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

Breast Invasive Carcinoma (Primary solid tumor)

16 April 2014 | analyses__2014_04_16

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 (2014): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1Q52N72

Overview

Introduction

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

Summary

Testing the association between copy number variation 80 arm-level events and 12 molecular subtypes across 1033 patients, 552 significant findings detected with P value < 0.05 and Q value < 0.25.

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

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 80 arm-level events and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 552 significant findings detected.


		Clinical Features	MRNA CNMF	MRNA CHIERARCHICAL	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nCNV (%)	nWild-Type	Chi-square test	Fisher's exact test	Chi-square test	Chi-square test	Fisher's exact test	Fisher's exact test	Chi-square test	Fisher's exact test	Chi-square test	Fisher's exact test	Fisher's exact test	Fisher's exact test
1p gain	197 (19%)	836	3.72e-09 (2.59e-06)	3.98e-09 (2.77e-06)	3.05e-20 (2.76e-17)	1.64e-10 (1.21e-07)	4.93e-06 (0.00279)	6.26e-05 (0.0308)	1.98e-19 (1.78e-16)	3.3e-15 (2.8e-12)	3.01e-10 (2.19e-07)	1.58e-15 (1.35e-12)	9.91e-11 (7.4e-08)	7.85e-10 (5.61e-07)
2p gain	117 (11%)	916	2.64e-15 (2.25e-12)	3.98e-15 (3.38e-12)	2.99e-19 (2.67e-16)	3.39e-12 (2.65e-09)	6.33e-11 (4.75e-08)	1.09e-10 (8.11e-08)	1.25e-28 (1.17e-25)	4.53e-28 (4.25e-25)	3.46e-19 (3.09e-16)	6.65e-20 (5.98e-17)	1.03e-22 (9.49e-20)	2.58e-15 (2.2e-12)
2q gain	71 (7%)	962	1.08e-07 (6.94e-05)	5.08e-08 (3.34e-05)	2.47e-09 (1.74e-06)	2.23e-06 (0.0013)	5.77e-07 (0.000351)	7.71e-06 (0.00424)	2.2e-14 (1.83e-11)	6.43e-14 (5.28e-11)	5.52e-08 (3.62e-05)	5.44e-11 (4.1e-08)	2.88e-12 (2.26e-09)	3.64e-09 (2.54e-06)
10p gain	203 (20%)	830	6.7e-10 (4.81e-07)	2.31e-08 (1.55e-05)	3.39e-29 (3.19e-26)	5.96e-15 (5.04e-12)	1.29e-05 (0.00689)	1.25e-05 (0.00673)	5.89e-19 (5.25e-16)	9.47e-18 (8.31e-15)	1.33e-13 (1.08e-10)	8.23e-18 (7.24e-15)	6.22e-12 (4.84e-09)	4.5e-12 (3.51e-09)
21q gain	188 (18%)	845	5.21e-10 (3.75e-07)	6.2e-07 (0.000377)	1.58e-14 (1.31e-11)	3.17e-09 (2.23e-06)	0.000202 (0.0891)	7.86e-05 (0.0377)	1.37e-16 (1.19e-13)	1.47e-17 (1.29e-14)	3.4e-07 (0.00021)	4e-14 (3.32e-11)	6.23e-09 (4.3e-06)	1.47e-07 (9.33e-05)
4p loss	337 (33%)	696	1.03e-14 (8.63e-12)	4.87e-14 (4.02e-11)	8.12e-36 (7.69e-33)	5.65e-21 (5.13e-18)	2.37e-07 (0.000148)	3.95e-07 (0.000243)	6.39e-29 (6e-26)	2.1e-27 (1.97e-24)	9.59e-23 (8.81e-20)	6.08e-26 (5.65e-23)	4.24e-20 (3.82e-17)	6.17e-18 (5.43e-15)
4q loss	299 (29%)	734	3.43e-08 (2.29e-05)	1.93e-08 (1.3e-05)	9.61e-27 (8.97e-24)	1.85e-12 (1.47e-09)	0.000127 (0.0588)	0.000354 (0.149)	1.49e-18 (1.32e-15)	3.46e-18 (3.06e-15)	1.54e-12 (1.22e-09)	4.78e-17 (4.17e-14)	5.08e-14 (4.19e-11)	1.82e-11 (1.39e-08)
5p loss	133 (13%)	900	7.17e-17 (6.26e-14)	5.82e-12 (4.54e-09)	1.81e-38 (1.72e-35)	1.08e-21 (9.81e-19)	1.51e-07 (9.53e-05)	1.91e-09 (1.35e-06)	1.12e-39 (1.07e-36)	2.66e-27 (2.49e-24)	3.76e-19 (3.36e-16)	4.21e-27 (3.93e-24)	1.31e-22 (1.2e-19)	1.91e-19 (1.71e-16)
5q loss	219 (21%)	814	1.25e-26 (1.17e-23)	3.12e-21 (2.83e-18)	4.19e-78 (4.02e-75)	5.72e-45 (5.46e-42)	3e-13 (2.42e-10)	5.49e-14 (4.52e-11)	1.09e-63 (1.05e-60)	7.18e-51 (6.87e-48)	4.45e-47 (4.25e-44)	5.35e-51 (5.12e-48)	4.72e-41 (4.5e-38)	2.68e-36 (2.54e-33)
9q loss	278 (27%)	755	0.000199 (0.0884)	3.55e-06 (0.00204)	7.71e-31 (7.25e-28)	6.57e-16 (5.64e-13)	6.52e-06 (0.00362)	0.000581 (0.238)	1.01e-14 (8.45e-12)	7.51e-13 (6.01e-10)	1.39e-13 (1.12e-10)	6.46e-16 (5.55e-13)	4.15e-11 (3.14e-08)	6.17e-10 (4.44e-07)
12q loss	124 (12%)	909	7.12e-10 (5.11e-07)	4.76e-09 (3.29e-06)	4.46e-20 (4.02e-17)	1.34e-21 (1.22e-18)	0.000246 (0.107)	2.75e-06 (0.0016)	2.7e-22 (2.47e-19)	1.06e-17 (9.31e-15)	3.1e-14 (2.57e-11)	1.21e-14 (1.01e-11)	1.05e-12 (8.4e-10)	9.06e-13 (7.24e-10)
14q loss	251 (24%)	782	1.2e-14 (1.01e-11)	5.9e-10 (4.25e-07)	9.74e-38 (9.25e-35)	6.72e-22 (6.13e-19)	5.79e-06 (0.00325)	4.45e-06 (0.00253)	3.68e-32 (3.48e-29)	2.2e-24 (2.03e-21)	1.23e-24 (1.14e-21)	1.92e-26 (1.78e-23)	8.33e-19 (7.42e-16)	5.57e-18 (4.91e-15)
16q loss	575 (56%)	458	3.55e-09 (2.48e-06)	9.94e-11 (7.41e-08)	3.47e-09 (2.43e-06)	9.04e-10 (6.45e-07)	5.4e-05 (0.027)	1.62e-07 (0.000102)	5.85e-21 (5.3e-18)	7.33e-17 (6.39e-14)	1.81e-11 (1.39e-08)	7.72e-12 (5.99e-09)	1.5e-07 (9.48e-05)	1.3e-07 (8.25e-05)
17q loss	264 (26%)	769	2.5e-12 (1.97e-09)	1.35e-10 (9.97e-08)	3.1e-26 (2.88e-23)	1.08e-16 (9.4e-14)	8.25e-11 (6.18e-08)	2.07e-11 (1.58e-08)	4.55e-20 (4.1e-17)	3.66e-18 (3.23e-15)	1.04e-14 (8.71e-12)	4.73e-16 (4.08e-13)	2.33e-08 (1.56e-05)	4.16e-10 (3.01e-07)
6p gain	202 (20%)	831	5.32e-07 (0.000325)	1.05e-05 (0.00566)	2.38e-32 (2.25e-29)	7.33e-16 (6.27e-13)	0.000177 (0.0795)	0.0113 (1.00)	7.02e-21 (6.35e-18)	9.73e-17 (8.46e-14)	2.07e-16 (1.79e-13)	1.56e-18 (1.38e-15)	5.54e-16 (4.77e-13)	5.4e-13 (4.34e-10)
6q gain	147 (14%)	886	1.58e-07 (9.92e-05)	3.32e-05 (0.0169)	2.61e-31 (2.46e-28)	7.57e-12 (5.88e-09)	1.32e-05 (0.00705)	0.00735 (1.00)	1.42e-16 (1.23e-13)	1.7e-11 (1.3e-08)	4.46e-15 (3.78e-12)	1.21e-14 (1.01e-11)	9.03e-14 (7.38e-11)	1.69e-11 (1.3e-08)
18p gain	170 (16%)	863	1.1e-06 (0.000655)	6.37e-08 (4.16e-05)	4.62e-18 (4.08e-15)	1.87e-14 (1.56e-11)	0.00147 (0.544)	4.82e-05 (0.0243)	1.71e-16 (1.48e-13)	1.23e-18 (1.1e-15)	3.37e-12 (2.64e-09)	1.43e-13 (1.16e-10)	6.33e-11 (4.75e-08)	5.8e-14 (4.77e-11)
22q gain	94 (9%)	939	1.66e-05 (0.0088)	1.76e-06 (0.00104)	9.18e-12 (7.09e-09)	0.000256 (0.11)	8.26e-06 (0.00451)	0.00376 (1.00)	1.92e-10 (1.42e-07)	7.66e-15 (6.45e-12)	2.18e-06 (0.00128)	3.42e-10 (2.48e-07)	1.55e-06 (0.000918)	8.55e-08 (5.52e-05)
3p loss	178 (17%)	855	4.18e-06 (0.00238)	6.71e-05 (0.0328)	8.92e-18 (7.83e-15)	6.3e-09 (4.33e-06)	0.000703 (0.287)	5.68e-05 (0.0283)	8.08e-12 (6.27e-09)	8.7e-08 (5.61e-05)	8.54e-07 (0.000516)	8.46e-07 (0.000512)	1.24e-07 (7.9e-05)	0.000138 (0.0632)
9p gain	134 (13%)	899	2.15e-10 (1.58e-07)	4.73e-08 (3.11e-05)	4.39e-16 (3.79e-13)	4.89e-05 (0.0246)	0.00513 (1.00)	1.69e-06 (0.001)	1.32e-13 (1.07e-10)	8.87e-09 (6.07e-06)	7.47e-05 (0.0358)	5.1e-06 (0.00287)	0.00276 (0.914)	0.00034 (0.144)
18q gain	147 (14%)	886	7.26e-05 (0.0351)	0.000119 (0.0551)	7.65e-14 (6.28e-11)	7.94e-05 (0.0379)	0.13 (1.00)	0.0416 (1.00)	9.69e-11 (7.25e-08)	1.02e-09 (7.21e-07)	0.000151 (0.0686)	9.12e-06 (0.00495)	0.000124 (0.0573)	1.94e-05 (0.0102)
9p loss	307 (30%)	726	1.79e-05 (0.00942)	6.23e-05 (0.0306)	1.98e-41 (1.88e-38)	6.78e-16 (5.81e-13)	0.00266 (0.892)	0.385 (1.00)	1.46e-16 (1.26e-13)	1.19e-11 (9.14e-09)	2.35e-11 (1.79e-08)	9.74e-10 (6.93e-07)	1.64e-09 (1.15e-06)	1.67e-05 (0.00883)
13q loss	423 (41%)	610	5.59e-05 (0.0279)	6.32e-06 (0.00352)	1.26e-24 (1.16e-21)	7.26e-08 (4.71e-05)	0.294 (1.00)	0.189 (1.00)	1.02e-10 (7.61e-08)	4.14e-11 (3.13e-08)	8.33e-08 (5.39e-05)	4.24e-08 (2.81e-05)	5.92e-08 (3.87e-05)	4.86e-06 (0.00275)
15q loss	308 (30%)	725	1.95e-05 (0.0102)	1.14e-05 (0.00613)	1.61e-31 (1.52e-28)	9.84e-14 (8.04e-11)	0.00426 (1.00)	0.00195 (0.685)	1.99e-16 (1.72e-13)	1.43e-13 (1.16e-10)	5.19e-14 (4.28e-11)	1.39e-17 (1.22e-14)	2.66e-12 (2.09e-09)	9.82e-10 (6.98e-07)
17p loss	553 (54%)	480	1.51e-09 (1.07e-06)	0.0254 (1.00)	1.58e-23 (1.45e-20)	4.63e-08 (3.05e-05)	2e-07 (0.000125)	0.000123 (0.0569)	1.13e-15 (9.7e-13)	2.28e-05 (0.0118)	8.97e-09 (6.12e-06)	1.55e-07 (9.77e-05)	6.52e-06 (0.00362)	0.00275 (0.914)
19p loss	186 (18%)	847	2.62e-05 (0.0136)	2.68e-05 (0.0138)	5.93e-25 (5.49e-22)	4.89e-13 (3.94e-10)	0.0231 (1.00)	0.0273 (1.00)	2.56e-11 (1.94e-08)	2.08e-10 (1.53e-07)	7.66e-14 (6.28e-11)	1.33e-07 (8.43e-05)	1.87e-10 (1.38e-07)	3.52e-06 (0.00203)
3q gain	205 (20%)	828	0.00105 (0.407)	6.06e-06 (0.00339)	9.5e-19 (8.46e-16)	1.66e-11 (1.28e-08)	0.018 (1.00)	0.135 (1.00)	1.02e-13 (8.34e-11)	4.67e-13 (3.76e-10)	7.04e-12 (5.48e-09)	5.63e-11 (4.24e-08)	3.97e-10 (2.87e-07)	7.85e-10 (5.61e-07)
8q gain	511 (49%)	522	2.72e-05 (0.0139)	0.00279 (0.914)	2.4e-25 (2.23e-22)	6.91e-13 (5.54e-10)	0.14 (1.00)	0.501 (1.00)	6.53e-15 (5.51e-12)	1.7e-10 (1.25e-07)	6.63e-09 (4.55e-06)	1.5e-12 (1.19e-09)	8.64e-12 (6.69e-09)	1.15e-08 (7.87e-06)
20q gain	434 (42%)	599	7.43e-05 (0.0358)	0.0074 (1.00)	1.81e-37 (1.72e-34)	4.37e-13 (3.52e-10)	0.0468 (1.00)	0.424 (1.00)	2.81e-10 (2.05e-07)	2.08e-07 (0.00013)	5.55e-09 (3.83e-06)	7.08e-08 (4.6e-05)	9.9e-06 (0.00535)	7.57e-06 (0.00417)
12p loss	145 (14%)	888	0.00164 (0.598)	0.000298 (0.128)	1.38e-08 (9.35e-06)	5.11e-08 (3.36e-05)	0.0171 (1.00)	0.0114 (1.00)	2.18e-08 (1.46e-05)	3.09e-08 (2.06e-05)	3.19e-07 (0.000198)	6.36e-08 (4.15e-05)	5.97e-06 (0.00335)	8.87e-05 (0.0421)
19q loss	155 (15%)	878	0.00372 (1.00)	0.000338 (0.143)	1.86e-22 (1.7e-19)	2.01e-08 (1.35e-05)	0.108 (1.00)	0.108 (1.00)	5.08e-10 (3.67e-07)	2.45e-10 (1.79e-07)	3.03e-07 (0.000188)	2.94e-05 (0.015)	4.21e-09 (2.92e-06)	0.000197 (0.0876)
12p gain	224 (22%)	809	0.00222 (0.76)	0.000545 (0.225)	8.84e-22 (8.06e-19)	1.31e-08 (8.92e-06)	0.143 (1.00)	0.0276 (1.00)	2.43e-07 (0.000151)	1.42e-09 (1e-06)	4.48e-08 (2.96e-05)	0.000153 (0.0693)	0.000151 (0.0686)	0.00188 (0.67)
16p gain	454 (44%)	579	0.000147 (0.0672)	0.00292 (0.936)	1.44e-09 (1.02e-06)	3.12e-06 (0.00181)	0.00799 (1.00)	0.00689 (1.00)	3.35e-12 (2.63e-09)	8.99e-07 (0.000542)	0.000517 (0.215)	0.00154 (0.565)	3.62e-05 (0.0183)	2.7e-05 (0.0139)
7p loss	108 (10%)	925	0.0427 (1.00)	0.00135 (0.508)	1.39e-12 (1.11e-09)	0.000128 (0.0589)	0.0891 (1.00)	0.215 (1.00)	2.84e-05 (0.0145)	8.56e-06 (0.00466)	8.01e-05 (0.0382)	6.91e-06 (0.00383)	2.82e-05 (0.0144)	0.000277 (0.119)
8p loss	375 (36%)	658	7.41e-06 (0.0041)	0.0118 (1.00)	1.76e-18 (1.56e-15)	1.09e-06 (0.000653)	0.112 (1.00)	0.213 (1.00)	2.43e-12 (1.92e-09)	8.87e-06 (0.00482)	5.11e-07 (0.000313)	9.09e-07 (0.000546)	5.03e-06 (0.00284)	0.00151 (0.558)
10q loss	224 (22%)	809	0.00356 (1.00)	0.00137 (0.515)	1.04e-13 (8.47e-11)	1.27e-12 (1.01e-09)	0.00113 (0.434)	0.0225 (1.00)	6.12e-11 (4.6e-08)	1.73e-08 (1.17e-05)	2.73e-06 (0.00159)	1.06e-07 (6.81e-05)	6.93e-05 (0.0338)	0.000603 (0.247)
11p loss	263 (25%)	770	0.0126 (1.00)	0.0672 (1.00)	3.38e-20 (3.05e-17)	3.37e-09 (2.36e-06)	0.011 (1.00)	0.00878 (1.00)	9.94e-11 (7.41e-08)	3.88e-06 (0.00223)	1.35e-05 (0.00718)	1.32e-05 (0.00705)	2.65e-05 (0.0137)	0.000178 (0.0801)
20p loss	87 (8%)	946	0.00392 (1.00)	0.000715 (0.29)	1.95e-12 (1.54e-09)	2.12e-11 (1.62e-08)	0.107 (1.00)	0.297 (1.00)	1.29e-11 (9.96e-09)	1.43e-10 (1.06e-07)	7.31e-09 (5.01e-06)	5.22e-07 (0.000319)	1.43e-07 (9.08e-05)	1.59e-08 (1.08e-05)
20q loss	51 (5%)	982	0.00797 (1.00)	0.0068 (1.00)	6.5e-08 (4.23e-05)	3.07e-12 (2.41e-09)	0.125 (1.00)	0.0774 (1.00)	2.92e-10 (2.12e-07)	3.44e-08 (2.29e-05)	1.83e-06 (0.00108)	1.15e-07 (7.36e-05)	1.44e-06 (0.000856)	1.21e-08 (8.25e-06)
11q gain	91 (9%)	942	0.396 (1.00)	0.829 (1.00)	2.81e-08 (1.88e-05)	0.00209 (0.724)	0.959 (1.00)	0.717 (1.00)	0.000237 (0.103)	5.91e-05 (0.0293)	0.000254 (0.11)	2.6e-06 (0.00152)	8.04e-06 (0.0044)	3.68e-05 (0.0186)
17q gain	214 (21%)	819	2.74e-08 (1.84e-05)	1.89e-05 (0.00991)	7.01e-26 (6.5e-23)	6.52e-07 (0.000396)	0.532 (1.00)	0.0121 (1.00)	6.33e-15 (5.35e-12)	1.78e-08 (1.2e-05)	7.42e-08 (4.81e-05)	0.00288 (0.932)	0.291 (1.00)	0.00108 (0.42)
20p gain	399 (39%)	634	5.32e-05 (0.0266)	0.00701 (1.00)	8.11e-32 (7.66e-29)	3.61e-08 (2.4e-05)	0.00379 (1.00)	0.0392 (1.00)	9e-07 (0.000542)	1.04e-05 (0.00562)	3.99e-08 (2.65e-05)	1.32e-06 (0.000787)	0.00146 (0.543)	0.00101 (0.397)
2p loss	175 (17%)	858	0.012 (1.00)	6.35e-05 (0.0311)	2.27e-12 (1.79e-09)	9.51e-06 (0.00515)	0.00102 (0.4)	0.0015 (0.556)	3.12e-06 (0.00181)	4.35e-11 (3.29e-08)	0.00112 (0.431)	5e-05 (0.0251)	0.00578 (1.00)	0.000312 (0.133)
7q gain	252 (24%)	781	0.00134 (0.508)	0.00909 (1.00)	2.78e-11 (2.11e-08)	0.000214 (0.094)	0.0371 (1.00)	0.0689 (1.00)	3.2e-06 (0.00185)	4.3e-07 (0.000264)	6.95e-05 (0.0338)	0.000128 (0.0588)	0.00904 (1.00)	0.0012 (0.455)
xq gain	133 (13%)	900	0.000972 (0.384)	8.96e-05 (0.0425)	6.13e-08 (4.01e-05)	0.00642 (1.00)	0.689 (1.00)	0.0445 (1.00)	4.15e-06 (0.00237)	4.18e-06 (0.00238)	8.21e-07 (0.000498)	2.2e-06 (0.00129)	0.00142 (0.528)	0.00976 (1.00)
1p loss	234 (23%)	799	0.00157 (0.575)	4.42e-06 (0.00251)	1.44e-21 (1.31e-18)	2.02e-07 (0.000126)	0.527 (1.00)	0.482 (1.00)	2.2e-06 (0.00129)	9.88e-14 (8.06e-11)	0.00748 (1.00)	9.05e-05 (0.0428)	0.312 (1.00)	0.182 (1.00)
6q loss	260 (25%)	773	0.000811 (0.326)	0.000235 (0.103)	2.52e-19 (2.26e-16)	7e-05 (0.034)	0.276 (1.00)	0.125 (1.00)	1.17e-07 (7.5e-05)	3.34e-05 (0.017)	0.0114 (1.00)	5.79e-05 (0.0288)	0.0127 (1.00)	0.0135 (1.00)
18q loss	310 (30%)	723	0.000199 (0.0884)	0.309 (1.00)	4.42e-14 (3.66e-11)	1.65e-07 (0.000103)	0.0379 (1.00)	0.29 (1.00)	2.69e-09 (1.89e-06)	0.0257 (1.00)	9.17e-05 (0.0433)	0.00157 (0.575)	8.05e-05 (0.0383)	0.0654 (1.00)
5q gain	200 (19%)	833	0.0123 (1.00)	0.0175 (1.00)	4.07e-24 (3.76e-21)	0.000566 (0.233)	0.00177 (0.634)	0.00175 (0.629)	0.000768 (0.311)	1.3e-05 (0.00696)	0.00772 (1.00)	0.00101 (0.395)	0.000494 (0.206)	0.000477 (0.2)
11q loss	350 (34%)	683	0.000165 (0.0744)	0.178 (1.00)	7.64e-23 (7.03e-20)	6.62e-09 (4.55e-06)	0.738 (1.00)	0.983 (1.00)	8.26e-15 (6.94e-12)	0.0042 (1.00)	0.064 (1.00)	0.000103 (0.0482)	0.105 (1.00)	0.0617 (1.00)
18p loss	309 (30%)	724	0.000251 (0.109)	0.402 (1.00)	8.97e-13 (7.18e-10)	1.07e-06 (0.000643)	0.217 (1.00)	0.777 (1.00)	1.41e-11 (1.09e-08)	0.0261 (1.00)	6.01e-05 (0.0296)	0.0192 (1.00)	0.00276 (0.914)	0.131 (1.00)
xq loss	173 (17%)	860	0.139 (1.00)	0.0319 (1.00)	6.27e-15 (5.3e-12)	3.03e-07 (0.000188)	0.0366 (1.00)	0.0247 (1.00)	3.52e-06 (0.00203)	3.89e-06 (0.00223)	0.000209 (0.092)	0.00188 (0.67)	0.0072 (1.00)	0.232 (1.00)
3p gain	136 (13%)	897	0.0949 (1.00)	0.00109 (0.421)	2.89e-11 (2.19e-08)	2.48e-05 (0.0129)	0.43 (1.00)	0.213 (1.00)	0.000913 (0.364)	3.36e-07 (0.000208)	0.00258 (0.871)	0.000143 (0.0653)	0.00276 (0.914)	0.0085 (1.00)
4p gain	75 (7%)	958	7e-05 (0.034)	0.00394 (1.00)	1.64e-15 (1.4e-12)	1.39e-05 (0.00741)	0.485 (1.00)	0.19 (1.00)	5.43e-07 (0.000331)	0.0041 (1.00)	0.00685 (1.00)	0.012 (1.00)	0.329 (1.00)	0.232 (1.00)
4q gain	71 (7%)	962	1.74e-06 (0.00103)	0.00254 (0.861)	4.94e-15 (4.19e-12)	0.000299 (0.128)	0.109 (1.00)	0.021 (1.00)	4.32e-07 (0.000265)	0.00491 (1.00)	0.0299 (1.00)	0.0168 (1.00)	0.23 (1.00)	0.331 (1.00)
10q gain	117 (11%)	916	0.0436 (1.00)	0.0201 (1.00)	5.5e-09 (3.8e-06)	0.0222 (1.00)	0.0311 (1.00)	0.0289 (1.00)	0.00663 (1.00)	0.000181 (0.081)	0.0145 (1.00)	0.000111 (0.052)	0.000215 (0.0943)	0.00461 (1.00)
11p gain	134 (13%)	899	0.784 (1.00)	0.858 (1.00)	1.54e-07 (9.74e-05)	0.00425 (1.00)	0.978 (1.00)	0.462 (1.00)	0.000913 (0.364)	0.00165 (0.598)	0.0128 (1.00)	7.89e-06 (0.00433)	0.000187 (0.0834)	7.31e-05 (0.0353)
12q gain	188 (18%)	845	0.00283 (0.917)	0.00138 (0.515)	1.29e-22 (1.18e-19)	2.58e-10 (1.89e-07)	0.293 (1.00)	0.449 (1.00)	3.85e-06 (0.00221)	3.57e-10 (2.59e-07)	0.00106 (0.412)	0.00955 (1.00)	0.18 (1.00)	0.172 (1.00)
19p gain	173 (17%)	860	0.00197 (0.69)	0.00093 (0.368)	2.82e-10 (2.05e-07)	0.0357 (1.00)	0.00738 (1.00)	0.013 (1.00)	1.85e-05 (0.00971)	6.2e-06 (0.00346)	0.00352 (1.00)	0.000112 (0.0525)	0.00113 (0.434)	0.0143 (1.00)
19q gain	207 (20%)	826	0.00516 (1.00)	0.00279 (0.914)	1.16e-11 (8.97e-09)	0.0245 (1.00)	0.0135 (1.00)	0.0256 (1.00)	5.93e-05 (0.0293)	3.44e-05 (0.0174)	0.00201 (0.701)	0.000111 (0.052)	0.00389 (1.00)	0.0203 (1.00)
2q loss	199 (19%)	834	0.133 (1.00)	0.00166 (0.6)	6.54e-13 (5.25e-10)	1.98e-05 (0.0103)	0.000444 (0.186)	0.000711 (0.29)	0.000971 (0.384)	1.44e-06 (0.000858)	0.00785 (1.00)	0.00216 (0.742)	0.0061 (1.00)	0.00396 (1.00)
3q loss	99 (10%)	934	0.00263 (0.883)	0.00231 (0.79)	1.7e-08 (1.15e-05)	5.87e-05 (0.0291)	0.189 (1.00)	0.0266 (1.00)	1.17e-07 (7.5e-05)	0.000166 (0.0747)	0.0238 (1.00)	0.0112 (1.00)	0.00119 (0.453)	0.257 (1.00)
16p loss	164 (16%)	869	0.166 (1.00)	0.228 (1.00)	2.63e-05 (0.0136)	0.00177 (0.634)	0.0217 (1.00)	0.0522 (1.00)	0.000793 (0.32)	0.0178 (1.00)	0.000493 (0.205)	0.00231 (0.79)	0.00018 (0.0806)	0.000117 (0.0546)
1q gain	673 (65%)	360	0.00124 (0.47)	0.91 (1.00)	7.22e-10 (5.17e-07)	7.32e-05 (0.0353)	0.59 (1.00)	0.243 (1.00)	1.14e-10 (8.42e-08)	0.574 (1.00)	0.403 (1.00)	0.868 (1.00)	0.608 (1.00)	0.174 (1.00)
13q gain	91 (9%)	942	0.302 (1.00)	0.259 (1.00)	1.53e-05 (0.0081)	0.00696 (1.00)	0.0203 (1.00)	0.0953 (1.00)	0.00513 (1.00)	0.000568 (0.233)	0.00429 (1.00)	0.000303 (0.129)	0.0213 (1.00)	0.0426 (1.00)
6p loss	177 (17%)	856	0.0484 (1.00)	0.00301 (0.961)	4.12e-14 (3.41e-11)	0.0192 (1.00)	0.754 (1.00)	0.0798 (1.00)	9.2e-05 (0.0433)	0.000113 (0.0528)	0.0844 (1.00)	0.00564 (1.00)	0.0506 (1.00)	0.0932 (1.00)
22q loss	467 (45%)	566	0.0542 (1.00)	0.00276 (0.914)	4.74e-14 (3.92e-11)	1.59e-06 (0.000943)	0.0178 (1.00)	0.00112 (0.431)	0.0556 (1.00)	0.000375 (0.157)	0.0101 (1.00)	0.00214 (0.737)	0.499 (1.00)	0.247 (1.00)
7p gain	295 (29%)	738	0.00694 (1.00)	0.183 (1.00)	2.06e-10 (1.51e-07)	0.00171 (0.617)	0.584 (1.00)	0.267 (1.00)	0.00104 (0.405)	0.00035 (0.148)	0.0173 (1.00)	0.021 (1.00)	0.138 (1.00)	0.014 (1.00)
14q gain	139 (13%)	894	0.00193 (0.682)	0.101 (1.00)	4.07e-09 (2.83e-06)	0.00364 (1.00)	0.48 (1.00)	0.254 (1.00)	3.94e-06 (0.00226)	0.00191 (0.677)	0.0029 (0.932)	0.0229 (1.00)	0.0182 (1.00)	0.0111 (1.00)
1q loss	53 (5%)	980	0.0216 (1.00)	0.00502 (1.00)	0.000792 (0.32)	0.0129 (1.00)	0.34 (1.00)	0.468 (1.00)	0.000543 (0.225)	0.000253 (0.11)	0.00644 (1.00)	0.04 (1.00)	0.528 (1.00)	0.295 (1.00)
7q loss	116 (11%)	917	0.0448 (1.00)	0.0113 (1.00)	7.41e-06 (0.0041)	0.224 (1.00)	0.697 (1.00)	0.797 (1.00)	0.0197 (1.00)	0.000202 (0.0891)	0.0374 (1.00)	0.00161 (0.587)	0.00206 (0.716)	0.0135 (1.00)
10p loss	169 (16%)	864	0.28 (1.00)	0.0743 (1.00)	8.17e-06 (0.00447)	2.08e-05 (0.0108)	0.258 (1.00)	0.42 (1.00)	0.000885 (0.353)	0.00211 (0.73)	0.00776 (1.00)	0.00261 (0.879)	0.0329 (1.00)	0.185 (1.00)
21q loss	168 (16%)	865	0.0329 (1.00)	0.0528 (1.00)	1.27e-12 (1.01e-09)	0.0003 (0.128)	0.772 (1.00)	0.972 (1.00)	0.0141 (1.00)	0.0027 (0.901)	0.00479 (1.00)	0.0202 (1.00)	0.003 (0.96)	0.0431 (1.00)
5p gain	302 (29%)	731	0.0127 (1.00)	0.857 (1.00)	6.69e-18 (5.89e-15)	0.0601 (1.00)	0.936 (1.00)	0.294 (1.00)	0.124 (1.00)	0.292 (1.00)	0.00555 (1.00)	0.0183 (1.00)	0.104 (1.00)	0.0852 (1.00)
8p gain	282 (27%)	751	0.163 (1.00)	0.0702 (1.00)	8.97e-08 (5.77e-05)	0.00409 (1.00)	0.8 (1.00)	0.402 (1.00)	0.00316 (1.00)	0.000829 (0.333)	0.132 (1.00)	0.0693 (1.00)	0.00194 (0.684)	0.0214 (1.00)
9q gain	111 (11%)	922	0.164 (1.00)	0.161 (1.00)	1.49e-09 (1.06e-06)	0.427 (1.00)	0.944 (1.00)	0.182 (1.00)	0.00279 (0.914)	0.028 (1.00)	0.643 (1.00)	0.201 (1.00)	0.0973 (1.00)	0.0205 (1.00)
17p gain	105 (10%)	928	0.0424 (1.00)	0.184 (1.00)	5.43e-06 (0.00305)	0.037 (1.00)	0.675 (1.00)	0.347 (1.00)	0.000876 (0.35)	0.0995 (1.00)	0.00185 (0.659)	0.919 (1.00)	0.638 (1.00)	0.713 (1.00)
15q gain	85 (8%)	948	0.0863 (1.00)	0.309 (1.00)	0.00252 (0.856)	0.0616 (1.00)	0.444 (1.00)	0.238 (1.00)	0.0228 (1.00)	0.00483 (1.00)	0.0538 (1.00)	0.00137 (0.515)	0.278 (1.00)	0.25 (1.00)
16q gain	131 (13%)	902	0.411 (1.00)	0.108 (1.00)	0.0027 (0.901)	0.0163 (1.00)	0.327 (1.00)	0.324 (1.00)	0.193 (1.00)	0.0126 (1.00)	0.00525 (1.00)	0.0057 (1.00)	0.0196 (1.00)	0.00914 (1.00)
8q loss	87 (8%)	946	0.0175 (1.00)	0.209 (1.00)	0.00697 (1.00)	0.0679 (1.00)	0.751 (1.00)	0.318 (1.00)	0.388 (1.00)	0.493 (1.00)	0.3 (1.00)	0.299 (1.00)	0.245 (1.00)	0.521 (1.00)

