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

Brain Lower Grade Glioma (Primary solid tumor)

02 April 2015 | analyses__2015_04_02

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 (2015): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1668C7Q

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 81 arm-level events and 12 molecular subtypes across 513 patients, 395 significant findings detected with P value < 0.05 and Q value < 0.25.

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

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 81 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, 395 significant findings detected.


		Clinical Features	MRNA CNMF	MRNA CHIERARCHICAL	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
1p loss	184 (36%)	329	0.0285 (0.0808)	0.00014 (0.000895)	1e-05 (9.08e-05)	1e-05 (9.08e-05)	0.00034 (0.00194)	0.457 (0.648)	1e-05 (9.08e-05)	1e-05 (9.08e-05)	1e-05 (9.08e-05)	1e-05 (9.08e-05)	1e-05 (9.08e-05)	1e-05 (9.08e-05)
7p gain	121 (24%)	392	0.744 (0.916)	0.78 (0.952)	1e-05 (9.08e-05)	1e-05 (9.08e-05)	0.00047 (0.00248)	0.0118 (0.0408)	1e-05 (9.08e-05)	1e-05 (9.08e-05)	0.00264 (0.0115)	1e-05 (9.08e-05)	0.00037 (0.00209)	1e-05 (9.08e-05)
10p loss	83 (16%)	430	0.269 (0.438)	0.884 (1.00)	1e-05 (9.08e-05)	1e-05 (9.08e-05)	1e-05 (9.08e-05)	0.00104 (0.005)	1e-05 (9.08e-05)	1e-05 (9.08e-05)	4e-05 (0.000316)	1e-05 (9.08e-05)	1e-05 (9.08e-05)	1e-05 (9.08e-05)
10q loss	96 (19%)	417	0.269 (0.438)	0.885 (1.00)	1e-05 (9.08e-05)	1e-05 (9.08e-05)	2e-05 (0.000174)	0.00055 (0.00286)	1e-05 (9.08e-05)	1e-05 (9.08e-05)	1e-05 (9.08e-05)	1e-05 (9.08e-05)	1e-05 (9.08e-05)	1e-05 (9.08e-05)
19q loss	209 (41%)	304	0.182 (0.331)	0.0132 (0.0439)	1e-05 (9.08e-05)	1e-05 (9.08e-05)	0.0399 (0.104)	0.334 (0.52)	1e-05 (9.08e-05)	1e-05 (9.08e-05)	1e-05 (9.08e-05)	1e-05 (9.08e-05)	1e-05 (9.08e-05)	1e-05 (9.08e-05)
22q loss	57 (11%)	456	0.815 (0.98)	0.00659 (0.0249)	1e-05 (9.08e-05)	1e-05 (9.08e-05)	5e-05 (0.00038)	0.0392 (0.103)	1e-05 (9.08e-05)	1e-05 (9.08e-05)	0.452 (0.643)	0.0003 (0.00177)	0.0112 (0.0399)	0.00012 (0.000799)
1p gain	13 (3%)	500			0.00014 (0.000895)	0.00014 (0.000895)	0.0236 (0.07)	1 (1.00)	1e-05 (9.08e-05)	1e-05 (9.08e-05)	0.00549 (0.0214)	1e-05 (9.08e-05)	0.0123 (0.0419)	0.00012 (0.000799)
7q gain	151 (29%)	362	0.764 (0.935)	0.52 (0.705)	1e-05 (9.08e-05)	1e-05 (9.08e-05)	0.00403 (0.0166)	0.201 (0.358)	1e-05 (9.08e-05)	1e-05 (9.08e-05)	0.00332 (0.0139)	1e-05 (9.08e-05)	0.00056 (0.00288)	1e-05 (9.08e-05)
