	0.46 (1.00)	0.0016 (0.618)	0.0272 (1.00)	0.0912 (1.00)	0.0987 (1.00)
21q loss	0 (0%)	827	0.0238 (1.00)	0.269 (1.00)	1.67e-06 (0.00102)	0.0576 (1.00)	1 (1.00)	0.812 (1.00)	0.615 (1.00)	0.622 (1.00)	0.0408 (1.00)	0.364 (1.00)
Xq loss	0 (0%)	882	0.668 (1.00)	0.0736 (1.00)	0.000611 (0.259)	0.00451 (1.00)	0.0154 (1.00)	0.2 (1.00)	0.00209 (0.781)	0.000923 (0.376)	0.00233 (0.864)	0.000357 (0.165)
7p gain	0 (0%)	755	0.151 (1.00)	0.257 (1.00)	0.0621 (1.00)	0.0146 (1.00)	0.947 (1.00)	0.52 (1.00)	0.1 (1.00)	0.0459 (1.00)	0.51 (1.00)	0.469 (1.00)
11p gain	0 (0%)	846	0.943 (1.00)	0.606 (1.00)	0.00507 (1.00)	0.0342 (1.00)	0.318 (1.00)	0.155 (1.00)	0.336 (1.00)	0.705 (1.00)	0.0255 (1.00)	0.0604 (1.00)
13q gain	0 (0%)	866	0.525 (1.00)	0.619 (1.00)	0.0284 (1.00)	0.0306 (1.00)	0.0642 (1.00)	0.258 (1.00)	0.000625 (0.263)	0.0245 (1.00)	0.0529 (1.00)	0.0245 (1.00)
15q gain	0 (0%)	868	0.727 (1.00)	0.474 (1.00)	0.682 (1.00)	0.145 (1.00)	0.817 (1.00)	0.561 (1.00)	0.0548 (1.00)	0.141 (1.00)	0.391 (1.00)	0.428 (1.00)
16q gain	0 (0%)	857	0.531 (1.00)	0.215 (1.00)	0.000841 (0.347)	0.0705 (1.00)	0.134 (1.00)	0.775 (1.00)	0.134 (1.00)	0.0146 (1.00)	0.00434 (1.00)	0.000609 (0.259)
17p gain	0 (0%)	866	0.0217 (1.00)	0.396 (1.00)	0.00182 (0.689)	0.619 (1.00)	0.18 (1.00)	0.2 (1.00)	0.633 (1.00)	0.641 (1.00)	0.89 (1.00)	0.842 (1.00)
1q loss	0 (0%)	891	0.243 (1.00)	0.0336 (1.00)	0.00419 (1.00)	0.211 (1.00)	0.272 (1.00)	0.739 (1.00)	0.0172 (1.00)	0.0102 (1.00)	0.185 (1.00)	0.15 (1.00)
3q loss	0 (0%)	869	0.0197 (1.00)	0.00585 (1.00)	0.00104 (0.415)	0.00415 (1.00)	0.185 (1.00)	0.0657 (1.00)	0.00925 (1.00)	0.0314 (1.00)	0.00134 (0.531)	0.0279 (1.00)
8q loss	0 (0%)	867	0.507 (1.00)	0.526 (1.00)	0.203 (1.00)	0.103 (1.00)	0.688 (1.00)	0.566 (1.00)	0.0317 (1.00)	0.26 (1.00)	0.316 (1.00)	0.398 (1.00)

'1p gain' versus 'MRNA_CNMF'

P value = 1.33e-05 (Chi-square test), Q value = 0.0075

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	124	36	23	95	72	20	103	40
1P GAIN CNV	11	2	1	27	11	4	4	5
1P GAIN WILD-TYPE	113	34	22	68	61	16	99	35

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

'1p gain' versus 'MRNA_CHIERARCHICAL'

P value = 6.2e-07 (Fisher's exact test), Q value = 0.00039

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	125	248
1P GAIN CNV	14	34	17
1P GAIN WILD-TYPE	126	91	231

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

'1p gain' versus 'CN_CNMF'

P value = 3.78e-07 (Chi-square test), Q value = 0.00024

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
1P GAIN CNV	21	15	7	46	6
1P GAIN WILD-TYPE	326	207	65	177	43

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

'1p gain' versus 'RPPA_CNMF'

P value = 2.11e-05 (Fisher's exact test), Q value = 0.012

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	35	13	6
1P GAIN WILD-TYPE	112	120	111

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

'1p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.000125 (Fisher's exact test), Q value = 0.062

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	29
1P GAIN WILD-TYPE	141	105	97

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

'1p gain' versus 'MRNASEQ_CNMF'

P value = 1.32e-07 (Fisher's exact test), Q value = 8.6e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
1P GAIN CNV	48	11	28
1P GAIN WILD-TYPE	186	137	418

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

'1p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.53e-06 (Fisher's exact test), Q value = 0.0015

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
1P GAIN CNV	15	30	42
1P GAIN WILD-TYPE	201	378	162

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

'1p gain' versus 'MIRSEQ_CNMF'

P value = 3.47e-05 (Fisher's exact test), Q value = 0.019

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
1P GAIN CNV	17	27	45
1P GAIN WILD-TYPE	217	365	210

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

'1p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.24e-05 (Fisher's exact test), Q value = 0.012

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
1P GAIN CNV	27	19	43
1P GAIN WILD-TYPE	335	265	192

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

'1q gain' versus 'MRNA_CNMF'

P value = 7.04e-05 (Chi-square test), Q value = 0.037

Table S10. 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	124	36	23	95	72	20	103	40
1Q GAIN CNV	53	17	13	53	39	10	80	25
1Q GAIN WILD-TYPE	71	19	10	42	33	10	23	15

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

'1q gain' versus 'CN_CNMF'

P value = 3.02e-08 (Chi-square test), Q value = 2e-05

Table S11. Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
1Q GAIN CNV	171	124	63	104	25
1Q GAIN WILD-TYPE	176	98	9	119	24

Figure S11. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

'1q gain' versus 'METHLYATION_CNMF'

P value = 2.87e-15 (Chi-square test), Q value = 2.2e-12

Table S12. Gene #2: '1q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
1Q GAIN CNV	44	108	60	58	16	26
1Q GAIN WILD-TYPE	57	31	33	79	24	71

Figure S12. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2p gain' versus 'MRNA_CNMF'

P value = 1.06e-08 (Chi-square test), Q value = 7.3e-06

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	124	36	23	95	72	20	103	40
2P GAIN CNV	3	0	0	18	11	0	1	0
2P GAIN WILD-TYPE	121	36	23	77	61	20	102	40

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

'2p gain' versus 'MRNA_CHIERARCHICAL'

P value = 3.56e-11 (Fisher's exact test), Q value = 2.6e-08

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	125	248
2P GAIN CNV	0	25	8
2P GAIN WILD-TYPE	140	100	240

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

'2p gain' versus 'CN_CNMF'

P value = 3.7e-10 (Chi-square test), Q value = 2.6e-07

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
2P GAIN CNV	2	11	3	31	1
2P GAIN WILD-TYPE	345	211	69	192	48

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

'2p gain' versus 'METHLYATION_CNMF'

P value = 4.62e-05 (Chi-square test), Q value = 0.025

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
2P GAIN CNV	14	1	4	5	1	2
2P GAIN WILD-TYPE	87	138	89	132	39	95

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

'2p gain' versus 'RPPA_CNMF'

P value = 1.97e-08 (Fisher's exact test), Q value = 1.3e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
2P GAIN CNV	24	0	4
2P GAIN WILD-TYPE	123	133	113

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

'2p gain' versus 'RPPA_CHIERARCHICAL'

P value = 3.14e-08 (Fisher's exact test), Q value = 2.1e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	110	126
2P GAIN CNV	4	1	23
2P GAIN WILD-TYPE	157	109	103

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

'2p gain' versus 'MRNASEQ_CNMF'

P value = 7.82e-12 (Fisher's exact test), Q value = 5.7e-09

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
2P GAIN CNV	35	0	12
2P GAIN WILD-TYPE	199	148	434

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

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.35e-14 (Fisher's exact test), Q value = 5.5e-11

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
2P GAIN CNV	0	13	34
2P GAIN WILD-TYPE	216	395	170

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

'2p gain' versus 'MIRSEQ_CNMF'

P value = 7.96e-11 (Fisher's exact test), Q value = 5.7e-08

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
2P GAIN CNV	1	9	32
2P GAIN WILD-TYPE	233	383	223

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

'2p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.26e-08 (Fisher's exact test), Q value = 2.2e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
2P GAIN CNV	11	3	28
2P GAIN WILD-TYPE	351	281	207

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

'2q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1.99e-05 (Fisher's exact test), Q value = 0.011

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	125	248
2Q GAIN CNV	0	13	6
2Q GAIN WILD-TYPE	140	112	242

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

'2q gain' versus 'CN_CNMF'

P value = 0.000123 (Chi-square test), Q value = 0.061

Table S24. Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
2Q GAIN CNV	1	6	3	15	0
2Q GAIN WILD-TYPE	346	216	69	208	49

Figure S24. 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 = 1e-04

Table S25. 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 S25. 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 = 0.2

Table S26. 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 S26. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'2q gain' versus 'MRNASEQ_CNMF'

P value = 3.22e-06 (Fisher's exact test), Q value = 0.0019

Table S27. Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
2Q GAIN CNV	18	0	6
2Q GAIN WILD-TYPE	216	148	440

Figure S27. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.38e-07 (Fisher's exact test), Q value = 0.00047

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
2Q GAIN CNV	0	7	17
2Q GAIN WILD-TYPE	216	401	187

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

'2q gain' versus 'MIRSEQ_CNMF'

P value = 0.000367 (Fisher's exact test), Q value = 0.17

Table S29. Gene #4: '2q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
2Q GAIN CNV	1	5	14
2Q GAIN WILD-TYPE	233	387	241

Figure S29. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3p gain' versus 'CN_CNMF'

P value = 6.6e-07 (Chi-square test), Q value = 0.00042

Table S30. Gene #5: '3p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
3P GAIN CNV	5	19	11	14	8
3P GAIN WILD-TYPE	342	203	61	209	41

Figure S30. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #3: 'CN_CNMF'

'3q gain' versus 'CN_CNMF'

P value = 2.38e-09 (Chi-square test), Q value = 1.7e-06

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
3Q GAIN CNV	9	26	13	42	9
3Q GAIN WILD-TYPE	338	196	59	181	40

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

'3q gain' versus 'METHLYATION_CNMF'

P value = 0.000321 (Chi-square test), Q value = 0.15

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
3Q GAIN CNV	18	5	11	13	2	2
3Q GAIN WILD-TYPE	83	134	82	124	38	95

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

'3q gain' versus 'MRNASEQ_CNMF'

P value = 0.000357 (Fisher's exact test), Q value = 0.16

Table S33. Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
3Q GAIN CNV	41	7	46
3Q GAIN WILD-TYPE	193	141	400

Figure S33. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000108 (Fisher's exact test), Q value = 0.054

Table S34. Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
3Q GAIN CNV	11	46	37
3Q GAIN WILD-TYPE	205	362	167

Figure S34. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_CNMF'

P value = 4.79e-06 (Fisher's exact test), Q value = 0.0028

Table S35. Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

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

Figure S35. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.53e-06 (Fisher's exact test), Q value = 0.0015

Table S36. Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

Figure S36. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4p gain' versus 'MRNA_CNMF'

P value = 1.38e-06 (Chi-square test), Q value = 0.00086

Table S37. 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	124	36	23	95	72	20	103	40
4P GAIN CNV	15	0	0	0	1	0	1	0
4P GAIN WILD-TYPE	109	36	23	95	71	20	102	40

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

'4p gain' versus 'MRNA_CHIERARCHICAL'