'1p gain' versus 'MRNA_CNMF'

P value = 3.72e-09 (Chi-square test), Q value = 2.6e-06

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
1P GAIN MUTATED	2	3	17	40	7	18	6	5
1P GAIN WILD-TYPE	19	33	102	56	102	54	14	35

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

'1p gain' versus 'MRNA_CHIERARCHICAL'

P value = 3.98e-09 (Fisher's exact test), Q value = 2.8e-06

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
1P GAIN MUTATED	15	49	34
1P GAIN WILD-TYPE	107	76	232

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

'1p gain' versus 'CN_CNMF'

P value = 3.05e-20 (Chi-square test), Q value = 2.8e-17

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
1P GAIN MUTATED	42	38	7	100	10
1P GAIN WILD-TYPE	335	214	97	152	38

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

'1p gain' versus 'METHLYATION_CNMF'

P value = 1.64e-10 (Chi-square test), Q value = 1.2e-07

Table S4. Gene #1: '1p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	124	176	104	135	56	116
1P GAIN MUTATED	50	16	14	23	6	29
1P GAIN WILD-TYPE	74	160	90	112	50	87

Figure S4. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1p gain' versus 'RPPA_CNMF'

P value = 4.93e-06 (Fisher's exact test), Q value = 0.0028

Table S5. Gene #1: '1p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
1P GAIN MUTATED	49	18	13
1P GAIN WILD-TYPE	98	115	104

Figure S5. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'1p gain' versus 'RPPA_CHIERARCHICAL'

P value = 6.26e-05 (Fisher's exact test), Q value = 0.031

Table S6. Gene #1: '1p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	110	126
1P GAIN MUTATED	30	10	40
1P GAIN WILD-TYPE	131	100	86

Figure S6. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'1p gain' versus 'MRNASEQ_CNMF'

P value = 1.98e-19 (Chi-square test), Q value = 1.8e-16

Table S7. Gene #1: '1p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	190	95	257	169	260	48
1P GAIN MUTATED	80	13	23	41	32	5
1P GAIN WILD-TYPE	110	82	234	128	228	43

Figure S7. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.3e-15 (Fisher's exact test), Q value = 2.8e-12

Table S8. Gene #1: '1p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	339	433	247
1P GAIN MUTATED	40	61	93
1P GAIN WILD-TYPE	299	372	154

Figure S8. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p gain' versus 'MIRSEQ_CNMF'

P value = 3.01e-10 (Chi-square test), Q value = 2.2e-07

Table S9. Gene #1: '1p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	194	170	227	251	140	32
1P GAIN MUTATED	25	29	25	86	25	4
1P GAIN WILD-TYPE	169	141	202	165	115	28

Figure S9. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.58e-15 (Fisher's exact test), Q value = 1.4e-12

Table S10. Gene #1: '1p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	531	273	210
1P GAIN MUTATED	71	100	23
1P GAIN WILD-TYPE	460	173	187

Figure S10. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 9.91e-11 (Fisher's exact test), Q value = 7.4e-08

Table S11. Gene #1: '1p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	238	218
1P GAIN MUTATED	33	27	76
1P GAIN WILD-TYPE	215	211	142

Figure S11. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'1p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.85e-10 (Fisher's exact test), Q value = 5.6e-07

Table S12. Gene #1: '1p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	358	181
1P GAIN MUTATED	62	52	22
1P GAIN WILD-TYPE	103	306	159

Figure S12. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1q gain' versus 'CN_CNMF'

P value = 7.22e-10 (Chi-square test), Q value = 5.2e-07

Table S13. Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
1Q GAIN MUTATED	223	161	99	162	28
1Q GAIN WILD-TYPE	154	91	5	90	20

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

'1q gain' versus 'METHLYATION_CNMF'

P value = 7.32e-05 (Chi-square test), Q value = 0.035

Table S14. Gene #2: '1q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	124	176	104	135	56	116
1Q GAIN MUTATED	83	134	75	72	31	65
1Q GAIN WILD-TYPE	41	42	29	63	25	51

Figure S14. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1q gain' versus 'MRNASEQ_CNMF'

P value = 1.14e-10 (Chi-square test), Q value = 8.4e-08

Table S15. Gene #2: '1q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	190	95	257	169	260	48
1Q GAIN MUTATED	127	56	209	109	132	32
1Q GAIN WILD-TYPE	63	39	48	60	128	16

Figure S15. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2p gain' versus 'MRNA_CNMF'

P value = 2.64e-15 (Chi-square test), Q value = 2.2e-12

Table S16. Gene #3: '2p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
2P GAIN MUTATED	1	1	6	31	1	20	1	0
2P GAIN WILD-TYPE	20	35	113	65	108	52	19	40

Figure S16. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'2p gain' versus 'MRNA_CHIERARCHICAL'

P value = 3.98e-15 (Fisher's exact test), Q value = 3.4e-12

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
2P GAIN MUTATED	1	41	19
2P GAIN WILD-TYPE	121	84	247

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

'2p gain' versus 'CN_CNMF'

P value = 2.99e-19 (Chi-square test), Q value = 2.7e-16

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
2P GAIN MUTATED	12	23	7	69	6
2P GAIN WILD-TYPE	365	229	97	183	42

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

'2p gain' versus 'METHLYATION_CNMF'

P value = 3.39e-12 (Chi-square test), Q value = 2.7e-09

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	124	176	104	135	56	116
2P GAIN MUTATED	36	2	8	14	3	14
2P GAIN WILD-TYPE	88	174	96	121	53	102

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

'2p gain' versus 'RPPA_CNMF'

P value = 6.33e-11 (Fisher's exact test), Q value = 4.8e-08

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
2P GAIN MUTATED	40	2	9
2P GAIN WILD-TYPE	107	131	108

Figure S20. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'2p gain' versus 'RPPA_CHIERARCHICAL'

P value = 1.09e-10 (Fisher's exact test), Q value = 8.1e-08

Table S21. Gene #3: '2p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	110	126
2P GAIN MUTATED	9	4	38
2P GAIN WILD-TYPE	152	106	88

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

'2p gain' versus 'MRNASEQ_CNMF'

P value = 1.25e-28 (Chi-square test), Q value = 1.2e-25

Table S22. Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	190	95	257	169	260	48
2P GAIN MUTATED	59	2	6	37	11	0
2P GAIN WILD-TYPE	131	93	251	132	249	48

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

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.53e-28 (Fisher's exact test), Q value = 4.2e-25

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	339	433	247
2P GAIN MUTATED	4	35	76
2P GAIN WILD-TYPE	335	398	171

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

'2p gain' versus 'MIRSEQ_CNMF'

P value = 3.46e-19 (Chi-square test), Q value = 3.1e-16

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	194	170	227	251	140	32
2P GAIN MUTATED	13	5	4	66	19	4
2P GAIN WILD-TYPE	181	165	223	185	121	28

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

'2p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.65e-20 (Fisher's exact test), Q value = 6e-17

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	531	273	210
2P GAIN MUTATED	33	73	5
2P GAIN WILD-TYPE	498	200	205

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

'2p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.03e-22 (Fisher's exact test), Q value = 9.5e-20

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	238	218
2P GAIN MUTATED	11	4	65
2P GAIN WILD-TYPE	237	234	153

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

'2p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.58e-15 (Fisher's exact test), Q value = 2.2e-12

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	358	181
2P GAIN MUTATED	50	24	6
2P GAIN WILD-TYPE	115	334	175

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

'2q gain' versus 'MRNA_CNMF'

P value = 1.08e-07 (Chi-square test), Q value = 6.9e-05

Table S28. Gene #4: '2q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
2Q GAIN MUTATED	1	1	5	18	1	14	0	0
2Q GAIN WILD-TYPE	20	35	114	78	108	58	20	40

Figure S28. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'2q gain' versus 'MRNA_CHIERARCHICAL'

P value = 5.08e-08 (Fisher's exact test), Q value = 3.3e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
2Q GAIN MUTATED	1	25	14
2Q GAIN WILD-TYPE	121	100	252

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

'2q gain' versus 'CN_CNMF'

P value = 2.47e-09 (Chi-square test), Q value = 1.7e-06

Table S30. Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
2Q GAIN MUTATED	9	15	6	40	1
2Q GAIN WILD-TYPE	368	237	98	212	47

Figure S30. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

'2q gain' versus 'METHLYATION_CNMF'

P value = 2.23e-06 (Chi-square test), Q value = 0.0013

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	124	176	104	135	56	116
2Q GAIN MUTATED	20	2	7	6	1	5
2Q GAIN WILD-TYPE	104	174	97	129	55	111

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

'2q gain' versus 'RPPA_CNMF'

P value = 5.77e-07 (Fisher's exact test), Q value = 0.00035

Table S32. Gene #4: '2q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
2Q GAIN MUTATED	26	2	4
2Q GAIN WILD-TYPE	121	131	113

Figure S32. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'2q gain' versus 'RPPA_CHIERARCHICAL'

P value = 7.71e-06 (Fisher's exact test), Q value = 0.0042

Table S33. Gene #4: '2q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	110	126
2Q GAIN MUTATED	6	3	23
2Q GAIN WILD-TYPE	155	107	103

Figure S33. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'2q gain' versus 'MRNASEQ_CNMF'

P value = 2.2e-14 (Chi-square test), Q value = 1.8e-11

Table S34. Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	190	95	257	169	260	48
2Q GAIN MUTATED	34	2	5	23	6	0
2Q GAIN WILD-TYPE	156	93	252	146	254	48

Figure S34. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.43e-14 (Fisher's exact test), Q value = 5.3e-11

Table S35. Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	339	433	247
2Q GAIN MUTATED	4	22	44
2Q GAIN WILD-TYPE	335	411	203

Figure S35. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_CNMF'

P value = 5.52e-08 (Chi-square test), Q value = 3.6e-05

Table S36. Gene #4: '2q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	194	170	227	251	140	32
2Q GAIN MUTATED	9	4	3	36	11	3
2Q GAIN WILD-TYPE	185	166	224	215	129	29

Figure S36. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.44e-11 (Fisher's exact test), Q value = 4.1e-08

Table S37. Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	531	273	210
2Q GAIN MUTATED	22	42	2
2Q GAIN WILD-TYPE	509	231	208

Figure S37. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.88e-12 (Fisher's exact test), Q value = 2.3e-09

Table S38. Gene #4: '2q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	238	218
2Q GAIN MUTATED	7	4	40
2Q GAIN WILD-TYPE	241	234	178

Figure S38. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'2q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.64e-09 (Fisher's exact test), Q value = 2.5e-06

Table S39. Gene #4: '2q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	358	181
2Q GAIN MUTATED	31	17	3
2Q GAIN WILD-TYPE	134	341	178

Figure S39. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3p gain' versus 'CN_CNMF'

P value = 2.89e-11 (Chi-square test), Q value = 2.2e-08

Table S40. Gene #5: '3p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
3P GAIN MUTATED	11	47	22	46	10
3P GAIN WILD-TYPE	366	205	82	206	38

Figure S40. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #3: 'CN_CNMF'

'3p gain' versus 'METHLYATION_CNMF'

P value = 2.48e-05 (Chi-square test), Q value = 0.013

Table S41. Gene #5: '3p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	124	176	104	135	56	116
3P GAIN MUTATED	29	12	12	16	2	7
3P GAIN WILD-TYPE	95	164	92	119	54	109

Figure S41. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.36e-07 (Fisher's exact test), Q value = 0.00021

Table S42. Gene #5: '3p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	339	433	247
3P GAIN MUTATED	19	70	46
3P GAIN WILD-TYPE	320	363	201

Figure S42. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000143 (Fisher's exact test), Q value = 0.065