11p loss	63 (12%)	450	1 (1.00)	0.0294 (0.0828)	1e-05 (9.08e-05)	1e-05 (9.08e-05)	0.0117 (0.0406)	0.725 (0.901)	1e-05 (9.08e-05)	1e-05 (9.08e-05)	1e-05 (9.08e-05)	7e-05 (0.000504)	0.435 (0.626)	0.0161 (0.0517)
14q loss	80 (16%)	433	0.468 (0.655)	0.266 (0.438)	0.00111 (0.00526)	0.0002 (0.00124)	0.0449 (0.113)	0.117 (0.234)	1e-05 (9.08e-05)	0.00024 (0.00146)	0.0101 (0.037)	0.00095 (0.00464)	0.0115 (0.0405)	0.00037 (0.00209)
5p gain	11 (2%)	502			0.00595 (0.023)	0.0032 (0.0135)	0.0217 (0.0655)	0.61 (0.791)	7e-05 (0.000504)	0.00043 (0.00232)	0.0249 (0.0729)	0.0271 (0.0777)	0.142 (0.272)	0.0159 (0.0516)
5q gain	8 (2%)	505			0.00486 (0.0194)	0.00025 (0.00151)			9e-05 (0.000639)	0.00012 (0.000799)	0.0129 (0.0432)	0.00075 (0.00372)	0.00769 (0.0285)	0.00045 (0.0024)
19q gain	25 (5%)	488			1e-05 (9.08e-05)	1e-05 (9.08e-05)	0.0577 (0.136)	0.396 (0.589)	1e-05 (9.08e-05)	1e-05 (9.08e-05)	0.00235 (0.0103)	1e-05 (9.08e-05)	1e-05 (9.08e-05)	1e-05 (9.08e-05)
20p gain	43 (8%)	470			1e-05 (9.08e-05)	1e-05 (9.08e-05)	0.0006 (0.00305)	0.175 (0.322)	1e-05 (9.08e-05)	1e-05 (9.08e-05)	0.161 (0.302)	1e-05 (9.08e-05)	0.00105 (0.00503)	1e-05 (9.08e-05)
20q gain	43 (8%)	470			1e-05 (9.08e-05)	1e-05 (9.08e-05)	0.00066 (0.00334)	0.145 (0.278)	1e-05 (9.08e-05)	1e-05 (9.08e-05)	0.052 (0.127)	1e-05 (9.08e-05)	3e-05 (0.000247)	1e-05 (9.08e-05)
4p loss	71 (14%)	442	1 (1.00)	0.782 (0.953)	0.00302 (0.013)	1e-05 (9.08e-05)	0.35 (0.537)	1 (1.00)	3e-05 (0.000247)	1e-05 (9.08e-05)	4e-05 (0.000316)	0.00032 (0.00187)	5e-05 (0.00038)	2e-05 (0.000174)
4q loss	92 (18%)	421	1 (1.00)	0.404 (0.593)	0.00692 (0.0259)	1e-05 (9.08e-05)	0.259 (0.432)	0.932 (1.00)	7e-05 (0.000504)	1e-05 (9.08e-05)	0.00017 (0.00107)	0.00126 (0.00592)	1e-05 (9.08e-05)	1e-05 (9.08e-05)
8p loss	17 (3%)	496	0.616 (0.797)	0.043 (0.109)	4e-05 (0.000316)	0.00012 (0.000799)	0.0187 (0.0582)	0.152 (0.289)	1e-05 (9.08e-05)	4e-05 (0.000316)	0.115 (0.231)	0.00115 (0.00543)	0.818 (0.983)	0.00033 (0.0019)
11q loss	21 (4%)	492			0.00024 (0.00146)	4e-05 (0.000316)	0.0179 (0.0562)	0.647 (0.83)	1e-05 (9.08e-05)	1e-05 (9.08e-05)	0.027 (0.0776)	7e-05 (0.000504)	0.489 (0.675)	0.00033 (0.0019)
10p gain	57 (11%)	456	1 (1.00)	0.0419 (0.108)	1e-05 (9.08e-05)	1e-05 (9.08e-05)	0.0204 (0.0622)	0.553 (0.739)	1e-05 (9.08e-05)	1e-05 (9.08e-05)	0.055 (0.133)	0.294 (0.47)	0.476 (0.661)	0.00516 (0.0205)
11p gain	31 (6%)	482			0.0326 (0.0886)	0.00096 (0.00467)	0.026 (0.0757)	0.11 (0.224)	0.0115 (0.0405)	0.0121 (0.0415)	0.0933 (0.197)	0.0243 (0.0719)	0.407 (0.597)	0.00785 (0.029)
19p gain	100 (19%)	413	0.223 (0.388)	1 (1.00)	1e-05 (9.08e-05)	1e-05 (9.08e-05)	0.674 (0.857)	0.424 (0.615)	1e-05 (9.08e-05)	1e-05 (9.08e-05)	0.00027 (0.00161)	0.0396 (0.103)	0.235 (0.405)	0.00314 (0.0133)
