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

Uterine Corpus Endometrioid Carcinoma (Primary solid tumor)

16 April 2014 | analyses__2014_04_16

Maintainer Information

Citation Information

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

Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C18K77S8

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 524 patients, 413 significant findings detected with P value < 0.05 and Q value < 0.25.

1p gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
1q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 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', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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' and 'MRNASEQ_CNMF'.
6p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
6q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
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', and 'MRNASEQ_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', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
12q gain cnv correlated to 'CN_CNMF'.
13q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
14q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
16p gain cnv correlated to 'CN_CNMF'.
17p gain cnv correlated to 'CN_CNMF'.
17q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
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', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
19q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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 'MRNA_CHIERARCHICAL', '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', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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', and 'MIRSEQ_CNMF'.
2q loss cnv correlated to 'CN_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 'MRNA_CHIERARCHICAL', '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_CHIERARCHICAL'.
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' and 'MIRSEQ_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 '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_MATURE_CHIERARCHICAL'.
9p loss cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
9q loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_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', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_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', 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_CHIERARCHICAL'.
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', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
15q loss cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
16p 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'.
16q 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'.
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', and 'MIRSEQ_CHIERARCHICAL'.
18p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', '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', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
19q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
20p loss cnv correlated to 'CN_CNMF'.
21q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
22q loss cnv correlated to 'MRNA_CHIERARCHICAL', '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, 413 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	Chi-square test	Fisher's exact test	Chi-square test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
15q loss	106 (20%)	418	0.000567 (0.274)	4.17e-05 (0.0229)	3.8e-41 (3.39e-38)	1.92e-14 (1.56e-11)	0.00036 (0.178)	0.212 (1.00)	4.15e-23 (3.62e-20)	3.5e-21 (3.01e-18)	1.82e-17 (1.54e-14)	1.5e-15 (1.23e-12)	1.17e-07 (7.96e-05)	8.56e-09 (6.07e-06)
20q gain	125 (24%)	399	0.00202 (0.897)	0.000218 (0.112)	9.24e-43 (8.27e-40)	5.8e-12 (4.54e-09)	0.0303 (1.00)	0.378 (1.00)	8.54e-19 (7.23e-16)	8.8e-16 (7.23e-13)	7.21e-14 (5.75e-11)	1.19e-08 (8.35e-06)	7.98e-05 (0.0429)	3.59e-06 (0.00217)
4p loss	100 (19%)	424	0.00381 (1.00)	0.000454 (0.223)	3.46e-38 (3.08e-35)	1.13e-16 (9.39e-14)	0.00389 (1.00)	0.346 (1.00)	8.91e-23 (7.76e-20)	8.22e-20 (7.02e-17)	6.72e-17 (5.63e-14)	4.38e-14 (3.52e-11)	1.78e-06 (0.0011)	4.07e-10 (3.04e-07)
9q loss	117 (22%)	407	2.35e-05 (0.0133)	1.13e-06 (0.000718)	8.8e-49 (7.89e-46)	1.28e-11 (9.94e-09)	0.000759 (0.358)	0.205 (1.00)	4.2e-20 (3.6e-17)	4.06e-17 (3.41e-14)	5.86e-14 (4.69e-11)	1.69e-09 (1.24e-06)	0.000835 (0.393)	7.24e-07 (0.000468)
14q loss	56 (11%)	468	0.00202 (0.897)	0.000218 (0.112)	1.38e-23 (1.2e-20)	5.91e-11 (4.51e-08)	0.0419 (1.00)	0.00457 (1.00)	4.54e-12 (3.56e-09)	9.66e-11 (7.34e-08)	4.33e-10 (3.23e-07)	1.12e-11 (8.7e-09)	1.92e-05 (0.0109)	2.22e-05 (0.0126)
16p loss	94 (18%)	430	0.00202 (0.897)	0.000218 (0.112)	8.31e-38 (7.39e-35)	2.04e-13 (1.62e-10)	0.0713 (1.00)	0.157 (1.00)	1.93e-21 (1.67e-18)	6.6e-18 (5.58e-15)	5.68e-14 (4.55e-11)	3.12e-10 (2.34e-07)	2.68e-05 (0.0151)	2.47e-09 (1.79e-06)
16q loss	135 (26%)	389	0.000771 (0.363)	9.8e-05 (0.0524)	2.04e-48 (1.82e-45)	3.69e-14 (2.97e-11)	0.308 (1.00)	1 (1.00)	3.49e-22 (3.02e-19)	1.82e-19 (1.55e-16)	7.1e-16 (5.86e-13)	2.8e-10 (2.11e-07)	1.84e-06 (0.00113)	5.22e-10 (3.88e-07)
17p loss	122 (23%)	402	0.00324 (1.00)	0.000454 (0.223)	4.05e-58 (3.64e-55)	4.35e-16 (3.6e-13)	0.00274 (1.00)	0.827 (1.00)	2.85e-26 (2.5e-23)	4.03e-22 (3.49e-19)	6.94e-19 (5.89e-16)	1.01e-11 (7.86e-09)	0.000455 (0.223)	8.61e-07 (0.000553)
2p gain	92 (18%)	432	0.855 (1.00)	0.683 (1.00)	1.81e-24 (1.59e-21)	1.42e-08 (9.93e-06)	0.0736 (1.00)	0.831 (1.00)	1.79e-09 (1.3e-06)	1.62e-09 (1.18e-06)	2.14e-08 (1.48e-05)	4.49e-06 (0.00269)	0.000148 (0.0775)	1.43e-06 (0.000894)
2q gain	75 (14%)	449	0.343 (1.00)	1 (1.00)	7.76e-22 (6.71e-19)	4.83e-07 (0.000315)	0.0502 (1.00)	1 (1.00)	8.79e-08 (5.98e-05)	2.26e-07 (0.00015)	6.19e-07 (0.000401)	9.78e-06 (0.00578)	0.000154 (0.08)	3.06e-06 (0.00186)
3q gain	78 (15%)	446	0.617 (1.00)	0.847 (1.00)	8.89e-28 (7.83e-25)	1.02e-08 (7.21e-06)	0.163 (1.00)	0.0444 (1.00)	2.11e-12 (1.66e-09)	1.78e-14 (1.45e-11)	8.53e-10 (6.32e-07)	8.86e-08 (6.02e-05)	0.000299 (0.149)	9.53e-07 (0.000609)
5p gain	49 (9%)	475	0.902 (1.00)	0.312 (1.00)	6.3e-16 (5.2e-13)	1.3e-07 (8.79e-05)	0.0743 (1.00)	1 (1.00)	4.48e-11 (3.43e-08)	1.04e-08 (7.3e-06)	6.52e-09 (4.66e-06)	1.15e-06 (0.000731)	2.71e-05 (0.0152)	3.36e-06 (0.00203)
18p gain	68 (13%)	456	0.333 (1.00)	0.158 (1.00)	1.25e-26 (1.1e-23)	1.59e-09 (1.16e-06)	0.0184 (1.00)	0.0242 (1.00)	1.41e-16 (1.17e-13)	8.65e-16 (7.12e-13)	2.55e-14 (2.06e-11)	5.54e-11 (4.24e-08)	9.06e-07 (0.00058)	2.87e-11 (2.21e-08)
18q gain	41 (8%)	483	0.253 (1.00)	0.0902 (1.00)	4.68e-13 (3.71e-10)	5.71e-05 (0.0311)	0.292 (1.00)	0.0831 (1.00)	7.61e-09 (5.41e-06)	7.5e-09 (5.34e-06)	8.07e-08 (5.5e-05)	1.31e-06 (0.000821)	0.000118 (0.0624)	1.58e-06 (0.000983)
20p gain	107 (20%)	417	0.00809 (1.00)	0.00105 (0.488)	1.53e-34 (1.36e-31)	3.97e-11 (3.05e-08)	0.143 (1.00)	0.812 (1.00)	4.46e-16 (3.69e-13)	1.5e-13 (1.2e-10)	2.31e-11 (1.78e-08)	1.3e-07 (8.8e-05)	2.43e-05 (0.0138)	9.25e-06 (0.00548)
22q gain	31 (6%)	493			1.89e-08 (1.31e-05)	1.92e-09 (1.4e-06)	0.341 (1.00)	0.0519 (1.00)	1.96e-11 (1.52e-08)	2.26e-10 (1.7e-07)	5.19e-09 (3.72e-06)	3.78e-05 (0.0208)	5.19e-06 (0.0031)	1.4e-06 (0.000877)
4q loss	99 (19%)	425	0.151 (1.00)	0.0272 (1.00)	7.07e-40 (6.3e-37)	3.84e-17 (3.23e-14)	0.0198 (1.00)	0.346 (1.00)	2.46e-22 (2.14e-19)	1.95e-19 (1.66e-16)	1.7e-16 (1.41e-13)	8.75e-15 (7.13e-12)	1.34e-06 (0.000842)	7.96e-11 (6.06e-08)
5q loss	72 (14%)	452	0.0129 (1.00)	0.00193 (0.862)	1.23e-28 (1.08e-25)	9.2e-15 (7.49e-12)	0.00283 (1.00)	0.0233 (1.00)	6.07e-15 (4.96e-12)	3.57e-13 (2.83e-10)	2.43e-13 (1.93e-10)	1.14e-09 (8.41e-07)	2.78e-05 (0.0155)	7.66e-09 (5.44e-06)
8p loss	75 (14%)	449	0.00809 (1.00)	0.00105 (0.488)	3.22e-32 (2.86e-29)	7.57e-16 (6.24e-13)	0.04 (1.00)	0.58 (1.00)	3.68e-20 (3.15e-17)	9.99e-17 (8.34e-14)	2.84e-16 (2.36e-13)	3.63e-11 (2.79e-08)	5.5e-08 (3.76e-05)	3.37e-10 (2.52e-07)
9p loss	99 (19%)	425	0.000997 (0.467)	9.8e-05 (0.0524)	2.02e-41 (1.81e-38)	1.27e-10 (9.6e-08)	0.00599 (1.00)	0.168 (1.00)	5.67e-17 (4.75e-14)	1.23e-14 (9.97e-12)	6.62e-13 (5.23e-10)	9.35e-09 (6.62e-06)	0.00534 (1.00)	1.37e-06 (0.00086)
11q loss	68 (13%)	456			8.89e-25 (7.79e-22)	1.09e-09 (8.03e-07)	0.777 (1.00)	1 (1.00)	7.7e-12 (6.01e-09)	2.03e-10 (1.53e-07)	1.1e-09 (8.11e-07)	2.25e-06 (0.00137)	0.000168 (0.0872)	1.88e-06 (0.00116)
12q loss	34 (6%)	490			3.29e-14 (2.65e-11)	2.62e-05 (0.0148)	0.101 (1.00)	0.0429 (1.00)	4.65e-09 (3.34e-06)	2.94e-07 (0.000194)	1.3e-06 (0.000817)	1.07e-05 (0.0063)	0.000266 (0.133)	7.75e-05 (0.0418)
19p loss	57 (11%)	467			6.2e-20 (5.3e-17)	6.15e-13 (4.86e-10)	0.0523 (1.00)	0.393 (1.00)	1.82e-10 (1.37e-07)	4.57e-09 (3.29e-06)	1.01e-07 (6.88e-05)	1.66e-06 (0.00103)	1.63e-05 (0.00939)	1.11e-05 (0.00652)
21q loss	53 (10%)	471	0.00809 (1.00)	0.00105 (0.488)	3.24e-16 (2.69e-13)	5.89e-06 (0.00351)	0.11 (1.00)	0.393 (1.00)	5.86e-11 (4.48e-08)	1.4e-08 (9.79e-06)	2.48e-09 (1.79e-06)	4.12e-07 (0.00027)	8.84e-07 (0.000567)	1.11e-06 (0.000707)
22q loss	105 (20%)	419	0.00202 (0.897)	0.000218 (0.112)	1.17e-42 (1.05e-39)	2.56e-10 (1.92e-07)	0.0443 (1.00)	0.813 (1.00)	1.31e-15 (1.07e-12)	2.45e-14 (1.98e-11)	1.17e-11 (9.14e-09)	3.06e-09 (2.21e-06)	0.0121 (1.00)	0.000152 (0.0793)
xq loss	69 (13%)	455	0.00809 (1.00)	0.00105 (0.488)	1.89e-29 (1.67e-26)	2.82e-07 (0.000186)	2.71e-05 (0.0152)	0.059 (1.00)	2.21e-14 (1.79e-11)	1.18e-11 (9.2e-09)	1.12e-08 (7.87e-06)	2e-07 (0.000134)	0.000682 (0.325)	6.93e-05 (0.0374)
6p gain	76 (15%)	448	0.209 (1.00)	0.173 (1.00)	3.37e-25 (2.96e-22)	2.07e-07 (0.000138)	0.168 (1.00)	0.0935 (1.00)	1.07e-09 (7.91e-07)	2.41e-09 (1.75e-06)	3.8e-07 (0.00025)	3.91e-06 (0.00236)	0.00832 (1.00)	0.000291 (0.145)
19q gain	55 (10%)	469			2.46e-24 (2.15e-21)	2.66e-05 (0.015)	0.331 (1.00)	0.477 (1.00)	3.07e-15 (2.51e-12)	1.08e-14 (8.76e-12)	1.01e-10 (7.69e-08)	1.39e-07 (9.39e-05)	0.00371 (1.00)	0.000153 (0.0797)
3p loss	50 (10%)	474	0.0391 (1.00)	0.00466 (1.00)	1.84e-20 (1.58e-17)	5.87e-07 (0.000381)	0.00865 (1.00)	0.0444 (1.00)	4.67e-14 (3.75e-11)	1.49e-12 (1.17e-09)	1.52e-07 (0.000102)	1.71e-06 (0.00106)	0.00254 (1.00)	2.68e-05 (0.0151)
5p loss	54 (10%)	470	0.151 (1.00)	0.0272 (1.00)	8.03e-19 (6.81e-16)	2.96e-09 (2.14e-06)	0.0303 (1.00)	0.0242 (1.00)	1.77e-09 (1.29e-06)	4.73e-09 (3.39e-06)	4.54e-08 (3.12e-05)	5.43e-07 (0.000353)	0.00234 (1.00)	1.2e-05 (0.007)
7q loss	41 (8%)	483			3.11e-21 (2.68e-18)	2.22e-08 (1.54e-05)	0.0844 (1.00)	0.000752 (0.356)	8.23e-14 (6.56e-11)	2.94e-11 (2.26e-08)	1.7e-10 (1.29e-07)	1.31e-06 (0.000821)	0.00071 (0.337)	1.93e-07 (0.000129)
10p loss	40 (8%)	484	0.0391 (1.00)	0.00466 (1.00)	8.64e-19 (7.31e-16)	4.32e-07 (0.000282)	0.0823 (1.00)	0.477 (1.00)	1.18e-09 (8.65e-07)	1.51e-08 (1.06e-05)	7.11e-08 (4.86e-05)	5.59e-06 (0.00334)	0.00769 (1.00)	3.75e-05 (0.0207)
11p loss	72 (14%)	452			3.7e-28 (3.27e-25)	8.26e-11 (6.29e-08)	0.218 (1.00)	0.373 (1.00)	6.07e-15 (4.96e-12)	2.21e-12 (1.74e-09)	1.24e-09 (9.12e-07)	4.88e-07 (0.000317)	0.000591 (0.285)	1.14e-06 (0.000724)
12p loss	42 (8%)	482	0.137 (1.00)	0.0194 (1.00)	1.38e-17 (1.17e-14)	8.05e-05 (0.0432)	0.0355 (1.00)	0.106 (1.00)	2.88e-10 (2.16e-07)	2.35e-08 (1.62e-05)	1.69e-08 (1.18e-05)	6.69e-05 (0.0363)	0.000534 (0.259)	8.21e-05 (0.044)
17q loss	88 (17%)	436	0.00202 (0.897)	0.000218 (0.112)	1.63e-36 (1.44e-33)	5.35e-08 (3.67e-05)	0.0924 (1.00)	0.612 (1.00)	1.83e-14 (1.48e-11)	5.92e-12 (4.63e-09)	7.08e-09 (5.06e-06)	2.12e-07 (0.000141)	0.0149 (1.00)	0.0115 (1.00)
1p gain	46 (9%)	478	0.534 (1.00)	0.312 (1.00)	1.18e-10 (8.92e-08)	0.00165 (0.743)	0.065 (1.00)	0.137 (1.00)	3.69e-06 (0.00222)	0.000133 (0.0701)	3.42e-05 (0.0189)	1.23e-05 (0.00714)	0.000101 (0.0536)	0.00482 (1.00)
1p loss	22 (4%)	502			2.24e-09 (1.63e-06)	7.78e-07 (0.000502)	0.655 (1.00)	0.151 (1.00)	1.63e-05 (0.00939)	6.88e-05 (0.0372)	0.000204 (0.105)	1.13e-05 (0.00658)	0.0289 (1.00)	0.00338 (1.00)
6q loss	24 (5%)	500	0.379 (1.00)	0.0902 (1.00)	4.67e-09 (3.36e-06)	0.000123 (0.0651)	0.423 (1.00)	0.674 (1.00)	4.01e-06 (0.00241)	1.78e-05 (0.0102)	0.00043 (0.211)	1.52e-05 (0.00878)	0.0357 (1.00)	0.0208 (1.00)
7p loss	43 (8%)	481	0.0391 (1.00)	0.00466 (1.00)	1.09e-16 (9.1e-14)	0.000478 (0.233)	0.0684 (1.00)	0.0546 (1.00)	7.43e-10 (5.51e-07)	1.25e-08 (8.8e-06)	1.2e-06 (0.00076)	0.000381 (0.188)	0.0673 (1.00)	0.00139 (0.635)
8q loss	25 (5%)	499			3.82e-10 (2.85e-07)	3.47e-07 (0.000229)	0.333 (1.00)	1 (1.00)	8.28e-07 (0.000532)	4.52e-06 (0.0027)	2.3e-05 (0.0131)	0.00116 (0.534)	0.000617 (0.296)	0.000135 (0.0708)
10q loss	39 (7%)	485	0.137 (1.00)	0.0194 (1.00)	9.31e-17 (7.78e-14)	4.32e-07 (0.000282)	0.0907 (1.00)	0.731 (1.00)	1.76e-08 (1.23e-05)	2.06e-07 (0.000137)	1.54e-06 (0.000962)	0.000301 (0.149)	0.0434 (1.00)	0.00101 (0.472)
13q loss	89 (17%)	435	0.902 (1.00)	0.667 (1.00)	1.2e-28 (1.06e-25)	1.21e-06 (0.000761)	0.0492 (1.00)	0.142 (1.00)	8.65e-10 (6.4e-07)	3.4e-08 (2.35e-05)	3.34e-05 (0.0185)	3.78e-08 (2.6e-05)	0.0499 (1.00)	0.0302 (1.00)
18p loss	52 (10%)	472			2.08e-17 (1.75e-14)	1.53e-07 (0.000103)	0.417 (1.00)	1 (1.00)	1.88e-06 (0.00116)	1.26e-05 (0.00732)	0.00011 (0.0587)	0.000165 (0.0857)	0.00276 (1.00)	0.0162 (1.00)
18q loss	65 (12%)	459	0.536 (1.00)	0.272 (1.00)	1.15e-22 (9.97e-20)	9.38e-09 (6.63e-06)	0.627 (1.00)	1 (1.00)	1.09e-09 (8.05e-07)	1.56e-08 (1.09e-05)	1.21e-07 (8.22e-05)	3.6e-07 (0.000237)	0.00213 (0.931)	0.0015 (0.678)
19q loss	53 (10%)	471	0.253 (1.00)	0.0902 (1.00)	4.41e-17 (3.7e-14)	1.53e-07 (0.000103)	0.159 (1.00)	0.56 (1.00)	6.1e-08 (4.17e-05)	7.82e-07 (0.000504)	2.12e-06 (0.0013)	4.85e-05 (0.0265)	0.00129 (0.59)	0.000618 (0.296)
6q gain	61 (12%)	463	0.209 (1.00)	0.173 (1.00)	1.04e-19 (8.85e-17)	0.000278 (0.139)	0.0946 (1.00)	0.0444 (1.00)	1.11e-05 (0.00652)	1.37e-05 (0.0079)	0.000179 (0.0921)	0.00155 (0.701)	0.371 (1.00)	0.023 (1.00)
12p gain	66 (13%)	458	0.387 (1.00)	1 (1.00)	6.66e-13 (5.25e-10)	2.94e-05 (0.0164)	0.857 (1.00)	0.812 (1.00)	3.5e-06 (0.00212)	1.07e-05 (0.0063)	0.00211 (0.924)	0.0189 (1.00)	0.00108 (0.497)	0.000243 (0.123)
13q gain	28 (5%)	496	0.137 (1.00)	0.0194 (1.00)	1.71e-11 (1.33e-08)	0.000135 (0.0709)	0.224 (1.00)	0.477 (1.00)	1.68e-06 (0.00104)	1.04e-05 (0.00611)	3.86e-07 (0.000253)	0.000914 (0.429)	0.0371 (1.00)	0.00123 (0.562)
17q gain	28 (5%)	496			1.73e-08 (1.2e-05)	2.69e-05 (0.0151)	0.062 (1.00)	0.674 (1.00)	0.000116 (0.0616)	1.04e-05 (0.00611)	0.000222 (0.113)	0.0158 (1.00)	0.0705 (1.00)	0.00122 (0.561)
19p gain	50 (10%)	474	0.0391 (1.00)	0.00466 (1.00)	1.35e-22 (1.17e-19)	0.0006 (0.289)	0.812 (1.00)	0.155 (1.00)	5.48e-12 (4.3e-09)	1.74e-11 (1.34e-08)	7.11e-09 (5.07e-06)	3.58e-05 (0.0198)	0.0369 (1.00)	0.00326 (1.00)
21q gain	36 (7%)	488			6.22e-14 (4.97e-11)	0.00268 (1.00)	0.341 (1.00)	0.0519 (1.00)	2.19e-06 (0.00134)	1.74e-05 (0.00994)	1.14e-06 (0.000721)	5.92e-05 (0.0322)	0.129 (1.00)	0.00163 (0.734)
1q loss	13 (2%)	511			0.000153 (0.0797)	3.63e-05 (0.02)		0.14 (1.00)	4.84e-05 (0.0265)	0.000237 (0.12)	0.000287 (0.143)	0.00196 (0.875)	0.0388 (1.00)	0.00393 (1.00)
3q loss	30 (6%)	494	0.0391 (1.00)	0.00466 (1.00)	1.44e-11 (1.12e-08)	0.000197 (0.101)	0.0637 (1.00)	0.201 (1.00)	3.4e-08 (2.35e-05)	2.68e-07 (0.000178)	3.05e-06 (0.00186)	0.00337 (1.00)	0.0984 (1.00)	0.00122 (0.561)
1q gain	178 (34%)	346	0.174 (1.00)	0.201 (1.00)	0.000175 (0.0902)	0.24 (1.00)	0.0855 (1.00)	0.014 (1.00)	0.00024 (0.121)	0.000134 (0.0708)	0.000252 (0.127)	0.0552 (1.00)	0.919 (1.00)	0.401 (1.00)
8q gain	152 (29%)	372	0.0106 (1.00)	0.015 (1.00)	2.8e-21 (2.41e-18)	0.217 (1.00)	0.00029 (0.145)	0.728 (1.00)	1.15e-05 (0.0067)	1.28e-05 (0.00742)	0.002 (0.891)	0.000583 (0.281)	0.0853 (1.00)	0.131 (1.00)
3p gain	45 (9%)	479			2.98e-23 (2.6e-20)	0.0132 (1.00)	0.395 (1.00)	0.713 (1.00)	5.1e-05 (0.0279)	2.31e-05 (0.0131)	0.00398 (1.00)	0.00704 (1.00)	0.0651 (1.00)	0.0488 (1.00)
14q gain	36 (7%)	488	1 (1.00)	0.769 (1.00)	1.39e-07 (9.34e-05)	0.00594 (1.00)	0.225 (1.00)	1 (1.00)	5.89e-06 (0.00351)	2.26e-06 (0.00138)	0.00142 (0.645)	0.0207 (1.00)	0.345 (1.00)	0.00964 (1.00)
5q gain	19 (4%)	505			1.31e-05 (0.00759)	0.0428 (1.00)	0.297 (1.00)	1 (1.00)	0.000331 (0.164)	0.000739 (0.35)	0.00216 (0.944)	0.00491 (1.00)	0.0296 (1.00)	0.00662 (1.00)
6p loss	17 (3%)	507	0.379 (1.00)	0.0902 (1.00)	8.01e-06 (0.00475)	0.00734 (1.00)	0.261 (1.00)	0.367 (1.00)	0.000707 (0.337)	0.00187 (0.838)	0.0177 (1.00)	0.000505 (0.246)	0.318 (1.00)	0.222 (1.00)
4p gain	13 (2%)	511			2.91e-05 (0.0162)	0.912 (1.00)	0.451 (1.00)	0.00691 (1.00)	0.00125 (0.572)	0.0125 (1.00)	0.0106 (1.00)	0.0329 (1.00)	0.336 (1.00)	0.184 (1.00)
7p gain	64 (12%)	460	0.855 (1.00)	1 (1.00)	1.31e-20 (1.12e-17)	0.00747 (1.00)	0.811 (1.00)	0.45 (1.00)	0.0233 (1.00)	0.0817 (1.00)	0.0121 (1.00)	0.015 (1.00)	0.272 (1.00)	0.388 (1.00)
7q gain	62 (12%)	462	0.855 (1.00)	1 (1.00)	2.57e-19 (2.19e-16)	0.00894 (1.00)	0.842 (1.00)	0.173 (1.00)	0.15 (1.00)	0.218 (1.00)	0.0903 (1.00)	0.0614 (1.00)	0.607 (1.00)	1 (1.00)
8p gain	116 (22%)	408	0.355 (1.00)	0.468 (1.00)	1.2e-15 (9.87e-13)	0.938 (1.00)	0.0264 (1.00)	0.845 (1.00)	0.165 (1.00)	0.0715 (1.00)	0.212 (1.00)	0.101 (1.00)	0.569 (1.00)	0.268 (1.00)
9p gain	22 (4%)	502			0.000226 (0.114)	0.00832 (1.00)	0.0996 (1.00)	0.201 (1.00)	0.00529 (1.00)	0.00359 (1.00)	0.0266 (1.00)	0.0822 (1.00)	0.171 (1.00)	0.294 (1.00)
10p gain	116 (22%)	408	0.00713 (1.00)	0.0426 (1.00)	2.54e-07 (0.000168)	0.9 (1.00)	0.192 (1.00)	0.219 (1.00)	0.103 (1.00)	0.367 (1.00)	0.412 (1.00)	0.204 (1.00)	0.144 (1.00)	0.0486 (1.00)
10q gain	109 (21%)	415	0.00486 (1.00)	0.0374 (1.00)	2.1e-06 (0.00129)	0.858 (1.00)	0.117 (1.00)	0.156 (1.00)	0.172 (1.00)	0.394 (1.00)	0.243 (1.00)	0.0412 (1.00)	0.161 (1.00)	0.077 (1.00)
11p gain	22 (4%)	502	0.0391 (1.00)	0.0902 (1.00)	7.18e-07 (0.000465)	0.0841 (1.00)	0.0383 (1.00)	1 (1.00)	0.00529 (1.00)	0.0142 (1.00)	0.00258 (1.00)	0.0209 (1.00)	0.222 (1.00)	0.132 (1.00)
11q gain	19 (4%)	505			3.22e-06 (0.00196)	0.0937 (1.00)	0.157 (1.00)	0.712 (1.00)	0.0274 (1.00)	0.0665 (1.00)	0.143 (1.00)	0.108 (1.00)	0.735 (1.00)	0.259 (1.00)
12q gain	52 (10%)	472	0.387 (1.00)	1 (1.00)	5.81e-10 (4.32e-07)	0.0057 (1.00)	0.899 (1.00)	0.796 (1.00)	0.00209 (0.915)	0.00293 (1.00)	0.0755 (1.00)	0.164 (1.00)	0.0482 (1.00)	0.0218 (1.00)
16p gain	25 (5%)	499			9.78e-07 (0.000624)	0.00334 (1.00)	0.157 (1.00)	0.712 (1.00)	0.114 (1.00)	0.105 (1.00)	0.0118 (1.00)	0.0326 (1.00)	0.847 (1.00)	0.377 (1.00)
17p gain	12 (2%)	512			0.000492 (0.24)	0.293 (1.00)	0.326 (1.00)	0.558 (1.00)	0.0982 (1.00)	0.00309 (1.00)	0.0667 (1.00)	0.152 (1.00)	0.713 (1.00)	0.222 (1.00)
xq gain	63 (12%)	461	0.704 (1.00)	0.847 (1.00)	4.16e-22 (3.6e-19)	0.723 (1.00)	0.917 (1.00)	0.329 (1.00)	0.545 (1.00)	0.301 (1.00)	0.291 (1.00)	1 (1.00)	0.117 (1.00)	1 (1.00)
2q loss	16 (3%)	508			6.78e-06 (0.00402)	0.224 (1.00)		0.14 (1.00)	0.000602 (0.289)	0.00183 (0.823)	0.0227 (1.00)	0.0121 (1.00)	0.781 (1.00)	0.208 (1.00)
20p loss	18 (3%)	506			6.08e-05 (0.033)	0.28 (1.00)	0.466 (1.00)	0.201 (1.00)	0.027 (1.00)	0.0488 (1.00)	0.00775 (1.00)	0.00834 (1.00)	0.519 (1.00)	0.501 (1.00)
4q gain	8 (2%)	516			0.00605 (1.00)	0.619 (1.00)		0.14 (1.00)	0.0307 (1.00)	0.213 (1.00)	0.227 (1.00)	0.249 (1.00)	0.547 (1.00)	0.258 (1.00)
9q gain	9 (2%)	515			0.152 (1.00)	0.124 (1.00)		0.14 (1.00)	0.363 (1.00)	0.252 (1.00)	0.241 (1.00)	0.0786 (1.00)	0.336 (1.00)	0.728 (1.00)
15q gain	11 (2%)	513			0.00896 (1.00)	0.918 (1.00)		1 (1.00)	0.689 (1.00)	0.457 (1.00)	0.725 (1.00)	0.153 (1.00)	0.529 (1.00)	0.534 (1.00)
16q gain	9 (2%)	515			0.0435 (1.00)	0.423 (1.00)	0.858 (1.00)	0.558 (1.00)	0.172 (1.00)	0.252 (1.00)	0.121 (1.00)	0.404 (1.00)	0.771 (1.00)	0.426 (1.00)
2p loss	10 (2%)	514			0.00246 (1.00)	0.39 (1.00)		0.14 (1.00)	0.00761 (1.00)	0.0191 (1.00)	0.558 (1.00)	0.318 (1.00)	0.909 (1.00)	0.18 (1.00)
20q loss	9 (2%)	515			0.0033 (1.00)	0.0545 (1.00)	0.586 (1.00)	0.633 (1.00)	0.0369 (1.00)	0.0399 (1.00)	0.0311 (1.00)	0.0158 (1.00)	0.279 (1.00)	0.252 (1.00)

