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

Uterine Corpus Endometrioid Carcinoma (Primary solid tumor)

17 October 2014 | analyses__2014_10_17

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/C1FT8K0F

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 539 patients, 414 significant findings detected with P value < 0.05 and Q value < 0.25.

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

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 80 arm-level events and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 414 significant findings detected.


		Clinical Features	MRNA CNMF	MRNA CHIERARCHICAL	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
9q loss	122 (23%)	417	3e-05 (0.0164)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	0.00038 (0.185)	0.697 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	0.00086 (0.398)	2e-05 (0.0113)
8p loss	80 (15%)	459	0.00785 (1.00)	6e-05 (0.032)	1e-05 (0.00892)	1e-05 (0.00892)	0.0345 (1.00)	0.0265 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)
15q loss	109 (20%)	430	0.00061 (0.289)	6e-05 (0.032)	1e-05 (0.00892)	1e-05 (0.00892)	0.00097 (0.446)	0.485 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)
17p loss	130 (24%)	409	0.00362 (1.00)	0.00021 (0.106)	1e-05 (0.00892)	1e-05 (0.00892)	0.00318 (1.00)	0.369 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)
2p gain	95 (18%)	444	0.854 (1.00)	0.371 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	0.0569 (1.00)	0.242 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	4e-05 (0.0216)	0.00013 (0.0671)
2q gain	79 (15%)	460	0.344 (1.00)	0.6 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	0.0643 (1.00)	0.133 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	3e-05 (0.0164)	0.00024 (0.121)
3q gain	84 (16%)	455	0.619 (1.00)	0.253 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	0.104 (1.00)	0.159 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	0.00039 (0.19)	4e-05 (0.0216)
5p gain	51 (9%)	488	1 (1.00)	0.512 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	0.144 (1.00)	0.705 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	0.00014 (0.072)	1e-05 (0.00892)
18p gain	72 (13%)	467	0.334 (1.00)	0.242 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	0.0116 (1.00)	0.163 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)
18q gain	45 (8%)	494	0.253 (1.00)	0.044 (1.00)	1e-05 (0.00892)	2e-05 (0.0113)	0.279 (1.00)	0.0956 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	2e-05 (0.0113)	6e-05 (0.032)
20p gain	112 (21%)	427	0.00873 (1.00)	0.0494 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	0.162 (1.00)	0.742 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	0.00028 (0.14)	1e-05 (0.00892)
20q gain	132 (24%)	407	0.00192 (0.849)	0.008 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	0.0323 (1.00)	0.669 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)
22q gain	31 (6%)	508			1e-05 (0.00892)	1e-05 (0.00892)	0.371 (1.00)	0.187 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)
4p loss	105 (19%)	434	0.0038 (1.00)	0.00184 (0.815)	1e-05 (0.00892)	1e-05 (0.00892)	0.00131 (0.593)	0.189 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	2e-05 (0.0113)	1e-05 (0.00892)
4q loss	105 (19%)	434	0.151 (1.00)	0.00461 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	0.0131 (1.00)	0.187 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)
5q loss	74 (14%)	465	0.0132 (1.00)	0.00972 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	0.00122 (0.554)	0.00231 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	0.00015 (0.0768)	5e-05 (0.0269)
11p loss	75 (14%)	464			1e-05 (0.00892)	1e-05 (0.00892)	0.302 (1.00)	0.328 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	0.00037 (0.182)	1e-05 (0.00892)
11q loss	72 (13%)	467			1e-05 (0.00892)	1e-05 (0.00892)	0.852 (1.00)	0.788 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)
12q loss	36 (7%)	503			1e-05 (0.00892)	1e-05 (0.00892)	0.104 (1.00)	0.0154 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	6e-05 (0.032)	0.0004 (0.194)
14q loss	61 (11%)	478	0.00197 (0.867)	0.00052 (0.249)	1e-05 (0.00892)	1e-05 (0.00892)	0.0145 (1.00)	0.0488 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	0.00527 (1.00)	2e-05 (0.0113)
16q loss	138 (26%)	401	0.00067 (0.315)	0.00136 (0.613)	1e-05 (0.00892)	1e-05 (0.00892)	0.342 (1.00)	0.973 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	0.00023 (0.116)	1e-05 (0.00892)
17q loss	93 (17%)	446	0.00194 (0.856)	2e-05 (0.0113)	1e-05 (0.00892)	1e-05 (0.00892)	0.109 (1.00)	0.918 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	0.00457 (1.00)	0.00048 (0.23)
xq loss	70 (13%)	469	0.00792 (1.00)	0.00501 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	0.00013 (0.0671)	0.215 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	0.00322 (1.00)	1e-05 (0.00892)
19p gain	54 (10%)	485	0.0384 (1.00)	0.0292 (1.00)	1e-05 (0.00892)	0.00028 (0.14)	0.907 (1.00)	0.0736 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	0.00032 (0.159)	0.0828 (1.00)
19q gain	57 (11%)	482			1e-05 (0.00892)	6e-05 (0.032)	0.488 (1.00)	0.0431 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	0.00021 (0.106)	0.0137 (1.00)
21q gain	39 (7%)	500			1e-05 (0.00892)	0.00047 (0.226)	0.427 (1.00)	0.452 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	0.00034 (0.168)	0.235 (1.00)
3p loss	51 (9%)	488	0.0397 (1.00)	0.00068 (0.318)	1e-05 (0.00892)	1e-05 (0.00892)	0.022 (1.00)	0.125 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	0.0148 (1.00)	0.00011 (0.0572)
5p loss	55 (10%)	484	0.05 (1.00)	0.0394 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	0.00391 (1.00)	0.103 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	3e-05 (0.0164)	0.00101 (0.464)
7q loss	42 (8%)	497			1e-05 (0.00892)	1e-05 (0.00892)	0.0476 (1.00)	0.014 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	0.00214 (0.935)	0.00043 (0.208)
9p loss	103 (19%)	436	0.00109 (0.499)	2e-05 (0.0113)	1e-05 (0.00892)	1e-05 (0.00892)	0.0034 (1.00)	0.563 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	0.00891 (1.00)	0.00072 (0.336)
12p loss	43 (8%)	496	0.138 (1.00)	0.167 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	0.0424 (1.00)	0.0379 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	0.00037 (0.182)	0.00226 (0.981)
16p loss	97 (18%)	442	0.00209 (0.915)	0.00743 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	0.0942 (1.00)	0.318 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	0.00438 (1.00)	2e-05 (0.0113)
19p loss	59 (11%)	480			1e-05 (0.00892)	1e-05 (0.00892)	0.0973 (1.00)	0.269 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	0.00567 (1.00)	1e-05 (0.00892)
19q loss	56 (10%)	483	0.252 (1.00)	0.0172 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	0.247 (1.00)	0.719 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	0.0109 (1.00)	3e-05 (0.0164)
21q loss	54 (10%)	485	0.0394 (1.00)	0.0302 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	0.24 (1.00)	0.426 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	0.00379 (1.00)	1e-05 (0.00892)
22q loss	109 (20%)	430	0.00183 (0.813)	0.00766 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	0.0396 (1.00)	0.279 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	0.00328 (1.00)	0.0002 (0.102)
1p gain	50 (9%)	489	0.532 (1.00)	0.218 (1.00)	1e-05 (0.00892)	0.00046 (0.222)	0.0459 (1.00)	0.265 (1.00)	1e-05 (0.00892)	2e-05 (0.0113)	2e-05 (0.0113)	1e-05 (0.00892)	0.00222 (0.966)	0.00276 (1.00)