13q loss	116 (23%)	397	0.181 (0.331)	3e-05 (0.000247)	2e-05 (0.000174)	0.00566 (0.022)	0.0249 (0.0729)	0.629 (0.808)	0.0679 (0.153)	0.0014 (0.00651)	0.0342 (0.0914)	0.0132 (0.0439)	0.3 (0.476)	0.239 (0.409)
1q gain	23 (4%)	490			0.00012 (0.000799)	0.00059 (0.00302)	0.435 (0.626)	0.608 (0.791)	7e-05 (0.000504)	0.00304 (0.013)	0.121 (0.239)	0.032 (0.0879)	0.0314 (0.0872)	0.0559 (0.134)
8q gain	56 (11%)	457	0.0527 (0.128)	0.404 (0.593)	1e-05 (9.08e-05)	7e-05 (0.000504)	0.0119 (0.0412)	0.0576 (0.136)	0.00205 (0.0091)	0.00053 (0.00277)	0.19 (0.343)	0.12 (0.237)	0.069 (0.154)	0.0148 (0.0485)
18p gain	17 (3%)	496			0.00012 (0.000799)	0.00433 (0.0176)	0.0232 (0.0692)	0.445 (0.637)	0.0124 (0.0421)	0.0132 (0.0439)	0.841 (0.999)	0.0906 (0.192)	0.612 (0.793)	0.0367 (0.0972)
18q gain	13 (3%)	500			0.00085 (0.00417)	0.00337 (0.0141)	0.0797 (0.174)	0.598 (0.784)	0.00027 (0.00161)	0.00043 (0.00232)	0.512 (0.7)	0.0172 (0.0544)	0.182 (0.331)	0.00413 (0.0169)
xq gain	40 (8%)	473			1e-05 (9.08e-05)	1e-05 (9.08e-05)	0.114 (0.23)	0.419 (0.61)	0.00011 (0.000769)	3e-05 (0.000247)	0.0153 (0.05)	0.414 (0.604)	0.531 (0.716)	0.0113 (0.0401)
3p loss	30 (6%)	483			0.00504 (0.0201)	0.0588 (0.137)	0.00659 (0.0249)	0.269 (0.438)	0.0268 (0.0772)	0.066 (0.15)	0.00109 (0.00519)	0.00044 (0.00236)	0.195 (0.35)	0.00311 (0.0133)
5q loss	33 (6%)	480	0.444 (0.637)	0.237 (0.407)	1e-05 (9.08e-05)	0.00012 (0.000799)	0.02 (0.0615)	0.118 (0.236)	0.0114 (0.0404)	1e-05 (9.08e-05)	0.00013 (0.000848)	0.161 (0.302)	0.811 (0.978)	0.608 (0.791)
8q loss	11 (2%)	502			0.00018 (0.00113)	2e-05 (0.000174)	0.0799 (0.174)	0.364 (0.554)	5e-05 (0.00038)	0.00052 (0.00273)	0.0514 (0.126)	0.00073 (0.00366)	0.369 (0.559)	0.0001 (0.000704)
9p loss	118 (23%)	395	0.383 (0.577)	0.265 (0.438)	1e-05 (9.08e-05)	0.00042 (0.00229)	0.0326 (0.0886)	0.0195 (0.0604)	0.104 (0.215)	0.0002 (0.00124)	0.893 (1.00)	0.22 (0.385)	0.283 (0.456)	0.0341 (0.0912)
16q loss	22 (4%)	491			0.00602 (0.0232)	0.00264 (0.0115)	0.376 (0.57)	0.0657 (0.15)	0.0485 (0.12)	0.0197 (0.0607)	0.666 (0.85)	0.00365 (0.0151)	0.291 (0.465)	0.00899 (0.033)
21q loss	36 (7%)	477	0.618 (0.798)	0.043 (0.109)	1e-05 (9.08e-05)	0.00033 (0.0019)	0.464 (0.654)	0.654 (0.836)	0.00068 (0.00342)	3e-05 (0.000247)	0.248 (0.422)	0.0272 (0.0779)	0.508 (0.697)	0.287 (0.461)
xq loss	71 (14%)	442	0.84 (0.999)	0.268 (0.438)	0.23 (0.398)	0.0201 (0.0618)	0.0716 (0.159)	0.0319 (0.0879)	0.00039 (0.00217)	1e-05 (9.08e-05)	6e-05 (0.000452)	0.26 (0.433)	0.0819 (0.177)	0.0228 (0.0684)