Table S43. Gene #5: '3p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	531	273	210
3P GAIN MUTATED	65	53	14
3P GAIN WILD-TYPE	466	220	196

Figure S43. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3q gain' versus 'MRNA_CHIERARCHICAL'

P value = 6.06e-06 (Fisher's exact test), Q value = 0.0034

Table S44. Gene #6: '3q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
3Q GAIN MUTATED	9	38	64
3Q GAIN WILD-TYPE	113	87	202

Figure S44. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'3q gain' versus 'CN_CNMF'

P value = 9.5e-19 (Chi-square test), Q value = 8.5e-16

Table S45. Gene #6: '3q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
3Q GAIN MUTATED	20	59	26	88	12
3Q GAIN WILD-TYPE	357	193	78	164	36

Figure S45. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #3: 'CN_CNMF'

'3q gain' versus 'METHLYATION_CNMF'

P value = 1.66e-11 (Chi-square test), Q value = 1.3e-08

Table S46. Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	124	176	104	135	56	116
3Q GAIN MUTATED	49	15	19	23	7	10
3Q GAIN WILD-TYPE	75	161	85	112	49	106

Figure S46. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3q gain' versus 'MRNASEQ_CNMF'

P value = 1.02e-13 (Chi-square test), Q value = 8.3e-11

Table S47. Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	190	95	257	169	260	48
3Q GAIN MUTATED	75	7	36	35	50	1
3Q GAIN WILD-TYPE	115	88	221	134	210	47

Figure S47. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.67e-13 (Fisher's exact test), Q value = 3.8e-10

Table S48. Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	339	433	247
3Q GAIN MUTATED	30	91	83
3Q GAIN WILD-TYPE	309	342	164

Figure S48. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_CNMF'

P value = 7.04e-12 (Chi-square test), Q value = 5.5e-09

Table S49. Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	194	170	227	251	140	32
3Q GAIN MUTATED	35	15	31	89	29	2
3Q GAIN WILD-TYPE	159	155	196	162	111	30

Figure S49. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.63e-11 (Fisher's exact test), Q value = 4.2e-08

Table S50. Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	531	273	210
3Q GAIN MUTATED	88	92	21
3Q GAIN WILD-TYPE	443	181	189

Figure S50. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.97e-10 (Fisher's exact test), Q value = 2.9e-07

Table S51. Gene #6: '3q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	238	218
3Q GAIN MUTATED	33	28	75
3Q GAIN WILD-TYPE	215	210	143

Figure S51. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'3q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.85e-10 (Fisher's exact test), Q value = 5.6e-07

Table S52. Gene #6: '3q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	358	181
3Q GAIN MUTATED	62	52	22
3Q GAIN WILD-TYPE	103	306	159

Figure S52. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p gain' versus 'MRNA_CNMF'

P value = 7e-05 (Chi-square test), Q value = 0.034

Table S53. Gene #7: '4p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
4P GAIN MUTATED	1	2	22	3	3	4	0	2
4P GAIN WILD-TYPE	20	34	97	93	106	68	20	38

Figure S53. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'4p gain' versus 'CN_CNMF'

P value = 1.64e-15 (Chi-square test), Q value = 1.4e-12

Table S54. Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
4P GAIN MUTATED	5	48	3	15	4
4P GAIN WILD-TYPE	372	204	101	237	44

Figure S54. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

'4p gain' versus 'METHLYATION_CNMF'

P value = 1.39e-05 (Chi-square test), Q value = 0.0074

Table S55. Gene #7: '4p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	124	176	104	135	56	116
4P GAIN MUTATED	7	6	8	24	4	3
4P GAIN WILD-TYPE	117	170	96	111	52	113

Figure S55. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p gain' versus 'MRNASEQ_CNMF'

P value = 5.43e-07 (Chi-square test), Q value = 0.00033

Table S56. Gene #7: '4p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	190	95	257	169	260	48
4P GAIN MUTATED	8	5	7	12	40	2
4P GAIN WILD-TYPE	182	90	250	157	220	46

Figure S56. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q gain' versus 'MRNA_CNMF'

P value = 1.74e-06 (Chi-square test), Q value = 0.001

Table S57. Gene #8: '4q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
4Q GAIN MUTATED	1	2	23	2	3	2	0	2
4Q GAIN WILD-TYPE	20	34	96	94	106	70	20	38

Figure S57. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'4q gain' versus 'CN_CNMF'

P value = 4.94e-15 (Chi-square test), Q value = 4.2e-12

Table S58. Gene #8: '4q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
4Q GAIN MUTATED	5	45	2	13	6
4Q GAIN WILD-TYPE	372	207	102	239	42

Figure S58. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #3: 'CN_CNMF'

'4q gain' versus 'METHLYATION_CNMF'

P value = 0.000299 (Chi-square test), Q value = 0.13

Table S59. Gene #8: '4q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	124	176	104	135	56	116
4Q GAIN MUTATED	7	7	5	21	4	3
4Q GAIN WILD-TYPE	117	169	99	114	52	113

Figure S59. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q gain' versus 'MRNASEQ_CNMF'

P value = 4.32e-07 (Chi-square test), Q value = 0.00027

Table S60. Gene #8: '4q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	190	95	257	169	260	48
4Q GAIN MUTATED	8	4	7	10	39	2
4Q GAIN WILD-TYPE	182	91	250	159	221	46

Figure S60. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5p gain' versus 'CN_CNMF'

P value = 6.69e-18 (Chi-square test), Q value = 5.9e-15

Table S61. Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
5P GAIN MUTATED	54	113	49	74	12
5P GAIN WILD-TYPE	323	139	55	178	36

Figure S61. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

'5q gain' versus 'CN_CNMF'

P value = 4.07e-24 (Chi-square test), Q value = 3.8e-21

Table S62. Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
5Q GAIN MUTATED	44	83	47	16	10
5Q GAIN WILD-TYPE	333	169	57	236	38

Figure S62. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'

'5q gain' versus 'METHLYATION_CNMF'

P value = 0.000566 (Chi-square test), Q value = 0.23

Table S63. Gene #10: '5q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	124	176	104	135	56	116
5Q GAIN MUTATED	13	42	29	32	6	14
5Q GAIN WILD-TYPE	111	134	75	103	50	102

Figure S63. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.3e-05 (Fisher's exact test), Q value = 0.007

Table S64. Gene #10: '5q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	339	433	247
5Q GAIN MUTATED	70	103	24
5Q GAIN WILD-TYPE	269	330	223

Figure S64. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000494 (Fisher's exact test), Q value = 0.21

Table S65. Gene #10: '5q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	238	218
5Q GAIN MUTATED	63	48	25
5Q GAIN WILD-TYPE	185	190	193

Figure S65. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000477 (Fisher's exact test), Q value = 0.2

Table S66. Gene #10: '5q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	358	181
5Q GAIN MUTATED	17	87	32
5Q GAIN WILD-TYPE	148	271	149

Figure S66. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p gain' versus 'MRNA_CNMF'

P value = 5.32e-07 (Chi-square test), Q value = 0.00032

Table S67. Gene #11: '6p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
6P GAIN MUTATED	2	2	18	36	13	19	7	2
6P GAIN WILD-TYPE	19	34	101	60	96	53	13	38

Figure S67. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'6p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1.05e-05 (Fisher's exact test), Q value = 0.0057

Table S68. Gene #11: '6p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
6P GAIN MUTATED	10	40	49
6P GAIN WILD-TYPE	112	85	217

Figure S68. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6p gain' versus 'CN_CNMF'

P value = 2.38e-32 (Chi-square test), Q value = 2.2e-29

Table S69. Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
6P GAIN MUTATED	17	44	19	112	10
6P GAIN WILD-TYPE	360	208	85	140	38

Figure S69. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

'6p gain' versus 'METHLYATION_CNMF'

P value = 7.33e-16 (Chi-square test), Q value = 6.3e-13

Table S70. Gene #11: '6p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	124	176	104	135	56	116
6P GAIN MUTATED	54	11	23	32	2	15
6P GAIN WILD-TYPE	70	165	81	103	54	101

Figure S70. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6p gain' versus 'RPPA_CNMF'

P value = 0.000177 (Fisher's exact test), Q value = 0.079

Table S71. Gene #11: '6p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
6P GAIN MUTATED	45	19	14
6P GAIN WILD-TYPE	102	114	103

Figure S71. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'6p gain' versus 'MRNASEQ_CNMF'

P value = 7.02e-21 (Chi-square test), Q value = 6.4e-18

Table S72. Gene #11: '6p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	190	95	257	169	260	48
6P GAIN MUTATED	80	7	26	45	36	2
6P GAIN WILD-TYPE	110	88	231	124	224	46

Figure S72. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.73e-17 (Fisher's exact test), Q value = 8.5e-14

Table S73. Gene #11: '6p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	339	433	247
6P GAIN MUTATED	27	79	90
6P GAIN WILD-TYPE	312	354	157

Figure S73. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_CNMF'

P value = 2.07e-16 (Chi-square test), Q value = 1.8e-13

Table S74. Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	194	170	227	251	140	32
6P GAIN MUTATED	22	17	23	93	30	9
6P GAIN WILD-TYPE	172	153	204	158	110	23

Figure S74. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.56e-18 (Fisher's exact test), Q value = 1.4e-15

Table S75. Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	531	273	210
6P GAIN MUTATED	80	101	13
6P GAIN WILD-TYPE	451	172	197

Figure S75. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 5.54e-16 (Fisher's exact test), Q value = 4.8e-13

Table S76. Gene #11: '6p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	238	218
6P GAIN MUTATED	26	24	83
6P GAIN WILD-TYPE	222	214	135

Figure S76. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'6p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.4e-13 (Fisher's exact test), Q value = 4.3e-10

Table S77. Gene #11: '6p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	358	181
6P GAIN MUTATED	66	48	19
6P GAIN WILD-TYPE	99	310	162

Figure S77. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q gain' versus 'MRNA_CNMF'

P value = 1.58e-07 (Chi-square test), Q value = 9.9e-05

Table S78. Gene #12: '6q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
6Q GAIN MUTATED	1	0	9	29	11	13	7	2
6Q GAIN WILD-TYPE	20	36	110	67	98	59	13	38

Figure S78. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'6q gain' versus 'MRNA_CHIERARCHICAL'

P value = 3.32e-05 (Fisher's exact test), Q value = 0.017

Table S79. Gene #12: '6q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
6Q GAIN MUTATED	7	32	33
6Q GAIN WILD-TYPE	115	93	233

Figure S79. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6q gain' versus 'CN_CNMF'

P value = 2.61e-31 (Chi-square test), Q value = 2.5e-28

Table S80. Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
6Q GAIN MUTATED	13	21	13	93	7
6Q GAIN WILD-TYPE	364	231	91	159	41

Figure S80. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

'6q gain' versus 'METHLYATION_CNMF'

P value = 7.57e-12 (Chi-square test), Q value = 5.9e-09

Table S81. Gene #12: '6q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	124	176	104	135	56	116
6Q GAIN MUTATED	41	6	15	18	2	14
6Q GAIN WILD-TYPE	83	170	89	117	54	102

Figure S81. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6q gain' versus 'RPPA_CNMF'

P value = 1.32e-05 (Fisher's exact test), Q value = 0.007

Table S82. Gene #12: '6q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
6Q GAIN MUTATED	38	10	10
6Q GAIN WILD-TYPE	109	123	107

Figure S82. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'6q gain' versus 'MRNASEQ_CNMF'

P value = 1.42e-16 (Chi-square test), Q value = 1.2e-13

Table S83. Gene #12: '6q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	190	95	257	169	260	48
6Q GAIN MUTATED	60	5	20	35	19	2
6Q GAIN WILD-TYPE	130	90	237	134	241	46

Figure S83. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.7e-11 (Fisher's exact test), Q value = 1.3e-08

Table S84. Gene #12: '6q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	339	433	247
6Q GAIN MUTATED	22	52	67
6Q GAIN WILD-TYPE	317	381	180

Figure S84. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6q gain' versus 'MIRSEQ_CNMF'

P value = 4.46e-15 (Chi-square test), Q value = 3.8e-12

Table S85. Gene #12: '6q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	194	170	227	251	140	32
6Q GAIN MUTATED	15	12	15	75	19	5
6Q GAIN WILD-TYPE	179	158	212	176	121	27

Figure S85. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.21e-14 (Fisher's exact test), Q value = 1e-11

Table S86. Gene #12: '6q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	531	273	210
6Q GAIN MUTATED	52	78	11
6Q GAIN WILD-TYPE	479	195	199

Figure S86. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 9.03e-14 (Fisher's exact test), Q value = 7.4e-11

Table S87. Gene #12: '6q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	238	218
6Q GAIN MUTATED	19	17	67
6Q GAIN WILD-TYPE	229	221	151

Figure S87. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'6q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.69e-11 (Fisher's exact test), Q value = 1.3e-08

Table S88. Gene #12: '6q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	358	181
6Q GAIN MUTATED	54	35	14
6Q GAIN WILD-TYPE	111	323	167

Figure S88. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

P value = 2.06e-10 (Chi-square test), Q value = 1.5e-07

Table S89. Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
7P GAIN MUTATED	69	73	54	86	13
7P GAIN WILD-TYPE	308	179	50	166	35

Figure S89. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00035 (Fisher's exact test), Q value = 0.15

Table S90. Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	339	433	247
7P GAIN MUTATED	75	125	92
7P GAIN WILD-TYPE	264	308	155

Figure S90. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 2.78e-11 (Chi-square test), Q value = 2.1e-08

Table S91. Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
7Q GAIN MUTATED	56	55	48	82	11
7Q GAIN WILD-TYPE	321	197	56	170	37

Figure S91. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 0.000214 (Chi-square test), Q value = 0.094

Table S92. Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	124	176	104	135	56	116
7Q GAIN MUTATED	48	36	24	34	7	19
7Q GAIN WILD-TYPE	76	140	80	101	49	97

Figure S92. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 3.2e-06 (Chi-square test), Q value = 0.0019

Table S93. Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	190	95	257	169	260	48
7Q GAIN MUTATED	69	16	62	49	51	2
7Q GAIN WILD-TYPE	121	79	195	120	209	46

Figure S93. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.3e-07 (Fisher's exact test), Q value = 0.00026

Table S94. Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	339	433	247
7Q GAIN MUTATED	61	96	92
7Q GAIN WILD-TYPE	278	337	155

Figure S94. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_CNMF'

P value = 6.95e-05 (Chi-square test), Q value = 0.034

Table S95. Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	194	170	227	251	140	32
7Q GAIN MUTATED	43	40	41	87	23	11
7Q GAIN WILD-TYPE	151	130	186	164	117	21

Figure S95. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000128 (Fisher's exact test), Q value = 0.059

Table S96. Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	531	273	210
7Q GAIN MUTATED	112	92	41
7Q GAIN WILD-TYPE	419	181	169

Figure S96. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

P value = 8.97e-08 (Chi-square test), Q value = 5.8e-05

Table S97. Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
8P GAIN MUTATED	73	68	39	75	27
8P GAIN WILD-TYPE	304	184	65	177	21

Figure S97. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'MRNA_CNMF'

P value = 2.72e-05 (Chi-square test), Q value = 0.014

Table S98. Gene #16: '8q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
8Q GAIN MUTATED	14	12	74	62	44	35	15	14
8Q GAIN WILD-TYPE	7	24	45	34	65	37	5	26

Figure S98. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'8q gain' versus 'CN_CNMF'

P value = 2.4e-25 (Chi-square test), Q value = 2.2e-22

Table S99. Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
8Q GAIN MUTATED	112	152	44	161	42
8Q GAIN WILD-TYPE	265	100	60	91	6

Figure S99. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 6.91e-13 (Chi-square test), Q value = 5.5e-10

Table S100. Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	124	176	104	135	56	116
8Q GAIN MUTATED	87	49	50	81	19	51
8Q GAIN WILD-TYPE	37	127	54	54	37	65

Figure S100. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 6.53e-15 (Chi-square test), Q value = 5.5e-12

Table S101. Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	190	95	257	169	260	48
8Q GAIN MUTATED	127	36	80	88	154	18
8Q GAIN WILD-TYPE	63	59	177	81	106	30

Figure S101. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.7e-10 (Fisher's exact test), Q value = 1.3e-07

Table S102. Gene #16: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	339	433	247
8Q GAIN MUTATED	120	230	153
8Q GAIN WILD-TYPE	219	203	94

Figure S102. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_CNMF'

P value = 6.63e-09 (Chi-square test), Q value = 4.5e-06

Table S103. Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	194	170	227	251	140	32
8Q GAIN MUTATED	92	59	92	157	85	16
8Q GAIN WILD-TYPE	102	111	135	94	55	16

Figure S103. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.5e-12 (Fisher's exact test), Q value = 1.2e-09

Table S104. Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	531	273	210
8Q GAIN MUTATED	252	180	69
8Q GAIN WILD-TYPE	279	93	141

Figure S104. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 8.64e-12 (Fisher's exact test), Q value = 6.7e-09

Table S105. Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	238	218
8Q GAIN MUTATED	113	80	145
8Q GAIN WILD-TYPE	135	158	73

Figure S105. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.15e-08 (Fisher's exact test), Q value = 7.9e-06

Table S106. Gene #16: '8q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	358	181
8Q GAIN MUTATED	110	165	63
8Q GAIN WILD-TYPE	55	193	118

Figure S106. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p gain' versus 'MRNA_CNMF'

P value = 2.15e-10 (Chi-square test), Q value = 1.6e-07

Table S107. Gene #17: '9p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
9P GAIN MUTATED	1	2	3	34	14	9	0	5
9P GAIN WILD-TYPE	20	34	116	62	95	63	20	35

Figure S107. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'9p gain' versus 'MRNA_CHIERARCHICAL'

P value = 4.73e-08 (Fisher's exact test), Q value = 3.1e-05

Table S108. Gene #17: '9p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
9P GAIN MUTATED	11	37	20
9P GAIN WILD-TYPE	111	88	246

Figure S108. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9p gain' versus 'CN_CNMF'

P value = 4.39e-16 (Chi-square test), Q value = 3.8e-13

Table S109. Gene #17: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
9P GAIN MUTATED	23	13	28	62	8
9P GAIN WILD-TYPE	354	239	76	190	40

Figure S109. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'

'9p gain' versus 'METHLYATION_CNMF'

P value = 4.89e-05 (Chi-square test), Q value = 0.025

Table S110. Gene #17: '9p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	124	176	104	135	56	116
9P GAIN MUTATED	32	18	9	15	2	12
9P GAIN WILD-TYPE	92	158	95	120	54	104

Figure S110. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p gain' versus 'RPPA_CHIERARCHICAL'

P value = 1.69e-06 (Fisher's exact test), Q value = 0.001

Table S111. Gene #17: '9p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	110	126
9P GAIN MUTATED	10	10	34
9P GAIN WILD-TYPE	151	100	92

Figure S111. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'9p gain' versus 'MRNASEQ_CNMF'

P value = 1.32e-13 (Chi-square test), Q value = 1.1e-10

Table S112. Gene #17: '9p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	190	95	257	169	260	48
9P GAIN MUTATED	58	5	27	22	15	7
9P GAIN WILD-TYPE	132	90	230	147	245	41

Figure S112. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.87e-09 (Fisher's exact test), Q value = 6.1e-06

Table S113. Gene #17: '9p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	339	433	247
9P GAIN MUTATED	28	44	62
9P GAIN WILD-TYPE	311	389	185

Figure S113. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p gain' versus 'MIRSEQ_CNMF'

P value = 7.47e-05 (Chi-square test), Q value = 0.036

Table S114. Gene #17: '9p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	194	170	227	251	140	32
9P GAIN MUTATED	24	14	20	55	14	3
9P GAIN WILD-TYPE	170	156	207	196	126	29

Figure S114. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.1e-06 (Fisher's exact test), Q value = 0.0029

Table S115. Gene #17: '9p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	531	273	210
9P GAIN MUTATED	54	59	17
9P GAIN WILD-TYPE	477	214	193

Figure S115. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00034 (Fisher's exact test), Q value = 0.14

Table S116. Gene #17: '9p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	358	181
9P GAIN MUTATED	35	47	12
9P GAIN WILD-TYPE	130	311	169

Figure S116. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q gain' versus 'CN_CNMF'

P value = 1.49e-09 (Chi-square test), Q value = 1.1e-06

Table S117. Gene #18: '9q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
9Q GAIN MUTATED	24	15	28	38	6
9Q GAIN WILD-TYPE	353	237	76	214	42

Figure S117. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #3: 'CN_CNMF'

'10p gain' versus 'MRNA_CNMF'

P value = 6.7e-10 (Chi-square test), Q value = 4.8e-07

Table S118. Gene #19: '10p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
10P GAIN MUTATED	2	4	17	42	11	26	6	4
10P GAIN WILD-TYPE	19	32	102	54	98	46	14	36

Figure S118. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'10p gain' versus 'MRNA_CHIERARCHICAL'

P value = 2.31e-08 (Fisher's exact test), Q value = 1.5e-05

Table S119. Gene #19: '10p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
10P GAIN MUTATED	16	52	44
10P GAIN WILD-TYPE	106	73	222

Figure S119. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'10p gain' versus 'CN_CNMF'

P value = 3.39e-29 (Chi-square test), Q value = 3.2e-26

Table S120. Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
10P GAIN MUTATED	22	48	15	110	8
10P GAIN WILD-TYPE	355	204	89	142	40

Figure S120. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

'10p gain' versus 'METHLYATION_CNMF'

P value = 5.96e-15 (Chi-square test), Q value = 5e-12

Table S121. Gene #19: '10p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	124	176	104	135	56	116
10P GAIN MUTATED	54	11	18	24	3	21
10P GAIN WILD-TYPE	70	165	86	111	53	95

Figure S121. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p gain' versus 'RPPA_CNMF'

P value = 1.29e-05 (Fisher's exact test), Q value = 0.0069

Table S122. Gene #19: '10p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
10P GAIN MUTATED	52	17	20
10P GAIN WILD-TYPE	95	116	97

Figure S122. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'10p gain' versus 'RPPA_CHIERARCHICAL'

P value = 1.25e-05 (Fisher's exact test), Q value = 0.0067

Table S123. Gene #19: '10p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	110	126
10P GAIN MUTATED	23	19	47
10P GAIN WILD-TYPE	138	91	79

Figure S123. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'10p gain' versus 'MRNASEQ_CNMF'

P value = 5.89e-19 (Chi-square test), Q value = 5.3e-16

Table S124. Gene #19: '10p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	190	95	257	169	260	48
10P GAIN MUTATED	80	10	24	45	36	6
10P GAIN WILD-TYPE	110	85	233	124	224	42

Figure S124. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.47e-18 (Fisher's exact test), Q value = 8.3e-15