6p gain	80 (15%)	459	0.21 (1.00)	0.666 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	0.0986 (1.00)	0.833 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	0.00215 (0.937)	0.0202 (1.00)
12p gain	71 (13%)	468	0.385 (1.00)	0.69 (1.00)	1e-05 (0.00892)	2e-05 (0.0113)	0.915 (1.00)	0.971 (1.00)	1e-05 (0.00892)	3e-05 (0.0164)	0.00035 (0.173)	0.00026 (0.13)	0.00417 (1.00)	0.00359 (1.00)
13q gain	30 (6%)	509	0.136 (1.00)	0.00726 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	0.251 (1.00)	0.0125 (1.00)	2e-05 (0.0113)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	0.00728 (1.00)	0.0233 (1.00)
17q gain	30 (6%)	509			1e-05 (0.00892)	1e-05 (0.00892)	0.0398 (1.00)	1 (1.00)	2e-05 (0.0113)	1e-05 (0.00892)	2e-05 (0.0113)	0.00019 (0.0971)	0.0504 (1.00)	0.0909 (1.00)
1p loss	25 (5%)	514			1e-05 (0.00892)	1e-05 (0.00892)	0.788 (1.00)	0.362 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	5e-05 (0.0269)	1e-05 (0.00892)	0.294 (1.00)	0.00064 (0.302)
1q loss	14 (3%)	525			1e-05 (0.00892)	8e-05 (0.0419)			5e-05 (0.0269)	8e-05 (0.0419)	1e-05 (0.00892)	1e-05 (0.00892)	0.525 (1.00)	0.00726 (1.00)
6q loss	25 (5%)	514	0.38 (1.00)	0.0301 (1.00)	1e-05 (0.00892)	0.0001 (0.0522)	0.473 (1.00)	0.803 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	0.00024 (0.121)	3e-05 (0.0164)	0.0121 (1.00)	0.0031 (1.00)
7p loss	44 (8%)	495	0.0385 (1.00)	0.194 (1.00)	1e-05 (0.00892)	0.00037 (0.182)	0.0366 (1.00)	0.554 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	0.0614 (1.00)	0.0611 (1.00)
8q loss	25 (5%)	514			1e-05 (0.00892)	1e-05 (0.00892)	0.326 (1.00)	0.84 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	2e-05 (0.0113)	0.00092 (0.424)	0.00936 (1.00)
10p loss	43 (8%)	496	0.0389 (1.00)	0.0302 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	0.0556 (1.00)	0.185 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	0.025 (1.00)	0.00408 (1.00)
10q loss	40 (7%)	499	0.138 (1.00)	0.167 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	0.0539 (1.00)	0.169 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	2e-05 (0.0113)	1e-05 (0.00892)	0.0307 (1.00)	0.00454 (1.00)
13q loss	93 (17%)	446	0.903 (1.00)	0.193 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	0.0252 (1.00)	0.496 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	3e-05 (0.0164)	0.165 (1.00)	0.00236 (1.00)
18q loss	65 (12%)	474	0.534 (1.00)	0.514 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	0.529 (1.00)	1 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	0.0118 (1.00)	0.0006 (0.285)
8q gain	159 (29%)	380	0.0108 (1.00)	0.0294 (1.00)	1e-05 (0.00892)	0.0414 (1.00)	0.0003 (0.149)	0.0219 (1.00)	1e-05 (0.00892)	0.00064 (0.302)	0.00042 (0.204)	7e-05 (0.0368)	0.00054 (0.258)	0.0074 (1.00)
3q loss	31 (6%)	508	0.0393 (1.00)	0.00071 (0.332)	1e-05 (0.00892)	6e-05 (0.032)	0.0637 (1.00)	0.266 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	0.00175 (0.78)	0.0123 (1.00)	0.0971 (1.00)
18p loss	52 (10%)	487			1e-05 (0.00892)	1e-05 (0.00892)	0.475 (1.00)	0.564 (1.00)	1e-05 (0.00892)	0.00678 (1.00)	0.0001 (0.0522)	0.00027 (0.135)	0.0169 (1.00)	0.00328 (1.00)
5q gain	20 (4%)	519			1e-05 (0.00892)	0.0355 (1.00)	0.372 (1.00)	0.292 (1.00)	0.00037 (0.182)	0.00131 (0.593)	0.0012 (0.546)	0.00019 (0.0971)	0.227 (1.00)	0.00014 (0.072)
1q gain	188 (35%)	351	0.181 (1.00)	0.0101 (1.00)	2e-05 (0.0113)	0.187 (1.00)	0.0941 (1.00)	0.0162 (1.00)	6e-05 (0.032)	0.00076 (0.353)	1e-05 (0.00892)	0.00926 (1.00)	0.902 (1.00)	0.0773 (1.00)
6q gain	64 (12%)	475	0.208 (1.00)	0.662 (1.00)	1e-05 (0.00892)	0.00057 (0.272)	0.053 (1.00)	0.757 (1.00)	2e-05 (0.0113)	0.00089 (0.411)	0.0011 (0.503)	0.00012 (0.0623)	0.0155 (1.00)	0.302 (1.00)
14q gain	37 (7%)	502	1 (1.00)	0.841 (1.00)	1e-05 (0.00892)	0.00204 (0.896)	0.0856 (1.00)	0.693 (1.00)	1e-05 (0.00892)	0.00012 (0.0623)	0.00179 (0.797)	0.00882 (1.00)	0.0939 (1.00)	0.309 (1.00)
6p loss	18 (3%)	521	0.379 (1.00)	0.0295 (1.00)	1e-05 (0.00892)	0.00146 (0.654)	0.363 (1.00)	1 (1.00)	0.00036 (0.177)	3e-05 (0.0164)	0.00675 (1.00)	0.00067 (0.315)	0.0681 (1.00)	0.0244 (1.00)
3p gain	49 (9%)	490			1e-05 (0.00892)	0.00905 (1.00)	0.301 (1.00)	0.947 (1.00)	5e-05 (0.0269)	0.00911 (1.00)	0.00142 (0.638)	0.0008 (0.371)	0.0144 (1.00)	0.0366 (1.00)
2q loss	17 (3%)	522			1e-05 (0.00892)	0.113 (1.00)			0.00023 (0.116)	0.0615 (1.00)	0.023 (1.00)	0.186 (1.00)	0.415 (1.00)	0.801 (1.00)
4p gain	14 (3%)	525			5e-05 (0.0269)	0.847 (1.00)	0.375 (1.00)	0.0362 (1.00)	0.00059 (0.281)	0.0102 (1.00)	0.00478 (1.00)	0.00552 (1.00)	0.348 (1.00)	0.435 (1.00)
7p gain	67 (12%)	472	0.855 (1.00)	0.906 (1.00)	1e-05 (0.00892)	0.00119 (0.543)	0.847 (1.00)	0.865 (1.00)	0.0185 (1.00)	0.091 (1.00)	0.0102 (1.00)	0.384 (1.00)	0.0322 (1.00)	0.0525 (1.00)
7q gain	66 (12%)	473	0.857 (1.00)	0.905 (1.00)	1e-05 (0.00892)	0.00136 (0.613)	0.855 (1.00)	0.537 (1.00)	0.121 (1.00)	0.165 (1.00)	0.0599 (1.00)	0.371 (1.00)	0.0905 (1.00)	0.212 (1.00)
8p gain	118 (22%)	421	0.356 (1.00)	0.402 (1.00)	1e-05 (0.00892)	0.881 (1.00)	0.0204 (1.00)	0.215 (1.00)	0.19 (1.00)	0.88 (1.00)	0.207 (1.00)	0.0978 (1.00)	0.116 (1.00)	0.507 (1.00)
9p gain	22 (4%)	517			0.00012 (0.0623)	0.00369 (1.00)	0.0948 (1.00)	0.326 (1.00)	0.00503 (1.00)	0.0432 (1.00)	0.00439 (1.00)	0.0427 (1.00)	0.102 (1.00)	0.368 (1.00)
10p gain	117 (22%)	422	0.00717 (1.00)	0.0875 (1.00)	1e-05 (0.00892)	0.873 (1.00)	0.195 (1.00)	0.815 (1.00)	0.124 (1.00)	0.127 (1.00)	0.72 (1.00)	0.0247 (1.00)	0.533 (1.00)	0.0351 (1.00)
10q gain	109 (20%)	430	0.00484 (1.00)	0.0884 (1.00)	7e-05 (0.0368)	0.731 (1.00)	0.123 (1.00)	0.662 (1.00)	0.204 (1.00)	0.211 (1.00)	0.478 (1.00)	0.00451 (1.00)	0.565 (1.00)	0.0603 (1.00)
11p gain	23 (4%)	516	0.0399 (1.00)	0.196 (1.00)	1e-05 (0.00892)	0.0444 (1.00)	0.0573 (1.00)	0.114 (1.00)	0.00282 (1.00)	0.00399 (1.00)	0.00304 (1.00)	0.0112 (1.00)	0.229 (1.00)	0.363 (1.00)
11q gain	19 (4%)	520			1e-05 (0.00892)	0.112 (1.00)	0.178 (1.00)	0.0117 (1.00)	0.0313 (1.00)	0.159 (1.00)	0.0738 (1.00)	0.106 (1.00)	0.885 (1.00)	0.654 (1.00)
12q gain	54 (10%)	485	0.385 (1.00)	0.689 (1.00)	2e-05 (0.0113)	0.00867 (1.00)	0.962 (1.00)	0.98 (1.00)	0.00308 (1.00)	0.008 (1.00)	0.031 (1.00)	0.132 (1.00)	0.202 (1.00)	0.274 (1.00)
16p gain	27 (5%)	512			1e-05 (0.00892)	0.0024 (1.00)	0.18 (1.00)	0.632 (1.00)	0.0487 (1.00)	0.0735 (1.00)	0.0155 (1.00)	0.0716 (1.00)	0.145 (1.00)	0.358 (1.00)
xq gain	65 (12%)	474	0.705 (1.00)	0.926 (1.00)	1e-05 (0.00892)	0.466 (1.00)	0.872 (1.00)	0.335 (1.00)	0.681 (1.00)	0.318 (1.00)	0.528 (1.00)	0.659 (1.00)	0.175 (1.00)	0.803 (1.00)
2p loss	11 (2%)	528			0.0002 (0.102)	0.301 (1.00)			0.00458 (1.00)	0.0897 (1.00)	0.465 (1.00)	0.133 (1.00)	0.555 (1.00)	0.722 (1.00)
20p loss	19 (4%)	520			1e-05 (0.00892)	0.209 (1.00)	0.469 (1.00)	0.666 (1.00)	0.0264 (1.00)	0.00529 (1.00)	0.00689 (1.00)	0.0272 (1.00)	0.418 (1.00)	0.43 (1.00)
20q loss	9 (2%)	530			0.00043 (0.208)	0.0886 (1.00)	0.642 (1.00)	1 (1.00)	0.0356 (1.00)	0.00316 (1.00)	0.0514 (1.00)	0.0185 (1.00)	0.177 (1.00)	0.246 (1.00)
4q gain	8 (1%)	531			0.00446 (1.00)	0.622 (1.00)			0.03 (1.00)	0.144 (1.00)	0.271 (1.00)	0.1 (1.00)	0.797 (1.00)	0.635 (1.00)
9q gain	9 (2%)	530			0.0311 (1.00)	0.168 (1.00)			0.363 (1.00)	0.58 (1.00)	0.158 (1.00)	0.358 (1.00)	0.66 (1.00)	0.264 (1.00)
15q gain	11 (2%)	528			0.00063 (0.298)	0.915 (1.00)			0.692 (1.00)	0.503 (1.00)	0.466 (1.00)	0.943 (1.00)	1 (1.00)	0.249 (1.00)
16q gain	10 (2%)	529			0.012 (1.00)	0.0514 (1.00)	0.945 (1.00)	0.84 (1.00)	0.172 (1.00)	0.268 (1.00)	0.0917 (1.00)	0.489 (1.00)	0.62 (1.00)	0.796 (1.00)
17p gain	12 (2%)	527			0.00153 (0.684)	0.162 (1.00)	0.223 (1.00)	1 (1.00)	0.105 (1.00)	0.0041 (1.00)	0.0763 (1.00)	0.0468 (1.00)	0.346 (1.00)	0.666 (1.00)