P value = 2.66e-05 (Fisher's exact test), Q value = 0.015

Table S38. Gene #7: '4p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	125	248
4P GAIN CNV	0	0	17
4P GAIN WILD-TYPE	140	125	231

Figure S38. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'4p gain' versus 'CN_CNMF'

P value = 1.12e-06 (Chi-square test), Q value = 7e-04

Table S39. Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
4P GAIN CNV	1	19	2	4	3
4P GAIN WILD-TYPE	346	203	70	219	46

Figure S39. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

'4p gain' versus 'METHLYATION_CNMF'

P value = 4.15e-05 (Chi-square test), Q value = 0.022

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
4P GAIN CNV	0	1	4	12	0	0
4P GAIN WILD-TYPE	101	138	89	125	40	97

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

'4p gain' versus 'MIRSEQ_CNMF'

P value = 0.000222 (Fisher's exact test), Q value = 0.11

Table S41. Gene #7: '4p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

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

Figure S41. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4q gain' versus 'MRNA_CNMF'

P value = 1.38e-06 (Chi-square test), Q value = 0.00086

Table S42. 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	124	36	23	95	72	20	103	40
4Q GAIN CNV	15	0	0	0	1	0	1	0
4Q GAIN WILD-TYPE	109	36	23	95	71	20	102	40

Figure S42. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'4q gain' versus 'MRNA_CHIERARCHICAL'

P value = 2.66e-05 (Fisher's exact test), Q value = 0.015

Table S43. Gene #8: '4q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	125	248
4Q GAIN CNV	0	0	17
4Q GAIN WILD-TYPE	140	125	231

Figure S43. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'4q gain' versus 'CN_CNMF'

P value = 1.27e-08 (Chi-square test), Q value = 8.7e-06

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
4Q GAIN CNV	1	20	1	2	3
4Q GAIN WILD-TYPE	346	202	71	221	46

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

'4q gain' versus 'METHLYATION_CNMF'

P value = 0.000389 (Chi-square test), Q value = 0.18

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
4Q GAIN CNV	0	1	3	10	0	0
4Q GAIN WILD-TYPE	101	138	90	127	40	97

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

'4q gain' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S46. Gene #8: '4q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

Figure S46. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5p gain' versus 'CN_CNMF'

P value = 4.56e-10 (Chi-square test), Q value = 3.2e-07

Table S47. Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
5P GAIN CNV	30	61	26	43	12
5P GAIN WILD-TYPE	317	161	46	180	37

Figure S47. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

'5q gain' versus 'CN_CNMF'

P value = 7.31e-17 (Chi-square test), Q value = 5.7e-14

Table S48. Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
5Q GAIN CNV	20	46	25	8	9
5Q GAIN WILD-TYPE	327	176	47	215	40

Figure S48. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'

'5q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000152 (Fisher's exact test), Q value = 0.075

Table S49. Gene #10: '5q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
5Q GAIN CNV	23	65	10
5Q GAIN WILD-TYPE	193	343	194

Figure S49. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_CNMF'

P value = 0.000236 (Fisher's exact test), Q value = 0.11

Table S50. Gene #10: '5q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
5Q GAIN CNV	22	64	16
5Q GAIN WILD-TYPE	212	328	239

Figure S50. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6p gain' versus 'MRNA_CNMF'

P value = 0.000185 (Chi-square test), Q value = 0.09

Table S51. 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	124	36	23	95	72	20	103	40
6P GAIN CNV	11	0	0	20	12	5	10	0
6P GAIN WILD-TYPE	113	36	23	75	60	15	93	40

Figure S51. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'6p gain' versus 'MRNA_CHIERARCHICAL'

P value = 4.92e-05 (Fisher's exact test), Q value = 0.026

Table S52. Gene #11: '6p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	125	248
6P GAIN CNV	4	24	30
6P GAIN WILD-TYPE	136	101	218

Figure S52. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6p gain' versus 'CN_CNMF'

P value = 1e-14 (Chi-square test), Q value = 7.6e-12

Table S53. Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
6P GAIN CNV	11	15	15	52	11
6P GAIN WILD-TYPE	336	207	57	171	38

Figure S53. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

'6p gain' versus 'METHLYATION_CNMF'

P value = 6.04e-11 (Chi-square test), Q value = 4.3e-08

Table S54. Gene #11: '6p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
6P GAIN CNV	31	8	14	14	1	1
6P GAIN WILD-TYPE	70	131	79	123	39	96

Figure S54. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6p gain' versus 'MRNASEQ_CNMF'

P value = 1.69e-09 (Fisher's exact test), Q value = 1.2e-06

Table S55. Gene #11: '6p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
6P GAIN CNV	50	3	39
6P GAIN WILD-TYPE	184	145	407

Figure S55. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.84e-09 (Fisher's exact test), Q value = 2.7e-06

Table S56. Gene #11: '6p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
6P GAIN CNV	5	45	42
6P GAIN WILD-TYPE	211	363	162

Figure S56. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_CNMF'

P value = 2.95e-09 (Fisher's exact test), Q value = 2e-06

Table S57. Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
6P GAIN CNV	9	32	53
6P GAIN WILD-TYPE	225	360	202

Figure S57. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.86e-09 (Fisher's exact test), Q value = 2.7e-06

Table S58. Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
6P GAIN CNV	34	11	49
6P GAIN WILD-TYPE	328	273	186

Figure S58. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6q gain' versus 'CN_CNMF'

P value = 1.72e-14 (Chi-square test), Q value = 1.3e-11

Table S59. Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
6Q GAIN CNV	5	5	10	39	2
6Q GAIN WILD-TYPE	342	217	62	184	47

Figure S59. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

'6q gain' versus 'RPPA_CNMF'

P value = 0.000535 (Fisher's exact test), Q value = 0.23

Table S60. Gene #12: '6q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
6Q GAIN CNV	20	7	2
6Q GAIN WILD-TYPE	127	126	115

Figure S60. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'6q gain' versus 'MRNASEQ_CNMF'

P value = 4.89e-06 (Fisher's exact test), Q value = 0.0029

Table S61. Gene #12: '6q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
6Q GAIN CNV	31	2	22
6Q GAIN WILD-TYPE	203	146	424

Figure S61. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.35e-06 (Fisher's exact test), Q value = 0.002

Table S62. Gene #12: '6q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
6Q GAIN CNV	2	28	25
6Q GAIN WILD-TYPE	214	380	179

Figure S62. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6q gain' versus 'MIRSEQ_CNMF'

P value = 6.69e-05 (Fisher's exact test), Q value = 0.035

Table S63. Gene #12: '6q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
6Q GAIN CNV	6	18	30
6Q GAIN WILD-TYPE	228	374	225

Figure S63. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.4e-06 (Fisher's exact test), Q value = 0.002

Table S64. Gene #12: '6q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
6Q GAIN CNV	18	6	30
6Q GAIN WILD-TYPE	344	278	205

Figure S64. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000482 (Fisher's exact test), Q value = 0.21

Table S65. Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
7Q GAIN CNV	17	48	42
7Q GAIN WILD-TYPE	199	360	162

Figure S65. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

P value = 5.71e-15 (Chi-square test), Q value = 4.4e-12

Table S66. Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
8P GAIN CNV	33	42	30	46	24
8P GAIN WILD-TYPE	314	180	42	177	25

Figure S66. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

'8p gain' versus 'METHLYATION_CNMF'

P value = 0.00037 (Chi-square test), Q value = 0.17

Table S67. Gene #15: '8p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
8P GAIN CNV	28	21	20	31	6	4
8P GAIN WILD-TYPE	73	118	73	106	34	93

Figure S67. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p gain' versus 'MRNASEQ_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.12

Table S68. Gene #15: '8p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
8P GAIN CNV	44	13	104
8P GAIN WILD-TYPE	190	135	342

Figure S68. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.18e-05 (Fisher's exact test), Q value = 0.0068

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
8P GAIN CNV	21	102	38
8P GAIN WILD-TYPE	195	306	166

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

'8q gain' versus 'MRNA_CNMF'

P value = 2.29e-05 (Chi-square test), Q value = 0.013

Table S70. 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	124	36	23	95	72	20	103	40
8Q GAIN CNV	72	13	14	52	34	11	35	7
8Q GAIN WILD-TYPE	52	23	9	43	38	9	68	33

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

'8q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.000315 (Fisher's exact test), Q value = 0.15

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	125	248
8Q GAIN CNV	45	63	130
8Q GAIN WILD-TYPE	95	62	118

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

'8q gain' versus 'CN_CNMF'

P value = 1.33e-23 (Chi-square test), Q value = 1.1e-20

Table S72. Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
8Q GAIN CNV	72	118	35	118	38
8Q GAIN WILD-TYPE	275	104	37	105	11

Figure S72. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 8.16e-13 (Chi-square test), Q value = 6e-10

Table S73. Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
8Q GAIN CNV	54	29	37	79	10	20
8Q GAIN WILD-TYPE	47	110	56	58	30	77

Figure S73. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 1.36e-08 (Fisher's exact test), Q value = 9.3e-06

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
8Q GAIN CNV	120	33	207
8Q GAIN WILD-TYPE	114	115	239

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

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.11e-07 (Fisher's exact test), Q value = 7.2e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
8Q GAIN CNV	59	200	101
8Q GAIN WILD-TYPE	157	208	103

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

'8q gain' versus 'MIRSEQ_CNMF'

P value = 1.05e-09 (Fisher's exact test), Q value = 7.3e-07

Table S76. Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
8Q GAIN CNV	61	172	138
8Q GAIN WILD-TYPE	173	220	117

Figure S76. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.51e-06 (Fisher's exact test), Q value = 0.0032

Table S77. Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
8Q GAIN CNV	162	88	121
8Q GAIN WILD-TYPE	200	196	114

Figure S77. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9p gain' versus 'MRNA_CNMF'

P value = 1.38e-08 (Chi-square test), Q value = 9.4e-06

Table S78. 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	124	36	23	95	72	20	103	40
9P GAIN CNV	3	1	0	24	4	0	7	2
9P GAIN WILD-TYPE	121	35	23	71	68	20	96	38

Figure S78. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'9p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1.6e-08 (Fisher's exact test), Q value = 1.1e-05

Table S79. Gene #17: '9p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	125	248
9P GAIN CNV	4	27	10
9P GAIN WILD-TYPE	136	98	238

Figure S79. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9p gain' versus 'CN_CNMF'

P value = 1.79e-08 (Chi-square test), Q value = 1.2e-05

Table S80. Gene #17: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
9P GAIN CNV	9	10	13	32	4
9P GAIN WILD-TYPE	338	212	59	191	45

Figure S80. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'

'9p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.000106 (Fisher's exact test), Q value = 0.054

Table S81. 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 S81. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'9p gain' versus 'MRNASEQ_CNMF'

P value = 8.46e-08 (Fisher's exact test), Q value = 5.6e-05

Table S82. Gene #17: '9p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
9P GAIN CNV	38	7	17
9P GAIN WILD-TYPE	196	141	429

Figure S82. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.98e-09 (Fisher's exact test), Q value = 2.7e-06

Table S83. Gene #17: '9p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
9P GAIN CNV	7	18	37
9P GAIN WILD-TYPE	209	390	167

Figure S83. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p gain' versus 'MIRSEQ_CNMF'

P value = 1.11e-06 (Fisher's exact test), Q value = 0.00069

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

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

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

'9p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.44e-07 (Fisher's exact test), Q value = 9.3e-05

Table S85. Gene #17: '9p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

Figure S85. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9q gain' versus 'CN_CNMF'

P value = 0.000148 (Chi-square test), Q value = 0.073

Table S86. Gene #18: '9q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
9Q GAIN CNV	10	12	12	19	3
9Q GAIN WILD-TYPE	337	210	60	204	46

Figure S86. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #3: 'CN_CNMF'