'1p gain' versus 'CN_CNMF'

P value = 1.18e-10 (Chi-square test), Q value = 8.9e-08

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
1P GAIN MUTATED	6	5	34	1	0
1P GAIN WILD-TYPE	299	43	120	11	5

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

'1p gain' versus 'MRNASEQ_CNMF'

P value = 3.69e-06 (Fisher's exact test), Q value = 0.0022

Table S2. Gene #1: '1p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
1P GAIN MUTATED	36	5	5
1P GAIN WILD-TYPE	188	145	140

Figure S2. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000133 (Fisher's exact test), Q value = 0.07

Table S3. Gene #1: '1p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	132	240
1P GAIN MUTATED	6	5	35
1P GAIN WILD-TYPE	141	127	205

Figure S3. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p gain' versus 'MIRSEQ_CNMF'

P value = 3.42e-05 (Fisher's exact test), Q value = 0.019

Table S4. Gene #1: '1p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	159	141
1P GAIN MUTATED	30	3	10
1P GAIN WILD-TYPE	175	156	131

Figure S4. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.23e-05 (Fisher's exact test), Q value = 0.0071

Table S5. Gene #1: '1p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	216	281
1P GAIN MUTATED	2	5	36
1P GAIN WILD-TYPE	6	211	245

Figure S5. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000101 (Fisher's exact test), Q value = 0.054