'1p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
1P GAIN MUTATED	38	6	2	0	4
1P GAIN WILD-TYPE	131	299	17	9	33

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

'1p gain' versus 'METHLYATION_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.22

Table S2. Gene #1: '1p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
1P GAIN MUTATED	30	5	10
1P GAIN WILD-TYPE	135	84	161

Figure S2. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S3. Gene #1: '1p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
1P GAIN MUTATED	6	38	5
1P GAIN WILD-TYPE	145	192	144

Figure S3. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S4. Gene #1: '1p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
1P GAIN MUTATED	12	31	6
1P GAIN WILD-TYPE	204	138	139

Figure S4. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p gain' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S5. Gene #1: '1p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
1P GAIN MUTATED	36	10	3
1P GAIN WILD-TYPE	190	133	158

Figure S5. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S6. Gene #1: '1p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
1P GAIN MUTATED	4	2	27	16
1P GAIN WILD-TYPE	137	58	96	190

Figure S6. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1q gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S7. Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
1Q GAIN MUTATED	57	90	12	8	21
1Q GAIN WILD-TYPE	112	215	7	1	16

Figure S7. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

'1q gain' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.032

Table S8. Gene #2: '1q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
1Q GAIN MUTATED	72	75	36
1Q GAIN WILD-TYPE	79	155	113

Figure S8. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S9. Gene #2: '1q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
1Q GAIN MUTATED	72	74	41
1Q GAIN WILD-TYPE	154	69	120

Figure S9. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
2P GAIN MUTATED	62	9	10	3	11
2P GAIN WILD-TYPE	107	296	9	6	26

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

'2p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S11. Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
2P GAIN MUTATED	53	9	11
2P GAIN WILD-TYPE	112	80	160

Figure S11. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S12. Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
2P GAIN MUTATED	16	68	9
2P GAIN WILD-TYPE	135	162	140

Figure S12. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S13. Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
2P GAIN MUTATED	25	59	9
2P GAIN WILD-TYPE	191	110	136

Figure S13. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S14. Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
2P GAIN MUTATED	66	17	11
2P GAIN WILD-TYPE	160	126	150

Figure S14. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S15. Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
2P GAIN MUTATED	10	8	48	28
2P GAIN WILD-TYPE	131	52	75	178

Figure S15. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.022

Table S16. Gene #3: '2p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
2P GAIN MUTATED	42	20	8
2P GAIN WILD-TYPE	130	76	122

Figure S16. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'2p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.067

Table S17. Gene #3: '2p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
2P GAIN MUTATED	35	7	28
2P GAIN WILD-TYPE	109	108	111

Figure S17. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S18. Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
2Q GAIN MUTATED	52	7	8	3	9
2Q GAIN WILD-TYPE	117	298	11	6	28

Figure S18. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

'2q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
2Q GAIN MUTATED	47	7	10
2Q GAIN WILD-TYPE	118	82	161

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

'2q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S20. Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
2Q GAIN MUTATED	13	57	7
2Q GAIN WILD-TYPE	138	173	142

Figure S20. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S21. Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
2Q GAIN MUTATED	19	50	8
2Q GAIN WILD-TYPE	197	119	137

Figure S21. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S22. Gene #4: '2q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
2Q GAIN MUTATED	55	16	8
2Q GAIN WILD-TYPE	171	127	153

Figure S22. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S23. Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
2Q GAIN MUTATED	8	5	42	24
2Q GAIN WILD-TYPE	133	55	81	182

Figure S23. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.016

Table S24. Gene #4: '2q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
2Q GAIN MUTATED	39	16	7
2Q GAIN WILD-TYPE	133	80	123

Figure S24. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'2q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.12

Table S25. Gene #4: '2q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
2Q GAIN MUTATED	31	6	25
2Q GAIN WILD-TYPE	113	109	114

Figure S25. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S26. Gene #5: '3p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
3P GAIN MUTATED	31	2	1	3	12
3P GAIN WILD-TYPE	138	303	18	6	25

Figure S26. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #3: 'CN_CNMF'

'3p gain' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.027

Table S27. Gene #5: '3p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
3P GAIN MUTATED	4	35	9
3P GAIN WILD-TYPE	147	195	140

Figure S27. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
3Q GAIN MUTATED	62	4	2	3	13
3Q GAIN WILD-TYPE	107	301	17	6	24

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

'3q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S29. Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
3Q GAIN MUTATED	54	9	11
3Q GAIN WILD-TYPE	111	80	160

Figure S29. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S30. Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
3Q GAIN MUTATED	6	66	10
3Q GAIN WILD-TYPE	145	164	139

Figure S30. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S31. Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
3Q GAIN MUTATED	18	55	9
3Q GAIN WILD-TYPE	198	114	136

Figure S31. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S32. Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
3Q GAIN MUTATED	64	11	9
3Q GAIN WILD-TYPE	162	132	152

Figure S32. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S33. Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
3Q GAIN MUTATED	12	0	46	26
3Q GAIN WILD-TYPE	129	60	77	180

Figure S33. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.19

Table S34. Gene #6: '3q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
3Q GAIN MUTATED	43	17	10
3Q GAIN WILD-TYPE	129	79	120

Figure S34. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'3q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.022

Table S35. Gene #6: '3q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
3Q GAIN MUTATED	41	8	21
3Q GAIN WILD-TYPE	103	107	118

Figure S35. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p gain' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.027

Table S36. Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
4P GAIN MUTATED	13	0	0	0	1
4P GAIN WILD-TYPE	156	305	19	9	36

Figure S36. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

'5p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S37. Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
5P GAIN MUTATED	43	3	4	1	0
5P GAIN WILD-TYPE	126	302	15	8	37

Figure S37. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

'5p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S38. Gene #9: '5p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
5P GAIN MUTATED	34	5	5
5P GAIN WILD-TYPE	131	84	166

Figure S38. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S39. Gene #9: '5p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
5P GAIN MUTATED	5	44	1
5P GAIN WILD-TYPE	146	186	148

Figure S39. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S40. Gene #9: '5p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
5P GAIN MUTATED	10	38	2
5P GAIN WILD-TYPE	206	131	143

Figure S40. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S41. Gene #9: '5p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
5P GAIN MUTATED	41	9	1
5P GAIN WILD-TYPE	185	134	160

Figure S41. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S42. Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
5P GAIN MUTATED	1	5	34	11
5P GAIN WILD-TYPE	140	55	89	195

Figure S42. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.072

Table S43. Gene #9: '5p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
5P GAIN MUTATED	30	8	4
5P GAIN WILD-TYPE	142	88	126

Figure S43. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S44. Gene #9: '5p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
5P GAIN MUTATED	32	1	9
5P GAIN WILD-TYPE	112	114	130

Figure S44. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S45. Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
5Q GAIN MUTATED	15	1	3	1	0
5Q GAIN WILD-TYPE	154	304	16	8	37

Figure S45. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'

'5q gain' versus 'MRNASEQ_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.18

Table S46. Gene #10: '5q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
5Q GAIN MUTATED	3	16	0
5Q GAIN WILD-TYPE	148	214	149

Figure S46. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.097

Table S47. Gene #10: '5q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
5Q GAIN MUTATED	0	3	12	5
5Q GAIN WILD-TYPE	141	57	111	201

Figure S47. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.072

Table S48. Gene #10: '5q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
5Q GAIN MUTATED	14	0	3
5Q GAIN WILD-TYPE	130	115	136

Figure S48. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S49. Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
6P GAIN MUTATED	61	5	1	1	12
6P GAIN WILD-TYPE	108	300	18	8	25

Figure S49. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

'6p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S50. Gene #11: '6p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
6P GAIN MUTATED	49	12	11
6P GAIN WILD-TYPE	116	77	160

Figure S50. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S51. Gene #11: '6p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
6P GAIN MUTATED	6	60	14
6P GAIN WILD-TYPE	145	170	135

Figure S51. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S52. Gene #11: '6p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
6P GAIN MUTATED	19	48	13
6P GAIN WILD-TYPE	197	121	132

Figure S52. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S53. Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
6P GAIN MUTATED	56	13	11
6P GAIN WILD-TYPE	170	130	150

Figure S53. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S54. Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
6P GAIN MUTATED	11	1	38	30
6P GAIN WILD-TYPE	130	59	85	176

Figure S54. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S55. Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
6Q GAIN MUTATED	46	5	1	1	11
6Q GAIN WILD-TYPE	123	300	18	8	26

Figure S55. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

'6q gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S56. Gene #12: '6q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
6Q GAIN MUTATED	6	44	14
6Q GAIN WILD-TYPE	145	186	135

Figure S56. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.062

Table S57. Gene #12: '6q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
6Q GAIN MUTATED	11	1	27	25
6Q GAIN WILD-TYPE	130	59	96	181

Figure S57. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S58. Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
7P GAIN MUTATED	33	9	12	2	11
7P GAIN WILD-TYPE	136	296	7	7	26

Figure S58. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S59. Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
7Q GAIN MUTATED	30	12	12	2	10
7Q GAIN WILD-TYPE	139	293	7	7	27

Figure S59. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

'8p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S60. Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
8P GAIN MUTATED	43	29	8	2	36
8P GAIN WILD-TYPE	126	276	11	7	1

Figure S60. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S61. Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
8Q GAIN MUTATED	80	31	8	3	37
8Q GAIN WILD-TYPE	89	274	11	6	0

Figure S61. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'RPPA_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.15

Table S62. Gene #16: '8q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

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

Figure S62. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S63. Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
8Q GAIN MUTATED	29	94	34
8Q GAIN WILD-TYPE	122	136	115

Figure S63. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8q gain' versus 'MIRSEQ_CNMF'

P value = 0.00042 (Fisher's exact test), Q value = 0.2

Table S64. Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
8Q GAIN MUTATED	86	37	33
8Q GAIN WILD-TYPE	140	106	128

Figure S64. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.037

Table S65. Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
8Q GAIN MUTATED	33	8	53	62
8Q GAIN WILD-TYPE	108	52	70	144

Figure S65. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9p gain' versus 'CN_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.062

Table S66. Gene #17: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
9P GAIN MUTATED	18	3	0	0	1
9P GAIN WILD-TYPE	151	302	19	9	36

Figure S66. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'

'10p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S67. Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
10P GAIN MUTATED	41	46	7	4	19
10P GAIN WILD-TYPE	128	259	12	5	18

Figure S67. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

'10q gain' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.037

Table S68. Gene #20: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
10Q GAIN MUTATED	36	45	8	4	16
10Q GAIN WILD-TYPE	133	260	11	5	21

Figure S68. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

'11p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S69. Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
11P GAIN MUTATED	17	0	4	0	2
11P GAIN WILD-TYPE	152	305	15	9	35

Figure S69. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

'11q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S70. Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
11Q GAIN MUTATED	13	0	3	0	3
11Q GAIN WILD-TYPE	156	305	16	9	34

Figure S70. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S71. Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
12P GAIN MUTATED	42	14	7	3	5
12P GAIN WILD-TYPE	127	291	12	6	32

Figure S71. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S72. Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
12P GAIN MUTATED	35	14	8
12P GAIN WILD-TYPE	130	75	163

Figure S72. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S73. Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
12P GAIN MUTATED	10	50	9
12P GAIN WILD-TYPE	141	180	140

Figure S73. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.016

Table S74. Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
12P GAIN MUTATED	21	39	9
12P GAIN WILD-TYPE	195	130	136

Figure S74. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.17

Table S75. Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
12P GAIN MUTATED	45	16	10
12P GAIN WILD-TYPE	181	127	151

Figure S75. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.13

Table S76. Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
12P GAIN MUTATED	10	5	31	25
12P GAIN WILD-TYPE	131	55	92	181