'10p gain' versus 'MRNA_CNMF'

P value = 7.38e-11 (Chi-square test), Q value = 5.3e-08

Table S87. 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	124	36	23	95	72	20	103	40
10P GAIN CNV	10	3	0	33	18	2	3	3
10P GAIN WILD-TYPE	114	33	23	62	54	18	100	37

Figure S87. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'10p gain' versus 'MRNA_CHIERARCHICAL'

P value = 9.62e-08 (Fisher's exact test), Q value = 6.3e-05

Table S88. Gene #19: '10p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	125	248
10P GAIN CNV	11	38	23
10P GAIN WILD-TYPE	129	87	225

Figure S88. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'10p gain' versus 'CN_CNMF'

P value = 5.04e-15 (Chi-square test), Q value = 3.8e-12

Table S89. Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
10P GAIN CNV	11	23	10	60	6
10P GAIN WILD-TYPE	336	199	62	163	43

Figure S89. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

'10p gain' versus 'METHLYATION_CNMF'

P value = 3.37e-15 (Chi-square test), Q value = 2.6e-12

Table S90. Gene #19: '10p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
10P GAIN CNV	34	4	11	14	0	2
10P GAIN WILD-TYPE	67	135	82	123	40	95

Figure S90. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p gain' versus 'RPPA_CNMF'

P value = 2.39e-05 (Fisher's exact test), Q value = 0.013

Table S91. Gene #19: '10p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

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

Figure S91. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'10p gain' versus 'RPPA_CHIERARCHICAL'

P value = 1.42e-06 (Fisher's exact test), Q value = 0.00088

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

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

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

'10p gain' versus 'MRNASEQ_CNMF'

P value = 1.15e-15 (Fisher's exact test), Q value = 8.8e-13

Table S93. Gene #19: '10p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
10P GAIN CNV	66	7	29
10P GAIN WILD-TYPE	168	141	417

Figure S93. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.46e-16 (Fisher's exact test), Q value = 1.9e-13

Table S94. Gene #19: '10p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
10P GAIN CNV	8	33	61
10P GAIN WILD-TYPE	208	375	143

Figure S94. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p gain' versus 'MIRSEQ_CNMF'

P value = 2.44e-12 (Fisher's exact test), Q value = 1.8e-09

Table S95. Gene #19: '10p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

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

Figure S95. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.15e-14 (Fisher's exact test), Q value = 1.6e-11

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

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

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

'10q gain' versus 'CN_CNMF'

P value = 0.000533 (Chi-square test), Q value = 0.23

Table S97. Gene #20: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
10Q GAIN CNV	5	10	7	19	4
10Q GAIN WILD-TYPE	342	212	65	204	45

Figure S97. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

'11q gain' versus 'CN_CNMF'

P value = 0.000131 (Chi-square test), Q value = 0.065

Table S98. Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
11Q GAIN CNV	9	7	2	22	6
11Q GAIN WILD-TYPE	338	215	70	201	43

Figure S98. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 9e-14 (Chi-square test), Q value = 6.7e-11

Table S99. Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
12P GAIN CNV	4	44	15	44	8
12P GAIN WILD-TYPE	343	178	57	179	41

Figure S99. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 4.76e-05 (Chi-square test), Q value = 0.025

Table S100. Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
12P GAIN CNV	19	9	11	25	1	2
12P GAIN WILD-TYPE	82	130	82	112	39	95

Figure S100. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 9.11e-05 (Fisher's exact test), Q value = 0.047

Table S101. Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
12P GAIN CNV	43	6	59
12P GAIN WILD-TYPE	191	142	387

Figure S101. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000256 (Fisher's exact test), Q value = 0.12

Table S102. Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
12P GAIN CNV	14	54	40
12P GAIN WILD-TYPE	202	354	164

Figure S102. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_CNMF'

P value = 0.000371 (Fisher's exact test), Q value = 0.17

Table S103. Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
12P GAIN CNV	17	43	48
12P GAIN WILD-TYPE	217	349	207

Figure S103. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12q gain' versus 'CN_CNMF'

P value = 1.81e-15 (Chi-square test), Q value = 1.4e-12

Table S104. Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
12Q GAIN CNV	5	46	16	14	6
12Q GAIN WILD-TYPE	342	176	56	209	43

Figure S104. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

'12q gain' versus 'METHLYATION_CNMF'

P value = 8.74e-05 (Chi-square test), Q value = 0.045

Table S105. Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
12Q GAIN CNV	4	13	11	24	1	1
12Q GAIN WILD-TYPE	97	126	82	113	39	96

Figure S105. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q gain' versus 'MRNASEQ_CNMF'

P value = 5.13e-06 (Fisher's exact test), Q value = 0.003

Table S106. Gene #26: '14q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
14Q GAIN CNV	14	2	57
14Q GAIN WILD-TYPE	220	146	389

Figure S106. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000453 (Fisher's exact test), Q value = 0.2

Table S107. Gene #26: '14q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
14Q GAIN CNV	10	52	11
14Q GAIN WILD-TYPE	206	356	193

Figure S107. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_CNMF'

P value = 8.16e-05 (Fisher's exact test), Q value = 0.042

Table S108. Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
14Q GAIN CNV	7	49	19
14Q GAIN WILD-TYPE	227	343	236

Figure S108. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16p gain' versus 'MRNA_CNMF'

P value = 1.01e-05 (Chi-square test), Q value = 0.0058

Table S109. 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	124	36	23	95	72	20	103	40
16P GAIN CNV	41	6	8	18	15	5	53	10
16P GAIN WILD-TYPE	83	30	15	77	57	15	50	30

Figure S109. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'16p gain' versus 'MRNA_CHIERARCHICAL'

P value = 8.07e-05 (Fisher's exact test), Q value = 0.042

Table S110. Gene #28: '16p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	125	248
16P GAIN CNV	38	22	96
16P GAIN WILD-TYPE	102	103	152

Figure S110. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'16p gain' versus 'METHLYATION_CNMF'

P value = 5.27e-07 (Chi-square test), Q value = 0.00033

Table S111. Gene #28: '16p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
16P GAIN CNV	17	54	30	40	3	11
16P GAIN WILD-TYPE	84	85	63	97	37	86

Figure S111. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16p gain' versus 'RPPA_CNMF'

P value = 0.000119 (Fisher's exact test), Q value = 0.059

Table S112. Gene #28: '16p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
16P GAIN CNV	30	58	32
16P GAIN WILD-TYPE	117	75	85

Figure S112. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'16p gain' versus 'RPPA_CHIERARCHICAL'

P value = 6.58e-05 (Fisher's exact test), Q value = 0.035

Table S113. 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	40	20
16P GAIN WILD-TYPE	101	70	106

Figure S113. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 1.2e-05 (Fisher's exact test), Q value = 0.0068

Table S114. Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
16P GAIN CNV	44	38	159
16P GAIN WILD-TYPE	190	110	287

Figure S114. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.56e-06 (Fisher's exact test), Q value = 0.0015

Table S115. Gene #28: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
16P GAIN CNV	54	150	37
16P GAIN WILD-TYPE	162	258	167

Figure S115. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MRNA_CNMF'

P value = 4.01e-07 (Chi-square test), Q value = 0.00026

Table S116. 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	124	36	23	95	72	20	103	40
17Q GAIN CNV	35	6	2	6	4	2	4	5
17Q GAIN WILD-TYPE	89	30	21	89	68	18	99	35

Figure S116. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'17q gain' versus 'CN_CNMF'

P value = 2.64e-18 (Chi-square test), Q value = 2.1e-15

Table S117. Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
17Q GAIN CNV	23	70	8	13	9
17Q GAIN WILD-TYPE	324	152	64	210	40

Figure S117. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 3.27e-06 (Chi-square test), Q value = 0.002

Table S118. Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
17Q GAIN CNV	5	13	15	37	6	7
17Q GAIN WILD-TYPE	96	126	78	100	34	90

Figure S118. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 0.000108 (Fisher's exact test), Q value = 0.054

Table S119. Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
17Q GAIN CNV	17	18	84
17Q GAIN WILD-TYPE	217	130	362

Figure S119. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.19e-06 (Fisher's exact test), Q value = 0.00074

Table S120. Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
17Q GAIN CNV	26	82	11
17Q GAIN WILD-TYPE	190	326	193

Figure S120. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p gain' versus 'CN_CNMF'

P value = 2.57e-07 (Chi-square test), Q value = 0.00017

Table S121. Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
18P GAIN CNV	12	25	4	35	11
18P GAIN WILD-TYPE	335	197	68	188	38

Figure S121. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 1.03e-07 (Chi-square test), Q value = 6.7e-05

Table S122. Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
18P GAIN CNV	22	5	8	11	0	1
18P GAIN WILD-TYPE	79	134	85	126	40	96

Figure S122. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p gain' versus 'MRNASEQ_CNMF'

P value = 3.57e-06 (Fisher's exact test), Q value = 0.0021

Table S123. Gene #32: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
18P GAIN CNV	37	2	44
18P GAIN WILD-TYPE	197	146	402

Figure S123. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.42e-07 (Fisher's exact test), Q value = 9.2e-05

Table S124. Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
18P GAIN CNV	4	45	34
18P GAIN WILD-TYPE	212	363	170

Figure S124. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_CNMF'

P value = 1.52e-05 (Fisher's exact test), Q value = 0.0086

Table S125. Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
18P GAIN CNV	11	28	42
18P GAIN WILD-TYPE	223	364	213

Figure S125. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000104 (Fisher's exact test), Q value = 0.053

Table S126. Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
18P GAIN CNV	28	15	38
18P GAIN WILD-TYPE	334	269	197

Figure S126. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18q gain' versus 'CN_CNMF'

P value = 6.69e-06 (Chi-square test), Q value = 0.0039

Table S127. Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
18Q GAIN CNV	11	21	5	30	10
18Q GAIN WILD-TYPE	336	201	67	193	39

Figure S127. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

'18q gain' versus 'MRNASEQ_CNMF'

P value = 0.000346 (Fisher's exact test), Q value = 0.16

Table S128. Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
18Q GAIN CNV	24	2	46
18Q GAIN WILD-TYPE	210	146	400

Figure S128. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.95e-05 (Fisher's exact test), Q value = 0.051

Table S129. Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
18Q GAIN CNV	5	43	24
18Q GAIN WILD-TYPE	211	365	180

Figure S129. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'CN_CNMF'

P value = 0.000382 (Chi-square test), Q value = 0.17

Table S130. Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
19P GAIN CNV	15	11	11	27	5
19P GAIN WILD-TYPE	332	211	61	196	44

Figure S130. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

'19q gain' versus 'CN_CNMF'

P value = 0.000415 (Chi-square test), Q value = 0.19

Table S131. Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
19Q GAIN CNV	17	19	13	30	7
19Q GAIN WILD-TYPE	330	203	59	193	42

Figure S131. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'MRNA_CNMF'

P value = 3.66e-05 (Chi-square test), Q value = 0.02

Table S132. 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	124	36	23	95	72	20	103	40
20P GAIN CNV	42	6	6	26	32	13	21	6
20P GAIN WILD-TYPE	82	30	17	69	40	7	82	34

Figure S132. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20p gain' versus 'CN_CNMF'

P value = 3.08e-23 (Chi-square test), Q value = 2.4e-20

Table S133. Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
20P GAIN CNV	27	95	34	69	14
20P GAIN WILD-TYPE	320	127	38	154	35

Figure S133. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 3.06e-08 (Chi-square test), Q value = 2.1e-05

Table S134. Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
20P GAIN CNV	20	21	29	56	6	10
20P GAIN WILD-TYPE	81	118	64	81	34	87

Figure S134. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p gain' versus 'MIRSEQ_CNMF'

P value = 0.000293 (Fisher's exact test), Q value = 0.14

Table S135. Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
20P GAIN CNV	39	116	77
20P GAIN WILD-TYPE	195	276	178