Table S125. Gene #19: '10p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	339	433	247
10P GAIN MUTATED	31	74	96
10P GAIN WILD-TYPE	308	359	151

Figure S125. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p gain' versus 'MIRSEQ_CNMF'

P value = 1.33e-13 (Chi-square test), Q value = 1.1e-10

Table S126. Gene #19: '10p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	194	170	227	251	140	32
10P GAIN MUTATED	34	18	21	91	30	5
10P GAIN WILD-TYPE	160	152	206	160	110	27

Figure S126. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.23e-18 (Fisher's exact test), Q value = 7.2e-15

Table S127. Gene #19: '10p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	531	273	210
10P GAIN MUTATED	80	103	16
10P GAIN WILD-TYPE	451	170	194

Figure S127. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.22e-12 (Fisher's exact test), Q value = 4.8e-09

Table S128. Gene #19: '10p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	238	218
10P GAIN MUTATED	33	23	76
10P GAIN WILD-TYPE	215	215	142

Figure S128. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.5e-12 (Fisher's exact test), Q value = 3.5e-09

Table S129. Gene #19: '10p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	358	181
10P GAIN MUTATED	64	50	18
10P GAIN WILD-TYPE	101	308	163

Figure S129. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q gain' versus 'CN_CNMF'

P value = 5.5e-09 (Chi-square test), Q value = 3.8e-06

Table S130. Gene #20: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
10Q GAIN MUTATED	15	31	13	53	5
10Q GAIN WILD-TYPE	362	221	91	199	43

Figure S130. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

'10q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000181 (Fisher's exact test), Q value = 0.081

Table S131. Gene #20: '10q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	339	433	247
10Q GAIN MUTATED	21	55	41
10Q GAIN WILD-TYPE	318	378	206

Figure S131. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000111 (Fisher's exact test), Q value = 0.052

Table S132. Gene #20: '10q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	531	273	210
10Q GAIN MUTATED	51	50	14
10Q GAIN WILD-TYPE	480	223	196

Figure S132. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000215 (Fisher's exact test), Q value = 0.094

Table S133. Gene #20: '10q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	238	218
10Q GAIN MUTATED	24	14	39
10Q GAIN WILD-TYPE	224	224	179

Figure S133. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11p gain' versus 'CN_CNMF'

P value = 1.54e-07 (Chi-square test), Q value = 9.7e-05

Table S134. Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
11P GAIN MUTATED	19	44	14	51	6
11P GAIN WILD-TYPE	358	208	90	201	42

Figure S134. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

'11p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.89e-06 (Fisher's exact test), Q value = 0.0043

Table S135. Gene #21: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	531	273	210
11P GAIN MUTATED	70	52	10
11P GAIN WILD-TYPE	461	221	200

Figure S135. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000187 (Fisher's exact test), Q value = 0.083

Table S136. Gene #21: '11p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	238	218
11P GAIN MUTATED	39	14	37
11P GAIN WILD-TYPE	209	224	181

Figure S136. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.31e-05 (Fisher's exact test), Q value = 0.035

Table S137. Gene #21: '11p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	358	181
11P GAIN MUTATED	30	52	8
11P GAIN WILD-TYPE	135	306	173

Figure S137. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q gain' versus 'CN_CNMF'

P value = 2.81e-08 (Chi-square test), Q value = 1.9e-05

Table S138. Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
11Q GAIN MUTATED	11	20	10	44	6
11Q GAIN WILD-TYPE	366	232	94	208	42

Figure S138. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

'11q gain' versus 'MRNASEQ_CNMF'

P value = 0.000237 (Chi-square test), Q value = 0.1

Table S139. Gene #22: '11q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	190	95	257	169	260	48
11Q GAIN MUTATED	27	5	15	25	19	0
11Q GAIN WILD-TYPE	163	90	242	144	241	48

Figure S139. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.91e-05 (Fisher's exact test), Q value = 0.029

Table S140. Gene #22: '11q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	339	433	247
11Q GAIN MUTATED	16	37	38
11Q GAIN WILD-TYPE	323	396	209

Figure S140. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_CNMF'

P value = 0.000254 (Chi-square test), Q value = 0.11

Table S141. Gene #22: '11q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	194	170	227	251	140	32
11Q GAIN MUTATED	15	5	15	39	12	2
11Q GAIN WILD-TYPE	179	165	212	212	128	30

Figure S141. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.6e-06 (Fisher's exact test), Q value = 0.0015

Table S142. Gene #22: '11q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	531	273	210
11Q GAIN MUTATED	36	44	8
11Q GAIN WILD-TYPE	495	229	202

Figure S142. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 8.04e-06 (Fisher's exact test), Q value = 0.0044

Table S143. Gene #22: '11q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	238	218
11Q GAIN MUTATED	18	8	35
11Q GAIN WILD-TYPE	230	230	183

Figure S143. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.68e-05 (Fisher's exact test), Q value = 0.019

Table S144. Gene #22: '11q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	358	181
11Q GAIN MUTATED	27	29	5
11Q GAIN WILD-TYPE	138	329	176

Figure S144. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.000545 (Fisher's exact test), Q value = 0.23

Table S145. Gene #23: '12p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
12P GAIN MUTATED	13	37	64
12P GAIN WILD-TYPE	109	88	202

Figure S145. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'12p gain' versus 'CN_CNMF'

P value = 8.84e-22 (Chi-square test), Q value = 8.1e-19

Table S146. Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
12P GAIN MUTATED	18	84	27	84	11
12P GAIN WILD-TYPE	359	168	77	168	37

Figure S146. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 1.31e-08 (Chi-square test), Q value = 8.9e-06

Table S147. Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	124	176	104	135	56	116
12P GAIN MUTATED	37	20	20	50	6	15
12P GAIN WILD-TYPE	87	156	84	85	50	101

Figure S147. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 2.43e-07 (Chi-square test), Q value = 0.00015

Table S148. Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	190	95	257	169	260	48
12P GAIN MUTATED	60	10	33	43	70	5
12P GAIN WILD-TYPE	130	85	224	126	190	43

Figure S148. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.42e-09 (Fisher's exact test), Q value = 1e-06

Table S149. Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	339	433	247
12P GAIN MUTATED	36	113	72
12P GAIN WILD-TYPE	303	320	175

Figure S149. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_CNMF'

P value = 4.48e-08 (Chi-square test), Q value = 3e-05

Table S150. Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	194	170	227	251	140	32
12P GAIN MUTATED	31	18	39	85	36	8
12P GAIN WILD-TYPE	163	152	188	166	104	24

Figure S150. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000153 (Fisher's exact test), Q value = 0.069

Table S151. Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	531	273	210
12P GAIN MUTATED	108	80	29
12P GAIN WILD-TYPE	423	193	181

Figure S151. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000151 (Fisher's exact test), Q value = 0.069

Table S152. Gene #23: '12p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	238	218
12P GAIN MUTATED	49	35	67
12P GAIN WILD-TYPE	199	203	151

Figure S152. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12q gain' versus 'CN_CNMF'

P value = 1.29e-22 (Chi-square test), Q value = 1.2e-19

Table S153. Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
12Q GAIN MUTATED	18	92	28	40	10
12Q GAIN WILD-TYPE	359	160	76	212	38

Figure S153. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

'12q gain' versus 'METHLYATION_CNMF'

P value = 2.58e-10 (Chi-square test), Q value = 1.9e-07

Table S154. Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	124	176	104	135	56	116
12Q GAIN MUTATED	15	24	18	52	6	10
12Q GAIN WILD-TYPE	109	152	86	83	50	106

Figure S154. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12q gain' versus 'MRNASEQ_CNMF'

P value = 3.85e-06 (Chi-square test), Q value = 0.0022

Table S155. Gene #24: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	190	95	257	169	260	48
12Q GAIN MUTATED	23	11	33	42	70	5
12Q GAIN WILD-TYPE	167	84	224	127	190	43

Figure S155. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.57e-10 (Fisher's exact test), Q value = 2.6e-07

Table S156. Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	339	433	247
12Q GAIN MUTATED	34	118	32
12Q GAIN WILD-TYPE	305	315	215

Figure S156. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q gain' versus 'CN_CNMF'

P value = 1.53e-05 (Chi-square test), Q value = 0.0081

Table S157. Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
13Q GAIN MUTATED	15	25	7	40	4
13Q GAIN WILD-TYPE	362	227	97	212	44

Figure S157. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

'13q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000568 (Fisher's exact test), Q value = 0.23

Table S158. Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	339	433	247
13Q GAIN MUTATED	16	40	34
13Q GAIN WILD-TYPE	323	393	213

Figure S158. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000303 (Fisher's exact test), Q value = 0.13

Table S159. Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	531	273	210
13Q GAIN MUTATED	39	40	10
13Q GAIN WILD-TYPE	492	233	200

Figure S159. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q gain' versus 'CN_CNMF'

P value = 4.07e-09 (Chi-square test), Q value = 2.8e-06

Table S160. Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
14Q GAIN MUTATED	26	60	21	24	8
14Q GAIN WILD-TYPE	351	192	83	228	40

Figure S160. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

'14q gain' versus 'MRNASEQ_CNMF'

P value = 3.94e-06 (Chi-square test), Q value = 0.0023

Table S161. Gene #26: '14q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	190	95	257	169	260	48
14Q GAIN MUTATED	12	12	35	41	38	0
14Q GAIN WILD-TYPE	178	83	222	128	222	48

Figure S161. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNA_CNMF'

P value = 0.000147 (Chi-square test), Q value = 0.067

Table S162. Gene #28: '16p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
16P GAIN MUTATED	11	14	52	33	73	35	12	14
16P GAIN WILD-TYPE	10	22	67	63	36	37	8	26

Figure S162. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'16p gain' versus 'CN_CNMF'

P value = 1.44e-09 (Chi-square test), Q value = 1e-06

Table S163. Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
16P GAIN MUTATED	143	123	75	92	21
16P GAIN WILD-TYPE	234	129	29	160	27

Figure S163. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

'16p gain' versus 'METHLYATION_CNMF'

P value = 3.12e-06 (Chi-square test), Q value = 0.0018

Table S164. Gene #28: '16p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	124	176	104	135	56	116
16P GAIN MUTATED	40	94	52	58	14	32
16P GAIN WILD-TYPE	84	82	52	77	42	84

Figure S164. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 3.35e-12 (Chi-square test), Q value = 2.6e-09

Table S165. Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	190	95	257	169	260	48
16P GAIN MUTATED	49	36	159	80	110	17
16P GAIN WILD-TYPE	141	59	98	89	150	31

Figure S165. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.99e-07 (Fisher's exact test), Q value = 0.00054

Table S166. Gene #28: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	339	433	247
16P GAIN MUTATED	156	220	75
16P GAIN WILD-TYPE	183	213	172

Figure S166. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_CNMF'

P value = 0.000517 (Chi-square test), Q value = 0.21

Table S167. Gene #28: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	194	170	227	251	140	32
16P GAIN MUTATED	99	69	113	88	54	20
16P GAIN WILD-TYPE	95	101	114	163	86	12

Figure S167. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.62e-05 (Fisher's exact test), Q value = 0.018

Table S168. Gene #28: '16p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	238	218
16P GAIN MUTATED	124	109	66
16P GAIN WILD-TYPE	124	129	152

Figure S168. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.7e-05 (Fisher's exact test), Q value = 0.014

Table S169. Gene #28: '16p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	358	181
16P GAIN MUTATED	45	170	84
16P GAIN WILD-TYPE	120	188	97

Figure S169. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p gain' versus 'CN_CNMF'

P value = 5.43e-06 (Chi-square test), Q value = 0.003

Table S170. Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
17P GAIN MUTATED	20	46	11	21	7
17P GAIN WILD-TYPE	357	206	93	231	41

Figure S170. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'MRNA_CNMF'

P value = 2.74e-08 (Chi-square test), Q value = 1.8e-05

Table S171. Gene #31: '17q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
17Q GAIN MUTATED	3	8	47	8	10	12	5	5
17Q GAIN WILD-TYPE	18	28	72	88	99	60	15	35

Figure S171. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'17q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1.89e-05 (Fisher's exact test), Q value = 0.0099

Table S172. Gene #31: '17q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
17Q GAIN MUTATED	16	11	71
17Q GAIN WILD-TYPE	106	114	195

Figure S172. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17q gain' versus 'CN_CNMF'

P value = 7.01e-26 (Chi-square test), Q value = 6.5e-23

Table S173. Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
17Q GAIN MUTATED	36	111	18	34	15
17Q GAIN WILD-TYPE	341	141	86	218	33

Figure S173. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 6.52e-07 (Chi-square test), Q value = 4e-04

Table S174. Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	124	176	104	135	56	116
17Q GAIN MUTATED	15	30	29	52	9	19
17Q GAIN WILD-TYPE	109	146	75	83	47	97

Figure S174. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 6.33e-15 (Chi-square test), Q value = 5.3e-12

Table S175. Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	190	95	257	169	260	48
17Q GAIN MUTATED	21	14	30	35	100	10
17Q GAIN WILD-TYPE	169	81	227	134	160	38

Figure S175. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.78e-08 (Fisher's exact test), Q value = 1.2e-05

Table S176. Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	339	433	247
17Q GAIN MUTATED	56	126	28
17Q GAIN WILD-TYPE	283	307	219

Figure S176. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_CNMF'

P value = 7.42e-08 (Chi-square test), Q value = 4.8e-05

Table S177. Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	194	170	227	251	140	32
17Q GAIN MUTATED	40	22	52	38	54	3
17Q GAIN WILD-TYPE	154	148	175	213	86	29

Figure S177. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18p gain' versus 'MRNA_CNMF'

P value = 1.1e-06 (Chi-square test), Q value = 0.00066

Table S178. Gene #32: '18p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
18P GAIN MUTATED	1	1	19	35	16	10	4	1
18P GAIN WILD-TYPE	20	35	100	61	93	62	16	39

Figure S178. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'18p gain' versus 'MRNA_CHIERARCHICAL'

P value = 6.37e-08 (Fisher's exact test), Q value = 4.2e-05

Table S179. Gene #32: '18p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
18P GAIN MUTATED	7	41	39
18P GAIN WILD-TYPE	115	84	227

Figure S179. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18p gain' versus 'CN_CNMF'

P value = 4.62e-18 (Chi-square test), Q value = 4.1e-15

Table S180. Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
18P GAIN MUTATED	17	40	20	81	12
18P GAIN WILD-TYPE	360	212	84	171	36

Figure S180. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 1.87e-14 (Chi-square test), Q value = 1.6e-11

Table S181. Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	124	176	104	135	56	116
18P GAIN MUTATED	48	14	10	18	1	14
18P GAIN WILD-TYPE	76	162	94	117	55	102

Figure S181. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p gain' versus 'RPPA_CHIERARCHICAL'

P value = 4.82e-05 (Fisher's exact test), Q value = 0.024

Table S182. Gene #32: '18p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	110	126
18P GAIN MUTATED	22	10	38
18P GAIN WILD-TYPE	139	100	88

Figure S182. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'18p gain' versus 'MRNASEQ_CNMF'

P value = 1.71e-16 (Chi-square test), Q value = 1.5e-13

Table S183. Gene #32: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	190	95	257	169	260	48
18P GAIN MUTATED	71	5	31	22	40	0
18P GAIN WILD-TYPE	119	90	226	147	220	48

Figure S183. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.23e-18 (Fisher's exact test), Q value = 1.1e-15

Table S184. Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	339	433	247
18P GAIN MUTATED	19	66	84
18P GAIN WILD-TYPE	320	367	163

Figure S184. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_CNMF'

P value = 3.37e-12 (Chi-square test), Q value = 2.6e-09

Table S185. Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	194	170	227	251	140	32
18P GAIN MUTATED	26	11	25	79	17	5
18P GAIN WILD-TYPE	168	159	202	172	123	27

Figure S185. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.43e-13 (Fisher's exact test), Q value = 1.2e-10

Table S186. Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	531	273	210
18P GAIN MUTATED	65	84	14
18P GAIN WILD-TYPE	466	189	196

Figure S186. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.33e-11 (Fisher's exact test), Q value = 4.8e-08

Table S187. Gene #32: '18p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	238	218
18P GAIN MUTATED	30	19	68
18P GAIN WILD-TYPE	218	219	150

Figure S187. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.8e-14 (Fisher's exact test), Q value = 4.8e-11

Table S188. Gene #32: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	358	181
18P GAIN MUTATED	60	47	10
18P GAIN WILD-TYPE	105	311	171

Figure S188. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q gain' versus 'MRNA_CNMF'

P value = 7.26e-05 (Chi-square test), Q value = 0.035

Table S189. Gene #33: '18q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
18Q GAIN MUTATED	2	1	21	29	17	5	4	1
18Q GAIN WILD-TYPE	19	35	98	67	92	67	16	39

Figure S189. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'18q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.000119 (Fisher's exact test), Q value = 0.055

Table S190. Gene #33: '18q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
18Q GAIN MUTATED	7	31	42
18Q GAIN WILD-TYPE	115	94	224

Figure S190. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18q gain' versus 'CN_CNMF'

P value = 7.65e-14 (Chi-square test), Q value = 6.3e-11

Table S191. Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
18Q GAIN MUTATED	14	36	21	64	12
18Q GAIN WILD-TYPE	363	216	83	188	36

Figure S191. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

'18q gain' versus 'METHLYATION_CNMF'

P value = 7.94e-05 (Chi-square test), Q value = 0.038

Table S192. Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	124	176	104	135	56	116
18Q GAIN MUTATED	31	14	11	18	2	12
18Q GAIN WILD-TYPE	93	162	93	117	54	104

Figure S192. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q gain' versus 'MRNASEQ_CNMF'

P value = 9.69e-11 (Chi-square test), Q value = 7.2e-08

Table S193. Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	190	95	257	169	260	48
18Q GAIN MUTATED	54	5	32	11	43	0
18Q GAIN WILD-TYPE	136	90	225	158	217	48

Figure S193. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.02e-09 (Fisher's exact test), Q value = 7.2e-07

Table S194. Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	339	433	247
18Q GAIN MUTATED	19	68	58
18Q GAIN WILD-TYPE	320	365	189

Figure S194. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_CNMF'

P value = 0.000151 (Chi-square test), Q value = 0.069

Table S195. Gene #33: '18q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	194	170	227	251	140	32
18Q GAIN MUTATED	24	11	25	56	21	4
18Q GAIN WILD-TYPE	170	159	202	195	119	28

Figure S195. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.12e-06 (Fisher's exact test), Q value = 0.005

Table S196. Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	531	273	210
18Q GAIN MUTATED	68	59	14
18Q GAIN WILD-TYPE	463	214	196

Figure S196. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000124 (Fisher's exact test), Q value = 0.057

Table S197. Gene #33: '18q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	238	218
18Q GAIN MUTATED	27	20	47
18Q GAIN WILD-TYPE	221	218	171

Figure S197. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.94e-05 (Fisher's exact test), Q value = 0.01

Table S198. Gene #33: '18q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	358	181
18Q GAIN MUTATED	37	47	10
18Q GAIN WILD-TYPE	128	311	171

Figure S198. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p gain' versus 'CN_CNMF'

P value = 2.82e-10 (Chi-square test), Q value = 2.1e-07

Table S199. Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
19P GAIN MUTATED	31	37	27	71	7
19P GAIN WILD-TYPE	346	215	77	181	41

Figure S199. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

'19p gain' versus 'MRNASEQ_CNMF'

P value = 1.85e-05 (Chi-square test), Q value = 0.0097

Table S200. Gene #34: '19p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	190	95	257	169	260	48
19P GAIN MUTATED	56	12	33	30	35	5
19P GAIN WILD-TYPE	134	83	224	139	225	43

Figure S200. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.2e-06 (Fisher's exact test), Q value = 0.0035

Table S201. Gene #34: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	339	433	247
19P GAIN MUTATED	41	63	67
19P GAIN WILD-TYPE	298	370	180

Figure S201. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000112 (Fisher's exact test), Q value = 0.052

Table S202. Gene #34: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	531	273	210
19P GAIN MUTATED	73	69	28
19P GAIN WILD-TYPE	458	204	182

Figure S202. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q gain' versus 'CN_CNMF'

P value = 1.16e-11 (Chi-square test), Q value = 9e-09

Table S203. Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
19Q GAIN MUTATED	35	49	30	82	11
19Q GAIN WILD-TYPE	342	203	74	170	37

Figure S203. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 5.93e-05 (Chi-square test), Q value = 0.029

Table S204. Gene #35: '19q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	190	95	257	169	260	48
19Q GAIN MUTATED	62	14	38	36	49	6
19Q GAIN WILD-TYPE	128	81	219	133	211	42

Figure S204. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.44e-05 (Fisher's exact test), Q value = 0.017

Table S205. Gene #35: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	339	433	247
19Q GAIN MUTATED	50	81	74
19Q GAIN WILD-TYPE	289	352	173

Figure S205. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000111 (Fisher's exact test), Q value = 0.052

Table S206. Gene #35: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	531	273	210
19Q GAIN MUTATED	91	80	34
19Q GAIN WILD-TYPE	440	193	176

Figure S206. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MRNA_CNMF'

P value = 5.32e-05 (Chi-square test), Q value = 0.027

Table S207. Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
20P GAIN MUTATED	8	13	49	42	34	41	15	7
20P GAIN WILD-TYPE	13	23	70	54	75	31	5	33

Figure S207. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20p gain' versus 'CN_CNMF'

P value = 8.11e-32 (Chi-square test), Q value = 7.7e-29

Table S208. Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
20P GAIN MUTATED	55	143	60	120	21
20P GAIN WILD-TYPE	322	109	44	132	27

Figure S208. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 3.61e-08 (Chi-square test), Q value = 2.4e-05

Table S209. Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	124	176	104	135	56	116
20P GAIN MUTATED	51	42	46	76	13	38
20P GAIN WILD-TYPE	73	134	58	59	43	78

Figure S209. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 9e-07 (Chi-square test), Q value = 0.00054

Table S210. Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	190	95	257	169	260	48
20P GAIN MUTATED	79	25	75	89	114	13
20P GAIN WILD-TYPE	111	70	182	80	146	35

Figure S210. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.04e-05 (Fisher's exact test), Q value = 0.0056

Table S211. Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	339	433	247
20P GAIN MUTATED	97	194	104
20P GAIN WILD-TYPE	242	239	143

Figure S211. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_CNMF'

P value = 3.99e-08 (Chi-square test), Q value = 2.6e-05

Table S212. Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	194	170	227	251	140	32
20P GAIN MUTATED	82	37	73	117	64	20
20P GAIN WILD-TYPE	112	133	154	134	76	12

Figure S212. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.32e-06 (Fisher's exact test), Q value = 0.00079

Table S213. Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	531	273	210
20P GAIN MUTATED	220	123	50
20P GAIN WILD-TYPE	311	150	160

Figure S213. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MRNA_CNMF'