Table S6. Gene #1: '1p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	175	117	90
1P GAIN MUTATED	30	5	3
1P GAIN WILD-TYPE	145	112	87

Figure S6. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'1q gain' versus 'CN_CNMF'

P value = 0.000175 (Chi-square test), Q value = 0.09

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
1Q GAIN MUTATED	91	26	50	6	5
1Q GAIN WILD-TYPE	214	22	104	6	0

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

'1q gain' versus 'MRNASEQ_CNMF'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
1Q GAIN MUTATED	70	70	36
1Q GAIN WILD-TYPE	154	80	109

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

'1q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000134 (Fisher's exact test), Q value = 0.071

Table S9. Gene #2: '1q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	132	240
1Q GAIN MUTATED	37	64	75
1Q GAIN WILD-TYPE	110	68	165

Figure S9. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_CNMF'

P value = 0.000252 (Fisher's exact test), Q value = 0.13

Table S10. Gene #2: '1q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	159	141
1Q GAIN MUTATED	63	43	68
1Q GAIN WILD-TYPE	142	116	73

Figure S10. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2p gain' versus 'CN_CNMF'

P value = 1.81e-24 (Chi-square test), Q value = 1.6e-21

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
2P GAIN MUTATED	9	24	56	2	1
2P GAIN WILD-TYPE	296	24	98	10	4

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

'2p gain' versus 'METHLYATION_CNMF'

P value = 1.42e-08 (Fisher's exact test), Q value = 9.9e-06

Table S12. Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	94	164
2P GAIN MUTATED	48	11	11
2P GAIN WILD-TYPE	104	83	153

Figure S12. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2p gain' versus 'MRNASEQ_CNMF'

P value = 1.79e-09 (Fisher's exact test), Q value = 1.3e-06

Table S13. Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
2P GAIN MUTATED	66	16	9
2P GAIN WILD-TYPE	158	134	136

Figure S13. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.62e-09 (Fisher's exact test), Q value = 1.2e-06

Table S14. Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	132	240
2P GAIN MUTATED	9	13	69
2P GAIN WILD-TYPE	138	119	171

Figure S14. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_CNMF'

P value = 2.14e-08 (Fisher's exact test), Q value = 1.5e-05

Table S15. Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	159	141
2P GAIN MUTATED	61	12	16
2P GAIN WILD-TYPE	144	147	125

Figure S15. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.49e-06 (Fisher's exact test), Q value = 0.0027

Table S16. Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	216	281
2P GAIN MUTATED	0	19	70
2P GAIN WILD-TYPE	8	197	211

Figure S16. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000148 (Fisher's exact test), Q value = 0.078

Table S17. Gene #3: '2p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	175	117	90
2P GAIN MUTATED	41	7	18
2P GAIN WILD-TYPE	134	110	72

Figure S17. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'2p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.43e-06 (Fisher's exact test), Q value = 0.00089

Table S18. Gene #3: '2p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	198	154
2P GAIN MUTATED	2	53	11
2P GAIN WILD-TYPE	28	145	143

Figure S18. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q gain' versus 'CN_CNMF'

P value = 7.76e-22 (Chi-square test), Q value = 6.7e-19

Table S19. Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
2Q GAIN MUTATED	6	22	45	1	1
2Q GAIN WILD-TYPE	299	26	109	11	4

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

'2q gain' versus 'METHLYATION_CNMF'

P value = 4.83e-07 (Fisher's exact test), Q value = 0.00031

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	94	164
2Q GAIN MUTATED	41	9	10
2Q GAIN WILD-TYPE	111	85	154

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

'2q gain' versus 'MRNASEQ_CNMF'

P value = 8.79e-08 (Fisher's exact test), Q value = 6e-05

Table S21. Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
2Q GAIN MUTATED	54	13	7
2Q GAIN WILD-TYPE	170	137	138

Figure S21. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.26e-07 (Fisher's exact test), Q value = 0.00015

Table S22. Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	132	240
2Q GAIN MUTATED	8	10	56
2Q GAIN WILD-TYPE	139	122	184

Figure S22. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_CNMF'

P value = 6.19e-07 (Fisher's exact test), Q value = 4e-04

Table S23. Gene #4: '2q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	159	141
2Q GAIN MUTATED	50	9	14
2Q GAIN WILD-TYPE	155	150	127

Figure S23. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.78e-06 (Fisher's exact test), Q value = 0.0058

Table S24. Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	216	281
2Q GAIN MUTATED	0	14	59
2Q GAIN WILD-TYPE	8	202	222

Figure S24. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000154 (Fisher's exact test), Q value = 0.08

Table S25. Gene #4: '2q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	175	117	90
2Q GAIN MUTATED	36	5	15
2Q GAIN WILD-TYPE	139	112	75

Figure S25. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'2q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.06e-06 (Fisher's exact test), Q value = 0.0019

Table S26. Gene #4: '2q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	198	154
2Q GAIN MUTATED	1	46	9
2Q GAIN WILD-TYPE	29	152	145

Figure S26. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3p gain' versus 'CN_CNMF'

P value = 2.98e-23 (Chi-square test), Q value = 2.6e-20

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
3P GAIN MUTATED	2	7	25	9	2
3P GAIN WILD-TYPE	303	41	129	3	3

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

'3p gain' versus 'MRNASEQ_CNMF'

P value = 5.1e-05 (Fisher's exact test), Q value = 0.028

Table S28. Gene #5: '3p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
3P GAIN MUTATED	32	3	9
3P GAIN WILD-TYPE	192	147	136

Figure S28. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.31e-05 (Fisher's exact test), Q value = 0.013

Table S29. Gene #5: '3p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	132	240
3P GAIN MUTATED	8	2	34
3P GAIN WILD-TYPE	139	130	206

Figure S29. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3q gain' versus 'CN_CNMF'

P value = 8.89e-28 (Chi-square test), Q value = 7.8e-25

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
3Q GAIN MUTATED	5	9	52	10	2
3Q GAIN WILD-TYPE	300	39	102	2	3

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

'3q gain' versus 'METHLYATION_CNMF'

P value = 1.02e-08 (Fisher's exact test), Q value = 7.2e-06

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	94	164
3Q GAIN MUTATED	47	11	10
3Q GAIN WILD-TYPE	105	83	154

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

'3q gain' versus 'MRNASEQ_CNMF'

P value = 2.11e-12 (Fisher's exact test), Q value = 1.7e-09

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
3Q GAIN MUTATED	62	5	10
3Q GAIN WILD-TYPE	162	145	135

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

'3q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.78e-14 (Fisher's exact test), Q value = 1.4e-11

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	132	240
3Q GAIN MUTATED	9	2	66
3Q GAIN WILD-TYPE	138	130	174

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

'3q gain' versus 'MIRSEQ_CNMF'

P value = 8.53e-10 (Fisher's exact test), Q value = 6.3e-07

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	159	141
3Q GAIN MUTATED	56	9	10
3Q GAIN WILD-TYPE	149	150	131

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

'3q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.86e-08 (Fisher's exact test), Q value = 6e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	216	281
3Q GAIN MUTATED	2	11	62
3Q GAIN WILD-TYPE	6	205	219

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

'3q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000299 (Fisher's exact test), Q value = 0.15

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	175	117	90
3Q GAIN MUTATED	40	7	16
3Q GAIN WILD-TYPE	135	110	74

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

'3q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9.53e-07 (Fisher's exact test), Q value = 0.00061

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	198	154
3Q GAIN MUTATED	3	51	9
3Q GAIN WILD-TYPE	27	147	145

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

'4p gain' versus 'CN_CNMF'

P value = 2.91e-05 (Chi-square test), Q value = 0.016

Table S38. Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
4P GAIN MUTATED	0	1	12	0	0
4P GAIN WILD-TYPE	305	47	142	12	5

Figure S38. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

'5p gain' versus 'CN_CNMF'

P value = 6.3e-16 (Chi-square test), Q value = 5.2e-13

Table S39. Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
5P GAIN MUTATED	3	5	40	0	1
5P GAIN WILD-TYPE	302	43	114	12	4

Figure S39. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

'5p gain' versus 'METHLYATION_CNMF'

P value = 1.3e-07 (Fisher's exact test), Q value = 8.8e-05

Table S40. Gene #9: '5p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	94	164
5P GAIN MUTATED	32	4	5
5P GAIN WILD-TYPE	120	90	159

Figure S40. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5p gain' versus 'MRNASEQ_CNMF'

P value = 4.48e-11 (Fisher's exact test), Q value = 3.4e-08

Table S41. Gene #9: '5p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
5P GAIN MUTATED	43	5	1
5P GAIN WILD-TYPE	181	145	144

Figure S41. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.04e-08 (Fisher's exact test), Q value = 7.3e-06

Table S42. Gene #9: '5p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	132	240
5P GAIN MUTATED	2	5	42
5P GAIN WILD-TYPE	145	127	198

Figure S42. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_CNMF'

P value = 6.52e-09 (Fisher's exact test), Q value = 4.7e-06

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	159	141
5P GAIN MUTATED	37	1	10
5P GAIN WILD-TYPE	168	158	131

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

'5p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.15e-06 (Fisher's exact test), Q value = 0.00073

Table S44. Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	216	281
5P GAIN MUTATED	2	5	41
5P GAIN WILD-TYPE	6	211	240

Figure S44. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.71e-05 (Fisher's exact test), Q value = 0.015

Table S45. Gene #9: '5p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	175	117	90
5P GAIN MUTATED	30	2	7
5P GAIN WILD-TYPE	145	115	83

Figure S45. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.36e-06 (Fisher's exact test), Q value = 0.002

Table S46. Gene #9: '5p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	198	154
5P GAIN MUTATED	2	34	3
5P GAIN WILD-TYPE	28	164	151

Figure S46. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q gain' versus 'CN_CNMF'

P value = 1.31e-05 (Chi-square test), Q value = 0.0076

Table S47. Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
5Q GAIN MUTATED	1	3	14	0	1
5Q GAIN WILD-TYPE	304	45	140	12	4

Figure S47. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'

'5q gain' versus 'MRNASEQ_CNMF'

P value = 0.000331 (Fisher's exact test), Q value = 0.16

Table S48. Gene #10: '5q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
5Q GAIN MUTATED	16	3	0
5Q GAIN WILD-TYPE	208	147	145

Figure S48. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6p gain' versus 'CN_CNMF'

P value = 3.37e-25 (Chi-square test), Q value = 3e-22

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
6P GAIN MUTATED	6	5	57	7	1
6P GAIN WILD-TYPE	299	43	97	5	4

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

'6p gain' versus 'METHLYATION_CNMF'

P value = 2.07e-07 (Fisher's exact test), Q value = 0.00014

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	94	164
6P GAIN MUTATED	44	14	10
6P GAIN WILD-TYPE	108	80	154

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

'6p gain' versus 'MRNASEQ_CNMF'

P value = 1.07e-09 (Fisher's exact test), Q value = 7.9e-07

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
6P GAIN MUTATED	57	5	14
6P GAIN WILD-TYPE	167	145	131

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

'6p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.41e-09 (Fisher's exact test), Q value = 1.8e-06

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	132	240
6P GAIN MUTATED	13	4	59
6P GAIN WILD-TYPE	134	128	181

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

'6p gain' versus 'MIRSEQ_CNMF'

P value = 3.8e-07 (Fisher's exact test), Q value = 0.00025

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	159	141
6P GAIN MUTATED	52	11	12
6P GAIN WILD-TYPE	153	148	129

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

'6p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.91e-06 (Fisher's exact test), Q value = 0.0024

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	216	281
6P GAIN MUTATED	3	14	58
6P GAIN WILD-TYPE	5	202	223

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

'6p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000291 (Fisher's exact test), Q value = 0.14

Table S55. Gene #11: '6p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	198	154
6P GAIN MUTATED	4	48	13
6P GAIN WILD-TYPE	26	150	141

Figure S55. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q gain' versus 'CN_CNMF'

P value = 1.04e-19 (Chi-square test), Q value = 8.8e-17

Table S56. Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
6Q GAIN MUTATED	5	5	43	7	1
6Q GAIN WILD-TYPE	300	43	111	5	4

Figure S56. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

'6q gain' versus 'METHLYATION_CNMF'

P value = 0.000278 (Fisher's exact test), Q value = 0.14

Table S57. Gene #12: '6q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	94	164
6Q GAIN MUTATED	33	9	11
6Q GAIN WILD-TYPE	119	85	153

Figure S57. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6q gain' versus 'MRNASEQ_CNMF'

P value = 1.11e-05 (Fisher's exact test), Q value = 0.0065

Table S58. Gene #12: '6q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
6Q GAIN MUTATED	42	5	14
6Q GAIN WILD-TYPE	182	145	131

Figure S58. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.37e-05 (Fisher's exact test), Q value = 0.0079

Table S59. Gene #12: '6q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	132	240
6Q GAIN MUTATED	13	4	44
6Q GAIN WILD-TYPE	134	128	196

Figure S59. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6q gain' versus 'MIRSEQ_CNMF'

P value = 0.000179 (Fisher's exact test), Q value = 0.092

Table S60. Gene #12: '6q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	159	141
6Q GAIN MUTATED	40	11	10
6Q GAIN WILD-TYPE	165	148	131

Figure S60. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 1.31e-20 (Chi-square test), Q value = 1.1e-17

Table S61. Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
7P GAIN MUTATED	8	24	27	4	1
7P GAIN WILD-TYPE	297	24	127	8	4

Figure S61. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7q gain' versus 'CN_CNMF'

P value = 2.57e-19 (Chi-square test), Q value = 2.2e-16

Table S62. Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
7Q GAIN MUTATED	11	24	22	4	1
7Q GAIN WILD-TYPE	294	24	132	8	4

Figure S62. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

'8p gain' versus 'CN_CNMF'

P value = 1.2e-15 (Chi-square test), Q value = 9.9e-13

Table S63. Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
8P GAIN MUTATED	39	22	41	12	2
8P GAIN WILD-TYPE	266	26	113	0	3

Figure S63. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'CN_CNMF'

P value = 2.8e-21 (Chi-square test), Q value = 2.4e-18

Table S64. Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
8Q GAIN MUTATED	41	26	70	12	3
8Q GAIN WILD-TYPE	264	22	84	0	2

Figure S64. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'RPPA_CNMF'

P value = 0.00029 (Chi-square test), Q value = 0.14

Table S65. 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 S65. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 1.15e-05 (Fisher's exact test), Q value = 0.0067

Table S66. Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
8Q GAIN MUTATED	90	29	33
8Q GAIN WILD-TYPE	134	121	112

Figure S66. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.28e-05 (Fisher's exact test), Q value = 0.0074

Table S67. Gene #16: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	132	240
8Q GAIN MUTATED	35	23	94
8Q GAIN WILD-TYPE	112	109	146

Figure S67. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p gain' versus 'CN_CNMF'

P value = 0.000226 (Chi-square test), Q value = 0.11

Table S68. Gene #17: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
9P GAIN MUTATED	4	2	16	0	0
9P GAIN WILD-TYPE	301	46	138	12	5

Figure S68. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'

'10p gain' versus 'CN_CNMF'

P value = 2.54e-07 (Chi-square test), Q value = 0.00017

Table S69. Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
10P GAIN MUTATED	47	24	37	6	2
10P GAIN WILD-TYPE	258	24	117	6	3

Figure S69. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

'10q gain' versus 'CN_CNMF'

P value = 2.1e-06 (Chi-square test), Q value = 0.0013

Table S70. Gene #20: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
10Q GAIN MUTATED	46	23	33	5	2
10Q GAIN WILD-TYPE	259	25	121	7	3

Figure S70. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

'11p gain' versus 'CN_CNMF'

P value = 7.18e-07 (Chi-square test), Q value = 0.00046

Table S71. Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
11P GAIN MUTATED	0	6	15	1	0
11P GAIN WILD-TYPE	305	42	139	11	5

Figure S71. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

'11q gain' versus 'CN_CNMF'

P value = 3.22e-06 (Chi-square test), Q value = 0.002

Table S72. Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
11Q GAIN MUTATED	0	6	12	1	0
11Q GAIN WILD-TYPE	305	42	142	11	5

Figure S72. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 6.66e-13 (Chi-square test), Q value = 5.3e-10

Table S73. Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
12P GAIN MUTATED	11	14	37	1	3
12P GAIN WILD-TYPE	294	34	117	11	2

Figure S73. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 2.94e-05 (Fisher's exact test), Q value = 0.016