Figure S135. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20q gain' versus 'MRNA_CNMF'

P value = 1.44e-05 (Chi-square test), Q value = 0.0081

Table S136. 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	124	36	23	95	72	20	103	40
20Q GAIN CNV	56	7	5	26	33	12	21	10
20Q GAIN WILD-TYPE	68	29	18	69	39	8	82	30

Figure S136. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20q gain' versus 'CN_CNMF'

P value = 3.32e-29 (Chi-square test), Q value = 2.6e-26

Table S137. Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
20Q GAIN CNV	31	118	32	78	17
20Q GAIN WILD-TYPE	316	104	40	145	32

Figure S137. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 2.35e-14 (Chi-square test), Q value = 1.8e-11

Table S138. Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
20Q GAIN CNV	22	23	34	72	7	10
20Q GAIN WILD-TYPE	79	116	59	65	33	87

Figure S138. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 3.01e-05 (Fisher's exact test), Q value = 0.016

Table S139. Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
20Q GAIN CNV	70	27	168
20Q GAIN WILD-TYPE	164	121	278

Figure S139. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.95e-06 (Fisher's exact test), Q value = 0.0018

Table S140. Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
20Q GAIN CNV	46	163	56
20Q GAIN WILD-TYPE	170	245	148

Figure S140. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 5.37e-06 (Fisher's exact test), Q value = 0.0031

Table S141. Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
20Q GAIN CNV	43	141	86
20Q GAIN WILD-TYPE	191	251	169

Figure S141. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'21q gain' versus 'MRNA_CNMF'

P value = 5.97e-05 (Chi-square test), Q value = 0.031

Table S142. 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	124	36	23	95	72	20	103	40
21Q GAIN CNV	12	0	1	17	19	5	7	2
21Q GAIN WILD-TYPE	112	36	22	78	53	15	96	38

Figure S142. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'21q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.092

Table S143. Gene #38: '21q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	125	248
21Q GAIN CNV	7	27	29
21Q GAIN WILD-TYPE	133	98	219

Figure S143. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'21q gain' versus 'CN_CNMF'

P value = 7.1e-10 (Chi-square test), Q value = 5e-07

Table S144. Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
21Q GAIN CNV	13	21	16	44	10
21Q GAIN WILD-TYPE	334	201	56	179	39

Figure S144. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

'21q gain' versus 'METHLYATION_CNMF'

P value = 4.67e-09 (Chi-square test), Q value = 3.2e-06

Table S145. Gene #38: '21q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
21Q GAIN CNV	26	7	17	10	1	2
21Q GAIN WILD-TYPE	75	132	76	127	39	95

Figure S145. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'21q gain' versus 'MRNASEQ_CNMF'

P value = 2.05e-11 (Fisher's exact test), Q value = 1.5e-08

Table S146. Gene #38: '21q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
21Q GAIN CNV	55	3	38
21Q GAIN WILD-TYPE	179	145	408

Figure S146. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.13e-10 (Fisher's exact test), Q value = 8e-08

Table S147. Gene #38: '21q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
21Q GAIN CNV	6	42	48
21Q GAIN WILD-TYPE	210	366	156

Figure S147. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'21q gain' versus 'MIRSEQ_CNMF'

P value = 3.95e-05 (Fisher's exact test), Q value = 0.021

Table S148. Gene #38: '21q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

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

Figure S148. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'21q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.66e-07 (Fisher's exact test), Q value = 0.00023

Table S149. Gene #38: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

Figure S149. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q gain' versus 'CN_CNMF'

P value = 3.75e-08 (Chi-square test), Q value = 2.5e-05

Table S150. Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
22Q GAIN CNV	2	10	1	26	4
22Q GAIN WILD-TYPE	345	212	71	197	45

Figure S150. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

'22q gain' versus 'MRNASEQ_CNMF'

P value = 4.84e-06 (Fisher's exact test), Q value = 0.0028

Table S151. Gene #39: '22q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
22Q GAIN CNV	23	0	15
22Q GAIN WILD-TYPE	211	148	431

Figure S151. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.57e-06 (Fisher's exact test), Q value = 0.00097

Table S152. Gene #39: '22q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
22Q GAIN CNV	2	13	23
22Q GAIN WILD-TYPE	214	395	181

Figure S152. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.03e-06 (Fisher's exact test), Q value = 0.00065

Table S153. Gene #39: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

Figure S153. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Xq gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.000165 (Fisher's exact test), Q value = 0.081

Table S154. Gene #40: 'Xq gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	125	248
XQ GAIN CNV	1	11	3
XQ GAIN WILD-TYPE	139	114	245

Figure S154. Get High-res Image Gene #40: 'Xq gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Xq gain' versus 'CN_CNMF'

P value = 0.000166 (Chi-square test), Q value = 0.082

Table S155. Gene #40: 'Xq gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
XQ GAIN CNV	2	3	2	14	0
XQ GAIN WILD-TYPE	345	219	70	209	49

Figure S155. Get High-res Image Gene #40: 'Xq gain' versus Molecular Subtype #3: 'CN_CNMF'

'Xq gain' versus 'MRNASEQ_CNMF'

P value = 0.000388 (Fisher's exact test), Q value = 0.18

Table S156. Gene #40: 'Xq gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
XQ GAIN CNV	13	0	6
XQ GAIN WILD-TYPE	221	148	440

Figure S156. Get High-res Image Gene #40: 'Xq gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Xq gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.47e-05 (Fisher's exact test), Q value = 0.0083

Table S157. Gene #40: 'Xq gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
XQ GAIN CNV	1	4	14
XQ GAIN WILD-TYPE	215	404	190

Figure S157. Get High-res Image Gene #40: 'Xq gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Xq gain' versus 'MIRSEQ_CNMF'

P value = 4.83e-05 (Fisher's exact test), Q value = 0.026

Table S158. Gene #40: 'Xq gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

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

Figure S158. Get High-res Image Gene #40: 'Xq gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Xq gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000182 (Fisher's exact test), Q value = 0.089

Table S159. Gene #40: 'Xq gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

Figure S159. Get High-res Image Gene #40: 'Xq gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1p loss' versus 'MRNA_CNMF'

P value = 0.000228 (Chi-square test), Q value = 0.11

Table S160. Gene #41: '1p 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	124	36	23	95	72	20	103	40
1P LOSS CNV	24	3	1	4	19	0	15	3
1P LOSS WILD-TYPE	100	33	22	91	53	20	88	37

Figure S160. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'1p loss' versus 'MRNA_CHIERARCHICAL'

P value = 3.98e-10 (Fisher's exact test), Q value = 2.8e-07

Table S161. Gene #41: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	125	248
1P LOSS CNV	7	4	58
1P LOSS WILD-TYPE	133	121	190

Figure S161. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

P value = 2.44e-23 (Chi-square test), Q value = 1.9e-20

Table S162. Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
1P LOSS CNV	13	57	30	17	6
1P LOSS WILD-TYPE	334	165	42	206	43

Figure S162. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 1.84e-06 (Chi-square test), Q value = 0.0011

Table S163. Gene #41: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
1P LOSS CNV	7	13	23	29	5	2
1P LOSS WILD-TYPE	94	126	70	108	35	95

Figure S163. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 3.92e-11 (Fisher's exact test), Q value = 2.8e-08

Table S164. Gene #41: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
1P LOSS CNV	14	5	92
1P LOSS WILD-TYPE	220	143	354

Figure S164. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.18e-13 (Fisher's exact test), Q value = 1.6e-10

Table S165. Gene #41: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
1P LOSS CNV	12	91	8
1P LOSS WILD-TYPE	204	317	196

Figure S165. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000177 (Fisher's exact test), Q value = 0.086

Table S166. Gene #41: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
1P LOSS CNV	69	33	18
1P LOSS WILD-TYPE	293	251	217

Figure S166. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2p loss' versus 'MRNA_CHIERARCHICAL'

P value = 3.09e-05 (Fisher's exact test), Q value = 0.017

Table S167. Gene #43: '2p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	125	248
2P LOSS CNV	6	3	36
2P LOSS WILD-TYPE	134	122	212

Figure S167. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'2p loss' versus 'CN_CNMF'

P value = 2.58e-12 (Chi-square test), Q value = 1.9e-09

Table S168. Gene #43: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
2P LOSS CNV	5	34	15	12	9
2P LOSS WILD-TYPE	342	188	57	211	40

Figure S168. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

'2p loss' versus 'METHLYATION_CNMF'

P value = 1.72e-07 (Chi-square test), Q value = 0.00011

Table S169. Gene #43: '2p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
2P LOSS CNV	1	7	9	24	1	0
2P LOSS WILD-TYPE	100	132	84	113	39	97

Figure S169. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2p loss' versus 'MRNASEQ_CNMF'

P value = 2.09e-07 (Fisher's exact test), Q value = 0.00013

Table S170. Gene #43: '2p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
2P LOSS CNV	6	5	59
2P LOSS WILD-TYPE	228	143	387

Figure S170. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.81e-07 (Fisher's exact test), Q value = 0.00049

Table S171. Gene #43: '2p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
2P LOSS CNV	10	55	5
2P LOSS WILD-TYPE	206	353	199

Figure S171. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_CNMF'

P value = 0.000265 (Fisher's exact test), Q value = 0.12

Table S172. Gene #43: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
2P LOSS CNV	10	48	13
2P LOSS WILD-TYPE	224	344	242

Figure S172. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00057 (Fisher's exact test), Q value = 0.24

Table S173. Gene #43: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
2P LOSS CNV	44	18	9
2P LOSS WILD-TYPE	318	266	226

Figure S173. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.000444 (Fisher's exact test), Q value = 0.2

Table S174. Gene #44: '2q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	125	248
2Q LOSS CNV	6	9	40
2Q LOSS WILD-TYPE	134	116	208

Figure S174. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'2q loss' versus 'CN_CNMF'

P value = 2.48e-12 (Chi-square test), Q value = 1.8e-09

Table S175. Gene #44: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
2Q LOSS CNV	5	41	16	21	8
2Q LOSS WILD-TYPE	342	181	56	202	41

Figure S175. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

'2q loss' versus 'METHLYATION_CNMF'

P value = 4.01e-06 (Chi-square test), Q value = 0.0024

Table S176. Gene #44: '2q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
2Q LOSS CNV	8	7	11	26	1	0
2Q LOSS WILD-TYPE	93	132	82	111	39	97

Figure S176. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2q loss' versus 'MRNASEQ_CNMF'

P value = 0.000387 (Fisher's exact test), Q value = 0.18

Table S177. Gene #44: '2q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
2Q LOSS CNV	19	5	61
2Q LOSS WILD-TYPE	215	143	385

Figure S177. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000322 (Fisher's exact test), Q value = 0.15

Table S178. Gene #44: '2q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
2Q LOSS CNV	11	59	15
2Q LOSS WILD-TYPE	205	349	189

Figure S178. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_CNMF'

P value = 0.000495 (Fisher's exact test), Q value = 0.22

Table S179. Gene #44: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
2Q LOSS CNV	10	53	24
2Q LOSS WILD-TYPE	224	339	231

Figure S179. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000423 (Fisher's exact test), Q value = 0.19

Table S180. Gene #44: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
2Q LOSS CNV	52	15	20
2Q LOSS WILD-TYPE	310	269	215

Figure S180. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'CN_CNMF'

P value = 2.58e-09 (Chi-square test), Q value = 1.8e-06

Table S181. Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
3P LOSS CNV	9	32	5	42	4
3P LOSS WILD-TYPE	338	190	67	181	45

Figure S181. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 3.42e-05 (Chi-square test), Q value = 0.019

Table S182. Gene #45: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
3P LOSS CNV	16	2	14	18	3	2
3P LOSS WILD-TYPE	85	137	79	119	37	95