P value = 7.43e-05 (Chi-square test), Q value = 0.036

Table S214. Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
20Q GAIN MUTATED	7	13	61	40	35	42	15	10
20Q GAIN WILD-TYPE	14	23	58	56	74	30	5	30

Figure S214. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20q gain' versus 'CN_CNMF'

P value = 1.81e-37 (Chi-square test), Q value = 1.7e-34

Table S215. Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
20Q GAIN MUTATED	60	164	59	127	24
20Q GAIN WILD-TYPE	317	88	45	125	24

Figure S215. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 4.37e-13 (Chi-square test), Q value = 3.5e-10

Table S216. Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	124	176	104	135	56	116
20Q GAIN MUTATED	55	45	53	88	12	38
20Q GAIN WILD-TYPE	69	131	51	47	44	78

Figure S216. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 2.81e-10 (Chi-square test), Q value = 2.1e-07

Table S217. Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	190	95	257	169	260	48
20Q GAIN MUTATED	83	26	73	92	138	16
20Q GAIN WILD-TYPE	107	69	184	77	122	32

Figure S217. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.08e-07 (Fisher's exact test), Q value = 0.00013

Table S218. Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	339	433	247
20Q GAIN MUTATED	103	216	109
20Q GAIN WILD-TYPE	236	217	138

Figure S218. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 5.55e-09 (Chi-square test), Q value = 3.8e-06

Table S219. Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	194	170	227	251	140	32
20Q GAIN MUTATED	85	41	82	123	78	20
20Q GAIN WILD-TYPE	109	129	145	128	62	12

Figure S219. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.08e-08 (Fisher's exact test), Q value = 4.6e-05

Table S220. Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	531	273	210
20Q GAIN MUTATED	249	127	53
20Q GAIN WILD-TYPE	282	146	157

Figure S220. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 9.9e-06 (Fisher's exact test), Q value = 0.0054

Table S221. Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	238	218
20Q GAIN MUTATED	119	72	109
20Q GAIN WILD-TYPE	129	166	109

Figure S221. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.57e-06 (Fisher's exact test), Q value = 0.0042

Table S222. Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	358	181
20Q GAIN MUTATED	75	175	50
20Q GAIN WILD-TYPE	90	183	131

Figure S222. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q gain' versus 'MRNA_CNMF'

P value = 5.21e-10 (Chi-square test), Q value = 3.8e-07

Table S223. Gene #38: '21q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
21Q GAIN MUTATED	2	2	16	31	11	31	8	3
21Q GAIN WILD-TYPE	19	34	103	65	98	41	12	37

Figure S223. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'21q gain' versus 'MRNA_CHIERARCHICAL'

P value = 6.2e-07 (Fisher's exact test), Q value = 0.00038

Table S224. Gene #38: '21q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
21Q GAIN MUTATED	11	45	48
21Q GAIN WILD-TYPE	111	80	218

Figure S224. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'21q gain' versus 'CN_CNMF'

P value = 1.58e-14 (Chi-square test), Q value = 1.3e-11

Table S225. Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
21Q GAIN MUTATED	29	42	20	85	12
21Q GAIN WILD-TYPE	348	210	84	167	36

Figure S225. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

'21q gain' versus 'METHLYATION_CNMF'

P value = 3.17e-09 (Chi-square test), Q value = 2.2e-06

Table S226. Gene #38: '21q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	124	176	104	135	56	116
21Q GAIN MUTATED	45	14	20	20	5	15
21Q GAIN WILD-TYPE	79	162	84	115	51	101

Figure S226. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'21q gain' versus 'RPPA_CNMF'

P value = 0.000202 (Fisher's exact test), Q value = 0.089

Table S227. Gene #38: '21q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
21Q GAIN MUTATED	47	16	22
21Q GAIN WILD-TYPE	100	117	95

Figure S227. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'21q gain' versus 'RPPA_CHIERARCHICAL'

P value = 7.86e-05 (Fisher's exact test), Q value = 0.038

Table S228. Gene #38: '21q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	110	126
21Q GAIN MUTATED	24	17	44
21Q GAIN WILD-TYPE	137	93	82

Figure S228. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'21q gain' versus 'MRNASEQ_CNMF'

P value = 1.37e-16 (Chi-square test), Q value = 1.2e-13

Table S229. Gene #38: '21q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	190	95	257	169	260	48
21Q GAIN MUTATED	64	7	25	54	33	2
21Q GAIN WILD-TYPE	126	88	232	115	227	46

Figure S229. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.47e-17 (Fisher's exact test), Q value = 1.3e-14

Table S230. Gene #38: '21q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	339	433	247
21Q GAIN MUTATED	25	71	89
21Q GAIN WILD-TYPE	314	362	158

Figure S230. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'21q gain' versus 'MIRSEQ_CNMF'

P value = 3.4e-07 (Chi-square test), Q value = 0.00021

Table S231. Gene #38: '21q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	194	170	227	251	140	32
21Q GAIN MUTATED	34	23	19	73	29	5
21Q GAIN WILD-TYPE	160	147	208	178	111	27

Figure S231. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'21q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-14 (Fisher's exact test), Q value = 3.3e-11

Table S232. Gene #38: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	531	273	210
21Q GAIN MUTATED	71	93	19
21Q GAIN WILD-TYPE	460	180	191

Figure S232. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'21q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.23e-09 (Fisher's exact test), Q value = 4.3e-06

Table S233. Gene #38: '21q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	238	218
21Q GAIN MUTATED	33	25	69
21Q GAIN WILD-TYPE	215	213	149

Figure S233. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'21q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.47e-07 (Fisher's exact test), Q value = 9.3e-05

Table S234. Gene #38: '21q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	358	181
21Q GAIN MUTATED	55	51	21
21Q GAIN WILD-TYPE	110	307	160

Figure S234. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q gain' versus 'MRNA_CNMF'

P value = 1.66e-05 (Chi-square test), Q value = 0.0088

Table S235. Gene #39: '22q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
22Q GAIN MUTATED	3	0	12	18	2	15	2	0
22Q GAIN WILD-TYPE	18	36	107	78	107	57	18	40

Figure S235. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'22q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1.76e-06 (Fisher's exact test), Q value = 0.001

Table S236. Gene #39: '22q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
22Q GAIN MUTATED	1	24	27
22Q GAIN WILD-TYPE	121	101	239

Figure S236. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'22q gain' versus 'CN_CNMF'

P value = 9.18e-12 (Chi-square test), Q value = 7.1e-09

Table S237. Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
22Q GAIN MUTATED	11	26	2	49	6
22Q GAIN WILD-TYPE	366	226	102	203	42

Figure S237. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

'22q gain' versus 'METHLYATION_CNMF'

P value = 0.000256 (Chi-square test), Q value = 0.11

Table S238. Gene #39: '22q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	124	176	104	135	56	116
22Q GAIN MUTATED	20	5	14	12	1	8
22Q GAIN WILD-TYPE	104	171	90	123	55	108

Figure S238. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q gain' versus 'RPPA_CNMF'

P value = 8.26e-06 (Fisher's exact test), Q value = 0.0045

Table S239. Gene #39: '22q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
22Q GAIN MUTATED	31	5	8
22Q GAIN WILD-TYPE	116	128	109

Figure S239. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'22q gain' versus 'MRNASEQ_CNMF'

P value = 1.92e-10 (Chi-square test), Q value = 1.4e-07

Table S240. Gene #39: '22q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	190	95	257	169	260	48
22Q GAIN MUTATED	34	1	6	28	22	1
22Q GAIN WILD-TYPE	156	94	251	141	238	47

Figure S240. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.66e-15 (Fisher's exact test), Q value = 6.5e-12

Table S241. Gene #39: '22q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	339	433	247
22Q GAIN MUTATED	3	43	46
22Q GAIN WILD-TYPE	336	390	201

Figure S241. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_CNMF'

P value = 2.18e-06 (Chi-square test), Q value = 0.0013

Table S242. Gene #39: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	194	170	227	251	140	32
22Q GAIN MUTATED	16	5	12	44	11	3
22Q GAIN WILD-TYPE	178	165	215	207	129	29

Figure S242. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'22q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.42e-10 (Fisher's exact test), Q value = 2.5e-07

Table S243. Gene #39: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	531	273	210
22Q GAIN MUTATED	37	50	4
22Q GAIN WILD-TYPE	494	223	206

Figure S243. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.55e-06 (Fisher's exact test), Q value = 0.00092

Table S244. Gene #39: '22q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	238	218
22Q GAIN MUTATED	17	8	37
22Q GAIN WILD-TYPE	231	230	181

Figure S244. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'22q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8.55e-08 (Fisher's exact test), Q value = 5.5e-05

Table S245. Gene #39: '22q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	358	181
22Q GAIN MUTATED	31	28	3
22Q GAIN WILD-TYPE	134	330	178

Figure S245. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq gain' versus 'MRNA_CHIERARCHICAL'

P value = 8.96e-05 (Fisher's exact test), Q value = 0.042

Table S246. Gene #40: 'xq gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
XQ GAIN MUTATED	8	33	40
XQ GAIN WILD-TYPE	114	92	226

Figure S246. Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'xq gain' versus 'CN_CNMF'

P value = 6.13e-08 (Chi-square test), Q value = 4e-05

Table S247. Gene #40: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
XQ GAIN MUTATED	17	39	18	49	10
XQ GAIN WILD-TYPE	360	213	86	203	38

Figure S247. Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

'xq gain' versus 'MRNASEQ_CNMF'

P value = 4.15e-06 (Chi-square test), Q value = 0.0024

Table S248. Gene #40: 'xq gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	190	95	257	169	260	48
XQ GAIN MUTATED	42	4	23	30	32	1
XQ GAIN WILD-TYPE	148	91	234	139	228	47

Figure S248. Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'xq gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.18e-06 (Fisher's exact test), Q value = 0.0024

Table S249. Gene #40: 'xq gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	339	433	247
XQ GAIN MUTATED	23	58	51
XQ GAIN WILD-TYPE	316	375	196

Figure S249. Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xq gain' versus 'MIRSEQ_CNMF'

P value = 8.21e-07 (Chi-square test), Q value = 5e-04

Table S250. Gene #40: 'xq gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	194	170	227	251	140	32
XQ GAIN MUTATED	20	5	22	54	21	4
XQ GAIN WILD-TYPE	174	165	205	197	119	28

Figure S250. Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xq gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.2e-06 (Fisher's exact test), Q value = 0.0013

Table S251. Gene #40: 'xq gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	531	273	210
XQ GAIN MUTATED	62	54	10
XQ GAIN WILD-TYPE	469	219	200

Figure S251. Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1p loss' versus 'MRNA_CHIERARCHICAL'

P value = 4.42e-06 (Fisher's exact test), Q value = 0.0025

Table S252. Gene #41: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
1P LOSS MUTATED	19	15	85
1P LOSS WILD-TYPE	103	110	181

Figure S252. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

P value = 1.44e-21 (Chi-square test), Q value = 1.3e-18

Table S253. Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
1P LOSS MUTATED	37	91	50	44	12
1P LOSS WILD-TYPE	340	161	54	208	36

Figure S253. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 2.02e-07 (Chi-square test), Q value = 0.00013

Table S254. Gene #41: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	124	176	104	135	56	116
1P LOSS MUTATED	18	29	38	45	8	14
1P LOSS WILD-TYPE	106	147	66	90	48	102

Figure S254. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 2.2e-06 (Chi-square test), Q value = 0.0013

Table S255. Gene #41: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	190	95	257	169	260	48
1P LOSS MUTATED	22	14	55	52	81	9
1P LOSS WILD-TYPE	168	81	202	117	179	39

Figure S255. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.88e-14 (Fisher's exact test), Q value = 8.1e-11

Table S256. Gene #41: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	339	433	247
1P LOSS MUTATED	53	150	30
1P LOSS WILD-TYPE	286	283	217

Figure S256. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.05e-05 (Fisher's exact test), Q value = 0.043

Table S257. Gene #41: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	531	273	210
1P LOSS MUTATED	148	44	36
1P LOSS WILD-TYPE	383	229	174

Figure S257. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1q loss' versus 'MRNASEQ_CNMF'

P value = 0.000543 (Chi-square test), Q value = 0.22

Table S258. Gene #42: '1q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	190	95	257	169	260	48
1Q LOSS MUTATED	8	2	4	14	24	1
1Q LOSS WILD-TYPE	182	93	253	155	236	47

Figure S258. Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000253 (Fisher's exact test), Q value = 0.11

Table S259. Gene #42: '1q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	339	433	247
1Q LOSS MUTATED	6	35	12
1Q LOSS WILD-TYPE	333	398	235

Figure S259. Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p loss' versus 'MRNA_CHIERARCHICAL'

P value = 6.35e-05 (Fisher's exact test), Q value = 0.031

Table S260. Gene #43: '2p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
2P LOSS MUTATED	15	11	67
2P LOSS WILD-TYPE	107	114	199

Figure S260. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'2p loss' versus 'CN_CNMF'

P value = 2.27e-12 (Chi-square test), Q value = 1.8e-09

Table S261. Gene #43: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
2P LOSS MUTATED	29	75	26	34	11
2P LOSS WILD-TYPE	348	177	78	218	37

Figure S261. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

'2p loss' versus 'METHLYATION_CNMF'

P value = 9.51e-06 (Chi-square test), Q value = 0.0052

Table S262. Gene #43: '2p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	124	176	104	135	56	116
2P LOSS MUTATED	13	28	20	38	4	7
2P LOSS WILD-TYPE	111	148	84	97	52	109

Figure S262. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2p loss' versus 'MRNASEQ_CNMF'

P value = 3.12e-06 (Chi-square test), Q value = 0.0018

Table S263. Gene #43: '2p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	190	95	257	169	260	48
2P LOSS MUTATED	18	11	44	28	70	2
2P LOSS WILD-TYPE	172	84	213	141	190	46

Figure S263. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.35e-11 (Fisher's exact test), Q value = 3.3e-08

Table S264. Gene #43: '2p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	339	433	247
2P LOSS MUTATED	42	113	18
2P LOSS WILD-TYPE	297	320	229

Figure S264. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.025

Table S265. Gene #43: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	531	273	210
2P LOSS MUTATED	116	32	23
2P LOSS WILD-TYPE	415	241	187

Figure S265. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000312 (Fisher's exact test), Q value = 0.13

Table S266. Gene #43: '2p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	358	181
2P LOSS MUTATED	16	77	20
2P LOSS WILD-TYPE	149	281	161

Figure S266. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q loss' versus 'CN_CNMF'

P value = 6.54e-13 (Chi-square test), Q value = 5.3e-10

Table S267. Gene #44: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
2Q LOSS MUTATED	29	79	28	49	14
2Q LOSS WILD-TYPE	348	173	76	203	34

Figure S267. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

'2q loss' versus 'METHLYATION_CNMF'

P value = 1.98e-05 (Chi-square test), Q value = 0.01

Table S268. Gene #44: '2q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	124	176	104	135	56	116
2Q LOSS MUTATED	22	27	18	44	5	11
2Q LOSS WILD-TYPE	102	149	86	91	51	105

Figure S268. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2q loss' versus 'RPPA_CNMF'

P value = 0.000444 (Fisher's exact test), Q value = 0.19

Table S269. Gene #44: '2q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
2Q LOSS MUTATED	32	36	10
2Q LOSS WILD-TYPE	115	97	107

Figure S269. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'2q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.44e-06 (Fisher's exact test), Q value = 0.00086

Table S270. Gene #44: '2q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	339	433	247
2Q LOSS MUTATED	43	115	37
2Q LOSS WILD-TYPE	296	318	210

Figure S270. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MRNA_CNMF'

P value = 4.18e-06 (Chi-square test), Q value = 0.0024

Table S271. Gene #45: '3p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
3P LOSS MUTATED	0	7	19	29	4	18	6	4
3P LOSS WILD-TYPE	21	29	100	67	105	54	14	36

Figure S271. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'3p loss' versus 'MRNA_CHIERARCHICAL'

P value = 6.71e-05 (Fisher's exact test), Q value = 0.033

Table S272. Gene #45: '3p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
3P LOSS MUTATED	15	38	34
3P LOSS WILD-TYPE	107	87	232

Figure S272. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'3p loss' versus 'CN_CNMF'

P value = 8.92e-18 (Chi-square test), Q value = 7.8e-15

Table S273. Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
3P LOSS MUTATED	23	52	13	85	5
3P LOSS WILD-TYPE	354	200	91	167	43

Figure S273. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 6.3e-09 (Chi-square test), Q value = 4.3e-06

Table S274. Gene #45: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	124	176	104	135	56	116
3P LOSS MUTATED	39	10	25	30	5	12
3P LOSS WILD-TYPE	85	166	79	105	51	104

Figure S274. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3p loss' versus 'RPPA_CHIERARCHICAL'

P value = 5.68e-05 (Fisher's exact test), Q value = 0.028

Table S275. Gene #45: '3p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	110	126
3P LOSS MUTATED	20	14	40
3P LOSS WILD-TYPE	141	96	86

Figure S275. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 8.08e-12 (Chi-square test), Q value = 6.3e-09

Table S276. Gene #45: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	190	95	257	169	260	48
3P LOSS MUTATED	55	10	18	49	38	4
3P LOSS WILD-TYPE	135	85	239	120	222	44

Figure S276. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.7e-08 (Fisher's exact test), Q value = 5.6e-05

Table S277. Gene #45: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	339	433	247
3P LOSS MUTATED	36	67	71
3P LOSS WILD-TYPE	303	366	176

Figure S277. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CNMF'

P value = 8.54e-07 (Chi-square test), Q value = 0.00052

Table S278. Gene #45: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	194	170	227	251	140	32
3P LOSS MUTATED	27	16	26	71	26	6
3P LOSS WILD-TYPE	167	154	201	180	114	26

Figure S278. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.46e-07 (Fisher's exact test), Q value = 0.00051

Table S279. Gene #45: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	531	273	210
3P LOSS MUTATED	77	74	21
3P LOSS WILD-TYPE	454	199	189

Figure S279. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.24e-07 (Fisher's exact test), Q value = 7.9e-05

Table S280. Gene #45: '3p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	238	218
3P LOSS MUTATED	33	24	64
3P LOSS WILD-TYPE	215	214	154

Figure S280. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'3p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000138 (Fisher's exact test), Q value = 0.063

Table S281. Gene #45: '3p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	358	181
3P LOSS MUTATED	46	55	20
3P LOSS WILD-TYPE	119	303	161

Figure S281. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

P value = 1.7e-08 (Chi-square test), Q value = 1.2e-05

Table S282. Gene #46: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
3Q LOSS MUTATED	10	32	9	44	4
3Q LOSS WILD-TYPE	367	220	95	208	44

Figure S282. Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

'3q loss' versus 'METHLYATION_CNMF'

P value = 5.87e-05 (Chi-square test), Q value = 0.029

Table S283. Gene #46: '3q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	124	176	104	135	56	116
3Q LOSS MUTATED	22	7	13	20	2	5
3Q LOSS WILD-TYPE	102	169	91	115	54	111

Figure S283. Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3q loss' versus 'MRNASEQ_CNMF'

P value = 1.17e-07 (Chi-square test), Q value = 7.5e-05

Table S284. Gene #46: '3q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	190	95	257	169	260	48
3Q LOSS MUTATED	24	5	8	34	23	2
3Q LOSS WILD-TYPE	166	90	249	135	237	46

Figure S284. Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000166 (Fisher's exact test), Q value = 0.075

Table S285. Gene #46: '3q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	339	433	247
3Q LOSS MUTATED	16	44	36
3Q LOSS WILD-TYPE	323	389	211

Figure S285. Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MRNA_CNMF'

P value = 1.03e-14 (Chi-square test), Q value = 8.6e-12

Table S286. Gene #47: '4p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
4P LOSS MUTATED	4	7	25	60	22	41	8	7
4P LOSS WILD-TYPE	17	29	94	36	87	31	12	33

Figure S286. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'4p loss' versus 'MRNA_CHIERARCHICAL'

P value = 4.87e-14 (Fisher's exact test), Q value = 4e-11

Table S287. Gene #47: '4p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
4P LOSS MUTATED	20	77	77
4P LOSS WILD-TYPE	102	48	189

Figure S287. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

P value = 8.12e-36 (Chi-square test), Q value = 7.7e-33

Table S288. Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
4P LOSS MUTATED	51	72	44	157	13
4P LOSS WILD-TYPE	326	180	60	95	35

Figure S288. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 5.65e-21 (Chi-square test), Q value = 5.1e-18

Table S289. Gene #47: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	124	176	104	135	56	116
4P LOSS MUTATED	84	33	34	32	7	30
4P LOSS WILD-TYPE	40	143	70	103	49	86

Figure S289. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p loss' versus 'RPPA_CNMF'

P value = 2.37e-07 (Fisher's exact test), Q value = 0.00015

Table S290. Gene #47: '4p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
4P LOSS MUTATED	77	39	25
4P LOSS WILD-TYPE	70	94	92

Figure S290. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'4p loss' versus 'RPPA_CHIERARCHICAL'

P value = 3.95e-07 (Fisher's exact test), Q value = 0.00024

Table S291. Gene #47: '4p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	110	126
4P LOSS MUTATED	45	27	69
4P LOSS WILD-TYPE	116	83	57

Figure S291. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 6.39e-29 (Chi-square test), Q value = 6e-26

Table S292. Gene #47: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	190	95	257	169	260	48
4P LOSS MUTATED	121	13	59	77	55	9
4P LOSS WILD-TYPE	69	82	198	92	205	39

Figure S292. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.1e-27 (Fisher's exact test), Q value = 2e-24

Table S293. Gene #47: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	339	433	247
4P LOSS MUTATED	60	124	150
4P LOSS WILD-TYPE	279	309	97

Figure S293. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_CNMF'

P value = 9.59e-23 (Chi-square test), Q value = 8.8e-20

Table S294. Gene #47: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	194	170	227	251	140	32
4P LOSS MUTATED	69	35	32	141	39	10
4P LOSS WILD-TYPE	125	135	195	110	101	22

Figure S294. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.08e-26 (Fisher's exact test), Q value = 5.7e-23

Table S295. Gene #47: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	531	273	210
4P LOSS MUTATED	143	155	28
4P LOSS WILD-TYPE	388	118	182

Figure S295. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.24e-20 (Fisher's exact test), Q value = 3.8e-17

Table S296. Gene #47: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	238	218
4P LOSS MUTATED	67	37	122
4P LOSS WILD-TYPE	181	201	96

Figure S296. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.17e-18 (Fisher's exact test), Q value = 5.4e-15

Table S297. Gene #47: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	358	181
4P LOSS MUTATED	99	96	31
4P LOSS WILD-TYPE	66	262	150

Figure S297. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'MRNA_CNMF'

P value = 3.43e-08 (Chi-square test), Q value = 2.3e-05

Table S298. Gene #48: '4q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
4Q LOSS MUTATED	4	7	24	47	21	36	7	7
4Q LOSS WILD-TYPE	17	29	95	49	88	36	13	33