Table S74. Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	94	164
12P GAIN MUTATED	31	14	7
12P GAIN WILD-TYPE	121	80	157

Figure S74. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 3.5e-06 (Fisher's exact test), Q value = 0.0021

Table S75. Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
12P GAIN MUTATED	47	9	9
12P GAIN WILD-TYPE	177	141	136

Figure S75. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.07e-05 (Fisher's exact test), Q value = 0.0063

Table S76. Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	132	240
12P GAIN MUTATED	10	7	48
12P GAIN WILD-TYPE	137	125	192

Figure S76. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000243 (Fisher's exact test), Q value = 0.12

Table S77. Gene #23: '12p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	198	154
12P GAIN MUTATED	6	34	7
12P GAIN WILD-TYPE	24	164	147

Figure S77. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q gain' versus 'CN_CNMF'

P value = 5.81e-10 (Chi-square test), Q value = 4.3e-07

Table S78. Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
12Q GAIN MUTATED	11	13	24	1	3
12Q GAIN WILD-TYPE	294	35	130	11	2

Figure S78. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

'13q gain' versus 'CN_CNMF'

P value = 1.71e-11 (Chi-square test), Q value = 1.3e-08

Table S79. Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
13Q GAIN MUTATED	1	0	25	1	1
13Q GAIN WILD-TYPE	304	48	129	11	4

Figure S79. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

'13q gain' versus 'METHLYATION_CNMF'

P value = 0.000135 (Fisher's exact test), Q value = 0.071

Table S80. Gene #25: '13q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	94	164
13Q GAIN MUTATED	16	7	1
13Q GAIN WILD-TYPE	136	87	163

Figure S80. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q gain' versus 'MRNASEQ_CNMF'

P value = 1.68e-06 (Fisher's exact test), Q value = 0.001

Table S81. Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
13Q GAIN MUTATED	25	1	2
13Q GAIN WILD-TYPE	199	149	143

Figure S81. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.04e-05 (Fisher's exact test), Q value = 0.0061

Table S82. Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	132	240
13Q GAIN MUTATED	2	1	25
13Q GAIN WILD-TYPE	145	131	215

Figure S82. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q gain' versus 'MIRSEQ_CNMF'

P value = 3.86e-07 (Fisher's exact test), Q value = 0.00025

Table S83. Gene #25: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	159	141
13Q GAIN MUTATED	25	2	1
13Q GAIN WILD-TYPE	180	157	140

Figure S83. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'14q gain' versus 'CN_CNMF'

P value = 1.39e-07 (Chi-square test), Q value = 9.3e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
14Q GAIN MUTATED	4	6	24	2	0
14Q GAIN WILD-TYPE	301	42	130	10	5

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

'14q gain' versus 'MRNASEQ_CNMF'

P value = 5.89e-06 (Fisher's exact test), Q value = 0.0035

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
14Q GAIN MUTATED	28	1	6
14Q GAIN WILD-TYPE	196	149	139

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

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.26e-06 (Fisher's exact test), Q value = 0.0014

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	132	240
14Q GAIN MUTATED	6	0	29
14Q GAIN WILD-TYPE	141	132	211

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

'16p gain' versus 'CN_CNMF'

P value = 9.78e-07 (Chi-square test), Q value = 0.00062

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
16P GAIN MUTATED	1	5	18	1	0
16P GAIN WILD-TYPE	304	43	136	11	5

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

'17p gain' versus 'CN_CNMF'

P value = 0.000492 (Chi-square test), Q value = 0.24

Table S88. Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
17P GAIN MUTATED	1	1	8	1	1
17P GAIN WILD-TYPE	304	47	146	11	4

Figure S88. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'CN_CNMF'

P value = 1.73e-08 (Chi-square test), Q value = 1.2e-05

Table S89. Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
17Q GAIN MUTATED	1	3	22	1	1
17Q GAIN WILD-TYPE	304	45	132	11	4

Figure S89. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 2.69e-05 (Fisher's exact test), Q value = 0.015

Table S90. Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	94	164
17Q GAIN MUTATED	20	3	2
17Q GAIN WILD-TYPE	132	91	162

Figure S90. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 0.000116 (Fisher's exact test), Q value = 0.062

Table S91. Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
17Q GAIN MUTATED	23	2	3
17Q GAIN WILD-TYPE	201	148	142

Figure S91. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.04e-05 (Fisher's exact test), Q value = 0.0061

Table S92. Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	132	240
17Q GAIN MUTATED	2	1	25
17Q GAIN WILD-TYPE	145	131	215

Figure S92. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_CNMF'

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

Table S93. Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	159	141
17Q GAIN MUTATED	22	3	3
17Q GAIN WILD-TYPE	183	156	138

Figure S93. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18p gain' versus 'CN_CNMF'

P value = 1.25e-26 (Chi-square test), Q value = 1.1e-23

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
18P GAIN MUTATED	3	5	59	1	0
18P GAIN WILD-TYPE	302	43	95	11	5

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

'18p gain' versus 'METHLYATION_CNMF'

P value = 1.59e-09 (Fisher's exact test), Q value = 1.2e-06

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	94	164
18P GAIN MUTATED	39	15	4
18P GAIN WILD-TYPE	113	79	160

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

'18p gain' versus 'MRNASEQ_CNMF'

P value = 1.41e-16 (Fisher's exact test), Q value = 1.2e-13

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
18P GAIN MUTATED	61	3	4
18P GAIN WILD-TYPE	163	147	141

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

'18p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.65e-16 (Fisher's exact test), Q value = 7.1e-13

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	132	240
18P GAIN MUTATED	4	2	62
18P GAIN WILD-TYPE	143	130	178

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

'18p gain' versus 'MIRSEQ_CNMF'

P value = 2.55e-14 (Fisher's exact test), Q value = 2.1e-11

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	159	141
18P GAIN MUTATED	55	3	7
18P GAIN WILD-TYPE	150	156	134

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

'18p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.54e-11 (Fisher's exact test), Q value = 4.2e-08

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	216	281
18P GAIN MUTATED	0	5	60
18P GAIN WILD-TYPE	8	211	221

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

'18p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 9.06e-07 (Fisher's exact test), Q value = 0.00058

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	175	117	90
18P GAIN MUTATED	37	2	14
18P GAIN WILD-TYPE	138	115	76

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 = 2.87e-11 (Fisher's exact test), Q value = 2.2e-08

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	198	154
18P GAIN MUTATED	2	49	2
18P GAIN WILD-TYPE	28	149	152

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

'18q gain' versus 'CN_CNMF'

P value = 4.68e-13 (Chi-square test), Q value = 3.7e-10

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
18Q GAIN MUTATED	3	3	34	1	0
18Q GAIN WILD-TYPE	302	45	120	11	5

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

'18q gain' versus 'METHLYATION_CNMF'

P value = 5.71e-05 (Fisher's exact test), Q value = 0.031

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	94	164
18Q GAIN MUTATED	22	10	3
18Q GAIN WILD-TYPE	130	84	161

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

'18q gain' versus 'MRNASEQ_CNMF'

P value = 7.61e-09 (Fisher's exact test), Q value = 5.4e-06

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
18Q GAIN MUTATED	36	2	3
18Q GAIN WILD-TYPE	188	148	142

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

'18q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.5e-09 (Fisher's exact test), Q value = 5.3e-06

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	132	240
18Q GAIN MUTATED	3	1	37
18Q GAIN WILD-TYPE	144	131	203

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

'18q gain' versus 'MIRSEQ_CNMF'

P value = 8.07e-08 (Fisher's exact test), Q value = 5.5e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	159	141
18Q GAIN MUTATED	32	1	7
18Q GAIN WILD-TYPE	173	158	134

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

'18q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.31e-06 (Fisher's exact test), Q value = 0.00082

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	216	281
18Q GAIN MUTATED	0	3	37
18Q GAIN WILD-TYPE	8	213	244

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

'18q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000118 (Fisher's exact test), Q value = 0.062

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	175	117	90
18Q GAIN MUTATED	24	1	7
18Q GAIN WILD-TYPE	151	116	83

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 = 1.58e-06 (Fisher's exact test), Q value = 0.00098

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	198	154
18Q GAIN MUTATED	2	29	1
18Q GAIN WILD-TYPE	28	169	153

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

'19p gain' versus 'CN_CNMF'

P value = 1.35e-22 (Chi-square test), Q value = 1.2e-19

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
19P GAIN MUTATED	0	2	46	2	0
19P GAIN WILD-TYPE	305	46	108	10	5

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

'19p gain' versus 'MRNASEQ_CNMF'

P value = 5.48e-12 (Fisher's exact test), Q value = 4.3e-09

Table S111. Gene #34: '19p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
19P GAIN MUTATED	44	1	4
19P GAIN WILD-TYPE	180	149	141

Figure S111. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.74e-11 (Fisher's exact test), Q value = 1.3e-08

Table S112. Gene #34: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	132	240
19P GAIN MUTATED	3	1	45
19P GAIN WILD-TYPE	144	131	195

Figure S112. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_CNMF'

P value = 7.11e-09 (Fisher's exact test), Q value = 5.1e-06

Table S113. Gene #34: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	159	141
19P GAIN MUTATED	40	5	4
19P GAIN WILD-TYPE	165	154	137

Figure S113. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.58e-05 (Fisher's exact test), Q value = 0.02

Table S114. Gene #34: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	216	281
19P GAIN MUTATED	3	8	38
19P GAIN WILD-TYPE	5	208	243

Figure S114. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q gain' versus 'CN_CNMF'

P value = 2.46e-24 (Chi-square test), Q value = 2.2e-21

Table S115. Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
19Q GAIN MUTATED	0	3	50	2	0
19Q GAIN WILD-TYPE	305	45	104	10	5

Figure S115. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

'19q gain' versus 'METHLYATION_CNMF'

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

Table S116. Gene #35: '19q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	94	164
19Q GAIN MUTATED	29	14	6
19Q GAIN WILD-TYPE	123	80	158

Figure S116. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 3.07e-15 (Fisher's exact test), Q value = 2.5e-12

Table S117. Gene #35: '19q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
19Q GAIN MUTATED	51	1	3
19Q GAIN WILD-TYPE	173	149	142

Figure S117. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.08e-14 (Fisher's exact test), Q value = 8.8e-12

Table S118. Gene #35: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	132	240
19Q GAIN MUTATED	2	1	52
19Q GAIN WILD-TYPE	145	131	188

Figure S118. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_CNMF'

P value = 1.01e-10 (Fisher's exact test), Q value = 7.7e-08

Table S119. Gene #35: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	159	141
19Q GAIN MUTATED	45	4	5
19Q GAIN WILD-TYPE	160	155	136

Figure S119. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.39e-07 (Fisher's exact test), Q value = 9.4e-05

Table S120. Gene #35: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	216	281
19Q GAIN MUTATED	3	6	45
19Q GAIN WILD-TYPE	5	210	236

Figure S120. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000153 (Fisher's exact test), Q value = 0.08

Table S121. Gene #35: '19q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	198	154
19Q GAIN MUTATED	1	37	8
19Q GAIN WILD-TYPE	29	161	146

Figure S121. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 1.53e-34 (Chi-square test), Q value = 1.4e-31

Table S122. Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
20P GAIN MUTATED	6	22	76	1	2
20P GAIN WILD-TYPE	299	26	78	11	3

Figure S122. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 3.97e-11 (Fisher's exact test), Q value = 3e-08

Table S123. Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	94	164
20P GAIN MUTATED	65	16	17
20P GAIN WILD-TYPE	87	78	147

Figure S123. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 4.46e-16 (Fisher's exact test), Q value = 3.7e-13

Table S124. Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
20P GAIN MUTATED	84	9	14
20P GAIN WILD-TYPE	140	141	131

Figure S124. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.5e-13 (Fisher's exact test), Q value = 1.2e-10

Table S125. Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	132	240
20P GAIN MUTATED	15	8	84
20P GAIN WILD-TYPE	132	124	156

Figure S125. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_CNMF'

P value = 2.31e-11 (Fisher's exact test), Q value = 1.8e-08

Table S126. Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	159	141
20P GAIN MUTATED	74	14	17
20P GAIN WILD-TYPE	131	145	124

Figure S126. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.3e-07 (Fisher's exact test), Q value = 8.8e-05

Table S127. Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	216	281
20P GAIN MUTATED	3	21	81
20P GAIN WILD-TYPE	5	195	200

Figure S127. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.43e-05 (Fisher's exact test), Q value = 0.014

Table S128. Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	175	117	90
20P GAIN MUTATED	61	15	16
20P GAIN WILD-TYPE	114	102	74

Figure S128. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9.25e-06 (Fisher's exact test), Q value = 0.0055

Table S129. Gene #36: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	198	154
20P GAIN MUTATED	6	67	19
20P GAIN WILD-TYPE	24	131	135

Figure S129. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q gain' versus 'MRNA_CHIERARCHICAL'

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

Table S130. Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	19	19	15
20Q GAIN MUTATED	0	0	6
20Q GAIN WILD-TYPE	19	19	9

Figure S130. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 9.24e-43 (Chi-square test), Q value = 8.3e-40

Table S131. Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
20Q GAIN MUTATED	7	25	90	1	2
20Q GAIN WILD-TYPE	298	23	64	11	3

Figure S131. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 5.8e-12 (Fisher's exact test), Q value = 4.5e-09

Table S132. Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	94	164
20Q GAIN MUTATED	73	19	21
20Q GAIN WILD-TYPE	79	75	143

Figure S132. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 8.54e-19 (Fisher's exact test), Q value = 7.2e-16

Table S133. Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
20Q GAIN MUTATED	97	10	18
20Q GAIN WILD-TYPE	127	140	127

Figure S133. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.8e-16 (Fisher's exact test), Q value = 7.2e-13

Table S134. Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	132	240
20Q GAIN MUTATED	19	9	97
20Q GAIN WILD-TYPE	128	123	143

Figure S134. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 7.21e-14 (Fisher's exact test), Q value = 5.8e-11

Table S135. Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	159	141
20Q GAIN MUTATED	86	18	17
20Q GAIN WILD-TYPE	119	141	124

Figure S135. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.19e-08 (Fisher's exact test), Q value = 8.4e-06

Table S136. Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	216	281
20Q GAIN MUTATED	4	25	92
20Q GAIN WILD-TYPE	4	191	189

Figure S136. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 7.98e-05 (Fisher's exact test), Q value = 0.043

Table S137. Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	175	117	90
20Q GAIN MUTATED	67	19	20
20Q GAIN WILD-TYPE	108	98	70

Figure S137. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.59e-06 (Fisher's exact test), Q value = 0.0022

Table S138. Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	198	154
20Q GAIN MUTATED	7	76	23
20Q GAIN WILD-TYPE	23	122	131

Figure S138. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q gain' versus 'CN_CNMF'

P value = 6.22e-14 (Chi-square test), Q value = 5e-11

Table S139. Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
21Q GAIN MUTATED	1	2	32	1	0
21Q GAIN WILD-TYPE	304	46	122	11	5

Figure S139. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

'21q gain' versus 'MRNASEQ_CNMF'

P value = 2.19e-06 (Fisher's exact test), Q value = 0.0013

Table S140. Gene #38: '21q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
21Q GAIN MUTATED	30	2	4
21Q GAIN WILD-TYPE	194	148	141

Figure S140. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.74e-05 (Fisher's exact test), Q value = 0.0099

Table S141. Gene #38: '21q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	132	240
21Q GAIN MUTATED	4	2	30
21Q GAIN WILD-TYPE	143	130	210

Figure S141. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'21q gain' versus 'MIRSEQ_CNMF'

P value = 1.14e-06 (Fisher's exact test), Q value = 0.00072

Table S142. Gene #38: '21q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	159	141
21Q GAIN MUTATED	29	3	3
21Q GAIN WILD-TYPE	176	156	138

Figure S142. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'21q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.92e-05 (Fisher's exact test), Q value = 0.032

Table S143. Gene #38: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	216	281
21Q GAIN MUTATED	2	4	29
21Q GAIN WILD-TYPE	6	212	252

Figure S143. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q gain' versus 'CN_CNMF'

P value = 1.89e-08 (Chi-square test), Q value = 1.3e-05

Table S144. Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
22Q GAIN MUTATED	3	3	24	0	1
22Q GAIN WILD-TYPE	302	45	130	12	4

Figure S144. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

'22q gain' versus 'METHLYATION_CNMF'