Figure S76. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12q gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S77. Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
12Q GAIN MUTATED	26	14	6	3	5
12Q GAIN WILD-TYPE	143	291	13	6	32

Figure S77. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

'13q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S78. Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
13Q GAIN MUTATED	27	0	0	1	2
13Q GAIN WILD-TYPE	142	305	19	8	35

Figure S78. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

'13q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S79. Gene #25: '13q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
13Q GAIN MUTATED	18	7	1
13Q GAIN WILD-TYPE	147	82	170

Figure S79. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S80. Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
13Q GAIN MUTATED	1	27	2
13Q GAIN WILD-TYPE	150	203	147

Figure S80. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S81. Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
13Q GAIN MUTATED	1	27	2
13Q GAIN WILD-TYPE	215	142	143

Figure S81. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S82. Gene #25: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
13Q GAIN MUTATED	28	0	2
13Q GAIN WILD-TYPE	198	143	159

Figure S82. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'13q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S83. Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
13Q GAIN MUTATED	2	0	23	5
13Q GAIN WILD-TYPE	139	60	100	201

Figure S83. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S84. Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
14Q GAIN MUTATED	26	4	1	0	6
14Q GAIN WILD-TYPE	143	301	18	9	31

Figure S84. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

'14q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S85. Gene #26: '14q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
14Q GAIN MUTATED	1	28	6
14Q GAIN WILD-TYPE	150	202	143

Figure S85. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.062

Table S86. Gene #26: '14q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
14Q GAIN MUTATED	6	23	6
14Q GAIN WILD-TYPE	210	146	139

Figure S86. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S87. Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
16P GAIN MUTATED	22	1	1	0	3
16P GAIN WILD-TYPE	147	304	18	9	34

Figure S87. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S88. Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
17Q GAIN MUTATED	25	1	0	1	3
17Q GAIN WILD-TYPE	144	304	19	8	34

Figure S88. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S89. Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
17Q GAIN MUTATED	23	2	2
17Q GAIN WILD-TYPE	142	87	169

Figure S89. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S90. Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
17Q GAIN MUTATED	2	25	3
17Q GAIN WILD-TYPE	149	205	146

Figure S90. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S91. Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
17Q GAIN MUTATED	4	24	2
17Q GAIN WILD-TYPE	212	145	143

Figure S91. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S92. Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
17Q GAIN MUTATED	25	2	3
17Q GAIN WILD-TYPE	201	141	158

Figure S92. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.097

Table S93. Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
17Q GAIN MUTATED	4	1	18	7
17Q GAIN WILD-TYPE	137	59	105	199

Figure S93. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S94. Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
18P GAIN MUTATED	65	3	3	0	1
18P GAIN WILD-TYPE	104	302	16	9	36

Figure S94. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S95. Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
18P GAIN MUTATED	45	13	4
18P GAIN WILD-TYPE	120	76	167

Figure S95. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S96. Gene #32: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
18P GAIN MUTATED	3	65	4
18P GAIN WILD-TYPE	148	165	145

Figure S96. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S97. Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
18P GAIN MUTATED	8	60	4
18P GAIN WILD-TYPE	208	109	141

Figure S97. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S98. Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
18P GAIN MUTATED	62	7	3
18P GAIN WILD-TYPE	164	136	158

Figure S98. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S99. Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
18P GAIN MUTATED	3	1	51	17
18P GAIN WILD-TYPE	138	59	72	189

Figure S99. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S100. Gene #32: '18p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
18P GAIN MUTATED	40	16	3
18P GAIN WILD-TYPE	132	80	127

Figure S100. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S101. Gene #32: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
18P GAIN MUTATED	33	2	24
18P GAIN WILD-TYPE	111	113	115

Figure S101. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S102. Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
18Q GAIN MUTATED	39	3	2	0	1
18Q GAIN WILD-TYPE	130	302	17	9	36

Figure S102. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

'18q gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S103. Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
18Q GAIN MUTATED	29	7	3
18Q GAIN WILD-TYPE	136	82	168

Figure S103. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S104. Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
18Q GAIN MUTATED	2	40	3
18Q GAIN WILD-TYPE	149	190	146

Figure S104. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S105. Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
18Q GAIN MUTATED	7	35	3
18Q GAIN WILD-TYPE	209	134	142

Figure S105. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S106. Gene #33: '18q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
18Q GAIN MUTATED	37	7	1
18Q GAIN WILD-TYPE	189	136	160

Figure S106. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S107. Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
18Q GAIN MUTATED	2	1	29	13
18Q GAIN WILD-TYPE	139	59	94	193

Figure S107. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S108. Gene #33: '18q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
18Q GAIN MUTATED	27	8	1
18Q GAIN WILD-TYPE	145	88	129

Figure S108. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.032

Table S109. Gene #33: '18q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
18Q GAIN MUTATED	22	1	13
18Q GAIN WILD-TYPE	122	114	126

Figure S109. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S110. Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
19P GAIN MUTATED	49	0	1	0	4
19P GAIN WILD-TYPE	120	305	18	9	33

Figure S110. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

'19p gain' versus 'METHLYATION_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.14

Table S111. Gene #34: '19p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
19P GAIN MUTATED	30	11	8
19P GAIN WILD-TYPE	135	78	163

Figure S111. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S112. Gene #34: '19p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
19P GAIN MUTATED	2	47	4
19P GAIN WILD-TYPE	149	183	145

Figure S112. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S113. Gene #34: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
19P GAIN MUTATED	11	39	3
19P GAIN WILD-TYPE	205	130	142

Figure S113. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S114. Gene #34: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
19P GAIN MUTATED	45	4	5
19P GAIN WILD-TYPE	181	139	156

Figure S114. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S115. Gene #34: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
19P GAIN MUTATED	7	1	30	16
19P GAIN WILD-TYPE	134	59	93	190

Figure S115. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.16

Table S116. Gene #34: '19p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
19P GAIN MUTATED	28	14	4
19P GAIN WILD-TYPE	144	82	126

Figure S116. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S117. Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
19Q GAIN MUTATED	51	0	2	0	4
19Q GAIN WILD-TYPE	118	305	17	9	33

Figure S117. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

'19q gain' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.032

Table S118. Gene #35: '19q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
19Q GAIN MUTATED	33	11	7
19Q GAIN WILD-TYPE	132	78	164

Figure S118. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S119. Gene #35: '19q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
19Q GAIN MUTATED	2	51	3
19Q GAIN WILD-TYPE	149	179	146

Figure S119. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S120. Gene #35: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
19Q GAIN MUTATED	10	44	2
19Q GAIN WILD-TYPE	206	125	143

Figure S120. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S121. Gene #35: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
19Q GAIN MUTATED	48	5	4
19Q GAIN WILD-TYPE	178	138	157

Figure S121. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S122. Gene #35: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
19Q GAIN MUTATED	5	1	39	12
19Q GAIN WILD-TYPE	136	59	84	194

Figure S122. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_MATURE_CNMF'

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

Table S123. Gene #35: '19q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
19Q GAIN MUTATED	29	15	4
19Q GAIN WILD-TYPE	143	81	126

Figure S123. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S124. Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
20P GAIN MUTATED	85	7	12	2	6
20P GAIN WILD-TYPE	84	298	7	7	31

Figure S124. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S125. Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
20P GAIN MUTATED	73	13	17
20P GAIN WILD-TYPE	92	76	154

Figure S125. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S126. Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
20P GAIN MUTATED	9	88	14
20P GAIN WILD-TYPE	142	142	135

Figure S126. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S127. Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
20P GAIN MUTATED	19	77	15
20P GAIN WILD-TYPE	197	92	130

Figure S127. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S128. Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
20P GAIN MUTATED	83	14	14
20P GAIN WILD-TYPE	143	129	147

Figure S128. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S129. Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
20P GAIN MUTATED	14	7	60	30
20P GAIN WILD-TYPE	127	53	63	176

Figure S129. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.14

Table S130. Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
20P GAIN MUTATED	58	20	18
20P GAIN WILD-TYPE	114	76	112

Figure S130. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S131. Gene #36: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
20P GAIN MUTATED	56	15	25
20P GAIN WILD-TYPE	88	100	114

Figure S131. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S132. Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
20Q GAIN MUTATED	103	8	12	2	7
20Q GAIN WILD-TYPE	66	297	7	7	30

Figure S132. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S133. Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
20Q GAIN MUTATED	83	16	21
20Q GAIN WILD-TYPE	82	73	150

Figure S133. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S134. Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
20Q GAIN MUTATED	10	102	18
20Q GAIN WILD-TYPE	141	128	131

Figure S134. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S135. Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
20Q GAIN MUTATED	22	89	19
20Q GAIN WILD-TYPE	194	80	126

Figure S135. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S136. Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
20Q GAIN MUTATED	97	15	18
20Q GAIN WILD-TYPE	129	128	143

Figure S136. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S137. Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
20Q GAIN MUTATED	19	7	68	36
20Q GAIN WILD-TYPE	122	53	55	170

Figure S137. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S138. Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
20Q GAIN MUTATED	70	23	19
20Q GAIN WILD-TYPE	102	73	111

Figure S138. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S139. Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
20Q GAIN MUTATED	64	18	30
20Q GAIN WILD-TYPE	80	97	109

Figure S139. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S140. Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
21Q GAIN MUTATED	35	1	0	0	3
21Q GAIN WILD-TYPE	134	304	19	9	34

Figure S140. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

'21q gain' versus 'METHLYATION_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.23

Table S141. Gene #38: '21q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
21Q GAIN MUTATED	24	7	5
21Q GAIN WILD-TYPE	141	82	166

Figure S141. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'21q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S142. Gene #38: '21q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
21Q GAIN MUTATED	2	33	4
21Q GAIN WILD-TYPE	149	197	145

Figure S142. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S143. Gene #38: '21q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
21Q GAIN MUTATED	4	31	4
21Q GAIN WILD-TYPE	212	138	141

Figure S143. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'21q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S144. Gene #38: '21q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
21Q GAIN MUTATED	34	2	3
21Q GAIN WILD-TYPE	192	141	158

Figure S144. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'21q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S145. Gene #38: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
21Q GAIN MUTATED	4	1	27	7
21Q GAIN WILD-TYPE	137	59	96	199

Figure S145. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'21q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.17

Table S146. Gene #38: '21q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
21Q GAIN MUTATED	23	10	2
21Q GAIN WILD-TYPE	149	86	128

Figure S146. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'22q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S147. Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
22Q GAIN MUTATED	27	3	0	1	0
22Q GAIN WILD-TYPE	142	302	19	8	37

Figure S147. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

'22q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S148. Gene #39: '22q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
22Q GAIN MUTATED	26	1	1
22Q GAIN WILD-TYPE	139	88	170