Figure S182. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3p loss' versus 'RPPA_CHIERARCHICAL'

P value = 5.31e-05 (Fisher's exact test), Q value = 0.028

Table S183. Gene #45: '3p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	110	126
3P LOSS CNV	14	4	27
3P LOSS WILD-TYPE	147	106	99

Figure S183. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 3.32e-05 (Fisher's exact test), Q value = 0.018

Table S184. Gene #45: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
3P LOSS CNV	42	8	34
3P LOSS WILD-TYPE	192	140	412

Figure S184. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000279 (Fisher's exact test), Q value = 0.13

Table S185. Gene #45: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
3P LOSS CNV	13	35	36
3P LOSS WILD-TYPE	203	373	168

Figure S185. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CNMF'

P value = 2.18e-06 (Fisher's exact test), Q value = 0.0013

Table S186. Gene #45: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
3P LOSS CNV	14	27	47
3P LOSS WILD-TYPE	220	365	208

Figure S186. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000443 (Fisher's exact test), Q value = 0.2

Table S187. Gene #45: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
3P LOSS CNV	39	14	35
3P LOSS WILD-TYPE	323	270	200

Figure S187. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'MRNA_CNMF'

P value = 4.5e-12 (Chi-square test), Q value = 3.3e-09

Table S188. 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	124	36	23	95	72	20	103	40
4P LOSS CNV	18	4	1	41	33	4	13	3
4P LOSS WILD-TYPE	106	32	22	54	39	16	90	37

Figure S188. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'4p loss' versus 'MRNA_CHIERARCHICAL'

P value = 1.24e-12 (Fisher's exact test), Q value = 9.1e-10

Table S189. Gene #47: '4p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	125	248
4P LOSS CNV	9	55	53
4P LOSS WILD-TYPE	131	70	195

Figure S189. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

P value = 9.98e-28 (Chi-square test), Q value = 7.9e-25

Table S190. Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
4P LOSS CNV	18	38	24	97	8
4P LOSS WILD-TYPE	329	184	48	126	41

Figure S190. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 3.87e-14 (Chi-square test), Q value = 2.9e-11

Table S191. Gene #47: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
4P LOSS CNV	44	19	22	14	4	3
4P LOSS WILD-TYPE	57	120	71	123	36	94

Figure S191. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p loss' versus 'RPPA_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.069

Table S192. Gene #47: '4p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
4P LOSS CNV	52	25	17
4P LOSS WILD-TYPE	95	108	100

Figure S192. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'4p loss' versus 'RPPA_CHIERARCHICAL'

P value = 7.57e-06 (Fisher's exact test), Q value = 0.0044

Table S193. 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	15	49
4P LOSS WILD-TYPE	131	95	77

Figure S193. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 2.85e-17 (Fisher's exact test), Q value = 2.2e-14

Table S194. Gene #47: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
4P LOSS CNV	92	7	76
4P LOSS WILD-TYPE	142	141	370

Figure S194. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.21e-18 (Fisher's exact test), Q value = 7.2e-15

Table S195. Gene #47: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
4P LOSS CNV	15	75	85
4P LOSS WILD-TYPE	201	333	119

Figure S195. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_CNMF'

P value = 6.76e-14 (Fisher's exact test), Q value = 5.1e-11

Table S196. Gene #47: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
4P LOSS CNV	21	66	93
4P LOSS WILD-TYPE	213	326	162

Figure S196. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.98e-15 (Fisher's exact test), Q value = 4.6e-12

Table S197. Gene #47: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
4P LOSS CNV	65	26	89
4P LOSS WILD-TYPE	297	258	146

Figure S197. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4q loss' versus 'MRNA_CNMF'

P value = 1.79e-06 (Chi-square test), Q value = 0.0011

Table S198. 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	124	36	23	95	72	20	103	40
4Q LOSS CNV	17	5	1	32	25	2	12	3
4Q LOSS WILD-TYPE	107	31	22	63	47	18	91	37

Figure S198. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'4q loss' versus 'MRNA_CHIERARCHICAL'

P value = 2.1e-08 (Fisher's exact test), Q value = 1.4e-05

Table S199. Gene #48: '4q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	125	248
4Q LOSS CNV	8	42	47
4Q LOSS WILD-TYPE	132	83	201

Figure S199. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 7.17e-21 (Chi-square test), Q value = 5.6e-18

Table S200. Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
4Q LOSS CNV	17	30	26	75	7
4Q LOSS WILD-TYPE	330	192	46	148	42

Figure S200. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 1.19e-10 (Chi-square test), Q value = 8.5e-08

Table S201. Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
4Q LOSS CNV	37	20	16	12	4	2
4Q LOSS WILD-TYPE	64	119	77	125	36	95

Figure S201. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 4.88e-12 (Fisher's exact test), Q value = 3.6e-09

Table S202. Gene #48: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
4Q LOSS CNV	73	6	68
4Q LOSS WILD-TYPE	161	142	378

Figure S202. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.13e-12 (Fisher's exact test), Q value = 8.3e-10

Table S203. Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
4Q LOSS CNV	13	66	68
4Q LOSS WILD-TYPE	203	342	136

Figure S203. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_CNMF'

P value = 4.17e-07 (Fisher's exact test), Q value = 0.00027

Table S204. Gene #48: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
4Q LOSS CNV	20	61	68
4Q LOSS WILD-TYPE	214	331	187

Figure S204. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.61e-10 (Fisher's exact test), Q value = 3.2e-07

Table S205. Gene #48: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
4Q LOSS CNV	51	26	72
4Q LOSS WILD-TYPE	311	258	163

Figure S205. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5p loss' versus 'MRNA_CNMF'

P value = 1.49e-08 (Chi-square test), Q value = 1e-05

Table S206. 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	124	36	23	95	72	20	103	40
5P LOSS CNV	4	2	2	24	9	0	3	0
5P LOSS WILD-TYPE	120	34	21	71	63	20	100	40

Figure S206. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'5p loss' versus 'MRNA_CHIERARCHICAL'

P value = 4.14e-06 (Fisher's exact test), Q value = 0.0024

Table S207. Gene #49: '5p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	125	248
5P LOSS CNV	3	24	17
5P LOSS WILD-TYPE	137	101	231

Figure S207. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'5p loss' versus 'CN_CNMF'

P value = 8.97e-21 (Chi-square test), Q value = 7e-18

Table S208. Gene #49: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
5P LOSS CNV	2	13	3	52	3
5P LOSS WILD-TYPE	345	209	69	171	46

Figure S208. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

'5p loss' versus 'METHLYATION_CNMF'

P value = 4.03e-12 (Chi-square test), Q value = 3e-09

Table S209. Gene #49: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
5P LOSS CNV	25	2	5	11	0	1
5P LOSS WILD-TYPE	76	137	88	126	40	96

Figure S209. 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 = 0.023

Table S210. 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 S210. 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 = 0.0039

Table S211. 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 S211. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'5p loss' versus 'MRNASEQ_CNMF'

P value = 1.79e-08 (Fisher's exact test), Q value = 1.2e-05

Table S212. Gene #49: '5p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
5P LOSS CNV	38	1	27
5P LOSS WILD-TYPE	196	147	419

Figure S212. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.4e-08 (Fisher's exact test), Q value = 2.3e-05

Table S213. Gene #49: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
5P LOSS CNV	4	27	35
5P LOSS WILD-TYPE	212	381	169

Figure S213. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_CNMF'

P value = 1.86e-14 (Fisher's exact test), Q value = 1.4e-11

Table S214. Gene #49: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
5P LOSS CNV	4	17	51
5P LOSS WILD-TYPE	230	375	204

Figure S214. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.1e-16 (Fisher's exact test), Q value = 8.5e-14

Table S215. Gene #49: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
5P LOSS CNV	19	3	50
5P LOSS WILD-TYPE	343	281	185

Figure S215. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'MRNA_CNMF'

P value = 4.14e-19 (Chi-square test), Q value = 3.2e-16

Table S216. 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	124	36	23	95	72	20	103	40
5Q LOSS CNV	9	3	3	44	13	0	3	1
5Q LOSS WILD-TYPE	115	33	20	51	59	20	100	39

Figure S216. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'5q loss' versus 'MRNA_CHIERARCHICAL'

P value = 9.95e-15 (Fisher's exact test), Q value = 7.6e-12

Table S217. Gene #50: '5q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	125	248
5Q LOSS CNV	5	47	24
5Q LOSS WILD-TYPE	135	78	224

Figure S217. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'5q loss' versus 'CN_CNMF'

P value = 4.59e-45 (Chi-square test), Q value = 3.7e-42

Table S218. Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
5Q LOSS CNV	4	15	4	94	7
5Q LOSS WILD-TYPE	343	207	68	129	42

Figure S218. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 1.21e-32 (Chi-square test), Q value = 9.6e-30

Table S219. Gene #50: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
5Q LOSS CNV	50	3	5	16	0	2
5Q LOSS WILD-TYPE	51	136	88	121	40	95

Figure S219. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5q loss' versus 'RPPA_CNMF'

P value = 1.86e-09 (Fisher's exact test), Q value = 1.3e-06

Table S220. 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	6	13
5Q LOSS WILD-TYPE	101	127	104

Figure S220. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'5q loss' versus 'RPPA_CHIERARCHICAL'

P value = 6.93e-11 (Fisher's exact test), Q value = 5e-08

Table S221. 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	8	45
5Q LOSS WILD-TYPE	149	102	81

Figure S221. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 4.87e-22 (Fisher's exact test), Q value = 3.8e-19

Table S222. Gene #50: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
5Q LOSS CNV	79	4	34
5Q LOSS WILD-TYPE	155	144	412

Figure S222. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.55e-24 (Fisher's exact test), Q value = 7.6e-21

Table S223. Gene #50: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
5Q LOSS CNV	7	35	75
5Q LOSS WILD-TYPE	209	373	129

Figure S223. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CNMF'

P value = 1.06e-27 (Fisher's exact test), Q value = 8.4e-25

Table S224. Gene #50: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
5Q LOSS CNV	9	23	89
5Q LOSS WILD-TYPE	225	369	166

Figure S224. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.15e-33 (Fisher's exact test), Q value = 9.2e-31

Table S225. Gene #50: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
5Q LOSS CNV	27	5	89
5Q LOSS WILD-TYPE	335	279	146

Figure S225. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6p loss' versus 'MRNA_CHIERARCHICAL'

P value = 9.32e-05 (Fisher's exact test), Q value = 0.048

Table S226. Gene #51: '6p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	125	248
6P LOSS CNV	21	4	44
6P LOSS WILD-TYPE	119	121	204

Figure S226. Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6p loss' versus 'CN_CNMF'

P value = 1.09e-09 (Chi-square test), Q value = 7.6e-07

Table S227. Gene #51: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
6P LOSS CNV	21	52	10	16	10
6P LOSS WILD-TYPE	326	170	62	207	39

Figure S227. Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

'6p loss' versus 'METHLYATION_CNMF'

P value = 4.96e-05 (Chi-square test), Q value = 0.026

Table S228. Gene #51: '6p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
6P LOSS CNV	4	13	11	29	2	4
6P LOSS WILD-TYPE	97	126	82	108	38	93

Figure S228. Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6p loss' versus 'MRNASEQ_CNMF'

P value = 1.23e-05 (Fisher's exact test), Q value = 0.007

Table S229. Gene #51: '6p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
6P LOSS CNV	14	12	78
6P LOSS WILD-TYPE	220	136	368

Figure S229. Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.85e-05 (Fisher's exact test), Q value = 0.01

Table S230. Gene #51: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
6P LOSS CNV	23	71	10
6P LOSS WILD-TYPE	193	337	194

Figure S230. Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000394 (Fisher's exact test), Q value = 0.18

Table S231. Gene #51: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
6P LOSS CNV	62	29	16
6P LOSS WILD-TYPE	300	255	219