Figure S298. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'4q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1.93e-08 (Fisher's exact test), Q value = 1.3e-05

Table S299. Gene #48: '4q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
4Q LOSS MUTATED	19	62	72
4Q LOSS WILD-TYPE	103	63	194

Figure S299. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 9.61e-27 (Chi-square test), Q value = 9e-24

Table S300. Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
4Q LOSS MUTATED	47	65	44	132	11
4Q LOSS WILD-TYPE	330	187	60	120	37

Figure S300. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 1.85e-12 (Chi-square test), Q value = 1.5e-09

Table S301. Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	124	176	104	135	56	116
4Q LOSS MUTATED	69	33	30	31	7	28
4Q LOSS WILD-TYPE	55	143	74	104	49	88

Figure S301. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q loss' versus 'RPPA_CNMF'

P value = 0.000127 (Fisher's exact test), Q value = 0.059

Table S302. Gene #48: '4q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
4Q LOSS MUTATED	65	35	25
4Q LOSS WILD-TYPE	82	98	92

Figure S302. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'4q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.000354 (Fisher's exact test), Q value = 0.15

Table S303. Gene #48: '4q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	110	126
4Q LOSS MUTATED	42	26	57
4Q LOSS WILD-TYPE	119	84	69

Figure S303. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 1.49e-18 (Chi-square test), Q value = 1.3e-15

Table S304. Gene #48: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	190	95	257	169	260	48
4Q LOSS MUTATED	97	12	55	72	51	9
4Q LOSS WILD-TYPE	93	83	202	97	209	39

Figure S304. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.46e-18 (Fisher's exact test), Q value = 3.1e-15

Table S305. Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	339	433	247
4Q LOSS MUTATED	53	120	123
4Q LOSS WILD-TYPE	286	313	124

Figure S305. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_CNMF'

P value = 1.54e-12 (Chi-square test), Q value = 1.2e-09

Table S306. Gene #48: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	194	170	227	251	140	32
4Q LOSS MUTATED	65	31	34	112	36	10
4Q LOSS WILD-TYPE	129	139	193	139	104	22

Figure S306. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.78e-17 (Fisher's exact test), Q value = 4.2e-14

Table S307. Gene #48: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	531	273	210
4Q LOSS MUTATED	134	128	26
4Q LOSS WILD-TYPE	397	145	184

Figure S307. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 5.08e-14 (Fisher's exact test), Q value = 4.2e-11

Table S308. Gene #48: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	238	218
4Q LOSS MUTATED	61	33	101
4Q LOSS WILD-TYPE	187	205	117

Figure S308. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.82e-11 (Fisher's exact test), Q value = 1.4e-08

Table S309. Gene #48: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	358	181
4Q LOSS MUTATED	79	90	26
4Q LOSS WILD-TYPE	86	268	155

Figure S309. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p loss' versus 'MRNA_CNMF'

P value = 7.17e-17 (Chi-square test), Q value = 6.3e-14

Table S310. Gene #49: '5p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
5P LOSS MUTATED	1	1	8	41	5	10	1	2
5P LOSS WILD-TYPE	20	35	111	55	104	62	19	38

Figure S310. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'5p loss' versus 'MRNA_CHIERARCHICAL'

P value = 5.82e-12 (Fisher's exact test), Q value = 4.5e-09

Table S311. Gene #49: '5p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
5P LOSS MUTATED	5	42	22
5P LOSS WILD-TYPE	117	83	244

Figure S311. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'5p loss' versus 'CN_CNMF'

P value = 1.81e-38 (Chi-square test), Q value = 1.7e-35

Table S312. Gene #49: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
5P LOSS MUTATED	12	16	4	94	7
5P LOSS WILD-TYPE	365	236	100	158	41

Figure S312. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

'5p loss' versus 'METHLYATION_CNMF'

P value = 1.08e-21 (Chi-square test), Q value = 9.8e-19

Table S313. Gene #49: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	124	176	104	135	56	116
5P LOSS MUTATED	49	4	7	14	1	15
5P LOSS WILD-TYPE	75	172	97	121	55	101

Figure S313. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5p loss' versus 'RPPA_CNMF'

P value = 1.51e-07 (Fisher's exact test), Q value = 9.5e-05

Table S314. Gene #49: '5p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
5P LOSS MUTATED	42	9	9
5P LOSS WILD-TYPE	105	124	108

Figure S314. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'5p loss' versus 'RPPA_CHIERARCHICAL'

P value = 1.91e-09 (Fisher's exact test), Q value = 1.3e-06

Table S315. Gene #49: '5p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	110	126
5P LOSS MUTATED	11	8	41
5P LOSS WILD-TYPE	150	102	85

Figure S315. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'5p loss' versus 'MRNASEQ_CNMF'

P value = 1.12e-39 (Chi-square test), Q value = 1.1e-36

Table S316. Gene #49: '5p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	190	95	257	169	260	48
5P LOSS MUTATED	80	3	4	24	20	1
5P LOSS WILD-TYPE	110	92	253	145	240	47

Figure S316. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.66e-27 (Fisher's exact test), Q value = 2.5e-24

Table S317. Gene #49: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	339	433	247
5P LOSS MUTATED	11	36	85
5P LOSS WILD-TYPE	328	397	162

Figure S317. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_CNMF'

P value = 3.76e-19 (Chi-square test), Q value = 3.4e-16

Table S318. Gene #49: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	194	170	227	251	140	32
5P LOSS MUTATED	14	14	3	73	22	4
5P LOSS WILD-TYPE	180	156	224	178	118	28

Figure S318. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.21e-27 (Fisher's exact test), Q value = 3.9e-24

Table S319. Gene #49: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	531	273	210
5P LOSS MUTATED	33	90	7
5P LOSS WILD-TYPE	498	183	203

Figure S319. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.31e-22 (Fisher's exact test), Q value = 1.2e-19

Table S320. Gene #49: '5p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	238	218
5P LOSS MUTATED	12	7	70
5P LOSS WILD-TYPE	236	231	148

Figure S320. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.91e-19 (Fisher's exact test), Q value = 1.7e-16

Table S321. Gene #49: '5p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	358	181
5P LOSS MUTATED	58	25	6
5P LOSS WILD-TYPE	107	333	175

Figure S321. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q loss' versus 'MRNA_CNMF'

P value = 1.25e-26 (Chi-square test), Q value = 1.2e-23

Table S322. Gene #50: '5q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
5Q LOSS MUTATED	2	3	14	61	4	20	5	3
5Q LOSS WILD-TYPE	19	33	105	35	105	52	15	37

Figure S322. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'5q loss' versus 'MRNA_CHIERARCHICAL'

P value = 3.12e-21 (Fisher's exact test), Q value = 2.8e-18

Table S323. Gene #50: '5q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
5Q LOSS MUTATED	9	68	35
5Q LOSS WILD-TYPE	113	57	231

Figure S323. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'5q loss' versus 'CN_CNMF'

P value = 4.19e-78 (Chi-square test), Q value = 4e-75

Table S324. Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
5Q LOSS MUTATED	16	28	5	160	10
5Q LOSS WILD-TYPE	361	224	99	92	38

Figure S324. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 5.72e-45 (Chi-square test), Q value = 5.5e-42

Table S325. Gene #50: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	124	176	104	135	56	116
5Q LOSS MUTATED	84	4	10	22	4	25
5Q LOSS WILD-TYPE	40	172	94	113	52	91

Figure S325. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5q loss' versus 'RPPA_CNMF'

P value = 3e-13 (Fisher's exact test), Q value = 2.4e-10

Table S326. Gene #50: '5q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
5Q LOSS MUTATED	66	11	18
5Q LOSS WILD-TYPE	81	122	99

Figure S326. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'5q loss' versus 'RPPA_CHIERARCHICAL'

P value = 5.49e-14 (Fisher's exact test), Q value = 4.5e-11

Table S327. Gene #50: '5q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	110	126
5Q LOSS MUTATED	20	13	62
5Q LOSS WILD-TYPE	141	97	64

Figure S327. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 1.09e-63 (Chi-square test), Q value = 1e-60

Table S328. Gene #50: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	190	95	257	169	260	48
5Q LOSS MUTATED	123	8	7	48	31	1
5Q LOSS WILD-TYPE	67	87	250	121	229	47

Figure S328. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.18e-51 (Fisher's exact test), Q value = 6.9e-48

Table S329. Gene #50: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	339	433	247
5Q LOSS MUTATED	20	57	141
5Q LOSS WILD-TYPE	319	376	106

Figure S329. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CNMF'

P value = 4.45e-47 (Chi-square test), Q value = 4.3e-44

Table S330. Gene #50: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	194	170	227	251	140	32
5Q LOSS MUTATED	20	15	7	133	33	6
5Q LOSS WILD-TYPE	174	155	220	118	107	26

Figure S330. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.35e-51 (Fisher's exact test), Q value = 5.1e-48

Table S331. Gene #50: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	531	273	210
5Q LOSS MUTATED	57	148	9
5Q LOSS WILD-TYPE	474	125	201

Figure S331. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.72e-41 (Fisher's exact test), Q value = 4.5e-38

Table S332. Gene #50: '5q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	238	218
5Q LOSS MUTATED	21	12	116
5Q LOSS WILD-TYPE	227	226	102

Figure S332. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.68e-36 (Fisher's exact test), Q value = 2.5e-33

Table S333. Gene #50: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	358	181
5Q LOSS MUTATED	97	40	12
5Q LOSS WILD-TYPE	68	318	169

Figure S333. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p loss' versus 'CN_CNMF'

P value = 4.12e-14 (Chi-square test), Q value = 3.4e-11

Table S334. Gene #51: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
6P LOSS MUTATED	34	80	22	27	14
6P LOSS WILD-TYPE	343	172	82	225	34

Figure S334. Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

'6p loss' versus 'MRNASEQ_CNMF'

P value = 9.2e-05 (Chi-square test), Q value = 0.043

Table S335. Gene #51: '6p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	190	95	257	169	260	48
6P LOSS MUTATED	20	14	38	26	70	6
6P LOSS WILD-TYPE	170	81	219	143	190	42

Figure S335. Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000113 (Fisher's exact test), Q value = 0.053

Table S336. Gene #51: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	339	433	247
6P LOSS MUTATED	47	99	28
6P LOSS WILD-TYPE	292	334	219

Figure S336. Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.000235 (Fisher's exact test), Q value = 0.1

Table S337. Gene #52: '6q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
6Q LOSS MUTATED	35	15	79
6Q LOSS WILD-TYPE	87	110	187

Figure S337. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6q loss' versus 'CN_CNMF'

P value = 2.52e-19 (Chi-square test), Q value = 2.3e-16

Table S338. Gene #52: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
6Q LOSS MUTATED	62	113	31	34	20
6Q LOSS WILD-TYPE	315	139	73	218	28

Figure S338. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

'6q loss' versus 'METHLYATION_CNMF'

P value = 7e-05 (Chi-square test), Q value = 0.034

Table S339. Gene #52: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	124	176	104	135	56	116
6Q LOSS MUTATED	22	48	25	55	8	23
6Q LOSS WILD-TYPE	102	128	79	80	48	93

Figure S339. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6q loss' versus 'MRNASEQ_CNMF'

P value = 1.17e-07 (Chi-square test), Q value = 7.5e-05

Table S340. Gene #52: '6q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	190	95	257	169	260	48
6Q LOSS MUTATED	27	22	55	39	101	12
6Q LOSS WILD-TYPE	163	73	202	130	159	36

Figure S340. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.34e-05 (Fisher's exact test), Q value = 0.017

Table S341. Gene #52: '6q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	339	433	247
6Q LOSS MUTATED	82	135	39
6Q LOSS WILD-TYPE	257	298	208

Figure S341. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.79e-05 (Fisher's exact test), Q value = 0.029

Table S342. Gene #52: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	531	273	210
6Q LOSS MUTATED	162	45	51
6Q LOSS WILD-TYPE	369	228	159

Figure S342. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7p loss' versus 'CN_CNMF'

P value = 1.39e-12 (Chi-square test), Q value = 1.1e-09

Table S343. Gene #53: '7p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
7P LOSS MUTATED	10	39	5	51	3
7P LOSS WILD-TYPE	367	213	99	201	45

Figure S343. Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #3: 'CN_CNMF'

'7p loss' versus 'METHLYATION_CNMF'

P value = 0.000128 (Chi-square test), Q value = 0.059

Table S344. Gene #53: '7p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	124	176	104	135	56	116
7P LOSS MUTATED	24	10	10	18	1	6
7P LOSS WILD-TYPE	100	166	94	117	55	110

Figure S344. Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p loss' versus 'MRNASEQ_CNMF'

P value = 2.84e-05 (Chi-square test), Q value = 0.015

Table S345. Gene #53: '7p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	190	95	257	169	260	48
7P LOSS MUTATED	33	2	13	23	32	3
7P LOSS WILD-TYPE	157	93	244	146	228	45

Figure S345. Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.56e-06 (Fisher's exact test), Q value = 0.0047

Table S346. Gene #53: '7p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	339	433	247
7P LOSS MUTATED	15	53	38
7P LOSS WILD-TYPE	324	380	209

Figure S346. Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7p loss' versus 'MIRSEQ_CNMF'

P value = 8.01e-05 (Chi-square test), Q value = 0.038

Table S347. Gene #53: '7p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	194	170	227	251	140	32
7P LOSS MUTATED	16	5	20	44	18	3
7P LOSS WILD-TYPE	178	165	207	207	122	29

Figure S347. Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.91e-06 (Fisher's exact test), Q value = 0.0038

Table S348. Gene #53: '7p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	531	273	210
7P LOSS MUTATED	54	45	7
7P LOSS WILD-TYPE	477	228	203

Figure S348. Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.82e-05 (Fisher's exact test), Q value = 0.014

Table S349. Gene #53: '7p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	238	218
7P LOSS MUTATED	16	11	36
7P LOSS WILD-TYPE	232	227	182

Figure S349. Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000277 (Fisher's exact test), Q value = 0.12

Table S350. Gene #53: '7p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	358	181
7P LOSS MUTATED	27	29	7
7P LOSS WILD-TYPE	138	329	174

Figure S350. Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q loss' versus 'CN_CNMF'

P value = 7.41e-06 (Chi-square test), Q value = 0.0041

Table S351. Gene #54: '7q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
7Q LOSS MUTATED	20	44	10	39	3
7Q LOSS WILD-TYPE	357	208	94	213	45

Figure S351. Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #3: 'CN_CNMF'

'7q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000202 (Fisher's exact test), Q value = 0.089

Table S352. Gene #54: '7q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	339	433	247
7Q LOSS MUTATED	22	68	24
7Q LOSS WILD-TYPE	317	365	223

Figure S352. Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'MRNA_CNMF'

P value = 7.41e-06 (Chi-square test), Q value = 0.0041

Table S353. Gene #55: '8p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
8P LOSS MUTATED	4	10	56	45	21	37	11	17
8P LOSS WILD-TYPE	17	26	63	51	88	35	9	23

Figure S353. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'8p loss' versus 'CN_CNMF'

P value = 1.76e-18 (Chi-square test), Q value = 1.6e-15

Table S354. Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
8P LOSS MUTATED	84	123	19	130	19
8P LOSS WILD-TYPE	293	129	85	122	29

Figure S354. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 1.09e-06 (Chi-square test), Q value = 0.00065

Table S355. Gene #55: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	124	176	104	135	56	116
8P LOSS MUTATED	54	39	37	66	10	39
8P LOSS WILD-TYPE	70	137	67	69	46	77

Figure S355. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 2.43e-12 (Chi-square test), Q value = 1.9e-09

Table S356. Gene #55: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	190	95	257	169	260	48
8P LOSS MUTATED	82	25	50	91	103	17
8P LOSS WILD-TYPE	108	70	207	78	157	31

Figure S356. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.87e-06 (Fisher's exact test), Q value = 0.0048

Table S357. Gene #55: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	339	433	247
8P LOSS MUTATED	90	167	111
8P LOSS WILD-TYPE	249	266	136

Figure S357. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_CNMF'

P value = 5.11e-07 (Chi-square test), Q value = 0.00031

Table S358. Gene #55: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	194	170	227	251	140	32
8P LOSS MUTATED	72	37	67	119	62	12
8P LOSS WILD-TYPE	122	133	160	132	78	20

Figure S358. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.09e-07 (Fisher's exact test), Q value = 0.00055

Table S359. Gene #55: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	531	273	210
8P LOSS MUTATED	191	128	50
8P LOSS WILD-TYPE	340	145	160

Figure S359. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 5.03e-06 (Fisher's exact test), Q value = 0.0028

Table S360. Gene #55: '8p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	238	218
8P LOSS MUTATED	96	56	97
8P LOSS WILD-TYPE	152	182	121

Figure S360. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9p loss' versus 'MRNA_CNMF'

P value = 1.79e-05 (Chi-square test), Q value = 0.0094

Table S361. Gene #57: '9p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
9P LOSS MUTATED	7	10	53	30	18	33	9	6
9P LOSS WILD-TYPE	14	26	66	66	91	39	11	34

Figure S361. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'9p loss' versus 'MRNA_CHIERARCHICAL'

P value = 6.23e-05 (Fisher's exact test), Q value = 0.031

Table S362. Gene #57: '9p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
9P LOSS MUTATED	21	41	104
9P LOSS WILD-TYPE	101	84	162

Figure S362. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

P value = 1.98e-41 (Chi-square test), Q value = 1.9e-38

Table S363. Gene #57: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
9P LOSS MUTATED	32	146	18	99	12
9P LOSS WILD-TYPE	345	106	86	153	36

Figure S363. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 6.78e-16 (Chi-square test), Q value = 5.8e-13

Table S364. Gene #57: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	124	176	104	135	56	116
9P LOSS MUTATED	46	20	37	70	11	18
9P LOSS WILD-TYPE	78	156	67	65	45	98

Figure S364. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 1.46e-16 (Chi-square test), Q value = 1.3e-13

Table S365. Gene #57: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	190	95	257	169	260	48
9P LOSS MUTATED	55	16	34	73	114	9
9P LOSS WILD-TYPE	135	79	223	96	146	39

Figure S365. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.19e-11 (Fisher's exact test), Q value = 9.1e-09

Table S366. Gene #57: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	339	433	247
9P LOSS MUTATED	54	166	81
9P LOSS WILD-TYPE	285	267	166

Figure S366. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_CNMF'

P value = 2.35e-11 (Chi-square test), Q value = 1.8e-08

Table S367. Gene #57: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	194	170	227	251	140	32
9P LOSS MUTATED	60	21	52	93	67	8
9P LOSS WILD-TYPE	134	149	175	158	73	24

Figure S367. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.74e-10 (Fisher's exact test), Q value = 6.9e-07

Table S368. Gene #57: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	531	273	210
9P LOSS MUTATED	168	105	28
9P LOSS WILD-TYPE	363	168	182

Figure S368. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.64e-09 (Fisher's exact test), Q value = 1.2e-06

Table S369. Gene #57: '9p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	238	218
9P LOSS MUTATED	74	35	89
9P LOSS WILD-TYPE	174	203	129

Figure S369. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.67e-05 (Fisher's exact test), Q value = 0.0088

Table S370. Gene #57: '9p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	358	181
9P LOSS MUTATED	64	104	30
9P LOSS WILD-TYPE	101	254	151

Figure S370. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q loss' versus 'MRNA_CNMF'

P value = 0.000199 (Chi-square test), Q value = 0.088

Table S371. Gene #58: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
9Q LOSS MUTATED	7	5	42	41	19	23	7	5
9Q LOSS WILD-TYPE	14	31	77	55	90	49	13	35

Figure S371. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'9q loss' versus 'MRNA_CHIERARCHICAL'

P value = 3.55e-06 (Fisher's exact test), Q value = 0.002

Table S372. Gene #58: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
9Q LOSS MUTATED	15	47	87
9Q LOSS WILD-TYPE	107	78	179

Figure S372. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 7.71e-31 (Chi-square test), Q value = 7.3e-28

Table S373. Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
9Q LOSS MUTATED	29	113	17	106	13
9Q LOSS WILD-TYPE	348	139	87	146	35

Figure S373. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 6.57e-16 (Chi-square test), Q value = 5.6e-13

Table S374. Gene #58: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	124	176	104	135	56	116
9Q LOSS MUTATED	56	18	28	59	6	19
9Q LOSS WILD-TYPE	68	158	76	76	50	97

Figure S374. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q loss' versus 'RPPA_CNMF'

P value = 6.52e-06 (Fisher's exact test), Q value = 0.0036

Table S375. Gene #58: '9q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
9Q LOSS MUTATED	65	29	23
9Q LOSS WILD-TYPE	82	104	94

Figure S375. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'9q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.000581 (Fisher's exact test), Q value = 0.24

Table S376. Gene #58: '9q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	110	126
9Q LOSS MUTATED	42	22	53
9Q LOSS WILD-TYPE	119	88	73

Figure S376. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 1.01e-14 (Chi-square test), Q value = 8.5e-12

Table S377. Gene #58: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	190	95	257	169	260	48
9Q LOSS MUTATED	74	10	32	52	98	7
9Q LOSS WILD-TYPE	116	85	225	117	162	41

Figure S377. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.51e-13 (Fisher's exact test), Q value = 6e-10

Table S378. Gene #58: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	339	433	247
9Q LOSS MUTATED	44	137	92
9Q LOSS WILD-TYPE	295	296	155

Figure S378. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_CNMF'

P value = 1.39e-13 (Chi-square test), Q value = 1.1e-10

Table S379. Gene #58: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	194	170	227	251	140	32
9Q LOSS MUTATED	44	18	44	106	51	6
9Q LOSS WILD-TYPE	150	152	183	145	89	26

Figure S379. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.46e-16 (Fisher's exact test), Q value = 5.6e-13

Table S380. Gene #58: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	531	273	210
9Q LOSS MUTATED	136	114	19
9Q LOSS WILD-TYPE	395	159	191

Figure S380. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.15e-11 (Fisher's exact test), Q value = 3.1e-08

Table S381. Gene #58: '9q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	238	218
9Q LOSS MUTATED	55	32	90
9Q LOSS WILD-TYPE	193	206	128

Figure S381. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.17e-10 (Fisher's exact test), Q value = 4.4e-07

Table S382. Gene #58: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	358	181
9Q LOSS MUTATED	70	85	22
9Q LOSS WILD-TYPE	95	273	159

Figure S382. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 8.17e-06 (Chi-square test), Q value = 0.0045

Table S383. Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
10P LOSS MUTATED	31	53	21	53	11
10P LOSS WILD-TYPE	346	199	83	199	37

Figure S383. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 2.08e-05 (Chi-square test), Q value = 0.011