Figure S148. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S149. Gene #39: '22q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
22Q GAIN MUTATED	0	31	0
22Q GAIN WILD-TYPE	151	199	149

Figure S149. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S150. Gene #39: '22q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
22Q GAIN MUTATED	3	28	0
22Q GAIN WILD-TYPE	213	141	145

Figure S150. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S151. Gene #39: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
22Q GAIN MUTATED	29	0	1
22Q GAIN WILD-TYPE	197	143	160

Figure S151. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'22q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S152. Gene #39: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
22Q GAIN MUTATED	2	0	22	6
22Q GAIN WILD-TYPE	139	60	101	200

Figure S152. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S153. Gene #39: '22q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
22Q GAIN MUTATED	24	2	2
22Q GAIN WILD-TYPE	148	94	128

Figure S153. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'22q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S154. Gene #39: '22q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
22Q GAIN MUTATED	22	1	5
22Q GAIN WILD-TYPE	122	114	134

Figure S154. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
XQ GAIN MUTATED	25	7	8	3	22
XQ GAIN WILD-TYPE	144	298	11	6	15

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

'1p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S156. Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
1P LOSS MUTATED	18	0	3	4	0
1P LOSS WILD-TYPE	151	305	16	5	37

Figure S156. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S157. Gene #41: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
1P LOSS MUTATED	20	1	0
1P LOSS WILD-TYPE	145	88	171

Figure S157. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S158. Gene #41: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
1P LOSS MUTATED	1	23	1
1P LOSS WILD-TYPE	150	207	148

Figure S158. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S159. Gene #41: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
1P LOSS MUTATED	5	20	0
1P LOSS WILD-TYPE	211	149	145

Figure S159. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.027

Table S160. Gene #41: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
1P LOSS MUTATED	22	2	1
1P LOSS WILD-TYPE	204	141	160

Figure S160. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S161. Gene #41: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
1P LOSS MUTATED	0	0	19	6
1P LOSS WILD-TYPE	141	60	104	200

Figure S161. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S162. Gene #42: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
1Q LOSS MUTATED	12	0	1	1	0
1Q LOSS WILD-TYPE	157	305	18	8	37

Figure S162. Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

'1q loss' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.042

Table S163. Gene #42: '1q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
1Q LOSS MUTATED	12	0	0
1Q LOSS WILD-TYPE	153	89	171

Figure S163. Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1q loss' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.027

Table S164. Gene #42: '1q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
1Q LOSS MUTATED	0	14	0
1Q LOSS WILD-TYPE	151	216	149

Figure S164. Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.042

Table S165. Gene #42: '1q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
1Q LOSS MUTATED	2	12	0
1Q LOSS WILD-TYPE	214	157	145

Figure S165. Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S166. Gene #42: '1q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
1Q LOSS MUTATED	14	0	0
1Q LOSS WILD-TYPE	212	143	161

Figure S166. Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S167. Gene #42: '1q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
1Q LOSS MUTATED	0	0	12	2
1Q LOSS WILD-TYPE	141	60	111	204

Figure S167. Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2p loss' versus 'CN_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.1

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
2P LOSS MUTATED	10	0	1	0	0
2P LOSS WILD-TYPE	159	305	18	9	37

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

'2q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S169. Gene #44: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
2Q LOSS MUTATED	16	0	1	0	0
2Q LOSS WILD-TYPE	153	305	18	9	37

Figure S169. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

'2q loss' versus 'MRNASEQ_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.12

Table S170. Gene #44: '2q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
2Q LOSS MUTATED	0	15	2
2Q LOSS WILD-TYPE	151	215	147

Figure S170. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S171. Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
3P LOSS MUTATED	45	0	3	2	1
3P LOSS WILD-TYPE	124	305	16	7	36

Figure S171. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S172. Gene #45: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
3P LOSS MUTATED	33	6	3
3P LOSS WILD-TYPE	132	83	168

Figure S172. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S173. Gene #45: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
3P LOSS MUTATED	1	46	2
3P LOSS WILD-TYPE	150	184	147

Figure S173. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S174. Gene #45: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
3P LOSS MUTATED	7	40	2
3P LOSS WILD-TYPE	209	129	143

Figure S174. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S175. Gene #45: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
3P LOSS MUTATED	40	6	3
3P LOSS WILD-TYPE	186	137	158

Figure S175. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S176. Gene #45: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
3P LOSS MUTATED	4	2	29	14
3P LOSS WILD-TYPE	137	58	94	192

Figure S176. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.057

Table S177. Gene #45: '3p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
3P LOSS MUTATED	26	3	11
3P LOSS WILD-TYPE	118	112	128

Figure S177. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S178. Gene #46: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
3Q LOSS MUTATED	27	0	1	2	1
3Q LOSS WILD-TYPE	142	305	18	7	36

Figure S178. Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

'3q loss' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.032

Table S179. Gene #46: '3q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
3Q LOSS MUTATED	20	3	2
3Q LOSS WILD-TYPE	145	86	169

Figure S179. Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S180. Gene #46: '3q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
3Q LOSS MUTATED	0	27	2
3Q LOSS WILD-TYPE	151	203	147

Figure S180. Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S181. Gene #46: '3q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
3Q LOSS MUTATED	3	24	2
3Q LOSS WILD-TYPE	213	145	143

Figure S181. Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S182. Gene #46: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
3Q LOSS MUTATED	25	1	3
3Q LOSS WILD-TYPE	201	142	158

Figure S182. Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S183. Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
4P LOSS MUTATED	91	4	4	4	2
4P LOSS WILD-TYPE	78	301	15	5	35

Figure S183. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S184. Gene #47: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
4P LOSS MUTATED	72	16	6
4P LOSS WILD-TYPE	93	73	165

Figure S184. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S185. Gene #47: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
4P LOSS MUTATED	6	90	8
4P LOSS WILD-TYPE	145	140	141

Figure S185. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S186. Gene #47: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
4P LOSS MUTATED	21	76	7
4P LOSS WILD-TYPE	195	93	138

Figure S186. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S187. Gene #47: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
4P LOSS MUTATED	84	11	8
4P LOSS WILD-TYPE	142	132	153

Figure S187. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S188. Gene #47: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
4P LOSS MUTATED	6	1	63	33
4P LOSS WILD-TYPE	135	59	60	173

Figure S188. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S189. Gene #47: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
4P LOSS MUTATED	55	26	12
4P LOSS WILD-TYPE	117	70	118

Figure S189. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S190. Gene #47: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
4P LOSS MUTATED	52	9	32
4P LOSS WILD-TYPE	92	106	107

Figure S190. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S191. Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
4Q LOSS MUTATED	92	3	4	4	2
4Q LOSS WILD-TYPE	77	302	15	5	35

Figure S191. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S192. Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
4Q LOSS MUTATED	73	15	5
4Q LOSS WILD-TYPE	92	74	166

Figure S192. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S193. Gene #48: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
4Q LOSS MUTATED	6	90	8
4Q LOSS WILD-TYPE	145	140	141

Figure S193. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S194. Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
4Q LOSS MUTATED	20	77	7
4Q LOSS WILD-TYPE	196	92	138

Figure S194. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S195. Gene #48: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
4Q LOSS MUTATED	84	11	8
4Q LOSS WILD-TYPE	142	132	153

Figure S195. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S196. Gene #48: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
4Q LOSS MUTATED	5	1	62	35
4Q LOSS WILD-TYPE	136	59	61	171

Figure S196. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S197. Gene #48: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
4Q LOSS MUTATED	53	28	11
4Q LOSS WILD-TYPE	119	68	119

Figure S197. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S198. Gene #48: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
4Q LOSS MUTATED	49	8	35
4Q LOSS WILD-TYPE	95	107	104

Figure S198. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S199. Gene #49: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
5P LOSS MUTATED	46	0	3	2	4
5P LOSS WILD-TYPE	123	305	16	7	33

Figure S199. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

'5p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S200. Gene #49: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
5P LOSS MUTATED	38	5	2
5P LOSS WILD-TYPE	127	84	169

Figure S200. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S201. Gene #49: '5p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
5P LOSS MUTATED	4	47	4
5P LOSS WILD-TYPE	147	183	145

Figure S201. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S202. Gene #49: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
5P LOSS MUTATED	10	41	4
5P LOSS WILD-TYPE	206	128	141

Figure S202. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S203. Gene #49: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
5P LOSS MUTATED	44	5	5
5P LOSS WILD-TYPE	182	138	156

Figure S203. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S204. Gene #49: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
5P LOSS MUTATED	2	0	35	17
5P LOSS WILD-TYPE	139	60	88	189

Figure S204. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.016

Table S205. Gene #49: '5p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
5P LOSS MUTATED	30	10	3
5P LOSS WILD-TYPE	142	86	127

Figure S205. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S206. Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
5Q LOSS MUTATED	66	0	2	2	4
5Q LOSS WILD-TYPE	103	305	17	7	33

Figure S206. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S207. Gene #50: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
5Q LOSS MUTATED	54	6	2
5Q LOSS WILD-TYPE	111	83	169

Figure S207. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S208. Gene #50: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
5Q LOSS MUTATED	4	65	5
5Q LOSS WILD-TYPE	147	165	144

Figure S208. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S209. Gene #50: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
5Q LOSS MUTATED	11	57	6
5Q LOSS WILD-TYPE	205	112	139

Figure S209. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S210. Gene #50: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
5Q LOSS MUTATED	62	6	5
5Q LOSS WILD-TYPE	164	137	156

Figure S210. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S211. Gene #50: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
5Q LOSS MUTATED	3	0	45	25
5Q LOSS WILD-TYPE	138	60	78	181

Figure S211. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.077

Table S212. Gene #50: '5q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
5Q LOSS MUTATED	38	14	7
5Q LOSS WILD-TYPE	134	82	123

Figure S212. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.027

Table S213. Gene #50: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
5Q LOSS MUTATED	31	4	24
5Q LOSS WILD-TYPE	113	111	115

Figure S213. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S214. Gene #51: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
6P LOSS MUTATED	15	0	2	1	0
6P LOSS WILD-TYPE	154	305	17	8	37

Figure S214. Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

'6p loss' versus 'MRNASEQ_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.18

Table S215. Gene #51: '6p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
6P LOSS MUTATED	1	16	1
6P LOSS WILD-TYPE	150	214	148

Figure S215. Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.016

Table S216. Gene #51: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
6P LOSS MUTATED	3	15	0
6P LOSS WILD-TYPE	213	154	145