Figure S231. Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6q loss' versus 'MRNA_CNMF'

P value = 4.71e-05 (Chi-square test), Q value = 0.025

Table S232. 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	124	36	23	95	72	20	103	40
6Q LOSS CNV	40	10	4	6	9	1	19	11
6Q LOSS WILD-TYPE	84	26	19	89	63	19	84	29

Figure S232. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'6q loss' versus 'MRNA_CHIERARCHICAL'

P value = 9.19e-07 (Fisher's exact test), Q value = 0.00058

Table S233. Gene #52: '6q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	125	248
6Q LOSS CNV	32	6	62
6Q LOSS WILD-TYPE	108	119	186

Figure S233. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6q loss' versus 'CN_CNMF'

P value = 1.2e-14 (Chi-square test), Q value = 9.1e-12

Table S234. Gene #52: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
6Q LOSS CNV	44	79	13	19	16
6Q LOSS WILD-TYPE	303	143	59	204	33

Figure S234. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

'6q loss' versus 'METHLYATION_CNMF'

P value = 6.48e-08 (Chi-square test), Q value = 4.3e-05

Table S235. Gene #52: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
6Q LOSS CNV	6	30	18	44	5	5
6Q LOSS WILD-TYPE	95	109	75	93	35	92

Figure S235. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6q loss' versus 'RPPA_CNMF'

P value = 0.00055 (Fisher's exact test), Q value = 0.24

Table S236. Gene #52: '6q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
6Q LOSS CNV	14	33	29
6Q LOSS WILD-TYPE	133	100	88

Figure S236. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'6q loss' versus 'MRNASEQ_CNMF'

P value = 2.4e-08 (Fisher's exact test), Q value = 1.6e-05

Table S237. Gene #52: '6q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
6Q LOSS CNV	18	27	114
6Q LOSS WILD-TYPE	216	121	332

Figure S237. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.38e-07 (Fisher's exact test), Q value = 0.00034

Table S238. Gene #52: '6q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
6Q LOSS CNV	46	98	15
6Q LOSS WILD-TYPE	170	310	189

Figure S238. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.54e-06 (Fisher's exact test), Q value = 0.0015

Table S239. Gene #52: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
6Q LOSS CNV	90	56	21
6Q LOSS WILD-TYPE	272	228	214

Figure S239. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7p loss' versus 'CN_CNMF'

P value = 9.93e-06 (Chi-square test), Q value = 0.0057

Table S240. Gene #53: '7p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
7P LOSS CNV	3	17	4	23	1
7P LOSS WILD-TYPE	344	205	68	200	48

Figure S240. Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #3: 'CN_CNMF'

'7p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000451 (Fisher's exact test), Q value = 0.2

Table S241. Gene #53: '7p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
7P LOSS CNV	3	24	20
7P LOSS WILD-TYPE	213	384	184

Figure S241. Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000466 (Fisher's exact test), Q value = 0.2

Table S242. Gene #53: '7p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
7P LOSS CNV	25	4	18
7P LOSS WILD-TYPE	337	280	217

Figure S242. Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7q loss' versus 'CN_CNMF'

P value = 0.000443 (Chi-square test), Q value = 0.2

Table S243. Gene #54: '7q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
7Q LOSS CNV	11	21	8	24	0
7Q LOSS WILD-TYPE	336	201	64	199	49

Figure S243. Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #3: 'CN_CNMF'

'7q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.37e-05 (Fisher's exact test), Q value = 0.0078

Table S244. Gene #54: '7q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
7Q LOSS CNV	38	5	18
7Q LOSS WILD-TYPE	324	279	217

Figure S244. Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8p loss' versus 'MRNA_CNMF'

P value = 0.000103 (Chi-square test), Q value = 0.052

Table S245. Gene #55: '8p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	124	36	23	95	72	20	103	40
8P LOSS CNV	54	9	4	24	29	4	16	15
8P LOSS WILD-TYPE	70	27	19	71	43	16	87	25

Figure S245. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'8p loss' versus 'CN_CNMF'

P value = 2.58e-15 (Chi-square test), Q value = 2e-12

Table S246. Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
8P LOSS CNV	56	97	10	92	15
8P LOSS WILD-TYPE	291	125	62	131	34

Figure S246. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 9.84e-08 (Chi-square test), Q value = 6.4e-05

Table S247. Gene #55: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
8P LOSS CNV	34	23	32	61	8	14
8P LOSS WILD-TYPE	67	116	61	76	32	83

Figure S247. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p loss' versus 'MRNA_CNMF'

P value = 2.39e-05 (Chi-square test), Q value = 0.013

Table S248. 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	124	36	23	95	72	20	103	40
9P LOSS CNV	42	8	5	17	26	5	11	2
9P LOSS WILD-TYPE	82	28	18	78	46	15	92	38

Figure S248. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 5.07e-19 (Chi-square test), Q value = 4e-16

Table S249. Gene #57: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
9P LOSS CNV	22	82	9	65	12
9P LOSS WILD-TYPE	325	140	63	158	37

Figure S249. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 1.08e-13 (Chi-square test), Q value = 8.1e-11

Table S250. Gene #57: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
9P LOSS CNV	23	5	29	48	8	3
9P LOSS WILD-TYPE	78	134	64	89	32	94

Figure S250. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 3.34e-06 (Fisher's exact test), Q value = 0.002

Table S251. Gene #57: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
9P LOSS CNV	56	11	112
9P LOSS WILD-TYPE	178	137	334

Figure S251. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.71e-06 (Fisher's exact test), Q value = 0.0045

Table S252. Gene #57: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
9P LOSS CNV	23	108	48
9P LOSS WILD-TYPE	193	300	156

Figure S252. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_CNMF'

P value = 5.65e-05 (Fisher's exact test), Q value = 0.03

Table S253. Gene #57: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
9P LOSS CNV	26	92	64
9P LOSS WILD-TYPE	208	300	191

Figure S253. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.37e-07 (Fisher's exact test), Q value = 0.00015

Table S254. Gene #57: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
9P LOSS CNV	92	29	61
9P LOSS WILD-TYPE	270	255	174

Figure S254. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 9.61e-16 (Chi-square test), Q value = 7.4e-13

Table S255. Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
9Q LOSS CNV	12	57	8	56	14
9Q LOSS WILD-TYPE	335	165	64	167	35

Figure S255. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 1.74e-12 (Chi-square test), Q value = 1.3e-09

Table S256. Gene #58: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
9Q LOSS CNV	30	3	17	36	3	2
9Q LOSS WILD-TYPE	71	136	76	101	37	95

Figure S256. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 9.07e-08 (Fisher's exact test), Q value = 6e-05

Table S257. Gene #58: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
9Q LOSS CNV	49	4	81
9Q LOSS WILD-TYPE	185	144	365

Figure S257. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.3e-06 (Fisher's exact test), Q value = 0.0048

Table S258. Gene #58: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
9Q LOSS CNV	14	79	41
9Q LOSS WILD-TYPE	202	329	163

Figure S258. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_CNMF'

P value = 4.12e-05 (Fisher's exact test), Q value = 0.022

Table S259. Gene #58: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
9Q LOSS CNV	18	64	56
9Q LOSS WILD-TYPE	216	328	199

Figure S259. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.12e-10 (Fisher's exact test), Q value = 1.5e-07

Table S260. Gene #58: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
9Q LOSS CNV	64	15	59
9Q LOSS WILD-TYPE	298	269	176

Figure S260. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 2.55e-06 (Chi-square test), Q value = 0.0015

Table S261. Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
10P LOSS CNV	6	28	8	27	6
10P LOSS WILD-TYPE	341	194	64	196	43

Figure S261. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

'10q loss' versus 'MRNA_CNMF'

P value = 0.000512 (Chi-square test), Q value = 0.22

Table S262. 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	124	36	23	95	72	20	103	40
10Q LOSS CNV	25	2	7	17	9	2	6	0
10Q LOSS WILD-TYPE	99	34	16	78	63	18	97	40

Figure S262. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'10q loss' versus 'CN_CNMF'

P value = 4.34e-14 (Chi-square test), Q value = 3.3e-11

Table S263. Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
10Q LOSS CNV	6	38	8	53	6
10Q LOSS WILD-TYPE	341	184	64	170	43

Figure S263. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 9.95e-07 (Chi-square test), Q value = 0.00062

Table S264. Gene #60: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
10Q LOSS CNV	23	6	15	23	3	1
10Q LOSS WILD-TYPE	78	133	78	114	37	96

Figure S264. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 5.36e-05 (Fisher's exact test), Q value = 0.028

Table S265. Gene #60: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
10Q LOSS CNV	41	5	60
10Q LOSS WILD-TYPE	193	143	386

Figure S265. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000363 (Fisher's exact test), Q value = 0.17

Table S266. Gene #60: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
10Q LOSS CNV	12	61	33
10Q LOSS WILD-TYPE	204	347	171

Figure S266. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 8.5e-15 (Chi-square test), Q value = 6.5e-12

Table S267. Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
11P LOSS CNV	12	58	15	54	5
11P LOSS WILD-TYPE	335	164	57	169	44

Figure S267. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 8.61e-08 (Chi-square test), Q value = 5.7e-05

Table S268. Gene #61: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
11P LOSS CNV	21	9	22	32	3	1
11P LOSS WILD-TYPE	80	130	71	105	37	96

Figure S268. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.61e-05 (Fisher's exact test), Q value = 0.03

Table S269. Gene #61: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
11P LOSS CNV	73	24	44
11P LOSS WILD-TYPE	289	260	191

Figure S269. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11q loss' versus 'MRNA_CNMF'

P value = 2.01e-07 (Chi-square test), Q value = 0.00013

Table S270. 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	124	36	23	95	72	20	103	40
11Q LOSS CNV	60	13	4	14	18	3	19	9
11Q LOSS WILD-TYPE	64	23	19	81	54	17	84	31

Figure S270. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'11q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.000327 (Fisher's exact test), Q value = 0.15

Table S271. Gene #62: '11q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	125	248
11Q LOSS CNV	36	19	85
11Q LOSS WILD-TYPE	104	106	163

Figure S271. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

P value = 2.04e-31 (Chi-square test), Q value = 1.6e-28

Table S272. Gene #62: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
11Q LOSS CNV	34	120	23	45	7
11Q LOSS WILD-TYPE	313	102	49	178	42

Figure S272. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

P value = 1.5e-11 (Chi-square test), Q value = 1.1e-08

Table S273. Gene #62: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
11Q LOSS CNV	16	27	34	58	8	4
11Q LOSS WILD-TYPE	85	112	59	79	32	93

Figure S273. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11q loss' versus 'MRNASEQ_CNMF'

P value = 4.03e-06 (Fisher's exact test), Q value = 0.0024

Table S274. Gene #62: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
11Q LOSS CNV	37	33	146
11Q LOSS WILD-TYPE	197	115	300

Figure S274. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.26e-05 (Fisher's exact test), Q value = 0.0072

Table S275. Gene #62: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
11Q LOSS CNV	55	131	30
11Q LOSS WILD-TYPE	161	277	174

Figure S275. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.01e-05 (Fisher's exact test), Q value = 0.016

Table S276. Gene #62: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
11Q LOSS CNV	121	59	44
11Q LOSS WILD-TYPE	241	225	191

Figure S276. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12p loss' versus 'METHLYATION_CNMF'

P value = 1.57e-06 (Chi-square test), Q value = 0.00097

Table S277. Gene #63: '12p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
12P LOSS CNV	18	7	1	10	7	1
12P LOSS WILD-TYPE	83	132	92	127	33	96

Figure S277. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p loss' versus 'MRNASEQ_CNMF'

P value = 7.88e-05 (Fisher's exact test), Q value = 0.041

Table S278. Gene #63: '12p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
12P LOSS CNV	33	6	23
12P LOSS WILD-TYPE	201	142	423