P value = 1.92e-09 (Fisher's exact test), Q value = 1.4e-06

Table S145. Gene #39: '22q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	94	164
22Q GAIN MUTATED	26	1	1
22Q GAIN WILD-TYPE	126	93	163

Figure S145. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q gain' versus 'MRNASEQ_CNMF'

P value = 1.96e-11 (Fisher's exact test), Q value = 1.5e-08

Table S146. Gene #39: '22q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
22Q GAIN MUTATED	31	0	0
22Q GAIN WILD-TYPE	193	150	145

Figure S146. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.26e-10 (Fisher's exact test), Q value = 1.7e-07

Table S147. Gene #39: '22q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	132	240
22Q GAIN MUTATED	0	0	31
22Q GAIN WILD-TYPE	147	132	209

Figure S147. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_CNMF'

P value = 5.19e-09 (Fisher's exact test), Q value = 3.7e-06

Table S148. Gene #39: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	159	141
22Q GAIN MUTATED	28	1	1
22Q GAIN WILD-TYPE	177	158	140

Figure S148. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'22q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.78e-05 (Fisher's exact test), Q value = 0.021

Table S149. Gene #39: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	216	281
22Q GAIN MUTATED	0	2	28
22Q GAIN WILD-TYPE	8	214	253

Figure S149. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 5.19e-06 (Fisher's exact test), Q value = 0.0031

Table S150. Gene #39: '22q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	175	117	90
22Q GAIN MUTATED	25	1	2
22Q GAIN WILD-TYPE	150	116	88

Figure S150. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'22q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.4e-06 (Fisher's exact test), Q value = 0.00088

Table S151. Gene #39: '22q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	198	154
22Q GAIN MUTATED	0	27	1
22Q GAIN WILD-TYPE	30	171	153

Figure S151. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq gain' versus 'CN_CNMF'

P value = 4.16e-22 (Chi-square test), Q value = 3.6e-19

Table S152. Gene #40: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
XQ GAIN MUTATED	10	19	23	9	2
XQ GAIN WILD-TYPE	295	29	131	3	3

Figure S152. Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'CN_CNMF'

P value = 2.24e-09 (Chi-square test), Q value = 1.6e-06

Table S153. Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
1P LOSS MUTATED	0	5	15	0	2
1P LOSS WILD-TYPE	305	43	139	12	3

Figure S153. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 7.78e-07 (Fisher's exact test), Q value = 5e-04

Table S154. Gene #41: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	94	164
1P LOSS MUTATED	17	1	0
1P LOSS WILD-TYPE	135	93	164

Figure S154. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 1.63e-05 (Fisher's exact test), Q value = 0.0094

Table S155. Gene #41: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
1P LOSS MUTATED	20	1	1
1P LOSS WILD-TYPE	204	149	144

Figure S155. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.88e-05 (Fisher's exact test), Q value = 0.037

Table S156. Gene #41: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	132	240
1P LOSS MUTATED	1	1	20
1P LOSS WILD-TYPE	146	131	220

Figure S156. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_CNMF'

P value = 0.000204 (Fisher's exact test), Q value = 0.1

Table S157. Gene #41: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	159	141
1P LOSS MUTATED	18	1	3
1P LOSS WILD-TYPE	187	158	138

Figure S157. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.13e-05 (Fisher's exact test), Q value = 0.0066

Table S158. Gene #41: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	216	281
1P LOSS MUTATED	1	0	21
1P LOSS WILD-TYPE	7	216	260

Figure S158. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1q loss' versus 'CN_CNMF'

P value = 0.000153 (Chi-square test), Q value = 0.08

Table S159. Gene #42: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
1Q LOSS MUTATED	0	2	11	0	0
1Q LOSS WILD-TYPE	305	46	143	12	5

Figure S159. Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

'1q loss' versus 'METHLYATION_CNMF'

P value = 3.63e-05 (Fisher's exact test), Q value = 0.02

Table S160. Gene #42: '1q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	94	164
1Q LOSS MUTATED	11	0	0
1Q LOSS WILD-TYPE	141	94	164

Figure S160. Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1q loss' versus 'MRNASEQ_CNMF'

P value = 4.84e-05 (Fisher's exact test), Q value = 0.027

Table S161. Gene #42: '1q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
1Q LOSS MUTATED	13	0	0
1Q LOSS WILD-TYPE	211	150	145

Figure S161. Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000237 (Fisher's exact test), Q value = 0.12

Table S162. Gene #42: '1q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	132	240
1Q LOSS MUTATED	0	0	13
1Q LOSS WILD-TYPE	147	132	227

Figure S162. Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1q loss' versus 'MIRSEQ_CNMF'

P value = 0.000287 (Fisher's exact test), Q value = 0.14

Table S163. Gene #42: '1q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	159	141
1Q LOSS MUTATED	12	0	1
1Q LOSS WILD-TYPE	193	159	140

Figure S163. Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2q loss' versus 'CN_CNMF'

P value = 6.78e-06 (Chi-square test), Q value = 0.004

Table S164. Gene #44: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
2Q LOSS MUTATED	0	2	14	0	0
2Q LOSS WILD-TYPE	305	46	140	12	5

Figure S164. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

'3p loss' versus 'CN_CNMF'

P value = 1.84e-20 (Chi-square test), Q value = 1.6e-17

Table S165. Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
3P LOSS MUTATED	0	5	44	0	1
3P LOSS WILD-TYPE	305	43	110	12	4

Figure S165. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 5.87e-07 (Fisher's exact test), Q value = 0.00038

Table S166. Gene #45: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	94	164
3P LOSS MUTATED	29	9	3
3P LOSS WILD-TYPE	123	85	161

Figure S166. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 4.67e-14 (Fisher's exact test), Q value = 3.7e-11

Table S167. Gene #45: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
3P LOSS MUTATED	46	1	2
3P LOSS WILD-TYPE	178	149	143

Figure S167. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.49e-12 (Fisher's exact test), Q value = 1.2e-09

Table S168. Gene #45: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	132	240
3P LOSS MUTATED	2	1	46
3P LOSS WILD-TYPE	145	131	194

Figure S168. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CNMF'

P value = 1.52e-07 (Fisher's exact test), Q value = 1e-04

Table S169. Gene #45: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	159	141
3P LOSS MUTATED	37	3	8
3P LOSS WILD-TYPE	168	156	133

Figure S169. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.71e-06 (Fisher's exact test), Q value = 0.0011

Table S170. Gene #45: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	216	281
3P LOSS MUTATED	1	5	42
3P LOSS WILD-TYPE	7	211	239

Figure S170. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.68e-05 (Fisher's exact test), Q value = 0.015

Table S171. Gene #45: '3p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	198	154
3P LOSS MUTATED	2	33	4
3P LOSS WILD-TYPE	28	165	150

Figure S171. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

P value = 1.44e-11 (Chi-square test), Q value = 1.1e-08

Table S172. Gene #46: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
3Q LOSS MUTATED	0	3	26	0	1
3Q LOSS WILD-TYPE	305	45	128	12	4

Figure S172. Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

'3q loss' versus 'METHLYATION_CNMF'

P value = 0.000197 (Fisher's exact test), Q value = 0.1

Table S173. Gene #46: '3q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	94	164
3Q LOSS MUTATED	18	4	2
3Q LOSS WILD-TYPE	134	90	162

Figure S173. Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3q loss' versus 'MRNASEQ_CNMF'

P value = 3.4e-08 (Fisher's exact test), Q value = 2.3e-05

Table S174. Gene #46: '3q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
3Q LOSS MUTATED	27	0	2
3Q LOSS WILD-TYPE	197	150	143

Figure S174. Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.68e-07 (Fisher's exact test), Q value = 0.00018

Table S175. Gene #46: '3q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	132	240
3Q LOSS MUTATED	2	0	27
3Q LOSS WILD-TYPE	145	132	213

Figure S175. Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_CNMF'

P value = 3.05e-06 (Fisher's exact test), Q value = 0.0019

Table S176. Gene #46: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	159	141
3Q LOSS MUTATED	24	3	1
3Q LOSS WILD-TYPE	181	156	140

Figure S176. Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.000454 (Fisher's exact test), Q value = 0.22

Table S177. Gene #47: '4p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	19	19	15
4P LOSS MUTATED	1	0	7
4P LOSS WILD-TYPE	18	19	8

Figure S177. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

P value = 3.46e-38 (Chi-square test), Q value = 3.1e-35

Table S178. Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
4P LOSS MUTATED	4	11	82	1	2
4P LOSS WILD-TYPE	301	37	72	11	3

Figure S178. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 1.13e-16 (Fisher's exact test), Q value = 9.4e-14

Table S179. Gene #47: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	94	164
4P LOSS MUTATED	63	20	6
4P LOSS WILD-TYPE	89	74	158

Figure S179. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 8.91e-23 (Fisher's exact test), Q value = 7.8e-20

Table S180. Gene #47: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
4P LOSS MUTATED	87	6	7
4P LOSS WILD-TYPE	137	144	138

Figure S180. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.22e-20 (Fisher's exact test), Q value = 7e-17

Table S181. Gene #47: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	132	240
4P LOSS MUTATED	7	6	87
4P LOSS WILD-TYPE	140	126	153

Figure S181. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_CNMF'

P value = 6.72e-17 (Fisher's exact test), Q value = 5.6e-14

Table S182. Gene #47: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	159	141
4P LOSS MUTATED	76	8	12
4P LOSS WILD-TYPE	129	151	129

Figure S182. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.38e-14 (Fisher's exact test), Q value = 3.5e-11

Table S183. Gene #47: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	216	281
4P LOSS MUTATED	4	10	82
4P LOSS WILD-TYPE	4	206	199

Figure S183. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.78e-06 (Fisher's exact test), Q value = 0.0011

Table S184. Gene #47: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	175	117	90
4P LOSS MUTATED	56	9	22
4P LOSS WILD-TYPE	119	108	68

Figure S184. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.07e-10 (Fisher's exact test), Q value = 3e-07

Table S185. Gene #47: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	198	154
4P LOSS MUTATED	6	70	11
4P LOSS WILD-TYPE	24	128	143

Figure S185. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 7.07e-40 (Chi-square test), Q value = 6.3e-37

Table S186. Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
4Q LOSS MUTATED	3	10	83	1	2
4Q LOSS WILD-TYPE	302	38	71	11	3

Figure S186. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 3.84e-17 (Fisher's exact test), Q value = 3.2e-14

Table S187. Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	94	164
4Q LOSS MUTATED	62	20	5
4Q LOSS WILD-TYPE	90	74	159

Figure S187. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 2.46e-22 (Fisher's exact test), Q value = 2.1e-19

Table S188. Gene #48: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
4Q LOSS MUTATED	86	7	6
4Q LOSS WILD-TYPE	138	143	139

Figure S188. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.95e-19 (Fisher's exact test), Q value = 1.7e-16

Table S189. Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	132	240
4Q LOSS MUTATED	7	6	86
4Q LOSS WILD-TYPE	140	126	154

Figure S189. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_CNMF'

P value = 1.7e-16 (Fisher's exact test), Q value = 1.4e-13

Table S190. Gene #48: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	159	141
4Q LOSS MUTATED	75	8	12
4Q LOSS WILD-TYPE	130	151	129

Figure S190. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.75e-15 (Fisher's exact test), Q value = 7.1e-12

Table S191. Gene #48: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	216	281
4Q LOSS MUTATED	4	9	82
4Q LOSS WILD-TYPE	4	207	199

Figure S191. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.34e-06 (Fisher's exact test), Q value = 0.00084

Table S192. Gene #48: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	175	117	90
4Q LOSS MUTATED	53	8	24
4Q LOSS WILD-TYPE	122	109	66

Figure S192. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.96e-11 (Fisher's exact test), Q value = 6.1e-08

Table S193. Gene #48: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	198	154
4Q LOSS MUTATED	5	70	10
4Q LOSS WILD-TYPE	25	128	144

Figure S193. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p loss' versus 'CN_CNMF'

P value = 8.03e-19 (Chi-square test), Q value = 6.8e-16

Table S194. Gene #49: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
5P LOSS MUTATED	0	9	43	1	1
5P LOSS WILD-TYPE	305	39	111	11	4

Figure S194. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

'5p loss' versus 'METHLYATION_CNMF'

P value = 2.96e-09 (Fisher's exact test), Q value = 2.1e-06

Table S195. Gene #49: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	94	164
5P LOSS MUTATED	35	7	3
5P LOSS WILD-TYPE	117	87	161

Figure S195. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5p loss' versus 'MRNASEQ_CNMF'

P value = 1.77e-09 (Fisher's exact test), Q value = 1.3e-06

Table S196. Gene #49: '5p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
5P LOSS MUTATED	45	4	5
5P LOSS WILD-TYPE	179	146	140

Figure S196. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.73e-09 (Fisher's exact test), Q value = 3.4e-06

Table S197. Gene #49: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	132	240
5P LOSS MUTATED	5	3	46
5P LOSS WILD-TYPE	142	129	194

Figure S197. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_CNMF'

P value = 4.54e-08 (Fisher's exact test), Q value = 3.1e-05

Table S198. Gene #49: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	159	141
5P LOSS MUTATED	42	6	6
5P LOSS WILD-TYPE	163	153	135

Figure S198. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.43e-07 (Fisher's exact test), Q value = 0.00035

Table S199. Gene #49: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	216	281
5P LOSS MUTATED	1	6	47
5P LOSS WILD-TYPE	7	210	234

Figure S199. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.2e-05 (Fisher's exact test), Q value = 0.007

Table S200. Gene #49: '5p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	198	154
5P LOSS MUTATED	2	37	5
5P LOSS WILD-TYPE	28	161	149

Figure S200. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q loss' versus 'CN_CNMF'

P value = 1.23e-28 (Chi-square test), Q value = 1.1e-25

Table S201. Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
5Q LOSS MUTATED	0	9	61	1	1
5Q LOSS WILD-TYPE	305	39	93	11	4

Figure S201. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 9.2e-15 (Fisher's exact test), Q value = 7.5e-12

Table S202. Gene #50: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	94	164
5Q LOSS MUTATED	49	8	3
5Q LOSS WILD-TYPE	103	86	161

Figure S202. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 6.07e-15 (Fisher's exact test), Q value = 5e-12

Table S203. Gene #50: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
5Q LOSS MUTATED	62	4	6
5Q LOSS WILD-TYPE	162	146	139

Figure S203. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.57e-13 (Fisher's exact test), Q value = 2.8e-10

Table S204. Gene #50: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	132	240
5Q LOSS MUTATED	7	3	62
5Q LOSS WILD-TYPE	140	129	178

Figure S204. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CNMF'

P value = 2.43e-13 (Fisher's exact test), Q value = 1.9e-10

Table S205. Gene #50: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	159	141
5Q LOSS MUTATED	58	6	7
5Q LOSS WILD-TYPE	147	153	134

Figure S205. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.14e-09 (Fisher's exact test), Q value = 8.4e-07

Table S206. Gene #50: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	216	281
5Q LOSS MUTATED	0	8	63
5Q LOSS WILD-TYPE	8	208	218

Figure S206. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.78e-05 (Fisher's exact test), Q value = 0.016

Table S207. Gene #50: '5q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	175	117	90
5Q LOSS MUTATED	40	5	13
5Q LOSS WILD-TYPE	135	112	77

Figure S207. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.66e-09 (Fisher's exact test), Q value = 5.4e-06

Table S208. Gene #50: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	198	154
5Q LOSS MUTATED	3	50	5
5Q LOSS WILD-TYPE	27	148	149

Figure S208. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p loss' versus 'CN_CNMF'

P value = 8.01e-06 (Chi-square test), Q value = 0.0047

Table S209. Gene #51: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
6P LOSS MUTATED	0	3	14	0	0
6P LOSS WILD-TYPE	305	45	140	12	5

Figure S209. Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

'6p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000505 (Fisher's exact test), Q value = 0.25

Table S210. Gene #51: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	216	281
6P LOSS MUTATED	1	0	13
6P LOSS WILD-TYPE	7	216	268

Figure S210. Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6q loss' versus 'CN_CNMF'

P value = 4.67e-09 (Chi-square test), Q value = 3.4e-06

Table S211. Gene #52: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
6Q LOSS MUTATED	0	3	21	0	0
6Q LOSS WILD-TYPE	305	45	133	12	5

Figure S211. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

'6q loss' versus 'METHLYATION_CNMF'