Figure S216. Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S217. Gene #52: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
6Q LOSS MUTATED	22	0	2	1	0
6Q LOSS WILD-TYPE	147	305	17	8	37

Figure S217. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

'6q loss' versus 'METHLYATION_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.052

Table S218. Gene #52: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
6Q LOSS MUTATED	15	4	0
6Q LOSS WILD-TYPE	150	85	171

Figure S218. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S219. Gene #52: '6q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
6Q LOSS MUTATED	1	23	1
6Q LOSS WILD-TYPE	150	207	148

Figure S219. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S220. Gene #52: '6q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
6Q LOSS MUTATED	3	22	0
6Q LOSS WILD-TYPE	213	147	145

Figure S220. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.12

Table S221. Gene #52: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
6Q LOSS MUTATED	19	3	1
6Q LOSS WILD-TYPE	207	140	160

Figure S221. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.016

Table S222. Gene #52: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
6Q LOSS MUTATED	0	0	14	9
6Q LOSS WILD-TYPE	141	60	109	197

Figure S222. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S223. Gene #53: '7p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
7P LOSS MUTATED	39	3	1	1	0
7P LOSS WILD-TYPE	130	302	18	8	37

Figure S223. Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #3: 'CN_CNMF'

'7p loss' versus 'METHLYATION_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.18

Table S224. Gene #53: '7p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
7P LOSS MUTATED	24	10	5
7P LOSS WILD-TYPE	141	79	166

Figure S224. Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S225. Gene #53: '7p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
7P LOSS MUTATED	1	39	4
7P LOSS WILD-TYPE	150	191	145

Figure S225. Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S226. Gene #53: '7p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
7P LOSS MUTATED	8	32	4
7P LOSS WILD-TYPE	208	137	141

Figure S226. Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S227. Gene #53: '7p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
7P LOSS MUTATED	36	2	6
7P LOSS WILD-TYPE	190	141	155

Figure S227. Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S228. Gene #53: '7p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
7P LOSS MUTATED	4	0	28	12
7P LOSS WILD-TYPE	137	60	95	194

Figure S228. Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S229. Gene #54: '7q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
7Q LOSS MUTATED	41	0	0	1	0
7Q LOSS WILD-TYPE	128	305	19	8	37

Figure S229. Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #3: 'CN_CNMF'

'7q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S230. Gene #54: '7q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
7Q LOSS MUTATED	29	9	1
7Q LOSS WILD-TYPE	136	80	170

Figure S230. Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S231. Gene #54: '7q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
7Q LOSS MUTATED	0	41	1
7Q LOSS WILD-TYPE	151	189	148

Figure S231. Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S232. Gene #54: '7q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
7Q LOSS MUTATED	4	36	2
7Q LOSS WILD-TYPE	212	133	143

Figure S232. Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S233. Gene #54: '7q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
7Q LOSS MUTATED	39	1	2
7Q LOSS WILD-TYPE	187	142	159

Figure S233. Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S234. Gene #54: '7q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
7Q LOSS MUTATED	2	0	32	8
7Q LOSS WILD-TYPE	139	60	91	198

Figure S234. Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00043 (Fisher's exact test), Q value = 0.21

Table S235. Gene #54: '7q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
7Q LOSS MUTATED	22	2	13
7Q LOSS WILD-TYPE	122	113	126

Figure S235. Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p loss' versus 'MRNA_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.032

Table S236. Gene #55: '8p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
8P LOSS MUTATED	0	5	0	0	0
8P LOSS WILD-TYPE	14	4	7	7	16

Figure S236. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S237. Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
8P LOSS MUTATED	75	3	1	1	0
8P LOSS WILD-TYPE	94	302	18	8	37

Figure S237. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S238. Gene #55: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
8P LOSS MUTATED	58	11	2
8P LOSS WILD-TYPE	107	78	169

Figure S238. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S239. Gene #55: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
8P LOSS MUTATED	3	71	3
8P LOSS WILD-TYPE	148	159	146

Figure S239. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S240. Gene #55: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
8P LOSS MUTATED	7	66	4
8P LOSS WILD-TYPE	209	103	141

Figure S240. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S241. Gene #55: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
8P LOSS MUTATED	70	3	4
8P LOSS WILD-TYPE	156	140	157

Figure S241. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S242. Gene #55: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
8P LOSS MUTATED	5	0	55	17
8P LOSS WILD-TYPE	136	60	68	189

Figure S242. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S243. Gene #55: '8p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
8P LOSS MUTATED	45	15	6
8P LOSS WILD-TYPE	127	81	124

Figure S243. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S244. Gene #55: '8p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
8P LOSS MUTATED	41	3	22
8P LOSS WILD-TYPE	103	112	117

Figure S244. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S245. Gene #56: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
8Q LOSS MUTATED	23	1	1	0	0
8Q LOSS WILD-TYPE	146	304	18	9	37

Figure S245. Get High-res Image Gene #56: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'

'8q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S246. Gene #56: '8q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
8Q LOSS MUTATED	20	3	0
8Q LOSS WILD-TYPE	145	86	171

Figure S246. Get High-res Image Gene #56: '8q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S247. Gene #56: '8q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
8Q LOSS MUTATED	0	23	2
8Q LOSS WILD-TYPE	151	207	147

Figure S247. Get High-res Image Gene #56: '8q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S248. Gene #56: '8q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
8Q LOSS MUTATED	1	22	2
8Q LOSS WILD-TYPE	215	147	143

Figure S248. Get High-res Image Gene #56: '8q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S249. Gene #56: '8q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
8Q LOSS MUTATED	22	0	2
8Q LOSS WILD-TYPE	204	143	159

Figure S249. Get High-res Image Gene #56: '8q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S250. Gene #56: '8q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
8Q LOSS MUTATED	2	0	17	5
8Q LOSS WILD-TYPE	139	60	106	201

Figure S250. Get High-res Image Gene #56: '8q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9p loss' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S251. Gene #57: '9p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
9P LOSS MUTATED	2	7	0	0	0
9P LOSS WILD-TYPE	12	2	7	7	16

Figure S251. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S252. Gene #57: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
9P LOSS MUTATED	90	2	6	1	4
9P LOSS WILD-TYPE	79	303	13	8	33

Figure S252. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S253. Gene #57: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
9P LOSS MUTATED	59	20	9
9P LOSS WILD-TYPE	106	69	162

Figure S253. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S254. Gene #57: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
9P LOSS MUTATED	6	83	13
9P LOSS WILD-TYPE	145	147	136

Figure S254. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S255. Gene #57: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
9P LOSS MUTATED	15	74	13
9P LOSS WILD-TYPE	201	95	132

Figure S255. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S256. Gene #57: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
9P LOSS MUTATED	76	10	14
9P LOSS WILD-TYPE	150	133	147

Figure S256. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S257. Gene #57: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
9P LOSS MUTATED	12	2	61	25
9P LOSS WILD-TYPE	129	58	62	181

Figure S257. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9q loss' versus 'MRNA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.016

Table S258. Gene #58: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
9Q LOSS MUTATED	0	9	0	0
9Q LOSS WILD-TYPE	14	8	12	10

Figure S258. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'9q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S259. Gene #58: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
9Q LOSS MUTATED	2	7	0	0	0
9Q LOSS WILD-TYPE	12	2	7	7	16

Figure S259. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S260. Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
9Q LOSS MUTATED	105	3	7	2	5
9Q LOSS WILD-TYPE	64	302	12	7	32

Figure S260. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S261. Gene #58: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
9Q LOSS MUTATED	71	22	13
9Q LOSS WILD-TYPE	94	67	158

Figure S261. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q loss' versus 'RPPA_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.19

Table S262. Gene #58: '9q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	37	39	12	41	24
9Q LOSS MUTATED	6	12	1	2	1	6
9Q LOSS WILD-TYPE	35	25	38	10	40	18

Figure S262. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S263. Gene #58: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
9Q LOSS MUTATED	8	97	15
9Q LOSS WILD-TYPE	143	133	134

Figure S263. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S264. Gene #58: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
9Q LOSS MUTATED	20	85	15
9Q LOSS WILD-TYPE	196	84	130

Figure S264. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S265. Gene #58: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
9Q LOSS MUTATED	89	14	16
9Q LOSS WILD-TYPE	137	129	145

Figure S265. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S266. Gene #58: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
9Q LOSS MUTATED	16	2	66	35
9Q LOSS WILD-TYPE	125	58	57	171

Figure S266. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S267. Gene #58: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
9Q LOSS MUTATED	55	15	33
9Q LOSS WILD-TYPE	89	100	106

Figure S267. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S268. Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
10P LOSS MUTATED	42	0	1	0	0
10P LOSS WILD-TYPE	127	305	18	9	37

Figure S268. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S269. Gene #59: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
10P LOSS MUTATED	31	5	1
10P LOSS WILD-TYPE	134	84	170

Figure S269. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S270. Gene #59: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
10P LOSS MUTATED	1	38	3
10P LOSS WILD-TYPE	150	192	146

Figure S270. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S271. Gene #59: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
10P LOSS MUTATED	5	34	3
10P LOSS WILD-TYPE	211	135	142

Figure S271. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S272. Gene #59: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
10P LOSS MUTATED	36	3	2
10P LOSS WILD-TYPE	190	140	159

Figure S272. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S273. Gene #59: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
10P LOSS MUTATED	2	1	27	11
10P LOSS WILD-TYPE	139	59	96	195

Figure S273. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S274. Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
10Q LOSS MUTATED	38	1	1	0	0
10Q LOSS WILD-TYPE	131	304	18	9	37

Figure S274. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S275. Gene #60: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
10Q LOSS MUTATED	28	6	1
10Q LOSS WILD-TYPE	137	83	170

Figure S275. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S276. Gene #60: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
10Q LOSS MUTATED	1	34	4
10Q LOSS WILD-TYPE	150	196	145

Figure S276. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S277. Gene #60: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
10Q LOSS MUTATED	6	29	4
10Q LOSS WILD-TYPE	210	140	141

Figure S277. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S278. Gene #60: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
10Q LOSS MUTATED	32	4	3
10Q LOSS WILD-TYPE	194	139	158

Figure S278. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S279. Gene #60: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
10Q LOSS MUTATED	3	1	24	11
10Q LOSS WILD-TYPE	138	59	99	195

Figure S279. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S280. Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
11P LOSS MUTATED	66	0	3	4	2
11P LOSS WILD-TYPE	103	305	16	5	35

Figure S280. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S281. Gene #61: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
11P LOSS MUTATED	53	12	5
11P LOSS WILD-TYPE	112	77	166