Figure S278. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.000244 (Fisher's exact test), Q value = 0.12

Table S279. Gene #64: '12q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	125	248
12Q LOSS CNV	3	18	12
12Q LOSS WILD-TYPE	137	107	236

Figure S279. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'12q loss' versus 'CN_CNMF'

P value = 9.88e-05 (Chi-square test), Q value = 0.05

Table S280. Gene #64: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
12Q LOSS CNV	10	9	4	27	2
12Q LOSS WILD-TYPE	337	213	68	196	47

Figure S280. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

'12q loss' versus 'METHLYATION_CNMF'

P value = 4.1e-09 (Chi-square test), Q value = 2.8e-06

Table S281. Gene #64: '12q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
12Q LOSS CNV	20	2	2	8	2	1
12Q LOSS WILD-TYPE	81	137	91	129	38	96

Figure S281. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12q loss' versus 'MRNASEQ_CNMF'

P value = 4.09e-08 (Fisher's exact test), Q value = 2.7e-05

Table S282. Gene #64: '12q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
12Q LOSS CNV	31	2	13
12Q LOSS WILD-TYPE	203	146	433

Figure S282. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.98e-07 (Fisher's exact test), Q value = 0.00013

Table S283. Gene #64: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
12Q LOSS CNV	4	14	28
12Q LOSS WILD-TYPE	212	394	176

Figure S283. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q loss' versus 'MIRSEQ_CNMF'

P value = 3.21e-06 (Fisher's exact test), Q value = 0.0019

Table S284. Gene #64: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
12Q LOSS CNV	6	13	31
12Q LOSS WILD-TYPE	228	379	224

Figure S284. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.34e-06 (Fisher's exact test), Q value = 0.00083

Table S285. Gene #64: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
12Q LOSS CNV	13	7	30
12Q LOSS WILD-TYPE	349	277	205

Figure S285. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'13q loss' versus 'MRNA_CNMF'

P value = 0.000134 (Chi-square test), Q value = 0.066

Table S286. 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	124	36	23	95	72	20	103	40
13Q LOSS CNV	58	10	4	31	25	4	22	5
13Q LOSS WILD-TYPE	66	26	19	64	47	16	81	35

Figure S286. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'13q loss' versus 'CN_CNMF'

P value = 1.62e-27 (Chi-square test), Q value = 1.3e-24

Table S287. Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
13Q LOSS CNV	28	100	31	80	28
13Q LOSS WILD-TYPE	319	122	41	143	21

Figure S287. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 2.84e-10 (Chi-square test), Q value = 2e-07

Table S288. Gene #65: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
13Q LOSS CNV	36	26	44	51	3	11
13Q LOSS WILD-TYPE	65	113	49	86	37	86

Figure S288. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 0.000411 (Fisher's exact test), Q value = 0.18

Table S289. Gene #65: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
13Q LOSS CNV	81	26	146
13Q LOSS WILD-TYPE	153	122	300

Figure S289. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000523 (Fisher's exact test), Q value = 0.23

Table S290. Gene #65: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
13Q LOSS CNV	44	142	67
13Q LOSS WILD-TYPE	172	266	137

Figure S290. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_CNMF'

P value = 2.49e-08 (Fisher's exact test), Q value = 1.7e-05

Table S291. Gene #65: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
13Q LOSS CNV	36	131	95
13Q LOSS WILD-TYPE	198	261	160

Figure S291. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'14q loss' versus 'MRNA_CNMF'

P value = 1.09e-10 (Chi-square test), Q value = 7.8e-08

Table S292. 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	124	36	23	95	72	20	103	40
14Q LOSS CNV	25	1	2	36	8	3	5	0
14Q LOSS WILD-TYPE	99	35	21	59	64	17	98	40

Figure S292. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'14q loss' versus 'MRNA_CHIERARCHICAL'

P value = 8.5e-08 (Fisher's exact test), Q value = 5.6e-05

Table S293. Gene #66: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	125	248
14Q LOSS CNV	7	38	35
14Q LOSS WILD-TYPE	133	87	213

Figure S293. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 2.6e-22 (Chi-square test), Q value = 2e-19

Table S294. Gene #66: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
14Q LOSS CNV	10	29	9	75	13
14Q LOSS WILD-TYPE	337	193	63	148	36

Figure S294. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 6.83e-16 (Chi-square test), Q value = 5.3e-13

Table S295. Gene #66: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
14Q LOSS CNV	39	5	16	18	1	3
14Q LOSS WILD-TYPE	62	134	77	119	39	94

Figure S295. 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 = 0.09

Table S296. 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 S296. 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 = 0.044

Table S297. 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 S297. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 2.46e-11 (Fisher's exact test), Q value = 1.8e-08

Table S298. Gene #66: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
14Q LOSS CNV	66	6	52
14Q LOSS WILD-TYPE	168	142	394

Figure S298. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.53e-11 (Fisher's exact test), Q value = 1.1e-08

Table S299. Gene #66: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
14Q LOSS CNV	11	53	60
14Q LOSS WILD-TYPE	205	355	144

Figure S299. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_CNMF'

P value = 5.57e-13 (Fisher's exact test), Q value = 4.1e-10

Table S300. Gene #66: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
14Q LOSS CNV	19	34	74
14Q LOSS WILD-TYPE	215	358	181

Figure S300. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'14q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.18e-13 (Fisher's exact test), Q value = 8.8e-11

Table S301. Gene #66: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
14Q LOSS CNV	36	20	71
14Q LOSS WILD-TYPE	326	264	164

Figure S301. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.000121 (Fisher's exact test), Q value = 0.06

Table S302. Gene #67: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	125	248
15Q LOSS CNV	13	37	49
15Q LOSS WILD-TYPE	127	88	199

Figure S302. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 3.85e-17 (Chi-square test), Q value = 3e-14

Table S303. Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
15Q LOSS CNV	19	37	28	68	10
15Q LOSS WILD-TYPE	328	185	44	155	39

Figure S303. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 4.94e-07 (Chi-square test), Q value = 0.00031

Table S304. Gene #67: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
15Q LOSS CNV	36	15	19	22	3	8
15Q LOSS WILD-TYPE	65	124	74	115	37	89

Figure S304. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 0.000106 (Fisher's exact test), Q value = 0.054

Table S305. Gene #67: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
15Q LOSS CNV	61	14	74
15Q LOSS WILD-TYPE	173	134	372

Figure S305. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000116 (Fisher's exact test), Q value = 0.058

Table S306. Gene #67: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
15Q LOSS CNV	22	74	53
15Q LOSS WILD-TYPE	194	334	151

Figure S306. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_CNMF'

P value = 7.41e-05 (Fisher's exact test), Q value = 0.039

Table S307. Gene #67: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
15Q LOSS CNV	27	63	67
15Q LOSS WILD-TYPE	207	329	188

Figure S307. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.04e-06 (Fisher's exact test), Q value = 0.0018

Table S308. Gene #67: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
15Q LOSS CNV	64	29	64
15Q LOSS WILD-TYPE	298	255	171

Figure S308. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16p loss' versus 'CN_CNMF'

P value = 1.42e-05 (Chi-square test), Q value = 0.008

Table S309. Gene #68: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
16P LOSS CNV	5	19	2	25	4
16P LOSS WILD-TYPE	342	203	70	198	45

Figure S309. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

'16p loss' versus 'METHLYATION_CNMF'

P value = 2.47e-05 (Chi-square test), Q value = 0.014

Table S310. Gene #68: '16p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
16P LOSS CNV	14	1	7	5	0	2
16P LOSS WILD-TYPE	87	138	86	132	40	95

Figure S310. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16p loss' versus 'MIRSEQ_CNMF'

P value = 0.000225 (Fisher's exact test), Q value = 0.11

Table S311. Gene #68: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
16P LOSS CNV	4	23	26
16P LOSS WILD-TYPE	230	369	229

Figure S311. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000233 (Fisher's exact test), Q value = 0.11

Table S312. Gene #68: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
16P LOSS CNV	20	7	26
16P LOSS WILD-TYPE	342	277	209

Figure S312. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'MRNA_CNMF'

P value = 7.08e-08 (Chi-square test), Q value = 4.7e-05

Table S313. 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	124	36	23	95	72	20	103	40
16Q LOSS CNV	59	20	13	16	33	7	62	23
16Q LOSS WILD-TYPE	65	16	10	79	39	13	41	17

Figure S313. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'16q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1.75e-13 (Fisher's exact test), Q value = 1.3e-10

Table S314. Gene #69: '16q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	125	248
16Q LOSS CNV	76	21	136
16Q LOSS WILD-TYPE	64	104	112

Figure S314. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'16q loss' versus 'CN_CNMF'

P value = 9.63e-12 (Chi-square test), Q value = 7e-09

Table S315. Gene #69: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
16Q LOSS CNV	161	107	46	50	26
16Q LOSS WILD-TYPE	186	115	26	173	23

Figure S315. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 6.1e-17 (Chi-square test), Q value = 4.7e-14

Table S316. Gene #69: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
16Q LOSS CNV	18	95	45	58	13	20
16Q LOSS WILD-TYPE	83	44	48	79	27	77

Figure S316. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16q loss' versus 'RPPA_CNMF'

P value = 8.18e-06 (Fisher's exact test), Q value = 0.0047

Table S317. Gene #69: '16q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
16Q LOSS CNV	40	73	54
16Q LOSS WILD-TYPE	107	60	63

Figure S317. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'16q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1.02e-09 (Fisher's exact test), Q value = 7.1e-07

Table S318. 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	25
16Q LOSS WILD-TYPE	71	58	101

Figure S318. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 1.01e-16 (Fisher's exact test), Q value = 7.8e-14

Table S319. Gene #69: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
16Q LOSS CNV	48	72	238
16Q LOSS WILD-TYPE	186	76	208

Figure S319. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.02e-20 (Fisher's exact test), Q value = 6.3e-17

Table S320. Gene #69: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
16Q LOSS CNV	116	209	33
16Q LOSS WILD-TYPE	100	199	171

Figure S320. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_CNMF'

P value = 9.39e-15 (Fisher's exact test), Q value = 7.1e-12

Table S321. Gene #69: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
16Q LOSS CNV	106	213	59
16Q LOSS WILD-TYPE	128	179	196

Figure S321. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.4e-18 (Fisher's exact test), Q value = 3.4e-15

Table S322. Gene #69: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
16Q LOSS CNV	162	167	49
16Q LOSS WILD-TYPE	200	117	186

Figure S322. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'MRNA_CNMF'

P value = 8.23e-06 (Chi-square test), Q value = 0.0048

Table S323. 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	124	36	23	95	72	20	103	40
17P LOSS CNV	58	19	11	40	47	3	27	15
17P LOSS WILD-TYPE	66	17	12	55	25	17	76	25

Figure S323. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17p loss' versus 'CN_CNMF'

P value = 6.2e-14 (Chi-square test), Q value = 4.6e-11

Table S324. Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
17P LOSS CNV	87	122	25	117	22
17P LOSS WILD-TYPE	260	100	47	106	27

Figure S324. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 5.8e-08 (Chi-square test), Q value = 3.9e-05

Table S325. Gene #70: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
17P LOSS CNV	38	47	47	75	14	16
17P LOSS WILD-TYPE	63	92	46	62	26	81

Figure S325. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q loss' versus 'MRNA_CNMF'

P value = 1.08e-10 (Chi-square test), Q value = 7.7e-08

Table S326. 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	124	36	23	95	72	20	103	40
17Q LOSS CNV	17	2	2	29	30	0	5	7
17Q LOSS WILD-TYPE	107	34	21	66	42	20	98	33

Figure S326. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1.72e-06 (Fisher's exact test), Q value = 0.0011

Table S327. Gene #71: '17q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	125	248
17Q LOSS CNV	12	41	39
17Q LOSS WILD-TYPE	128	84	209