P value = 0.000123 (Fisher's exact test), Q value = 0.065

Table S212. Gene #52: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	94	164
6Q LOSS MUTATED	13	5	0
6Q LOSS WILD-TYPE	139	89	164

Figure S212. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6q loss' versus 'MRNASEQ_CNMF'

P value = 4.01e-06 (Fisher's exact test), Q value = 0.0024

Table S213. Gene #52: '6q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
6Q LOSS MUTATED	22	1	1
6Q LOSS WILD-TYPE	202	149	144

Figure S213. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.78e-05 (Fisher's exact test), Q value = 0.01

Table S214. Gene #52: '6q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	132	240
6Q LOSS MUTATED	1	1	22
6Q LOSS WILD-TYPE	146	131	218

Figure S214. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_CNMF'

P value = 0.00043 (Fisher's exact test), Q value = 0.21

Table S215. Gene #52: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	159	141
6Q LOSS MUTATED	17	1	3
6Q LOSS WILD-TYPE	188	158	138

Figure S215. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.52e-05 (Fisher's exact test), Q value = 0.0088

Table S216. Gene #52: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	216	281
6Q LOSS MUTATED	1	0	20
6Q LOSS WILD-TYPE	7	216	261

Figure S216. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7p loss' versus 'CN_CNMF'

P value = 1.09e-16 (Chi-square test), Q value = 9.1e-14

Table S217. Gene #53: '7p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
7P LOSS MUTATED	3	1	38	0	1
7P LOSS WILD-TYPE	302	47	116	12	4

Figure S217. Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #3: 'CN_CNMF'

'7p loss' versus 'METHLYATION_CNMF'

P value = 0.000478 (Fisher's exact test), Q value = 0.23

Table S218. Gene #53: '7p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	94	164
7P LOSS MUTATED	23	10	5
7P LOSS WILD-TYPE	129	84	159

Figure S218. Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p loss' versus 'MRNASEQ_CNMF'

P value = 7.43e-10 (Fisher's exact test), Q value = 5.5e-07

Table S219. Gene #53: '7p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
7P LOSS MUTATED	38	1	4
7P LOSS WILD-TYPE	186	149	141

Figure S219. Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.25e-08 (Fisher's exact test), Q value = 8.8e-06

Table S220. Gene #53: '7p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	132	240
7P LOSS MUTATED	4	1	38
7P LOSS WILD-TYPE	143	131	202

Figure S220. Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7p loss' versus 'MIRSEQ_CNMF'

P value = 1.2e-06 (Fisher's exact test), Q value = 0.00076

Table S221. Gene #53: '7p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	159	141
7P LOSS MUTATED	33	6	3
7P LOSS WILD-TYPE	172	153	138

Figure S221. Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000381 (Fisher's exact test), Q value = 0.19

Table S222. Gene #53: '7p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	216	281
7P LOSS MUTATED	2	7	33
7P LOSS WILD-TYPE	6	209	248

Figure S222. Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7q loss' versus 'CN_CNMF'

P value = 3.11e-21 (Chi-square test), Q value = 2.7e-18

Table S223. Gene #54: '7q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
7Q LOSS MUTATED	0	0	40	0	1
7Q LOSS WILD-TYPE	305	48	114	12	4

Figure S223. Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #3: 'CN_CNMF'

'7q loss' versus 'METHLYATION_CNMF'

P value = 2.22e-08 (Fisher's exact test), Q value = 1.5e-05

Table S224. Gene #54: '7q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	94	164
7Q LOSS MUTATED	28	9	1
7Q LOSS WILD-TYPE	124	85	163

Figure S224. Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7q loss' versus 'MRNASEQ_CNMF'

P value = 8.23e-14 (Fisher's exact test), Q value = 6.6e-11

Table S225. Gene #54: '7q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
7Q LOSS MUTATED	40	0	1
7Q LOSS WILD-TYPE	184	150	144

Figure S225. Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.94e-11 (Fisher's exact test), Q value = 2.3e-08

Table S226. Gene #54: '7q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	132	240
7Q LOSS MUTATED	2	0	39
7Q LOSS WILD-TYPE	145	132	201

Figure S226. Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q loss' versus 'MIRSEQ_CNMF'

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

Table S227. Gene #54: '7q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	159	141
7Q LOSS MUTATED	36	2	2
7Q LOSS WILD-TYPE	169	157	139

Figure S227. Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.31e-06 (Fisher's exact test), Q value = 0.00082

Table S228. Gene #54: '7q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	216	281
7Q LOSS MUTATED	0	3	37
7Q LOSS WILD-TYPE	8	213	244

Figure S228. Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.93e-07 (Fisher's exact test), Q value = 0.00013

Table S229. Gene #54: '7q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	198	154
7Q LOSS MUTATED	0	33	2
7Q LOSS WILD-TYPE	30	165	152

Figure S229. Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

P value = 3.22e-32 (Chi-square test), Q value = 2.9e-29

Table S230. Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
8P LOSS MUTATED	4	3	67	0	1
8P LOSS WILD-TYPE	301	45	87	12	4

Figure S230. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 7.57e-16 (Fisher's exact test), Q value = 6.2e-13

Table S231. Gene #55: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	94	164
8P LOSS MUTATED	51	13	2
8P LOSS WILD-TYPE	101	81	162

Figure S231. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 3.68e-20 (Fisher's exact test), Q value = 3.1e-17

Table S232. Gene #55: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
8P LOSS MUTATED	68	3	3
8P LOSS WILD-TYPE	156	147	142

Figure S232. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.99e-17 (Fisher's exact test), Q value = 8.3e-14

Table S233. Gene #55: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	132	240
8P LOSS MUTATED	4	3	67
8P LOSS WILD-TYPE	143	129	173

Figure S233. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_CNMF'

P value = 2.84e-16 (Fisher's exact test), Q value = 2.4e-13

Table S234. Gene #55: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	159	141
8P LOSS MUTATED	61	5	5
8P LOSS WILD-TYPE	144	154	136

Figure S234. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.63e-11 (Fisher's exact test), Q value = 2.8e-08

Table S235. Gene #55: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	216	281
8P LOSS MUTATED	2	6	63
8P LOSS WILD-TYPE	6	210	218

Figure S235. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 5.5e-08 (Fisher's exact test), Q value = 3.8e-05

Table S236. Gene #55: '8p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	175	117	90
8P LOSS MUTATED	41	2	18
8P LOSS WILD-TYPE	134	115	72

Figure S236. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.37e-10 (Fisher's exact test), Q value = 2.5e-07

Table S237. Gene #55: '8p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	198	154
8P LOSS MUTATED	2	54	5
8P LOSS WILD-TYPE	28	144	149

Figure S237. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q loss' versus 'CN_CNMF'

P value = 3.82e-10 (Chi-square test), Q value = 2.9e-07

Table S238. Gene #56: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
8Q LOSS MUTATED	1	1	23	0	0
8Q LOSS WILD-TYPE	304	47	131	12	5

Figure S238. Get High-res Image Gene #56: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'

'8q loss' versus 'METHLYATION_CNMF'

P value = 3.47e-07 (Fisher's exact test), Q value = 0.00023

Table S239. Gene #56: '8q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	94	164
8Q LOSS MUTATED	20	3	0
8Q LOSS WILD-TYPE	132	91	164

Figure S239. Get High-res Image Gene #56: '8q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8q loss' versus 'MRNASEQ_CNMF'

P value = 8.28e-07 (Fisher's exact test), Q value = 0.00053

Table S240. Gene #56: '8q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
8Q LOSS MUTATED	23	0	2
8Q LOSS WILD-TYPE	201	150	143

Figure S240. Get High-res Image Gene #56: '8q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.52e-06 (Fisher's exact test), Q value = 0.0027

Table S241. Gene #56: '8q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	132	240
8Q LOSS MUTATED	2	0	23
8Q LOSS WILD-TYPE	145	132	217

Figure S241. Get High-res Image Gene #56: '8q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8q loss' versus 'MIRSEQ_CNMF'

P value = 2.3e-05 (Fisher's exact test), Q value = 0.013

Table S242. Gene #56: '8q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	159	141
8Q LOSS MUTATED	20	2	1
8Q LOSS WILD-TYPE	185	157	140

Figure S242. Get High-res Image Gene #56: '8q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000135 (Fisher's exact test), Q value = 0.071

Table S243. Gene #56: '8q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	198	154
8Q LOSS MUTATED	0	20	1
8Q LOSS WILD-TYPE	30	178	153

Figure S243. Get High-res Image Gene #56: '8q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p loss' versus 'MRNA_CHIERARCHICAL'

P value = 9.8e-05 (Fisher's exact test), Q value = 0.052

Table S244. Gene #57: '9p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	19	19	15
9P LOSS MUTATED	1	0	8
9P LOSS WILD-TYPE	18	19	7

Figure S244. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

P value = 2.02e-41 (Chi-square test), Q value = 1.8e-38

Table S245. Gene #57: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
9P LOSS MUTATED	2	14	83	0	0
9P LOSS WILD-TYPE	303	34	71	12	5

Figure S245. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 1.27e-10 (Fisher's exact test), Q value = 9.6e-08

Table S246. Gene #57: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	94	164
9P LOSS MUTATED	52	23	9
9P LOSS WILD-TYPE	100	71	155

Figure S246. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 5.67e-17 (Fisher's exact test), Q value = 4.7e-14

Table S247. Gene #57: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
9P LOSS MUTATED	80	6	13
9P LOSS WILD-TYPE	144	144	132

Figure S247. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.23e-14 (Fisher's exact test), Q value = 1e-11

Table S248. Gene #57: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	132	240
9P LOSS MUTATED	14	5	80
9P LOSS WILD-TYPE	133	127	160

Figure S248. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_CNMF'

P value = 6.62e-13 (Fisher's exact test), Q value = 5.2e-10

Table S249. Gene #57: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	159	141
9P LOSS MUTATED	71	14	10
9P LOSS WILD-TYPE	134	145	131

Figure S249. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.35e-09 (Fisher's exact test), Q value = 6.6e-06

Table S250. Gene #57: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	216	281
9P LOSS MUTATED	3	16	76
9P LOSS WILD-TYPE	5	200	205

Figure S250. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.37e-06 (Fisher's exact test), Q value = 0.00086

Table S251. Gene #57: '9p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	198	154
9P LOSS MUTATED	3	63	16
9P LOSS WILD-TYPE	27	135	138

Figure S251. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q loss' versus 'MRNA_CNMF'

P value = 2.35e-05 (Fisher's exact test), Q value = 0.013

Table S252. 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 S252. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'9q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1.13e-06 (Fisher's exact test), Q value = 0.00072

Table S253. Gene #58: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	19	19	15
9Q LOSS MUTATED	0	0	9
9Q LOSS WILD-TYPE	19	19	6

Figure S253. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 8.8e-49 (Chi-square test), Q value = 7.9e-46

Table S254. Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
9Q LOSS MUTATED	3	19	95	0	0
9Q LOSS WILD-TYPE	302	29	59	12	5

Figure S254. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 1.28e-11 (Fisher's exact test), Q value = 9.9e-09

Table S255. Gene #58: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	94	164
9Q LOSS MUTATED	62	26	13
9Q LOSS WILD-TYPE	90	68	151

Figure S255. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 4.2e-20 (Fisher's exact test), Q value = 3.6e-17

Table S256. Gene #58: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
9Q LOSS MUTATED	94	8	15
9Q LOSS WILD-TYPE	130	142	130

Figure S256. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.06e-17 (Fisher's exact test), Q value = 3.4e-14

Table S257. Gene #58: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	132	240
9Q LOSS MUTATED	16	7	94
9Q LOSS WILD-TYPE	131	125	146

Figure S257. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_CNMF'

P value = 5.86e-14 (Fisher's exact test), Q value = 4.7e-11

Table S258. Gene #58: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	159	141
9Q LOSS MUTATED	82	17	14
9Q LOSS WILD-TYPE	123	142	127

Figure S258. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9q loss' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S259. Gene #58: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	216	281
9Q LOSS MUTATED	4	21	88
9Q LOSS WILD-TYPE	4	195	193

Figure S259. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.24e-07 (Fisher's exact test), Q value = 0.00047

Table S260. Gene #58: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	198	154
9Q LOSS MUTATED	5	73	20
9Q LOSS WILD-TYPE	25	125	134

Figure S260. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 8.64e-19 (Chi-square test), Q value = 7.3e-16

Table S261. Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
10P LOSS MUTATED	0	2	38	0	0
10P LOSS WILD-TYPE	305	46	116	12	5

Figure S261. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 4.32e-07 (Fisher's exact test), Q value = 0.00028

Table S262. Gene #59: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	94	164
10P LOSS MUTATED	24	9	1
10P LOSS WILD-TYPE	128	85	163

Figure S262. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 1.18e-09 (Fisher's exact test), Q value = 8.7e-07

Table S263. Gene #59: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
10P LOSS MUTATED	36	1	3
10P LOSS WILD-TYPE	188	149	142

Figure S263. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.51e-08 (Fisher's exact test), Q value = 1.1e-05

Table S264. Gene #59: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	132	240
10P LOSS MUTATED	3	1	36
10P LOSS WILD-TYPE	144	131	204

Figure S264. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_CNMF'

P value = 7.11e-08 (Fisher's exact test), Q value = 4.9e-05

Table S265. Gene #59: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	159	141
10P LOSS MUTATED	32	2	4
10P LOSS WILD-TYPE	173	157	137

Figure S265. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.59e-06 (Fisher's exact test), Q value = 0.0033

Table S266. Gene #59: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	216	281
10P LOSS MUTATED	1	3	34
10P LOSS WILD-TYPE	7	213	247

Figure S266. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.75e-05 (Fisher's exact test), Q value = 0.021

Table S267. Gene #59: '10p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	198	154
10P LOSS MUTATED	1	29	3
10P LOSS WILD-TYPE	29	169	151

Figure S267. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 9.31e-17 (Chi-square test), Q value = 7.8e-14

Table S268. Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
10Q LOSS MUTATED	1	2	36	0	0
10Q LOSS WILD-TYPE	304	46	118	12	5

Figure S268. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 4.32e-07 (Fisher's exact test), Q value = 0.00028

Table S269. Gene #60: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	94	164
10Q LOSS MUTATED	24	9	1
10Q LOSS WILD-TYPE	128	85	163

Figure S269. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 1.76e-08 (Fisher's exact test), Q value = 1.2e-05

Table S270. Gene #60: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
10Q LOSS MUTATED	34	1	4
10Q LOSS WILD-TYPE	190	149	141

Figure S270. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.06e-07 (Fisher's exact test), Q value = 0.00014

Table S271. Gene #60: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	132	240
10Q LOSS MUTATED	4	1	34
10Q LOSS WILD-TYPE	143	131	206

Figure S271. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_CNMF'

P value = 1.54e-06 (Fisher's exact test), Q value = 0.00096

Table S272. Gene #60: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	159	141
10Q LOSS MUTATED	30	3	4
10Q LOSS WILD-TYPE	175	156	137

Figure S272. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000301 (Fisher's exact test), Q value = 0.15

Table S273. Gene #60: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	216	281
10Q LOSS MUTATED	1	5	31
10Q LOSS WILD-TYPE	7	211	250

Figure S273. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 3.7e-28 (Chi-square test), Q value = 3.3e-25

Table S274. Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
11P LOSS MUTATED	1	9	60	0	2
11P LOSS WILD-TYPE	304	39	94	12	3

Figure S274. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 8.26e-11 (Fisher's exact test), Q value = 6.3e-08

Table S275. Gene #61: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	94	164
11P LOSS MUTATED	45	17	5
11P LOSS WILD-TYPE	107	77	159

Figure S275. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p loss' versus 'MRNASEQ_CNMF'

P value = 6.07e-15 (Fisher's exact test), Q value = 5e-12

Table S276. Gene #61: '11p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
11P LOSS MUTATED	62	4	6
11P LOSS WILD-TYPE	162	146	139

Figure S276. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.21e-12 (Fisher's exact test), Q value = 1.7e-09

Table S277. Gene #61: '11p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	132	240
11P LOSS MUTATED	8	3	61
11P LOSS WILD-TYPE	139	129	179

Figure S277. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_CNMF'

P value = 1.24e-09 (Fisher's exact test), Q value = 9.1e-07

Table S278. Gene #61: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	159	141
11P LOSS MUTATED	53	8	9
11P LOSS WILD-TYPE	152	151	132