Table S384. Gene #59: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	124	176	104	135	56	116
10P LOSS MUTATED	34	21	16	34	9	7
10P LOSS WILD-TYPE	90	155	88	101	47	109

Figure S384. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q loss' versus 'CN_CNMF'

P value = 1.04e-13 (Chi-square test), Q value = 8.5e-11

Table S385. Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
10Q LOSS MUTATED	33	68	22	86	15
10Q LOSS WILD-TYPE	344	184	82	166	33

Figure S385. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 1.27e-12 (Chi-square test), Q value = 1e-09

Table S386. Gene #60: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	124	176	104	135	56	116
10Q LOSS MUTATED	53	20	24	47	9	11
10Q LOSS WILD-TYPE	71	156	80	88	47	105

Figure S386. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 6.12e-11 (Chi-square test), Q value = 4.6e-08

Table S387. Gene #60: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	190	95	257	169	260	48
10Q LOSS MUTATED	63	12	26	53	61	3
10Q LOSS WILD-TYPE	127	83	231	116	199	45

Figure S387. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.73e-08 (Fisher's exact test), Q value = 1.2e-05

Table S388. Gene #60: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	339	433	247
10Q LOSS MUTATED	40	100	78
10Q LOSS WILD-TYPE	299	333	169

Figure S388. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_CNMF'

P value = 2.73e-06 (Chi-square test), Q value = 0.0016

Table S389. Gene #60: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	194	170	227	251	140	32
10Q LOSS MUTATED	41	22	31	79	39	7
10Q LOSS WILD-TYPE	153	148	196	172	101	25

Figure S389. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.06e-07 (Fisher's exact test), Q value = 6.8e-05

Table S390. Gene #60: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	531	273	210
10Q LOSS MUTATED	103	90	26
10Q LOSS WILD-TYPE	428	183	184

Figure S390. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.93e-05 (Fisher's exact test), Q value = 0.034

Table S391. Gene #60: '10q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	238	218
10Q LOSS MUTATED	51	36	70
10Q LOSS WILD-TYPE	197	202	148

Figure S391. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000603 (Fisher's exact test), Q value = 0.25

Table S392. Gene #60: '10q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	358	181
10Q LOSS MUTATED	55	71	31
10Q LOSS WILD-TYPE	110	287	150

Figure S392. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 3.38e-20 (Chi-square test), Q value = 3.1e-17

Table S393. Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
11P LOSS MUTATED	33	97	29	94	10
11P LOSS WILD-TYPE	344	155	75	158	38

Figure S393. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 3.37e-09 (Chi-square test), Q value = 2.4e-06

Table S394. Gene #61: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	124	176	104	135	56	116
11P LOSS MUTATED	41	20	33	53	11	16
11P LOSS WILD-TYPE	83	156	71	82	45	100

Figure S394. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p loss' versus 'MRNASEQ_CNMF'

P value = 9.94e-11 (Chi-square test), Q value = 7.4e-08

Table S395. Gene #61: '11p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	190	95	257	169	260	48
11P LOSS MUTATED	57	17	26	61	87	12
11P LOSS WILD-TYPE	133	78	231	108	173	36

Figure S395. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.88e-06 (Fisher's exact test), Q value = 0.0022

Table S396. Gene #61: '11p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	339	433	247
11P LOSS MUTATED	55	126	79
11P LOSS WILD-TYPE	284	307	168

Figure S396. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_CNMF'

P value = 1.35e-05 (Chi-square test), Q value = 0.0072

Table S397. Gene #61: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	194	170	227	251	140	32
11P LOSS MUTATED	45	25	45	86	47	7
11P LOSS WILD-TYPE	149	145	182	165	93	25

Figure S397. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.32e-05 (Fisher's exact test), Q value = 0.007

Table S398. Gene #61: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	531	273	210
11P LOSS MUTATED	144	83	28
11P LOSS WILD-TYPE	387	190	182

Figure S398. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.65e-05 (Fisher's exact test), Q value = 0.014

Table S399. Gene #61: '11p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	238	218
11P LOSS MUTATED	58	38	75
11P LOSS WILD-TYPE	190	200	143

Figure S399. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000178 (Fisher's exact test), Q value = 0.08

Table S400. Gene #61: '11p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	358	181
11P LOSS MUTATED	56	88	27
11P LOSS WILD-TYPE	109	270	154

Figure S400. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q loss' versus 'MRNA_CNMF'

P value = 0.000165 (Chi-square test), Q value = 0.074

Table S401. Gene #62: '11q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
11Q LOSS MUTATED	5	16	64	27	26	26	6	15
11Q LOSS WILD-TYPE	16	20	55	69	83	46	14	25

Figure S401. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'11q loss' versus 'CN_CNMF'

P value = 7.64e-23 (Chi-square test), Q value = 7e-20

Table S402. Gene #62: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
11Q LOSS MUTATED	67	146	36	88	13
11Q LOSS WILD-TYPE	310	106	68	164	35

Figure S402. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

P value = 6.62e-09 (Chi-square test), Q value = 4.5e-06

Table S403. Gene #62: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	124	176	104	135	56	116
11Q LOSS MUTATED	38	43	44	73	16	23
11Q LOSS WILD-TYPE	86	133	60	62	40	93

Figure S403. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11q loss' versus 'MRNASEQ_CNMF'

P value = 8.26e-15 (Chi-square test), Q value = 6.9e-12

Table S404. Gene #62: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	190	95	257	169	260	48
11Q LOSS MUTATED	53	29	49	58	140	15
11Q LOSS WILD-TYPE	137	66	208	111	120	33

Figure S404. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000103 (Fisher's exact test), Q value = 0.048

Table S405. Gene #62: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	531	273	210
11Q LOSS MUTATED	209	83	50
11Q LOSS WILD-TYPE	322	190	160

Figure S405. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.000298 (Fisher's exact test), Q value = 0.13

Table S406. Gene #63: '12p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
12P LOSS MUTATED	10	32	32
12P LOSS WILD-TYPE	112	93	234

Figure S406. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'12p loss' versus 'CN_CNMF'

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

Table S407. Gene #63: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
12P LOSS MUTATED	33	36	11	64	1
12P LOSS WILD-TYPE	344	216	93	188	47

Figure S407. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

'12p loss' versus 'METHLYATION_CNMF'

P value = 5.11e-08 (Chi-square test), Q value = 3.4e-05

Table S408. Gene #63: '12p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	124	176	104	135	56	116
12P LOSS MUTATED	39	12	13	17	8	10
12P LOSS WILD-TYPE	85	164	91	118	48	106

Figure S408. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p loss' versus 'MRNASEQ_CNMF'

P value = 2.18e-08 (Chi-square test), Q value = 1.5e-05

Table S409. Gene #63: '12p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	190	95	257	169	260	48
12P LOSS MUTATED	53	13	18	26	29	4
12P LOSS WILD-TYPE	137	82	239	143	231	44

Figure S409. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.09e-08 (Fisher's exact test), Q value = 2.1e-05

Table S410. Gene #63: '12p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	339	433	247
12P LOSS MUTATED	32	47	64
12P LOSS WILD-TYPE	307	386	183

Figure S410. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p loss' versus 'MIRSEQ_CNMF'

P value = 3.19e-07 (Chi-square test), Q value = 2e-04

Table S411. Gene #63: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	194	170	227	251	140	32
12P LOSS MUTATED	25	14	14	59	27	4
12P LOSS WILD-TYPE	169	156	213	192	113	28

Figure S411. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.36e-08 (Fisher's exact test), Q value = 4.2e-05

Table S412. Gene #63: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	531	273	210
12P LOSS MUTATED	63	66	14
12P LOSS WILD-TYPE	468	207	196

Figure S412. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 5.97e-06 (Fisher's exact test), Q value = 0.0033

Table S413. Gene #63: '12p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	238	218
12P LOSS MUTATED	27	20	52
12P LOSS WILD-TYPE	221	218	166

Figure S413. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8.87e-05 (Fisher's exact test), Q value = 0.042

Table S414. Gene #63: '12p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	358	181
12P LOSS MUTATED	40	44	15
12P LOSS WILD-TYPE	125	314	166

Figure S414. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q loss' versus 'MRNA_CNMF'

P value = 7.12e-10 (Chi-square test), Q value = 5.1e-07

Table S415. Gene #64: '12q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
12Q LOSS MUTATED	2	3	7	32	5	6	2	2
12Q LOSS WILD-TYPE	19	33	112	64	104	66	18	38

Figure S415. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'12q loss' versus 'MRNA_CHIERARCHICAL'

P value = 4.76e-09 (Fisher's exact test), Q value = 3.3e-06

Table S416. Gene #64: '12q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
12Q LOSS MUTATED	6	35	18
12Q LOSS WILD-TYPE	116	90	248

Figure S416. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'12q loss' versus 'CN_CNMF'

P value = 4.46e-20 (Chi-square test), Q value = 4e-17

Table S417. Gene #64: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
12Q LOSS MUTATED	20	18	10	74	2
12Q LOSS WILD-TYPE	357	234	94	178	46

Figure S417. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

'12q loss' versus 'METHLYATION_CNMF'

P value = 1.34e-21 (Chi-square test), Q value = 1.2e-18

Table S418. Gene #64: '12q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	124	176	104	135	56	116
12Q LOSS MUTATED	49	6	13	10	2	8
12Q LOSS WILD-TYPE	75	170	91	125	54	108

Figure S418. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12q loss' versus 'RPPA_CNMF'

P value = 0.000246 (Fisher's exact test), Q value = 0.11

Table S419. Gene #64: '12q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
12Q LOSS MUTATED	31	9	8
12Q LOSS WILD-TYPE	116	124	109

Figure S419. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'12q loss' versus 'RPPA_CHIERARCHICAL'

P value = 2.75e-06 (Fisher's exact test), Q value = 0.0016

Table S420. Gene #64: '12q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	110	126
12Q LOSS MUTATED	12	5	31
12Q LOSS WILD-TYPE	149	105	95

Figure S420. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'12q loss' versus 'MRNASEQ_CNMF'

P value = 2.7e-22 (Chi-square test), Q value = 2.5e-19

Table S421. Gene #64: '12q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	190	95	257	169	260	48
12Q LOSS MUTATED	65	8	15	15	16	3
12Q LOSS WILD-TYPE	125	87	242	154	244	45

Figure S421. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.06e-17 (Fisher's exact test), Q value = 9.3e-15

Table S422. Gene #64: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	339	433	247
12Q LOSS MUTATED	22	28	72
12Q LOSS WILD-TYPE	317	405	175

Figure S422. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q loss' versus 'MIRSEQ_CNMF'

P value = 3.1e-14 (Chi-square test), Q value = 2.6e-11

Table S423. Gene #64: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	194	170	227	251	140	32
12Q LOSS MUTATED	13	16	7	66	16	3
12Q LOSS WILD-TYPE	181	154	220	185	124	29

Figure S423. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.21e-14 (Fisher's exact test), Q value = 1e-11

Table S424. Gene #64: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	531	273	210
12Q LOSS MUTATED	40	71	10
12Q LOSS WILD-TYPE	491	202	200

Figure S424. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.05e-12 (Fisher's exact test), Q value = 8.4e-10

Table S425. Gene #64: '12q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	238	218
12Q LOSS MUTATED	17	16	62
12Q LOSS WILD-TYPE	231	222	156

Figure S425. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9.06e-13 (Fisher's exact test), Q value = 7.2e-10

Table S426. Gene #64: '12q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	358	181
12Q LOSS MUTATED	53	30	12
12Q LOSS WILD-TYPE	112	328	169

Figure S426. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q loss' versus 'MRNA_CNMF'

P value = 5.59e-05 (Chi-square test), Q value = 0.028

Table S427. Gene #65: '13q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
13Q LOSS MUTATED	7	14	62	51	30	38	9	8
13Q LOSS WILD-TYPE	14	22	57	45	79	34	11	32

Figure S427. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'13q loss' versus 'MRNA_CHIERARCHICAL'

P value = 6.32e-06 (Fisher's exact test), Q value = 0.0035

Table S428. Gene #65: '13q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
13Q LOSS MUTATED	31	69	119
13Q LOSS WILD-TYPE	91	56	147

Figure S428. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 1.26e-24 (Chi-square test), Q value = 1.2e-21

Table S429. Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
13Q LOSS MUTATED	72	138	53	132	28
13Q LOSS WILD-TYPE	305	114	51	120	20

Figure S429. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 7.26e-08 (Chi-square test), Q value = 4.7e-05

Table S430. Gene #65: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	124	176	104	135	56	116
13Q LOSS MUTATED	71	51	52	63	12	38
13Q LOSS WILD-TYPE	53	125	52	72	44	78

Figure S430. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 1.02e-10 (Chi-square test), Q value = 7.6e-08

Table S431. Gene #65: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	190	95	257	169	260	48
13Q LOSS MUTATED	103	27	70	86	118	11
13Q LOSS WILD-TYPE	87	68	187	83	142	37

Figure S431. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.14e-11 (Fisher's exact test), Q value = 3.1e-08

Table S432. Gene #65: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	339	433	247
13Q LOSS MUTATED	90	194	131
13Q LOSS WILD-TYPE	249	239	116

Figure S432. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_CNMF'

P value = 8.33e-08 (Chi-square test), Q value = 5.4e-05

Table S433. Gene #65: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	194	170	227	251	140	32
13Q LOSS MUTATED	75	38	93	133	64	12
13Q LOSS WILD-TYPE	119	132	134	118	76	20

Figure S433. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'13q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.24e-08 (Fisher's exact test), Q value = 2.8e-05

Table S434. Gene #65: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	531	273	210
13Q LOSS MUTATED	220	141	54
13Q LOSS WILD-TYPE	311	132	156

Figure S434. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 5.92e-08 (Fisher's exact test), Q value = 3.9e-05

Table S435. Gene #65: '13q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	238	218
13Q LOSS MUTATED	90	67	118
13Q LOSS WILD-TYPE	158	171	100

Figure S435. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'13q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.86e-06 (Fisher's exact test), Q value = 0.0028

Table S436. Gene #65: '13q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	358	181
13Q LOSS MUTATED	89	135	51
13Q LOSS WILD-TYPE	76	223	130

Figure S436. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q loss' versus 'MRNA_CNMF'

P value = 1.2e-14 (Chi-square test), Q value = 1e-11

Table S437. Gene #66: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
14Q LOSS MUTATED	3	1	30	50	7	14	9	5
14Q LOSS WILD-TYPE	18	35	89	46	102	58	11	35

Figure S437. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'14q loss' versus 'MRNA_CHIERARCHICAL'

P value = 5.9e-10 (Fisher's exact test), Q value = 4.3e-07

Table S438. Gene #66: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
14Q LOSS MUTATED	14	56	49
14Q LOSS WILD-TYPE	108	69	217

Figure S438. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 9.74e-38 (Chi-square test), Q value = 9.3e-35

Table S439. Gene #66: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
14Q LOSS MUTATED	29	55	20	136	11
14Q LOSS WILD-TYPE	348	197	84	116	37

Figure S439. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 6.72e-22 (Chi-square test), Q value = 6.1e-19

Table S440. Gene #66: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	124	176	104	135	56	116
14Q LOSS MUTATED	74	16	26	32	8	22
14Q LOSS WILD-TYPE	50	160	78	103	48	94

Figure S440. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q loss' versus 'RPPA_CNMF'

P value = 5.79e-06 (Fisher's exact test), Q value = 0.0032

Table S441. Gene #66: '14q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
14Q LOSS MUTATED	54	16	25
14Q LOSS WILD-TYPE	93	117	92

Figure S441. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'14q loss' versus 'RPPA_CHIERARCHICAL'

P value = 4.45e-06 (Fisher's exact test), Q value = 0.0025

Table S442. Gene #66: '14q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	110	126
14Q LOSS MUTATED	24	21	50
14Q LOSS WILD-TYPE	137	89	76

Figure S442. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 3.68e-32 (Chi-square test), Q value = 3.5e-29

Table S443. Gene #66: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	190	95	257	169	260	48
14Q LOSS MUTATED	108	8	25	44	56	6
14Q LOSS WILD-TYPE	82	87	232	125	204	42

Figure S443. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.2e-24 (Fisher's exact test), Q value = 2e-21

Table S444. Gene #66: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	339	433	247
14Q LOSS MUTATED	42	83	122
14Q LOSS WILD-TYPE	297	350	125

Figure S444. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_CNMF'

P value = 1.23e-24 (Chi-square test), Q value = 1.1e-21

Table S445. Gene #66: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	194	170	227	251	140	32
14Q LOSS MUTATED	31	25	29	123	34	2
14Q LOSS WILD-TYPE	163	145	198	128	106	30

Figure S445. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'14q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.92e-26 (Fisher's exact test), Q value = 1.8e-23

Table S446. Gene #66: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	531	273	210
14Q LOSS MUTATED	88	133	23
14Q LOSS WILD-TYPE	443	140	187

Figure S446. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 8.33e-19 (Fisher's exact test), Q value = 7.4e-16

Table S447. Gene #66: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	238	218
14Q LOSS MUTATED	45	31	106
14Q LOSS WILD-TYPE	203	207	112

Figure S447. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'14q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.57e-18 (Fisher's exact test), Q value = 4.9e-15

Table S448. Gene #66: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	358	181
14Q LOSS MUTATED	88	68	26
14Q LOSS WILD-TYPE	77	290	155

Figure S448. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q loss' versus 'MRNA_CNMF'

P value = 1.95e-05 (Chi-square test), Q value = 0.01

Table S449. Gene #67: '15q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
15Q LOSS MUTATED	4	9	31	45	22	33	8	6
15Q LOSS WILD-TYPE	17	27	88	51	87	39	12	34

Figure S449. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'15q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1.14e-05 (Fisher's exact test), Q value = 0.0061

Table S450. Gene #67: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
15Q LOSS MUTATED	20	55	83
15Q LOSS WILD-TYPE	102	70	183

Figure S450. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 1.61e-31 (Chi-square test), Q value = 1.5e-28

Table S451. Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
15Q LOSS MUTATED	35	82	44	134	13
15Q LOSS WILD-TYPE	342	170	60	118	35

Figure S451. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 9.84e-14 (Chi-square test), Q value = 8e-11

Table S452. Gene #67: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	124	176	104	135	56	116
15Q LOSS MUTATED	69	26	33	49	10	24
15Q LOSS WILD-TYPE	55	150	71	86	46	92

Figure S452. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 1.99e-16 (Chi-square test), Q value = 1.7e-13

Table S453. Gene #67: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	190	95	257	169	260	48
15Q LOSS MUTATED	95	13	48	72	71	7
15Q LOSS WILD-TYPE	95	82	209	97	189	41

Figure S453. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.43e-13 (Fisher's exact test), Q value = 1.2e-10

Table S454. Gene #67: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	339	433	247
15Q LOSS MUTATED	56	138	112
15Q LOSS WILD-TYPE	283	295	135

Figure S454. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_CNMF'

P value = 5.19e-14 (Chi-square test), Q value = 4.3e-11

Table S455. Gene #67: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	194	170	227	251	140	32
15Q LOSS MUTATED	60	22	44	118	44	11
15Q LOSS WILD-TYPE	134	148	183	133	96	21

Figure S455. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.39e-17 (Fisher's exact test), Q value = 1.2e-14

Table S456. Gene #67: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	531	273	210
15Q LOSS MUTATED	151	126	22
15Q LOSS WILD-TYPE	380	147	188

Figure S456. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.66e-12 (Fisher's exact test), Q value = 2.1e-09

Table S457. Gene #67: '15q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	238	218
15Q LOSS MUTATED	72	34	98
15Q LOSS WILD-TYPE	176	204	120

Figure S457. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9.82e-10 (Fisher's exact test), Q value = 7e-07

Table S458. Gene #67: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	358	181
15Q LOSS MUTATED	78	97	29
15Q LOSS WILD-TYPE	87	261	152

Figure S458. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p loss' versus 'CN_CNMF'

P value = 2.63e-05 (Chi-square test), Q value = 0.014

Table S459. Gene #68: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
16P LOSS MUTATED	47	34	9	64	10
16P LOSS WILD-TYPE	330	218	95	188	38

Figure S459. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

'16p loss' versus 'MIRSEQ_CNMF'

P value = 0.000493 (Chi-square test), Q value = 0.21

Table S460. Gene #68: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	194	170	227	251	140	32
16P LOSS MUTATED	24	20	25	61	26	6
16P LOSS WILD-TYPE	170	150	202	190	114	26

Figure S460. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.081

Table S461. Gene #68: '16p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	238	218
16P LOSS MUTATED	27	36	55
16P LOSS WILD-TYPE	221	202	163

Figure S461. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000117 (Fisher's exact test), Q value = 0.055

Table S462. Gene #68: '16p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	358	181
16P LOSS MUTATED	46	45	27
16P LOSS WILD-TYPE	119	313	154

Figure S462. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q loss' versus 'MRNA_CNMF'

P value = 3.55e-09 (Chi-square test), Q value = 2.5e-06

Table S463. Gene #69: '16q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
16Q LOSS MUTATED	12	21	62	28	82	38	12	31
16Q LOSS WILD-TYPE	9	15	57	68	27	34	8	9

Figure S463. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'16q loss' versus 'MRNA_CHIERARCHICAL'

P value = 9.94e-11 (Fisher's exact test), Q value = 7.4e-08

Table S464. Gene #69: '16q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
16Q LOSS MUTATED	78	37	171
16Q LOSS WILD-TYPE	44	88	95

Figure S464. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'16q loss' versus 'CN_CNMF'

P value = 3.47e-09 (Chi-square test), Q value = 2.4e-06

Table S465. Gene #69: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
16Q LOSS MUTATED	229	131	80	105	30
16Q LOSS WILD-TYPE	148	121	24	147	18

Figure S465. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 9.04e-10 (Chi-square test), Q value = 6.4e-07

Table S466. Gene #69: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	124	176	104	135	56	116
16Q LOSS MUTATED	50	129	71	63	29	52
16Q LOSS WILD-TYPE	74	47	33	72	27	64

Figure S466. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16q loss' versus 'RPPA_CNMF'

P value = 5.4e-05 (Fisher's exact test), Q value = 0.027

Table S467. Gene #69: '16q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
16Q LOSS MUTATED	58	87	66
16Q LOSS WILD-TYPE	89	46	51

Figure S467. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'16q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1.62e-07 (Fisher's exact test), Q value = 1e-04

Table S468. Gene #69: '16q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	110	126
16Q LOSS MUTATED	106	63	42
16Q LOSS WILD-TYPE	55	47	84

Figure S468. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 5.85e-21 (Chi-square test), Q value = 5.3e-18

Table S469. Gene #69: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	190	95	257	169	260	48
16Q LOSS MUTATED	63	58	202	82	129	32
16Q LOSS WILD-TYPE	127	37	55	87	131	16