Figure S281. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S282. Gene #61: '11p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
11P LOSS MUTATED	3	64	7
11P LOSS WILD-TYPE	148	166	142

Figure S282. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S283. Gene #61: '11p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
11P LOSS MUTATED	13	54	7
11P LOSS WILD-TYPE	203	115	138

Figure S283. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S284. Gene #61: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
11P LOSS MUTATED	58	8	8
11P LOSS WILD-TYPE	168	135	153

Figure S284. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S285. Gene #61: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
11P LOSS MUTATED	7	0	43	24
11P LOSS WILD-TYPE	134	60	80	182

Figure S285. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.18

Table S286. Gene #61: '11p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
11P LOSS MUTATED	44	15	11
11P LOSS WILD-TYPE	128	81	119

Figure S286. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S287. Gene #61: '11p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
11P LOSS MUTATED	44	8	18
11P LOSS WILD-TYPE	100	107	121

Figure S287. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S288. Gene #62: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
11Q LOSS MUTATED	62	0	4	4	2
11Q LOSS WILD-TYPE	107	305	15	5	35

Figure S288. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S289. Gene #62: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
11Q LOSS MUTATED	52	11	6
11Q LOSS WILD-TYPE	113	78	165

Figure S289. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S290. Gene #62: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
11Q LOSS MUTATED	3	59	9
11Q LOSS WILD-TYPE	148	171	140

Figure S290. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S291. Gene #62: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
11Q LOSS MUTATED	10	53	8
11Q LOSS WILD-TYPE	206	116	137

Figure S291. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S292. Gene #62: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
11Q LOSS MUTATED	55	8	9
11Q LOSS WILD-TYPE	171	135	152

Figure S292. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S293. Gene #62: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
11Q LOSS MUTATED	8	0	44	20
11Q LOSS WILD-TYPE	133	60	79	186

Figure S293. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S294. Gene #62: '11q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
11Q LOSS MUTATED	49	10	10
11Q LOSS WILD-TYPE	123	86	120

Figure S294. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S295. Gene #62: '11q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
11Q LOSS MUTATED	46	8	15
11Q LOSS WILD-TYPE	98	107	124

Figure S295. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S296. Gene #63: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
12P LOSS MUTATED	41	0	0	0	2
12P LOSS WILD-TYPE	128	305	19	9	35

Figure S296. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

'12p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S297. Gene #63: '12p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
12P LOSS MUTATED	29	3	4
12P LOSS WILD-TYPE	136	86	167

Figure S297. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S298. Gene #63: '12p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
12P LOSS MUTATED	0	38	5
12P LOSS WILD-TYPE	151	192	144

Figure S298. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S299. Gene #63: '12p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
12P LOSS MUTATED	3	34	6
12P LOSS WILD-TYPE	213	135	139

Figure S299. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S300. Gene #63: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
12P LOSS MUTATED	35	2	4
12P LOSS WILD-TYPE	191	141	157

Figure S300. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S301. Gene #63: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
12P LOSS MUTATED	3	0	28	10
12P LOSS WILD-TYPE	138	60	95	196

Figure S301. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.18

Table S302. Gene #63: '12p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
12P LOSS MUTATED	26	5	4
12P LOSS WILD-TYPE	146	91	126

Figure S302. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S303. Gene #64: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
12Q LOSS MUTATED	34	0	0	0	2
12Q LOSS WILD-TYPE	135	305	19	9	35

Figure S303. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

'12q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S304. Gene #64: '12q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
12Q LOSS MUTATED	27	1	2
12Q LOSS WILD-TYPE	138	88	169

Figure S304. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S305. Gene #64: '12q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
12Q LOSS MUTATED	0	32	3
12Q LOSS WILD-TYPE	151	198	146

Figure S305. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S306. Gene #64: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
12Q LOSS MUTATED	1	30	4
12Q LOSS WILD-TYPE	215	139	141

Figure S306. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S307. Gene #64: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
12Q LOSS MUTATED	29	3	2
12Q LOSS WILD-TYPE	197	140	159

Figure S307. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S308. Gene #64: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
12Q LOSS MUTATED	1	0	24	9
12Q LOSS WILD-TYPE	140	60	99	197

Figure S308. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.032

Table S309. Gene #64: '12q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
12Q LOSS MUTATED	24	3	2
12Q LOSS WILD-TYPE	148	93	128

Figure S309. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-04 (Fisher's exact test), Q value = 0.19

Table S310. Gene #64: '12q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
12Q LOSS MUTATED	20	2	7
12Q LOSS WILD-TYPE	124	113	132

Figure S310. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S311. Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
13Q LOSS MUTATED	71	6	8	3	5
13Q LOSS WILD-TYPE	98	299	11	6	32

Figure S311. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S312. Gene #65: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
13Q LOSS MUTATED	51	17	13
13Q LOSS WILD-TYPE	114	72	158

Figure S312. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S313. Gene #65: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
13Q LOSS MUTATED	8	67	16
13Q LOSS WILD-TYPE	143	163	133

Figure S313. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S314. Gene #65: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
13Q LOSS MUTATED	26	50	15
13Q LOSS WILD-TYPE	190	119	130

Figure S314. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S315. Gene #65: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
13Q LOSS MUTATED	61	17	14
13Q LOSS WILD-TYPE	165	126	147

Figure S315. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'13q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.016

Table S316. Gene #65: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
13Q LOSS MUTATED	13	5	38	36
13Q LOSS WILD-TYPE	128	55	85	170

Figure S316. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00052 (Fisher's exact test), Q value = 0.25

Table S317. Gene #66: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
14Q LOSS MUTATED	1	5	0	0	0
14Q LOSS WILD-TYPE	13	4	7	7	16

Figure S317. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S318. Gene #66: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
14Q LOSS MUTATED	54	0	2	3	2
14Q LOSS WILD-TYPE	115	305	17	6	35

Figure S318. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S319. Gene #66: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
14Q LOSS MUTATED	40	7	1
14Q LOSS WILD-TYPE	125	82	170

Figure S319. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S320. Gene #66: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
14Q LOSS MUTATED	3	53	4
14Q LOSS WILD-TYPE	148	177	145

Figure S320. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S321. Gene #66: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
14Q LOSS MUTATED	8	48	4
14Q LOSS WILD-TYPE	208	121	141

Figure S321. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S322. Gene #66: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
14Q LOSS MUTATED	50	7	2
14Q LOSS WILD-TYPE	176	136	159

Figure S322. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'14q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S323. Gene #66: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
14Q LOSS MUTATED	2	1	39	17
14Q LOSS WILD-TYPE	139	59	84	189

Figure S323. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S324. Gene #66: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
14Q LOSS MUTATED	31	3	13
14Q LOSS WILD-TYPE	113	112	126

Figure S324. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q loss' versus 'MRNA_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.032

Table S325. Gene #67: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
15Q LOSS MUTATED	1	6	0	0	0
15Q LOSS WILD-TYPE	13	3	7	7	16

Figure S325. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S326. Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
15Q LOSS MUTATED	91	4	6	5	3
15Q LOSS WILD-TYPE	78	301	13	4	34

Figure S326. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S327. Gene #67: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
15Q LOSS MUTATED	70	18	8
15Q LOSS WILD-TYPE	95	71	163

Figure S327. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S328. Gene #67: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
15Q LOSS MUTATED	6	94	9
15Q LOSS WILD-TYPE	145	136	140

Figure S328. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S329. Gene #67: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
15Q LOSS MUTATED	21	80	8
15Q LOSS WILD-TYPE	195	89	137

Figure S329. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S330. Gene #67: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
15Q LOSS MUTATED	87	12	8
15Q LOSS WILD-TYPE	139	131	153

Figure S330. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S331. Gene #67: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
15Q LOSS MUTATED	7	1	61	38
15Q LOSS WILD-TYPE	134	59	62	168

Figure S331. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S332. Gene #67: '15q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
15Q LOSS MUTATED	58	23	13
15Q LOSS WILD-TYPE	114	73	117

Figure S332. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S333. Gene #67: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
15Q LOSS MUTATED	55	8	31
15Q LOSS WILD-TYPE	89	107	108

Figure S333. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S334. Gene #68: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
16P LOSS MUTATED	85	4	4	1	3
16P LOSS WILD-TYPE	84	301	15	8	34

Figure S334. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

'16p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S335. Gene #68: '16p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
16P LOSS MUTATED	61	20	6
16P LOSS WILD-TYPE	104	69	165

Figure S335. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S336. Gene #68: '16p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
16P LOSS MUTATED	4	84	8
16P LOSS WILD-TYPE	147	146	141

Figure S336. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S337. Gene #68: '16p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
16P LOSS MUTATED	18	70	8
16P LOSS WILD-TYPE	198	99	137

Figure S337. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S338. Gene #68: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
16P LOSS MUTATED	75	10	9
16P LOSS WILD-TYPE	151	133	152

Figure S338. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S339. Gene #68: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
16P LOSS MUTATED	7	2	56	29
16P LOSS WILD-TYPE	134	58	67	177

Figure S339. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S340. Gene #68: '16p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
16P LOSS MUTATED	46	7	33
16P LOSS WILD-TYPE	98	108	106

Figure S340. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S341. Gene #69: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
16Q LOSS MUTATED	112	14	7	1	4
16Q LOSS WILD-TYPE	57	291	12	8	33

Figure S341. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S342. Gene #69: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
16Q LOSS MUTATED	80	26	15
16Q LOSS WILD-TYPE	85	63	156

Figure S342. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S343. Gene #69: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
16Q LOSS MUTATED	14	110	14
16Q LOSS WILD-TYPE	137	120	135

Figure S343. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S344. Gene #69: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
16Q LOSS MUTATED	32	93	13
16Q LOSS WILD-TYPE	184	76	132

Figure S344. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S345. Gene #69: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
16Q LOSS MUTATED	98	21	15
16Q LOSS WILD-TYPE	128	122	146

Figure S345. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S346. Gene #69: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
16Q LOSS MUTATED	13	7	73	41
16Q LOSS WILD-TYPE	128	53	50	165

Figure S346. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.12

Table S347. Gene #69: '16q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
16Q LOSS MUTATED	66	30	22
16Q LOSS WILD-TYPE	106	66	108

Figure S347. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S348. Gene #69: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
16Q LOSS MUTATED	61	13	44
16Q LOSS WILD-TYPE	83	102	95

Figure S348. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'MRNA_CHIERARCHICAL'

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

Table S349. Gene #70: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
17P LOSS MUTATED	1	6	1	0	0
17P LOSS WILD-TYPE	13	3	6	7	16