Figure S327. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

P value = 8.88e-11 (Chi-square test), Q value = 6.4e-08

Table S328. Gene #71: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
17Q LOSS CNV	24	34	11	66	8
17Q LOSS WILD-TYPE	323	188	61	157	41

Figure S328. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

'17q loss' versus 'METHLYATION_CNMF'

P value = 7.48e-05 (Chi-square test), Q value = 0.039

Table S329. Gene #71: '17q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
17Q LOSS CNV	25	7	13	23	2	8
17Q LOSS WILD-TYPE	76	132	80	114	38	89

Figure S329. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q loss' versus 'RPPA_CNMF'

P value = 9.69e-10 (Fisher's exact test), Q value = 6.8e-07

Table S330. 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	19
17Q LOSS WILD-TYPE	96	126	98

Figure S330. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'17q loss' versus 'RPPA_CHIERARCHICAL'

P value = 6.4e-07 (Fisher's exact test), Q value = 4e-04

Table S331. 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	44
17Q LOSS WILD-TYPE	145	93	82

Figure S331. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'17q loss' versus 'MRNASEQ_CNMF'

P value = 1.9e-10 (Fisher's exact test), Q value = 1.3e-07

Table S332. Gene #71: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
17Q LOSS CNV	71	13	50
17Q LOSS WILD-TYPE	163	135	396

Figure S332. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.84e-08 (Fisher's exact test), Q value = 3.2e-05

Table S333. Gene #71: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
17Q LOSS CNV	20	54	60
17Q LOSS WILD-TYPE	196	354	144

Figure S333. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_CNMF'

P value = 9.64e-07 (Fisher's exact test), Q value = 6e-04

Table S334. Gene #71: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
17Q LOSS CNV	26	46	67
17Q LOSS WILD-TYPE	208	346	188

Figure S334. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.69e-05 (Fisher's exact test), Q value = 0.015

Table S335. Gene #71: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
17Q LOSS CNV	50	30	59
17Q LOSS WILD-TYPE	312	254	176

Figure S335. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p loss' versus 'MRNA_CNMF'

P value = 0.000377 (Chi-square test), Q value = 0.17

Table S336. 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	124	36	23	95	72	20	103	40
18P LOSS CNV	27	5	4	13	30	5	14	9
18P LOSS WILD-TYPE	97	31	19	82	42	15	89	31

Figure S336. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'18p loss' versus 'CN_CNMF'

P value = 6.18e-10 (Chi-square test), Q value = 4.3e-07

Table S337. Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
18P LOSS CNV	28	57	24	57	9
18P LOSS WILD-TYPE	319	165	48	166	40

Figure S337. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

P value = 3.32e-06 (Chi-square test), Q value = 0.002

Table S338. Gene #72: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
18P LOSS CNV	13	14	30	36	3	11
18P LOSS WILD-TYPE	88	125	63	101	37	86

Figure S338. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 6.11e-13 (Chi-square test), Q value = 4.5e-10

Table S339. Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
18Q LOSS CNV	24	58	26	61	8
18Q LOSS WILD-TYPE	323	164	46	162	41

Figure S339. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 7.01e-08 (Chi-square test), Q value = 4.6e-05

Table S340. Gene #73: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
18Q LOSS CNV	21	15	33	36	2	7
18Q LOSS WILD-TYPE	80	124	60	101	38	90

Figure S340. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p loss' versus 'MRNA_CNMF'

P value = 1.65e-05 (Chi-square test), Q value = 0.0093

Table S341. 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	124	36	23	95	72	20	103	40
19P LOSS CNV	17	4	0	5	15	1	1	0
19P LOSS WILD-TYPE	107	32	23	90	57	19	102	40

Figure S341. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'19p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.000461 (Fisher's exact test), Q value = 0.2

Table S342. Gene #74: '19p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	125	248
19P LOSS CNV	3	8	32
19P LOSS WILD-TYPE	137	117	216

Figure S342. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

P value = 7.77e-13 (Chi-square test), Q value = 5.7e-10

Table S343. Gene #74: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
19P LOSS CNV	1	38	2	19	7
19P LOSS WILD-TYPE	346	184	70	204	42

Figure S343. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

P value = 1.43e-08 (Chi-square test), Q value = 9.7e-06

Table S344. Gene #74: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
19P LOSS CNV	8	0	7	23	0	0
19P LOSS WILD-TYPE	93	139	86	114	40	97

Figure S344. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p loss' versus 'MRNASEQ_CNMF'

P value = 0.000554 (Fisher's exact test), Q value = 0.24

Table S345. Gene #74: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
19P LOSS CNV	26	2	37
19P LOSS WILD-TYPE	208	146	409

Figure S345. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000512 (Fisher's exact test), Q value = 0.22

Table S346. Gene #74: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
19P LOSS CNV	5	42	18
19P LOSS WILD-TYPE	211	366	186

Figure S346. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_CNMF'

P value = 0.000287 (Fisher's exact test), Q value = 0.13

Table S347. Gene #74: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
19P LOSS CNV	5	33	27
19P LOSS WILD-TYPE	229	359	228

Figure S347. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q loss' versus 'MRNA_CNMF'

P value = 7.41e-05 (Chi-square test), Q value = 0.039

Table S348. 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	124	36	23	95	72	20	103	40
19Q LOSS CNV	14	3	0	3	13	1	1	0
19Q LOSS WILD-TYPE	110	33	23	92	59	19	102	40

Figure S348. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'19q loss' versus 'CN_CNMF'

P value = 3.66e-10 (Chi-square test), Q value = 2.6e-07

Table S349. Gene #75: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
19Q LOSS CNV	2	30	0	15	6
19Q LOSS WILD-TYPE	345	192	72	208	43

Figure S349. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

P value = 1.62e-05 (Chi-square test), Q value = 0.0091

Table S350. Gene #75: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
19Q LOSS CNV	7	0	6	16	0	0
19Q LOSS WILD-TYPE	94	139	87	121	40	97

Figure S350. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.9e-06 (Fisher's exact test), Q value = 0.0051

Table S351. Gene #75: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
19Q LOSS CNV	1	36	14
19Q LOSS WILD-TYPE	215	372	190

Figure S351. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00046 (Fisher's exact test), Q value = 0.2

Table S352. Gene #75: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
19Q LOSS CNV	34	7	10
19Q LOSS WILD-TYPE	328	277	225

Figure S352. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p loss' versus 'CN_CNMF'

P value = 1.42e-06 (Chi-square test), Q value = 0.00088

Table S353. Gene #76: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
20P LOSS CNV	3	20	2	21	7
20P LOSS WILD-TYPE	344	202	70	202	42

Figure S353. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

'20p loss' versus 'METHLYATION_CNMF'

P value = 2.42e-05 (Chi-square test), Q value = 0.013

Table S354. Gene #76: '20p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
20P LOSS CNV	15	1	5	9	1	1
20P LOSS WILD-TYPE	86	138	88	128	39	96

Figure S354. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000252 (Fisher's exact test), Q value = 0.12

Table S355. Gene #76: '20p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
20P LOSS CNV	3	23	21
20P LOSS WILD-TYPE	213	385	183

Figure S355. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p loss' versus 'MIRSEQ_CNMF'

P value = 0.000176 (Fisher's exact test), Q value = 0.086

Table S356. Gene #76: '20p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
20P LOSS CNV	7	15	28
20P LOSS WILD-TYPE	227	377	227

Figure S356. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000223 (Fisher's exact test), Q value = 0.11

Table S357. Gene #76: '20p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
20P LOSS CNV	22	5	23
20P LOSS WILD-TYPE	340	279	212

Figure S357. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q loss' versus 'CN_CNMF'

P value = 6.97e-05 (Chi-square test), Q value = 0.036

Table S358. Gene #77: '20q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
20Q LOSS CNV	1	7	2	14	5
20Q LOSS WILD-TYPE	346	215	70	209	44

Figure S358. Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #3: 'CN_CNMF'

'20q loss' versus 'METHLYATION_CNMF'

P value = 2.82e-06 (Chi-square test), Q value = 0.0017

Table S359. Gene #77: '20q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
20Q LOSS CNV	11	0	1	3	0	1
20Q LOSS WILD-TYPE	90	139	92	134	40	96

Figure S359. Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00032 (Fisher's exact test), Q value = 0.15

Table S360. Gene #77: '20q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
20Q LOSS CNV	1	9	14
20Q LOSS WILD-TYPE	215	399	190

Figure S360. Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q loss' versus 'MIRSEQ_CNMF'

P value = 0.000443 (Fisher's exact test), Q value = 0.2

Table S361. Gene #77: '20q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
20Q LOSS CNV	3	7	18
20Q LOSS WILD-TYPE	231	385	237

Figure S361. Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.3e-05 (Fisher's exact test), Q value = 0.018

Table S362. Gene #77: '20q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
20Q LOSS CNV	8	2	18
20Q LOSS WILD-TYPE	354	282	217

Figure S362. Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'21q loss' versus 'CN_CNMF'

P value = 1.67e-06 (Chi-square test), Q value = 0.001

Table S363. Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
21Q LOSS CNV	9	31	9	28	9
21Q LOSS WILD-TYPE	338	191	63	195	40

Figure S363. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'MRNA_CNMF'

P value = 4.25e-05 (Chi-square test), Q value = 0.023

Table S364. 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	124	36	23	95	72	20	103	40
22Q LOSS CNV	63	17	7	17	19	5	37	13
22Q LOSS WILD-TYPE	61	19	16	78	53	15	66	27

Figure S364. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'22q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1.42e-07 (Fisher's exact test), Q value = 9.2e-05

Table S365. Gene #79: '22q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	125	248
22Q LOSS CNV	52	19	107
22Q LOSS WILD-TYPE	88	106	141

Figure S365. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 2.97e-06 (Chi-square test), Q value = 0.0018

Table S366. Gene #79: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
22Q LOSS CNV	90	93	34	64	25
22Q LOSS WILD-TYPE	257	129	38	159	24

Figure S366. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 5.32e-07 (Chi-square test), Q value = 0.00034

Table S367. Gene #79: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
22Q LOSS CNV	26	46	38	67	8	15
22Q LOSS WILD-TYPE	75	93	55	70	32	82

Figure S367. 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 = 0.21

Table S368. 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 S368. 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 = 0.0092

Table S369. 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 S369. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 2.18e-10 (Fisher's exact test), Q value = 1.5e-07

Table S370. Gene #79: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
22Q LOSS CNV	45	40	193
22Q LOSS WILD-TYPE	189	108	253

Figure S370. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.62e-11 (Fisher's exact test), Q value = 1.9e-08

Table S371. Gene #79: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
22Q LOSS CNV	74	173	31
22Q LOSS WILD-TYPE	142	235	173

Figure S371. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CNMF'

P value = 1.57e-08 (Fisher's exact test), Q value = 1.1e-05

Table S372. Gene #79: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
22Q LOSS CNV	68	170	55
22Q LOSS WILD-TYPE	166	222	200

Figure S372. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000171 (Fisher's exact test), Q value = 0.084

Table S373. Gene #79: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
22Q LOSS CNV	137	103	53
22Q LOSS WILD-TYPE	225	181	182

Figure S373. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Xq loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000357 (Fisher's exact test), Q value = 0.16

Table S374. Gene #80: 'Xq loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
XQ LOSS CNV	16	1	13
XQ LOSS WILD-TYPE	346	283	222

Figure S374. Get High-res Image Gene #80: 'Xq loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

Methods & Data

Input

Mutation data file = broad_values_by_arm.mutsig.cluster.txt
Molecular subtypes file = BRCA-TP.transferedmergedcluster.txt
Number of patients = 913
Number of significantly arm-level cnvs = 80
Number of molecular subtypes = 10
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

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

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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