Figure S278. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.88e-07 (Fisher's exact test), Q value = 0.00032

Table S279. Gene #61: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	216	281
11P LOSS MUTATED	3	11	56
11P LOSS WILD-TYPE	5	205	225

Figure S279. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.14e-06 (Fisher's exact test), Q value = 0.00072

Table S280. Gene #61: '11p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	198	154
11P LOSS MUTATED	1	53	12
11P LOSS WILD-TYPE	29	145	142

Figure S280. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

P value = 8.89e-25 (Chi-square test), Q value = 7.8e-22

Table S281. Gene #62: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
11Q LOSS MUTATED	1	11	54	0	2
11Q LOSS WILD-TYPE	304	37	100	12	3

Figure S281. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

P value = 1.09e-09 (Fisher's exact test), Q value = 8e-07

Table S282. Gene #62: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	94	164
11Q LOSS MUTATED	44	15	6
11Q LOSS WILD-TYPE	108	79	158

Figure S282. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11q loss' versus 'MRNASEQ_CNMF'

P value = 7.7e-12 (Fisher's exact test), Q value = 6e-09

Table S283. Gene #62: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
11Q LOSS MUTATED	56	4	8
11Q LOSS WILD-TYPE	168	146	137

Figure S283. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.03e-10 (Fisher's exact test), Q value = 1.5e-07

Table S284. Gene #62: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	132	240
11Q LOSS MUTATED	9	3	56
11Q LOSS WILD-TYPE	138	129	184

Figure S284. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_CNMF'

P value = 1.1e-09 (Fisher's exact test), Q value = 8.1e-07

Table S285. Gene #62: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	159	141
11Q LOSS MUTATED	52	9	7
11Q LOSS WILD-TYPE	153	150	134

Figure S285. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.25e-06 (Fisher's exact test), Q value = 0.0014

Table S286. Gene #62: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	216	281
11Q LOSS MUTATED	2	11	55
11Q LOSS WILD-TYPE	6	205	226

Figure S286. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000168 (Fisher's exact test), Q value = 0.087

Table S287. Gene #62: '11q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	175	117	90
11Q LOSS MUTATED	45	10	10
11Q LOSS WILD-TYPE	130	107	80

Figure S287. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.88e-06 (Fisher's exact test), Q value = 0.0012

Table S288. Gene #62: '11q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	198	154
11Q LOSS MUTATED	1	52	12
11Q LOSS WILD-TYPE	29	146	142

Figure S288. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12p loss' versus 'CN_CNMF'

P value = 1.38e-17 (Chi-square test), Q value = 1.2e-14

Table S289. Gene #63: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
12P LOSS MUTATED	0	3	38	1	0
12P LOSS WILD-TYPE	305	45	116	11	5

Figure S289. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

'12p loss' versus 'METHLYATION_CNMF'

P value = 8.05e-05 (Fisher's exact test), Q value = 0.043

Table S290. Gene #63: '12p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	94	164
12P LOSS MUTATED	24	7	4
12P LOSS WILD-TYPE	128	87	160

Figure S290. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p loss' versus 'MRNASEQ_CNMF'

P value = 2.88e-10 (Fisher's exact test), Q value = 2.2e-07

Table S291. Gene #63: '12p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
12P LOSS MUTATED	37	0	5
12P LOSS WILD-TYPE	187	150	140

Figure S291. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.35e-08 (Fisher's exact test), Q value = 1.6e-05

Table S292. Gene #63: '12p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	132	240
12P LOSS MUTATED	6	0	36
12P LOSS WILD-TYPE	141	132	204

Figure S292. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p loss' versus 'MIRSEQ_CNMF'

P value = 1.69e-08 (Fisher's exact test), Q value = 1.2e-05

Table S293. Gene #63: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	159	141
12P LOSS MUTATED	34	4	2
12P LOSS WILD-TYPE	171	155	139

Figure S293. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.69e-05 (Fisher's exact test), Q value = 0.036

Table S294. Gene #63: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	216	281
12P LOSS MUTATED	0	5	35
12P LOSS WILD-TYPE	8	211	246

Figure S294. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8.21e-05 (Fisher's exact test), Q value = 0.044

Table S295. Gene #63: '12p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	198	154
12P LOSS MUTATED	1	30	4
12P LOSS WILD-TYPE	29	168	150

Figure S295. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q loss' versus 'CN_CNMF'

P value = 3.29e-14 (Chi-square test), Q value = 2.7e-11

Table S296. Gene #64: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
12Q LOSS MUTATED	0	2	31	1	0
12Q LOSS WILD-TYPE	305	46	123	11	5

Figure S296. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

'12q loss' versus 'METHLYATION_CNMF'

P value = 2.62e-05 (Fisher's exact test), Q value = 0.015

Table S297. Gene #64: '12q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	94	164
12Q LOSS MUTATED	21	5	2
12Q LOSS WILD-TYPE	131	89	162

Figure S297. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12q loss' versus 'MRNASEQ_CNMF'

P value = 4.65e-09 (Fisher's exact test), Q value = 3.3e-06

Table S298. Gene #64: '12q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
12Q LOSS MUTATED	31	0	3
12Q LOSS WILD-TYPE	193	150	142

Figure S298. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.94e-07 (Fisher's exact test), Q value = 0.00019

Table S299. Gene #64: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	132	240
12Q LOSS MUTATED	4	0	30
12Q LOSS WILD-TYPE	143	132	210

Figure S299. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q loss' versus 'MIRSEQ_CNMF'

P value = 1.3e-06 (Fisher's exact test), Q value = 0.00082

Table S300. Gene #64: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	159	141
12Q LOSS MUTATED	27	2	3
12Q LOSS WILD-TYPE	178	157	138

Figure S300. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.07e-05 (Fisher's exact test), Q value = 0.0063

Table S301. Gene #64: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	216	281
12Q LOSS MUTATED	0	2	30
12Q LOSS WILD-TYPE	8	214	251

Figure S301. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000266 (Fisher's exact test), Q value = 0.13

Table S302. Gene #64: '12q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	175	117	90
12Q LOSS MUTATED	23	2	3
12Q LOSS WILD-TYPE	152	115	87

Figure S302. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.75e-05 (Fisher's exact test), Q value = 0.042

Table S303. Gene #64: '12q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	198	154
12Q LOSS MUTATED	1	25	2
12Q LOSS WILD-TYPE	29	173	152

Figure S303. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 1.2e-28 (Chi-square test), Q value = 1.1e-25

Table S304. Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
13Q LOSS MUTATED	4	20	63	1	1
13Q LOSS WILD-TYPE	301	28	91	11	4

Figure S304. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 1.21e-06 (Fisher's exact test), Q value = 0.00076

Table S305. Gene #65: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	94	164
13Q LOSS MUTATED	44	21	12
13Q LOSS WILD-TYPE	108	73	152

Figure S305. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 8.65e-10 (Fisher's exact test), Q value = 6.4e-07

Table S306. Gene #65: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
13Q LOSS MUTATED	65	8	16
13Q LOSS WILD-TYPE	159	142	129

Figure S306. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.4e-08 (Fisher's exact test), Q value = 2.3e-05

Table S307. Gene #65: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	132	240
13Q LOSS MUTATED	17	7	65
13Q LOSS WILD-TYPE	130	125	175

Figure S307. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_CNMF'

P value = 3.34e-05 (Fisher's exact test), Q value = 0.019

Table S308. Gene #65: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	159	141
13Q LOSS MUTATED	53	14	18
13Q LOSS WILD-TYPE	152	145	123

Figure S308. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'13q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.78e-08 (Fisher's exact test), Q value = 2.6e-05

Table S309. Gene #65: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	216	281
13Q LOSS MUTATED	6	17	62
13Q LOSS WILD-TYPE	2	199	219

Figure S309. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'MRNA_CHIERARCHICAL'

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

Table S310. Gene #66: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	19	19	15
14Q LOSS MUTATED	0	0	6
14Q LOSS WILD-TYPE	19	19	9

Figure S310. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 1.38e-23 (Chi-square test), Q value = 1.2e-20

Table S311. Gene #66: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
14Q LOSS MUTATED	0	4	49	1	2
14Q LOSS WILD-TYPE	305	44	105	11	3

Figure S311. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 5.91e-11 (Fisher's exact test), Q value = 4.5e-08

Table S312. Gene #66: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	94	164
14Q LOSS MUTATED	35	8	1
14Q LOSS WILD-TYPE	117	86	163

Figure S312. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 4.54e-12 (Fisher's exact test), Q value = 3.6e-09

Table S313. Gene #66: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
14Q LOSS MUTATED	49	3	4
14Q LOSS WILD-TYPE	175	147	141

Figure S313. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.66e-11 (Fisher's exact test), Q value = 7.3e-08

Table S314. Gene #66: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	132	240
14Q LOSS MUTATED	5	2	49
14Q LOSS WILD-TYPE	142	130	191

Figure S314. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_CNMF'

P value = 4.33e-10 (Fisher's exact test), Q value = 3.2e-07

Table S315. Gene #66: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	159	141
14Q LOSS MUTATED	43	2	9
14Q LOSS WILD-TYPE	162	157	132

Figure S315. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'14q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.12e-11 (Fisher's exact test), Q value = 8.7e-09

Table S316. Gene #66: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	216	281
14Q LOSS MUTATED	3	2	49
14Q LOSS WILD-TYPE	5	214	232

Figure S316. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.92e-05 (Fisher's exact test), Q value = 0.011

Table S317. Gene #66: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	175	117	90
14Q LOSS MUTATED	34	3	8
14Q LOSS WILD-TYPE	141	114	82

Figure S317. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'14q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.22e-05 (Fisher's exact test), Q value = 0.013

Table S318. Gene #66: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	198	154
14Q LOSS MUTATED	4	36	5
14Q LOSS WILD-TYPE	26	162	149

Figure S318. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q loss' versus 'MRNA_CHIERARCHICAL'

P value = 4.17e-05 (Fisher's exact test), Q value = 0.023

Table S319. Gene #67: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	19	19	15
15Q LOSS MUTATED	0	0	7
15Q LOSS WILD-TYPE	19	19	8

Figure S319. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 3.8e-41 (Chi-square test), Q value = 3.4e-38

Table S320. Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
15Q LOSS MUTATED	4	14	86	0	2
15Q LOSS WILD-TYPE	301	34	68	12	3

Figure S320. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 1.92e-14 (Fisher's exact test), Q value = 1.6e-11

Table S321. Gene #67: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	94	164
15Q LOSS MUTATED	61	24	8
15Q LOSS WILD-TYPE	91	70	156

Figure S321. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'15q loss' versus 'RPPA_CNMF'

P value = 0.00036 (Chi-square test), Q value = 0.18

Table S322. Gene #67: '15q 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
15Q LOSS MUTATED	1	11	2	1	1	3
15Q LOSS WILD-TYPE	40	26	37	11	40	21

Figure S322. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 4.15e-23 (Fisher's exact test), Q value = 3.6e-20

Table S323. Gene #67: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
15Q LOSS MUTATED	91	7	8
15Q LOSS WILD-TYPE	133	143	137

Figure S323. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.5e-21 (Fisher's exact test), Q value = 3e-18

Table S324. Gene #67: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	132	240
15Q LOSS MUTATED	9	5	92
15Q LOSS WILD-TYPE	138	127	148

Figure S324. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_CNMF'

P value = 1.82e-17 (Fisher's exact test), Q value = 1.5e-14

Table S325. Gene #67: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	159	141
15Q LOSS MUTATED	79	9	12
15Q LOSS WILD-TYPE	126	150	129

Figure S325. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.5e-15 (Fisher's exact test), Q value = 1.2e-12

Table S326. Gene #67: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	216	281
15Q LOSS MUTATED	5	10	85
15Q LOSS WILD-TYPE	3	206	196

Figure S326. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.17e-07 (Fisher's exact test), Q value = 8e-05

Table S327. Gene #67: '15q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	175	117	90
15Q LOSS MUTATED	61	9	18
15Q LOSS WILD-TYPE	114	108	72

Figure S327. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8.56e-09 (Fisher's exact test), Q value = 6.1e-06

Table S328. Gene #67: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	198	154
15Q LOSS MUTATED	6	69	13
15Q LOSS WILD-TYPE	24	129	141

Figure S328. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p loss' versus 'MRNA_CHIERARCHICAL'

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

Table S329. Gene #68: '16p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	19	19	15
16P LOSS MUTATED	0	0	6
16P LOSS WILD-TYPE	19	19	9

Figure S329. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'16p loss' versus 'CN_CNMF'

P value = 8.31e-38 (Chi-square test), Q value = 7.4e-35

Table S330. Gene #68: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
16P LOSS MUTATED	5	9	80	0	0
16P LOSS WILD-TYPE	300	39	74	12	5

Figure S330. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

'16p loss' versus 'METHLYATION_CNMF'

P value = 2.04e-13 (Fisher's exact test), Q value = 1.6e-10

Table S331. Gene #68: '16p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	94	164
16P LOSS MUTATED	53	25	6
16P LOSS WILD-TYPE	99	69	158

Figure S331. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16p loss' versus 'MRNASEQ_CNMF'

P value = 1.93e-21 (Fisher's exact test), Q value = 1.7e-18

Table S332. Gene #68: '16p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
16P LOSS MUTATED	82	5	7
16P LOSS WILD-TYPE	142	145	138

Figure S332. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.6e-18 (Fisher's exact test), Q value = 5.6e-15

Table S333. Gene #68: '16p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	132	240
16P LOSS MUTATED	9	4	81
16P LOSS WILD-TYPE	138	128	159

Figure S333. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_CNMF'

P value = 5.68e-14 (Fisher's exact test), Q value = 4.5e-11

Table S334. Gene #68: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	159	141
16P LOSS MUTATED	69	9	11
16P LOSS WILD-TYPE	136	150	130

Figure S334. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.12e-10 (Fisher's exact test), Q value = 2.3e-07

Table S335. Gene #68: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	216	281
16P LOSS MUTATED	2	12	75
16P LOSS WILD-TYPE	6	204	206

Figure S335. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.68e-05 (Fisher's exact test), Q value = 0.015

Table S336. Gene #68: '16p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	175	117	90
16P LOSS MUTATED	49	9	23
16P LOSS WILD-TYPE	126	108	67

Figure S336. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.47e-09 (Fisher's exact test), Q value = 1.8e-06

Table S337. Gene #68: '16p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	198	154
16P LOSS MUTATED	4	66	11
16P LOSS WILD-TYPE	26	132	143

Figure S337. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q loss' versus 'MRNA_CHIERARCHICAL'

P value = 9.8e-05 (Fisher's exact test), Q value = 0.052

Table S338. Gene #69: '16q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	19	19	15
16Q LOSS MUTATED	0	1	8
16Q LOSS WILD-TYPE	19	18	7

Figure S338. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'16q loss' versus 'CN_CNMF'

P value = 2.04e-48 (Chi-square test), Q value = 1.8e-45

Table S339. Gene #69: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
16Q LOSS MUTATED	15	13	107	0	0
16Q LOSS WILD-TYPE	290	35	47	12	5

Figure S339. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 3.69e-14 (Fisher's exact test), Q value = 3e-11

Table S340. Gene #69: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	94	164
16Q LOSS MUTATED	72	31	15
16Q LOSS WILD-TYPE	80	63	149

Figure S340. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 3.49e-22 (Fisher's exact test), Q value = 3e-19

Table S341. Gene #69: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
16Q LOSS MUTATED	107	15	13
16Q LOSS WILD-TYPE	117	135	132

Figure S341. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.82e-19 (Fisher's exact test), Q value = 1.5e-16

Table S342. Gene #69: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	132	240
16Q LOSS MUTATED	14	13	108
16Q LOSS WILD-TYPE	133	119	132

Figure S342. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_CNMF'

P value = 7.1e-16 (Fisher's exact test), Q value = 5.9e-13

Table S343. Gene #69: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	159	141
16Q LOSS MUTATED	92	15	22
16Q LOSS WILD-TYPE	113	144	119

Figure S343. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.8e-10 (Fisher's exact test), Q value = 2.1e-07

Table S344. Gene #69: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	216	281
16Q LOSS MUTATED	4	25	100
16Q LOSS WILD-TYPE	4	191	181

Figure S344. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.84e-06 (Fisher's exact test), Q value = 0.0011

Table S345. Gene #69: '16q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	175	117	90
16Q LOSS MUTATED	69	15	30
16Q LOSS WILD-TYPE	106	102	60