Figure S349. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S350. Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
17P LOSS MUTATED	120	3	4	1	2
17P LOSS WILD-TYPE	49	302	15	8	35

Figure S350. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S351. Gene #70: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
17P LOSS MUTATED	83	21	11
17P LOSS WILD-TYPE	82	68	160

Figure S351. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S352. Gene #70: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
17P LOSS MUTATED	4	108	15
17P LOSS WILD-TYPE	147	122	134

Figure S352. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S353. Gene #70: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
17P LOSS MUTATED	19	92	16
17P LOSS WILD-TYPE	197	77	129

Figure S353. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S354. Gene #70: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
17P LOSS MUTATED	102	9	16
17P LOSS WILD-TYPE	124	134	145

Figure S354. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S355. Gene #70: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
17P LOSS MUTATED	16	1	74	36
17P LOSS WILD-TYPE	125	59	49	170

Figure S355. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S356. Gene #70: '17p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
17P LOSS MUTATED	66	28	16
17P LOSS WILD-TYPE	106	68	114

Figure S356. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'17p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S357. Gene #70: '17p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
17P LOSS MUTATED	59	16	35
17P LOSS WILD-TYPE	85	99	104

Figure S357. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q loss' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S358. Gene #71: '17q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
17Q LOSS MUTATED	0	6	0	0	0
17Q LOSS WILD-TYPE	14	3	7	7	16

Figure S358. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S359. Gene #71: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
17Q LOSS MUTATED	84	2	4	1	2
17Q LOSS WILD-TYPE	85	303	15	8	35

Figure S359. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

'17q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S360. Gene #71: '17q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
17Q LOSS MUTATED	54	18	10
17Q LOSS WILD-TYPE	111	71	161

Figure S360. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S361. Gene #71: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
17Q LOSS MUTATED	4	74	13
17Q LOSS WILD-TYPE	147	156	136

Figure S361. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S362. Gene #71: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
17Q LOSS MUTATED	17	60	14
17Q LOSS WILD-TYPE	199	109	131

Figure S362. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S363. Gene #71: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
17Q LOSS MUTATED	68	8	14
17Q LOSS WILD-TYPE	158	135	147

Figure S363. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S364. Gene #71: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
17Q LOSS MUTATED	12	1	48	29
17Q LOSS WILD-TYPE	129	59	75	177

Figure S364. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00048 (Fisher's exact test), Q value = 0.23

Table S365. Gene #71: '17q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
17Q LOSS MUTATED	44	14	22
17Q LOSS WILD-TYPE	100	101	117

Figure S365. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S366. Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
18P LOSS MUTATED	38	1	6	4	3
18P LOSS WILD-TYPE	131	304	13	5	34

Figure S366. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S367. Gene #72: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
18P LOSS MUTATED	34	8	4
18P LOSS WILD-TYPE	131	81	167

Figure S367. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S368. Gene #72: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
18P LOSS MUTATED	5	40	7
18P LOSS WILD-TYPE	146	190	142

Figure S368. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p loss' versus 'MIRSEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.052

Table S369. Gene #72: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
18P LOSS MUTATED	36	8	7
18P LOSS WILD-TYPE	190	135	154

Figure S369. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 0.13

Table S370. Gene #72: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
18P LOSS MUTATED	5	2	22	22
18P LOSS WILD-TYPE	136	58	101	184

Figure S370. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S371. Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
18Q LOSS MUTATED	50	1	7	4	3
18Q LOSS WILD-TYPE	119	304	12	5	34

Figure S371. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S372. Gene #73: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
18Q LOSS MUTATED	42	11	6
18Q LOSS WILD-TYPE	123	78	165

Figure S372. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S373. Gene #73: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
18Q LOSS MUTATED	5	52	8
18Q LOSS WILD-TYPE	146	178	141

Figure S373. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S374. Gene #73: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
18Q LOSS MUTATED	19	38	8
18Q LOSS WILD-TYPE	197	131	137

Figure S374. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S375. Gene #73: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
18Q LOSS MUTATED	48	7	9
18Q LOSS WILD-TYPE	178	136	152

Figure S375. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S376. Gene #73: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
18Q LOSS MUTATED	6	1	35	22
18Q LOSS WILD-TYPE	135	59	88	184

Figure S376. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S377. Gene #74: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
19P LOSS MUTATED	51	0	5	2	1
19P LOSS WILD-TYPE	118	305	14	7	36

Figure S377. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S378. Gene #74: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
19P LOSS MUTATED	45	6	2
19P LOSS WILD-TYPE	120	83	169

Figure S378. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S379. Gene #74: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
19P LOSS MUTATED	4	48	5
19P LOSS WILD-TYPE	147	182	144

Figure S379. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S380. Gene #74: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
19P LOSS MUTATED	12	41	4
19P LOSS WILD-TYPE	204	128	141

Figure S380. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S381. Gene #74: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
19P LOSS MUTATED	46	5	6
19P LOSS WILD-TYPE	180	138	155

Figure S381. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S382. Gene #74: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
19P LOSS MUTATED	5	1	35	16
19P LOSS WILD-TYPE	136	59	88	190

Figure S382. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S383. Gene #74: '19p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
19P LOSS MUTATED	37	3	11
19P LOSS WILD-TYPE	107	112	128

Figure S383. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S384. Gene #75: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
19Q LOSS MUTATED	49	1	4	1	1
19Q LOSS WILD-TYPE	120	304	15	8	36

Figure S384. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S385. Gene #75: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
19Q LOSS MUTATED	37	8	4
19Q LOSS WILD-TYPE	128	81	167

Figure S385. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S386. Gene #75: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
19Q LOSS MUTATED	4	44	6
19Q LOSS WILD-TYPE	147	186	143

Figure S386. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S387. Gene #75: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
19Q LOSS MUTATED	10	39	5
19Q LOSS WILD-TYPE	206	130	140

Figure S387. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S388. Gene #75: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
19Q LOSS MUTATED	42	5	7
19Q LOSS WILD-TYPE	184	138	154

Figure S388. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S389. Gene #75: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
19Q LOSS MUTATED	6	1	28	19
19Q LOSS WILD-TYPE	135	59	95	187

Figure S389. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.016

Table S390. Gene #75: '19q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
19Q LOSS MUTATED	31	4	12
19Q LOSS WILD-TYPE	113	111	127

Figure S390. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S391. Gene #76: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
20P LOSS MUTATED	16	1	1	1	0
20P LOSS WILD-TYPE	153	304	18	8	37

Figure S391. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

'20q loss' versus 'CN_CNMF'

P value = 0.00043 (Fisher's exact test), Q value = 0.21

Table S392. Gene #77: '20q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
20Q LOSS MUTATED	7	0	1	1	0
20Q LOSS WILD-TYPE	162	305	18	8	37

Figure S392. Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #3: 'CN_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S393. Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
21Q LOSS MUTATED	44	4	2	4	0
21Q LOSS WILD-TYPE	125	301	17	5	37

Figure S393. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

'21q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S394. Gene #78: '21q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
21Q LOSS MUTATED	34	7	5
21Q LOSS WILD-TYPE	131	82	166

Figure S394. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'21q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S395. Gene #78: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
21Q LOSS MUTATED	7	45	1
21Q LOSS WILD-TYPE	144	185	148

Figure S395. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S396. Gene #78: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
21Q LOSS MUTATED	15	36	2
21Q LOSS WILD-TYPE	201	133	143

Figure S396. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S397. Gene #78: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
21Q LOSS MUTATED	44	6	2
21Q LOSS WILD-TYPE	182	137	159

Figure S397. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'21q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S398. Gene #78: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
21Q LOSS MUTATED	2	2	30	18
21Q LOSS WILD-TYPE	139	58	93	188

Figure S398. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S399. Gene #78: '21q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
21Q LOSS MUTATED	28	1	17
21Q LOSS WILD-TYPE	116	114	122

Figure S399. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S400. Gene #79: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
22Q LOSS MUTATED	96	3	4	3	3
22Q LOSS WILD-TYPE	73	302	15	6	34

Figure S400. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S401. Gene #79: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
22Q LOSS MUTATED	67	20	13
22Q LOSS WILD-TYPE	98	69	158

Figure S401. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S402. Gene #79: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
22Q LOSS MUTATED	6	83	17
22Q LOSS WILD-TYPE	145	147	132

Figure S402. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S403. Gene #79: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
22Q LOSS MUTATED	23	67	16
22Q LOSS WILD-TYPE	193	102	129

Figure S403. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S404. Gene #79: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
22Q LOSS MUTATED	80	10	17
22Q LOSS WILD-TYPE	146	133	144

Figure S404. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S405. Gene #79: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
22Q LOSS MUTATED	15	1	55	36
22Q LOSS WILD-TYPE	126	59	68	170

Figure S405. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.1

Table S406. Gene #79: '22q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
22Q LOSS MUTATED	50	15	29
22Q LOSS WILD-TYPE	94	100	110

Figure S406. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S407. Gene #80: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
XQ LOSS MUTATED	63	1	3	2	1
XQ LOSS WILD-TYPE	106	304	16	7	36

Figure S407. Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S408. Gene #80: 'xq loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
XQ LOSS MUTATED	42	11	6
XQ LOSS WILD-TYPE	123	78	165

Figure S408. Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xq loss' versus 'RPPA_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.067

Table S409. Gene #80: 'xq loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	37	39	12	41	24
XQ LOSS MUTATED	3	13	2	1	1	1
XQ LOSS WILD-TYPE	38	24	37	11	40	23

Figure S409. Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'xq loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S410. Gene #80: 'xq loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
XQ LOSS MUTATED	4	59	5
XQ LOSS WILD-TYPE	147	171	144

Figure S410. Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'xq loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S411. Gene #80: 'xq loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
XQ LOSS MUTATED	17	46	5
XQ LOSS WILD-TYPE	199	123	140

Figure S411. Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S412. Gene #80: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
XQ LOSS MUTATED	52	7	8
XQ LOSS WILD-TYPE	174	136	153

Figure S412. Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xq loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S413. Gene #80: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
XQ LOSS MUTATED	5	2	38	22
XQ LOSS WILD-TYPE	136	58	85	184

Figure S413. Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S414. Gene #80: 'xq loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
XQ LOSS MUTATED	41	4	13
XQ LOSS WILD-TYPE	103	111	126

Figure S414. Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtypes file = UCEC-TP.transferedmergedcluster.txt
Number of patients = 539
Number of significantly arm-level cnvs = 80
Number of molecular subtypes = 12
Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

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] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)

[2] 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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