Figure S469. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.33e-17 (Fisher's exact test), Q value = 6.4e-14

Table S470. Gene #69: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	339	433	247
16Q LOSS MUTATED	229	256	81
16Q LOSS WILD-TYPE	110	177	166

Figure S470. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_CNMF'

P value = 1.81e-11 (Chi-square test), Q value = 1.4e-08

Table S471. Gene #69: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	194	170	227	251	140	32
16Q LOSS MUTATED	119	99	152	97	70	28
16Q LOSS WILD-TYPE	75	71	75	154	70	4

Figure S471. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.72e-12 (Fisher's exact test), Q value = 6e-09

Table S472. Gene #69: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	531	273	210
16Q LOSS MUTATED	322	103	140
16Q LOSS WILD-TYPE	209	170	70

Figure S472. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.5e-07 (Fisher's exact test), Q value = 9.5e-05

Table S473. Gene #69: '16q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	238	218
16Q LOSS MUTATED	144	157	88
16Q LOSS WILD-TYPE	104	81	130

Figure S473. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.3e-07 (Fisher's exact test), Q value = 8.3e-05

Table S474. Gene #69: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	358	181
16Q LOSS MUTATED	63	203	123
16Q LOSS WILD-TYPE	102	155	58

Figure S474. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'MRNA_CNMF'

P value = 1.51e-09 (Chi-square test), Q value = 1.1e-06

Table S475. Gene #70: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
17P LOSS MUTATED	13	23	66	61	30	57	12	21
17P LOSS WILD-TYPE	8	13	53	35	79	15	8	19

Figure S475. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17p loss' versus 'CN_CNMF'

P value = 1.58e-23 (Chi-square test), Q value = 1.5e-20

Table S476. Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
17P LOSS MUTATED	132	166	47	186	22
17P LOSS WILD-TYPE	245	86	57	66	26

Figure S476. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 4.63e-08 (Chi-square test), Q value = 3.1e-05

Table S477. Gene #70: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	124	176	104	135	56	116
17P LOSS MUTATED	75	68	62	92	26	44
17P LOSS WILD-TYPE	49	108	42	43	30	72

Figure S477. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17p loss' versus 'RPPA_CNMF'

P value = 2e-07 (Fisher's exact test), Q value = 0.00012

Table S478. Gene #70: '17p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
17P LOSS MUTATED	107	56	56
17P LOSS WILD-TYPE	40	77	61

Figure S478. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'17p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.000123 (Fisher's exact test), Q value = 0.057

Table S479. Gene #70: '17p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	110	126
17P LOSS MUTATED	83	48	88
17P LOSS WILD-TYPE	78	62	38

Figure S479. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 1.13e-15 (Chi-square test), Q value = 9.7e-13

Table S480. Gene #70: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	190	95	257	169	260	48
17P LOSS MUTATED	114	45	92	132	141	22
17P LOSS WILD-TYPE	76	50	165	37	119	26

Figure S480. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.28e-05 (Fisher's exact test), Q value = 0.012

Table S481. Gene #70: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	339	433	247
17P LOSS MUTATED	152	236	158
17P LOSS WILD-TYPE	187	197	89

Figure S481. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CNMF'

P value = 8.97e-09 (Chi-square test), Q value = 6.1e-06

Table S482. Gene #70: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	194	170	227	251	140	32
17P LOSS MUTATED	108	66	97	165	87	20
17P LOSS WILD-TYPE	86	104	130	86	53	12

Figure S482. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.55e-07 (Fisher's exact test), Q value = 9.8e-05

Table S483. Gene #70: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	531	273	210
17P LOSS MUTATED	287	175	81
17P LOSS WILD-TYPE	244	98	129

Figure S483. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.52e-06 (Fisher's exact test), Q value = 0.0036

Table S484. Gene #70: '17p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	238	218
17P LOSS MUTATED	128	101	142
17P LOSS WILD-TYPE	120	137	76

Figure S484. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'17q loss' versus 'MRNA_CNMF'

P value = 2.5e-12 (Chi-square test), Q value = 2e-09

Table S485. Gene #71: '17q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
17Q LOSS MUTATED	4	4	22	50	12	34	4	12
17Q LOSS WILD-TYPE	17	32	97	46	97	38	16	28

Figure S485. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1.35e-10 (Fisher's exact test), Q value = 1e-07

Table S486. Gene #71: '17q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
17Q LOSS MUTATED	23	65	54
17Q LOSS WILD-TYPE	99	60	212

Figure S486. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

P value = 3.1e-26 (Chi-square test), Q value = 2.9e-23

Table S487. Gene #71: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
17Q LOSS MUTATED	50	56	21	130	7
17Q LOSS WILD-TYPE	327	196	83	122	41

Figure S487. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

'17q loss' versus 'METHLYATION_CNMF'

P value = 1.08e-16 (Chi-square test), Q value = 9.4e-14

Table S488. Gene #71: '17q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	124	176	104	135	56	116
17Q LOSS MUTATED	62	13	17	35	6	28
17Q LOSS WILD-TYPE	62	163	87	100	50	88

Figure S488. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q loss' versus 'RPPA_CNMF'

P value = 8.25e-11 (Fisher's exact test), Q value = 6.2e-08

Table S489. Gene #71: '17q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
17Q LOSS MUTATED	71	16	30
17Q LOSS WILD-TYPE	76	117	87

Figure S489. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'17q loss' versus 'RPPA_CHIERARCHICAL'

P value = 2.07e-11 (Fisher's exact test), Q value = 1.6e-08

Table S490. Gene #71: '17q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	110	126
17Q LOSS MUTATED	26	24	67
17Q LOSS WILD-TYPE	135	86	59

Figure S490. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'17q loss' versus 'MRNASEQ_CNMF'

P value = 4.55e-20 (Chi-square test), Q value = 4.1e-17

Table S491. Gene #71: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	190	95	257	169	260	48
17Q LOSS MUTATED	88	15	36	70	43	9
17Q LOSS WILD-TYPE	102	80	221	99	217	39

Figure S491. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.66e-18 (Fisher's exact test), Q value = 3.2e-15

Table S492. Gene #71: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	339	433	247
17Q LOSS MUTATED	54	89	118
17Q LOSS WILD-TYPE	285	344	129

Figure S492. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_CNMF'

P value = 1.04e-14 (Chi-square test), Q value = 8.7e-12

Table S493. Gene #71: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	194	170	227	251	140	32
17Q LOSS MUTATED	43	32	28	111	33	12
17Q LOSS WILD-TYPE	151	138	199	140	107	20

Figure S493. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.73e-16 (Fisher's exact test), Q value = 4.1e-13

Table S494. Gene #71: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	531	273	210
17Q LOSS MUTATED	113	120	26
17Q LOSS WILD-TYPE	418	153	184

Figure S494. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.33e-08 (Fisher's exact test), Q value = 1.6e-05

Table S495. Gene #71: '17q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	238	218
17Q LOSS MUTATED	51	40	87
17Q LOSS WILD-TYPE	197	198	131

Figure S495. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'17q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.16e-10 (Fisher's exact test), Q value = 3e-07

Table S496. Gene #71: '17q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	358	181
17Q LOSS MUTATED	75	71	32
17Q LOSS WILD-TYPE	90	287	149

Figure S496. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p loss' versus 'MRNA_CNMF'

P value = 0.000251 (Chi-square test), Q value = 0.11

Table S497. Gene #72: '18p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
18P LOSS MUTATED	6	11	36	27	19	38	9	13
18P LOSS WILD-TYPE	15	25	83	69	90	34	11	27

Figure S497. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'18p loss' versus 'CN_CNMF'

P value = 8.97e-13 (Chi-square test), Q value = 7.2e-10

Table S498. Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
18P LOSS MUTATED	60	105	38	95	11
18P LOSS WILD-TYPE	317	147	66	157	37

Figure S498. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

P value = 1.07e-06 (Chi-square test), Q value = 0.00064

Table S499. Gene #72: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	124	176	104	135	56	116
18P LOSS MUTATED	34	31	46	57	13	29
18P LOSS WILD-TYPE	90	145	58	78	43	87

Figure S499. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p loss' versus 'MRNASEQ_CNMF'

P value = 1.41e-11 (Chi-square test), Q value = 1.1e-08

Table S500. Gene #72: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	190	95	257	169	260	48
18P LOSS MUTATED	49	22	52	90	79	12
18P LOSS WILD-TYPE	141	73	205	79	181	36

Figure S500. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p loss' versus 'MIRSEQ_CNMF'

P value = 6.01e-05 (Chi-square test), Q value = 0.03

Table S501. Gene #72: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	194	170	227	251	140	32
18P LOSS MUTATED	66	34	50	88	55	13
18P LOSS WILD-TYPE	128	136	177	163	85	19

Figure S501. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18q loss' versus 'MRNA_CNMF'

P value = 0.000199 (Chi-square test), Q value = 0.088

Table S502. Gene #73: '18q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
18Q LOSS MUTATED	5	11	34	27	19	38	7	9
18Q LOSS WILD-TYPE	16	25	85	69	90	34	13	31

Figure S502. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 4.42e-14 (Chi-square test), Q value = 3.7e-11

Table S503. Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
18Q LOSS MUTATED	58	104	39	99	10
18Q LOSS WILD-TYPE	319	148	65	153	38

Figure S503. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 1.65e-07 (Chi-square test), Q value = 1e-04

Table S504. Gene #73: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	124	176	104	135	56	116
18Q LOSS MUTATED	43	31	46	58	12	26
18Q LOSS WILD-TYPE	81	145	58	77	44	90

Figure S504. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 2.69e-09 (Chi-square test), Q value = 1.9e-06

Table S505. Gene #73: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	190	95	257	169	260	48
18Q LOSS MUTATED	56	23	54	86	76	10
18Q LOSS WILD-TYPE	134	72	203	83	184	38

Figure S505. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q loss' versus 'MIRSEQ_CNMF'

P value = 9.17e-05 (Chi-square test), Q value = 0.043

Table S506. Gene #73: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	194	170	227	251	140	32
18Q LOSS MUTATED	65	35	49	94	49	13
18Q LOSS WILD-TYPE	129	135	178	157	91	19

Figure S506. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 8.05e-05 (Fisher's exact test), Q value = 0.038

Table S507. Gene #73: '18q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	238	218
18Q LOSS MUTATED	77	49	85
18Q LOSS WILD-TYPE	171	189	133

Figure S507. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19p loss' versus 'MRNA_CNMF'

P value = 2.62e-05 (Chi-square test), Q value = 0.014

Table S508. Gene #74: '19p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
19P LOSS MUTATED	3	6	30	20	8	25	1	2
19P LOSS WILD-TYPE	18	30	89	76	101	47	19	38

Figure S508. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'19p loss' versus 'MRNA_CHIERARCHICAL'

P value = 2.68e-05 (Fisher's exact test), Q value = 0.014

Table S509. Gene #74: '19p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
19P LOSS MUTATED	7	25	63
19P LOSS WILD-TYPE	115	100	203

Figure S509. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

P value = 5.93e-25 (Chi-square test), Q value = 5.5e-22

Table S510. Gene #74: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
19P LOSS MUTATED	14	88	9	67	8
19P LOSS WILD-TYPE	363	164	95	185	40

Figure S510. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

P value = 4.89e-13 (Chi-square test), Q value = 3.9e-10

Table S511. Gene #74: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	124	176	104	135	56	116
19P LOSS MUTATED	33	10	15	49	4	12
19P LOSS WILD-TYPE	91	166	89	86	52	104

Figure S511. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p loss' versus 'MRNASEQ_CNMF'

P value = 2.56e-11 (Chi-square test), Q value = 1.9e-08

Table S512. Gene #74: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	190	95	257	169	260	48
19P LOSS MUTATED	47	5	17	47	63	5
19P LOSS WILD-TYPE	143	90	240	122	197	43

Figure S512. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.08e-10 (Fisher's exact test), Q value = 1.5e-07

Table S513. Gene #74: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	339	433	247
19P LOSS MUTATED	25	105	54
19P LOSS WILD-TYPE	314	328	193

Figure S513. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_CNMF'

P value = 7.66e-14 (Chi-square test), Q value = 6.3e-11

Table S514. Gene #74: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	194	170	227	251	140	32
19P LOSS MUTATED	27	7	24	71	45	7
19P LOSS WILD-TYPE	167	163	203	180	95	25

Figure S514. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.33e-07 (Fisher's exact test), Q value = 8.4e-05

Table S515. Gene #74: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	531	273	210
19P LOSS MUTATED	102	66	13
19P LOSS WILD-TYPE	429	207	197

Figure S515. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.87e-10 (Fisher's exact test), Q value = 1.4e-07

Table S516. Gene #74: '19p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	238	218
19P LOSS MUTATED	42	16	66
19P LOSS WILD-TYPE	206	222	152

Figure S516. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.52e-06 (Fisher's exact test), Q value = 0.002

Table S517. Gene #74: '19p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	358	181
19P LOSS MUTATED	46	64	14
19P LOSS WILD-TYPE	119	294	167

Figure S517. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.000338 (Fisher's exact test), Q value = 0.14

Table S518. Gene #75: '19q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
19Q LOSS MUTATED	6	19	52
19Q LOSS WILD-TYPE	116	106	214

Figure S518. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 1.86e-22 (Chi-square test), Q value = 1.7e-19

Table S519. Gene #75: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
19Q LOSS MUTATED	12	79	5	51	8
19Q LOSS WILD-TYPE	365	173	99	201	40

Figure S519. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

P value = 2.01e-08 (Chi-square test), Q value = 1.4e-05

Table S520. Gene #75: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	124	176	104	135	56	116
19Q LOSS MUTATED	24	7	17	38	2	15
19Q LOSS WILD-TYPE	100	169	87	97	54	101

Figure S520. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q loss' versus 'MRNASEQ_CNMF'

P value = 5.08e-10 (Chi-square test), Q value = 3.7e-07

Table S521. Gene #75: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	190	95	257	169	260	48
19Q LOSS MUTATED	35	5	13	44	53	4
19Q LOSS WILD-TYPE	155	90	244	125	207	44

Figure S521. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.45e-10 (Fisher's exact test), Q value = 1.8e-07

Table S522. Gene #75: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	339	433	247
19Q LOSS MUTATED	18	90	46
19Q LOSS WILD-TYPE	321	343	201

Figure S522. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_CNMF'

P value = 3.03e-07 (Chi-square test), Q value = 0.00019

Table S523. Gene #75: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	194	170	227	251	140	32
19Q LOSS MUTATED	25	9	22	56	34	5
19Q LOSS WILD-TYPE	169	161	205	195	106	27

Figure S523. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.94e-05 (Fisher's exact test), Q value = 0.015

Table S524. Gene #75: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	531	273	210
19Q LOSS MUTATED	89	50	12
19Q LOSS WILD-TYPE	442	223	198

Figure S524. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.21e-09 (Fisher's exact test), Q value = 2.9e-06

Table S525. Gene #75: '19q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	238	218
19Q LOSS MUTATED	36	11	53
19Q LOSS WILD-TYPE	212	227	165

Figure S525. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000197 (Fisher's exact test), Q value = 0.088

Table S526. Gene #75: '19q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	358	181
19Q LOSS MUTATED	36	52	12
19Q LOSS WILD-TYPE	129	306	169

Figure S526. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p loss' versus 'CN_CNMF'

P value = 1.95e-12 (Chi-square test), Q value = 1.5e-09

Table S527. Gene #76: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
20P LOSS MUTATED	8	24	3	48	4
20P LOSS WILD-TYPE	369	228	101	204	44

Figure S527. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

'20p loss' versus 'METHLYATION_CNMF'

P value = 2.12e-11 (Chi-square test), Q value = 1.6e-08

Table S528. Gene #76: '20p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	124	176	104	135	56	116
20P LOSS MUTATED	32	6	9	11	3	2
20P LOSS WILD-TYPE	92	170	95	124	53	114

Figure S528. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p loss' versus 'MRNASEQ_CNMF'

P value = 1.29e-11 (Chi-square test), Q value = 1e-08

Table S529. Gene #76: '20p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	190	95	257	169	260	48
20P LOSS MUTATED	41	1	10	14	21	0
20P LOSS WILD-TYPE	149	94	247	155	239	48

Figure S529. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.43e-10 (Fisher's exact test), Q value = 1.1e-07

Table S530. Gene #76: '20p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	339	433	247
20P LOSS MUTATED	9	32	46
20P LOSS WILD-TYPE	330	401	201

Figure S530. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p loss' versus 'MIRSEQ_CNMF'

P value = 7.31e-09 (Chi-square test), Q value = 5e-06

Table S531. Gene #76: '20p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	194	170	227	251	140	32
20P LOSS MUTATED	7	5	10	44	13	2
20P LOSS WILD-TYPE	187	165	217	207	127	30

Figure S531. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.22e-07 (Fisher's exact test), Q value = 0.00032

Table S532. Gene #76: '20p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	531	273	210
20P LOSS MUTATED	31	43	7
20P LOSS WILD-TYPE	500	230	203

Figure S532. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.43e-07 (Fisher's exact test), Q value = 9.1e-05

Table S533. Gene #76: '20p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	238	218
20P LOSS MUTATED	10	9	37
20P LOSS WILD-TYPE	238	229	181

Figure S533. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.59e-08 (Fisher's exact test), Q value = 1.1e-05

Table S534. Gene #76: '20p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	358	181
20P LOSS MUTATED	33	16	7
20P LOSS WILD-TYPE	132	342	174

Figure S534. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q loss' versus 'CN_CNMF'

P value = 6.5e-08 (Chi-square test), Q value = 4.2e-05

Table S535. Gene #77: '20q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
20Q LOSS MUTATED	4	12	3	30	2
20Q LOSS WILD-TYPE	373	240	101	222	46

Figure S535. Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #3: 'CN_CNMF'

'20q loss' versus 'METHLYATION_CNMF'

P value = 3.07e-12 (Chi-square test), Q value = 2.4e-09

Table S536. Gene #77: '20q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	124	176	104	135	56	116
20Q LOSS MUTATED	24	3	2	6	1	1
20Q LOSS WILD-TYPE	100	173	102	129	55	115

Figure S536. Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q loss' versus 'MRNASEQ_CNMF'

P value = 2.92e-10 (Chi-square test), Q value = 2.1e-07

Table S537. Gene #77: '20q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	190	95	257	169	260	48
20Q LOSS MUTATED	29	1	7	6	8	0
20Q LOSS WILD-TYPE	161	94	250	163	252	48

Figure S537. Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.44e-08 (Fisher's exact test), Q value = 2.3e-05

Table S538. Gene #77: '20q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	339	433	247
20Q LOSS MUTATED	6	14	31
20Q LOSS WILD-TYPE	333	419	216

Figure S538. Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q loss' versus 'MIRSEQ_CNMF'

P value = 1.83e-06 (Chi-square test), Q value = 0.0011

Table S539. Gene #77: '20q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	194	170	227	251	140	32
20Q LOSS MUTATED	4	4	6	29	4	1
20Q LOSS WILD-TYPE	190	166	221	222	136	31

Figure S539. Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.15e-07 (Fisher's exact test), Q value = 7.4e-05

Table S540. Gene #77: '20q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	531	273	210
20Q LOSS MUTATED	11	31	6
20Q LOSS WILD-TYPE	520	242	204

Figure S540. Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.44e-06 (Fisher's exact test), Q value = 0.00086

Table S541. Gene #77: '20q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	238	218
20Q LOSS MUTATED	3	7	25
20Q LOSS WILD-TYPE	245	231	193

Figure S541. Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.21e-08 (Fisher's exact test), Q value = 8.2e-06

Table S542. Gene #77: '20q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	358	181
20Q LOSS MUTATED	24	5	6
20Q LOSS WILD-TYPE	141	353	175

Figure S542. Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q loss' versus 'CN_CNMF'

P value = 1.27e-12 (Chi-square test), Q value = 1e-09

Table S543. Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
21Q LOSS MUTATED	19	69	19	51	10
21Q LOSS WILD-TYPE	358	183	85	201	38

Figure S543. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

'21q loss' versus 'METHLYATION_CNMF'

P value = 3e-04 (Chi-square test), Q value = 0.13

Table S544. Gene #78: '21q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	124	176	104	135	56	116
21Q LOSS MUTATED	22	20	19	36	4	10
21Q LOSS WILD-TYPE	102	156	85	99	52	106

Figure S544. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 4.74e-14 (Chi-square test), Q value = 3.9e-11

Table S545. Gene #79: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
22Q LOSS MUTATED	117	142	72	111	25
22Q LOSS WILD-TYPE	260	110	32	141	23

Figure S545. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 1.59e-06 (Chi-square test), Q value = 0.00094

Table S546. Gene #79: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	124	176	104	135	56	116
22Q LOSS MUTATED	58	67	49	87	16	41
22Q LOSS WILD-TYPE	66	109	55	48	40	75

Figure S546. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000375 (Fisher's exact test), Q value = 0.16

Table S547. Gene #79: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	339	433	247
22Q LOSS MUTATED	158	218	86
22Q LOSS WILD-TYPE	181	215	161

Figure S547. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xq loss' versus 'CN_CNMF'

P value = 6.27e-15 (Chi-square test), Q value = 5.3e-12

Table S548. Gene #80: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	377	252	104	252	48
XQ LOSS MUTATED	20	66	14	68	5
XQ LOSS WILD-TYPE	357	186	90	184	43

Figure S548. Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 3.03e-07 (Chi-square test), Q value = 0.00019

Table S549. Gene #80: 'xq loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	124	176	104	135	56	116
XQ LOSS MUTATED	29	16	25	35	6	5
XQ LOSS WILD-TYPE	95	160	79	100	50	111

Figure S549. Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xq loss' versus 'MRNASEQ_CNMF'

P value = 3.52e-06 (Chi-square test), Q value = 0.002

Table S550. Gene #80: 'xq loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	190	95	257	169	260	48
XQ LOSS MUTATED	40	9	22	36	61	3
XQ LOSS WILD-TYPE	150	86	235	133	199	45

Figure S550. Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'xq loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.89e-06 (Fisher's exact test), Q value = 0.0022

Table S551. Gene #80: 'xq loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	339	433	247
XQ LOSS MUTATED	30	90	51
XQ LOSS WILD-TYPE	309	343	196

Figure S551. Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_CNMF'

P value = 0.000209 (Chi-square test), Q value = 0.092

Table S552. Gene #80: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	194	170	227	251	140	32
XQ LOSS MUTATED	34	8	39	56	27	6
XQ LOSS WILD-TYPE	160	162	188	195	113	26

Figure S552. Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtypes file = BRCA-TP.transferedmergedcluster.txt
Number of patients = 1033
Number of significantly arm-level cnvs = 80
Number of molecular subtypes = 12
Exclude genes that fewer than K tumors have mutations, K = 3

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References

[1] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)

[2] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)

[3] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)

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