Figure S345. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.22e-10 (Fisher's exact test), Q value = 3.9e-07

Table S346. Gene #69: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	198	154
16Q LOSS MUTATED	7	87	20
16Q LOSS WILD-TYPE	23	111	134

Figure S346. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.000454 (Fisher's exact test), Q value = 0.22

Table S347. Gene #70: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	19	19	15
17P LOSS MUTATED	1	0	7
17P LOSS WILD-TYPE	18	19	8

Figure S347. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 4.05e-58 (Chi-square test), Q value = 3.6e-55

Table S348. Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
17P LOSS MUTATED	3	12	107	0	0
17P LOSS WILD-TYPE	302	36	47	12	5

Figure S348. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 4.35e-16 (Fisher's exact test), Q value = 3.6e-13

Table S349. Gene #70: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	94	164
17P LOSS MUTATED	71	25	11
17P LOSS WILD-TYPE	81	69	153

Figure S349. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 2.85e-26 (Fisher's exact test), Q value = 2.5e-23

Table S350. Gene #70: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
17P LOSS MUTATED	102	5	14
17P LOSS WILD-TYPE	122	145	131

Figure S350. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.03e-22 (Fisher's exact test), Q value = 3.5e-19

Table S351. Gene #70: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	132	240
17P LOSS MUTATED	16	4	101
17P LOSS WILD-TYPE	131	128	139

Figure S351. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CNMF'

P value = 6.94e-19 (Fisher's exact test), Q value = 5.9e-16

Table S352. Gene #70: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	159	141
17P LOSS MUTATED	90	16	11
17P LOSS WILD-TYPE	115	143	130

Figure S352. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.01e-11 (Fisher's exact test), Q value = 7.9e-09

Table S353. Gene #70: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	216	281
17P LOSS MUTATED	4	19	94
17P LOSS WILD-TYPE	4	197	187

Figure S353. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000455 (Fisher's exact test), Q value = 0.22

Table S354. Gene #70: '17p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	175	117	90
17P LOSS MUTATED	61	17	24
17P LOSS WILD-TYPE	114	100	66

Figure S354. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'17p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8.61e-07 (Fisher's exact test), Q value = 0.00055

Table S355. Gene #70: '17p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	198	154
17P LOSS MUTATED	6	75	21
17P LOSS WILD-TYPE	24	123	133

Figure S355. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q loss' versus 'MRNA_CHIERARCHICAL'

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

Table S356. Gene #71: '17q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	19	19	15
17Q LOSS MUTATED	0	0	6
17Q LOSS WILD-TYPE	19	19	9

Figure S356. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

P value = 1.63e-36 (Chi-square test), Q value = 1.4e-33

Table S357. Gene #71: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
17Q LOSS MUTATED	2	11	75	0	0
17Q LOSS WILD-TYPE	303	37	79	12	5

Figure S357. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

'17q loss' versus 'METHLYATION_CNMF'

P value = 5.35e-08 (Fisher's exact test), Q value = 3.7e-05

Table S358. Gene #71: '17q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	94	164
17Q LOSS MUTATED	45	22	10
17Q LOSS WILD-TYPE	107	72	154

Figure S358. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q loss' versus 'MRNASEQ_CNMF'

P value = 1.83e-14 (Fisher's exact test), Q value = 1.5e-11

Table S359. Gene #71: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
17Q LOSS MUTATED	70	5	12
17Q LOSS WILD-TYPE	154	145	133

Figure S359. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.92e-12 (Fisher's exact test), Q value = 4.6e-09

Table S360. Gene #71: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	132	240
17Q LOSS MUTATED	14	4	69
17Q LOSS WILD-TYPE	133	128	171

Figure S360. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_CNMF'

P value = 7.08e-09 (Fisher's exact test), Q value = 5.1e-06

Table S361. Gene #71: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	159	141
17Q LOSS MUTATED	59	14	10
17Q LOSS WILD-TYPE	146	145	131

Figure S361. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.12e-07 (Fisher's exact test), Q value = 0.00014

Table S362. Gene #71: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	216	281
17Q LOSS MUTATED	4	15	64
17Q LOSS WILD-TYPE	4	201	217

Figure S362. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 2.08e-17 (Chi-square test), Q value = 1.7e-14

Table S363. Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
18P LOSS MUTATED	1	11	38	0	2
18P LOSS WILD-TYPE	304	37	116	12	3

Figure S363. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

P value = 1.53e-07 (Fisher's exact test), Q value = 1e-04

Table S364. Gene #72: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	94	164
18P LOSS MUTATED	33	9	4
18P LOSS WILD-TYPE	119	85	160

Figure S364. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p loss' versus 'MRNASEQ_CNMF'

P value = 1.88e-06 (Fisher's exact test), Q value = 0.0012

Table S365. Gene #72: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
18P LOSS MUTATED	40	6	6
18P LOSS WILD-TYPE	184	144	139

Figure S365. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.26e-05 (Fisher's exact test), Q value = 0.0073

Table S366. Gene #72: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	132	240
18P LOSS MUTATED	8	4	40
18P LOSS WILD-TYPE	139	128	200

Figure S366. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.059

Table S367. Gene #72: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	159	141
18P LOSS MUTATED	35	7	9
18P LOSS WILD-TYPE	170	152	132

Figure S367. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000165 (Fisher's exact test), Q value = 0.086

Table S368. Gene #72: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	216	281
18P LOSS MUTATED	3	10	38
18P LOSS WILD-TYPE	5	206	243

Figure S368. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18q loss' versus 'CN_CNMF'

P value = 1.15e-22 (Chi-square test), Q value = 1e-19

Table S369. Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
18Q LOSS MUTATED	1	13	49	0	2
18Q LOSS WILD-TYPE	304	35	105	12	3

Figure S369. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 9.38e-09 (Fisher's exact test), Q value = 6.6e-06

Table S370. Gene #73: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	94	164
18Q LOSS MUTATED	41	12	6
18Q LOSS WILD-TYPE	111	82	158

Figure S370. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 1.09e-09 (Fisher's exact test), Q value = 8e-07

Table S371. Gene #73: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
18Q LOSS MUTATED	52	6	7
18Q LOSS WILD-TYPE	172	144	138

Figure S371. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.56e-08 (Fisher's exact test), Q value = 1.1e-05

Table S372. Gene #73: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	132	240
18Q LOSS MUTATED	9	4	52
18Q LOSS WILD-TYPE	138	128	188

Figure S372. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_CNMF'

P value = 1.21e-07 (Fisher's exact test), Q value = 8.2e-05

Table S373. Gene #73: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	159	141
18Q LOSS MUTATED	47	9	8
18Q LOSS WILD-TYPE	158	150	133

Figure S373. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.6e-07 (Fisher's exact test), Q value = 0.00024

Table S374. Gene #73: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	216	281
18Q LOSS MUTATED	4	10	50
18Q LOSS WILD-TYPE	4	206	231

Figure S374. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

P value = 6.2e-20 (Chi-square test), Q value = 5.3e-17

Table S375. Gene #74: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
19P LOSS MUTATED	1	13	43	0	0
19P LOSS WILD-TYPE	304	35	111	12	5

Figure S375. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

P value = 6.15e-13 (Fisher's exact test), Q value = 4.9e-10

Table S376. Gene #74: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	94	164
19P LOSS MUTATED	42	7	2
19P LOSS WILD-TYPE	110	87	162

Figure S376. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p loss' versus 'MRNASEQ_CNMF'

P value = 1.82e-10 (Fisher's exact test), Q value = 1.4e-07

Table S377. Gene #74: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
19P LOSS MUTATED	48	5	4
19P LOSS WILD-TYPE	176	145	141

Figure S377. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.57e-09 (Fisher's exact test), Q value = 3.3e-06

Table S378. Gene #74: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	132	240
19P LOSS MUTATED	5	4	48
19P LOSS WILD-TYPE	142	128	192

Figure S378. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_CNMF'

P value = 1.01e-07 (Fisher's exact test), Q value = 6.9e-05

Table S379. Gene #74: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	159	141
19P LOSS MUTATED	42	6	7
19P LOSS WILD-TYPE	163	153	134

Figure S379. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.66e-06 (Fisher's exact test), Q value = 0.001

Table S380. Gene #74: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	216	281
19P LOSS MUTATED	2	7	46
19P LOSS WILD-TYPE	6	209	235

Figure S380. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.63e-05 (Fisher's exact test), Q value = 0.0094

Table S381. Gene #74: '19p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	175	117	90
19P LOSS MUTATED	38	5	7
19P LOSS WILD-TYPE	137	112	83

Figure S381. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.11e-05 (Fisher's exact test), Q value = 0.0065

Table S382. Gene #74: '19p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	198	154
19P LOSS MUTATED	4	40	6
19P LOSS WILD-TYPE	26	158	148

Figure S382. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 4.41e-17 (Chi-square test), Q value = 3.7e-14

Table S383. Gene #75: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
19Q LOSS MUTATED	2	12	39	0	0
19Q LOSS WILD-TYPE	303	36	115	12	5

Figure S383. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

P value = 1.53e-07 (Fisher's exact test), Q value = 1e-04

Table S384. Gene #75: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	94	164
19Q LOSS MUTATED	33	9	4
19Q LOSS WILD-TYPE	119	85	160

Figure S384. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q loss' versus 'MRNASEQ_CNMF'

P value = 6.1e-08 (Fisher's exact test), Q value = 4.2e-05

Table S385. Gene #75: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
19Q LOSS MUTATED	42	5	5
19Q LOSS WILD-TYPE	182	145	140

Figure S385. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.82e-07 (Fisher's exact test), Q value = 5e-04

Table S386. Gene #75: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	132	240
19Q LOSS MUTATED	6	4	42
19Q LOSS WILD-TYPE	141	128	198

Figure S386. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_CNMF'

P value = 2.12e-06 (Fisher's exact test), Q value = 0.0013

Table S387. Gene #75: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	159	141
19Q LOSS MUTATED	38	7	6
19Q LOSS WILD-TYPE	167	152	135

Figure S387. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.85e-05 (Fisher's exact test), Q value = 0.027

Table S388. Gene #75: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	216	281
19Q LOSS MUTATED	2	8	41
19Q LOSS WILD-TYPE	6	208	240

Figure S388. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p loss' versus 'CN_CNMF'

P value = 6.08e-05 (Chi-square test), Q value = 0.033

Table S389. Gene #76: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
20P LOSS MUTATED	1	4	13	0	0
20P LOSS WILD-TYPE	304	44	141	12	5

Figure S389. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 3.24e-16 (Chi-square test), Q value = 2.7e-13

Table S390. Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
21Q LOSS MUTATED	4	6	41	0	2
21Q LOSS WILD-TYPE	301	42	113	12	3

Figure S390. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

'21q loss' versus 'METHLYATION_CNMF'

P value = 5.89e-06 (Fisher's exact test), Q value = 0.0035

Table S391. Gene #78: '21q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	94	164
21Q LOSS MUTATED	30	9	5
21Q LOSS WILD-TYPE	122	85	159

Figure S391. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'21q loss' versus 'MRNASEQ_CNMF'

P value = 5.86e-11 (Fisher's exact test), Q value = 4.5e-08

Table S392. Gene #78: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
21Q LOSS MUTATED	45	7	1
21Q LOSS WILD-TYPE	179	143	144

Figure S392. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.4e-08 (Fisher's exact test), Q value = 9.8e-06

Table S393. Gene #78: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	132	240
21Q LOSS MUTATED	2	7	44
21Q LOSS WILD-TYPE	145	125	196

Figure S393. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_CNMF'

P value = 2.48e-09 (Fisher's exact test), Q value = 1.8e-06

Table S394. Gene #78: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	159	141
21Q LOSS MUTATED	40	2	8
21Q LOSS WILD-TYPE	165	157	133

Figure S394. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'21q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.12e-07 (Fisher's exact test), Q value = 0.00027

Table S395. Gene #78: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	216	281
21Q LOSS MUTATED	0	5	45
21Q LOSS WILD-TYPE	8	211	236

Figure S395. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 8.84e-07 (Fisher's exact test), Q value = 0.00057

Table S396. Gene #78: '21q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	175	117	90
21Q LOSS MUTATED	33	1	9
21Q LOSS WILD-TYPE	142	116	81

Figure S396. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'21q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.11e-06 (Fisher's exact test), Q value = 0.00071

Table S397. Gene #78: '21q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	198	154
21Q LOSS MUTATED	4	36	3
21Q LOSS WILD-TYPE	26	162	151

Figure S397. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q loss' versus 'MRNA_CHIERARCHICAL'

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

Table S398. Gene #79: '22q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	19	19	15
22Q LOSS MUTATED	0	0	6
22Q LOSS WILD-TYPE	19	19	9

Figure S398. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 1.17e-42 (Chi-square test), Q value = 1.1e-39

Table S399. Gene #79: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
22Q LOSS MUTATED	3	14	87	0	1
22Q LOSS WILD-TYPE	302	34	67	12	4

Figure S399. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 2.56e-10 (Fisher's exact test), Q value = 1.9e-07

Table S400. Gene #79: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	94	164
22Q LOSS MUTATED	58	25	13
22Q LOSS WILD-TYPE	94	69	151

Figure S400. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 1.31e-15 (Fisher's exact test), Q value = 1.1e-12

Table S401. Gene #79: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
22Q LOSS MUTATED	81	7	16
22Q LOSS WILD-TYPE	143	143	129

Figure S401. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.45e-14 (Fisher's exact test), Q value = 2e-11

Table S402. Gene #79: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	132	240
22Q LOSS MUTATED	17	5	82
22Q LOSS WILD-TYPE	130	127	158

Figure S402. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CNMF'

P value = 1.17e-11 (Fisher's exact test), Q value = 9.1e-09

Table S403. Gene #79: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	159	141
22Q LOSS MUTATED	73	17	12
22Q LOSS WILD-TYPE	132	142	129

Figure S403. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.06e-09 (Fisher's exact test), Q value = 2.2e-06

Table S404. Gene #79: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	216	281
22Q LOSS MUTATED	6	20	76
22Q LOSS WILD-TYPE	2	196	205

Figure S404. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000152 (Fisher's exact test), Q value = 0.079

Table S405. Gene #79: '22q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	198	154
22Q LOSS MUTATED	6	64	21
22Q LOSS WILD-TYPE	24	134	133

Figure S405. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq loss' versus 'CN_CNMF'

P value = 1.89e-29 (Chi-square test), Q value = 1.7e-26

Table S406. Gene #80: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
XQ LOSS MUTATED	1	7	61	0	0
XQ LOSS WILD-TYPE	304	41	93	12	5

Figure S406. Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 2.82e-07 (Fisher's exact test), Q value = 0.00019

Table S407. Gene #80: 'xq loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	94	164
XQ LOSS MUTATED	36	16	6
XQ LOSS WILD-TYPE	116	78	158

Figure S407. Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xq loss' versus 'RPPA_CNMF'

P value = 2.71e-05 (Chi-square test), Q value = 0.015

Table S408. 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 S408. Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'xq loss' versus 'MRNASEQ_CNMF'

P value = 2.21e-14 (Fisher's exact test), Q value = 1.8e-11

Table S409. Gene #80: 'xq loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
XQ LOSS MUTATED	59	5	4
XQ LOSS WILD-TYPE	165	145	141

Figure S409. Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'xq loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.18e-11 (Fisher's exact test), Q value = 9.2e-09

Table S410. Gene #80: 'xq loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	132	240
XQ LOSS MUTATED	6	4	58
XQ LOSS WILD-TYPE	141	128	182

Figure S410. Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_CNMF'

P value = 1.12e-08 (Fisher's exact test), Q value = 7.9e-06

Table S411. Gene #80: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	159	141
XQ LOSS MUTATED	49	8	8
XQ LOSS WILD-TYPE	156	151	133

Figure S411. Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xq loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-07 (Fisher's exact test), Q value = 0.00013

Table S412. Gene #80: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	216	281
XQ LOSS MUTATED	3	9	53
XQ LOSS WILD-TYPE	5	207	228

Figure S412. Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.93e-05 (Fisher's exact test), Q value = 0.037

Table S413. Gene #80: 'xq loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	198	154
XQ LOSS MUTATED	5	43	9
XQ LOSS WILD-TYPE	25	155	145

Figure S413. 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 = 524
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

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R

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] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)

[3] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)

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