2p gain	14 (3%)	499			0.016 (0.0517)	0.0145 (0.0476)	0.309 (0.489)	0.343 (0.53)	0.0722 (0.16)	0.00164 (0.00738)	0.607 (0.791)	0.0212 (0.0643)	0.89 (1.00)	0.0403 (0.104)
2q gain	13 (3%)	500			0.0383 (0.101)	0.0105 (0.0377)	0.309 (0.489)	0.348 (0.535)	0.0821 (0.177)	0.00082 (0.00405)	0.51 (0.698)	0.0178 (0.0562)	0.684 (0.865)	0.0457 (0.114)
6p gain	7 (1%)	506			0.227 (0.393)	0.0469 (0.116)	0.0385 (0.101)	0.513 (0.701)	0.767 (0.938)	0.00482 (0.0194)	0.0221 (0.0666)	0.0637 (0.146)	0.573 (0.762)	0.0332 (0.0895)
22q gain	23 (4%)	490			0.0111 (0.0399)	3e-05 (0.000247)	1 (1.00)	0.686 (0.866)	0.001 (0.00484)	0.0004 (0.0022)	0.119 (0.237)	0.528 (0.713)	0.0423 (0.108)	0.223 (0.388)
6q loss	63 (12%)	450			0.00013 (0.000848)	0.00153 (0.00698)	0.25 (0.424)	0.565 (0.752)	0.09 (0.191)	0.052 (0.127)	0.00134 (0.00626)	0.172 (0.319)	0.0129 (0.0432)	0.00013 (0.000848)
12q loss	51 (10%)	462	1 (1.00)	0.582 (0.77)	1e-05 (9.08e-05)	1e-05 (9.08e-05)	0.681 (0.863)	0.11 (0.224)	0.00142 (0.00654)	1e-05 (9.08e-05)	0.00655 (0.0249)	0.33 (0.516)	0.836 (0.998)	0.81 (0.978)
15q loss	51 (10%)	462	1 (1.00)	0.707 (0.884)	0.0288 (0.0814)	0.00215 (0.0095)	0.273 (0.442)	0.0456 (0.114)	0.00165 (0.00739)	1e-05 (9.08e-05)	0.238 (0.408)	0.473 (0.661)	0.0581 (0.136)	0.0843 (0.181)
xp loss	100 (19%)	413	0.839 (0.999)	0.0667 (0.151)	0.00056 (0.00288)	0.0994 (0.209)	0.00803 (0.0296)	0.00366 (0.0151)	0.197 (0.352)	1e-05 (9.08e-05)	0.0244 (0.0719)	0.351 (0.537)	0.0686 (0.154)	0.186 (0.338)
4p gain	13 (3%)	500			0.00075 (0.00372)	0.00663 (0.025)	0.0326 (0.0886)	0.896 (1.00)	0.0609 (0.141)	0.0171 (0.0543)	0.192 (0.345)	0.104 (0.215)	0.336 (0.523)	0.276 (0.448)
4q gain	6 (1%)	507			0.0397 (0.103)	0.0186 (0.0581)	0.113 (0.228)	0.67 (0.853)	0.0116 (0.0406)	0.00943 (0.0345)	0.267 (0.438)	0.15 (0.285)	0.385 (0.578)	0.226 (0.393)
8p gain	46 (9%)	467			5e-05 (0.00038)	0.00141 (0.00653)	0.0637 (0.146)	0.162 (0.302)	0.033 (0.0892)	0.0133 (0.0439)	0.387 (0.58)	0.412 (0.604)	0.209 (0.368)	0.0714 (0.159)
9q gain	24 (5%)	489			0.0119 (0.041)	0.105 (0.216)	0.26 (0.433)	0.0552 (0.133)	0.0276 (0.0786)	0.00434 (0.0176)	0.433 (0.625)	0.0104 (0.0376)	0.586 (0.771)	0.173 (0.321)
10q gain	12 (2%)	501			0.00164 (0.00738)	0.0195 (0.0604)	0.269 (0.438)	0.516 (0.701)	0.397 (0.59)	5e-05 (0.00038)	0.0779 (0.172)	0.0323 (0.0883)	0.574 (0.762)	0.211 (0.371)
11q gain	58 (11%)	455	0.616 (0.797)	0.581 (0.769)	0.178 (0.327)	0.0103 (0.0372)	0.08 (0.174)	0.0307 (0.0859)	0.0794 (0.174)	0.0635 (0.146)	0.546 (0.732)	0.0463 (0.115)	0.651 (0.834)	0.0317 (0.0879)
12p gain	33 (6%)	480	0.752 (0.924)	0.584 (0.77)	0.00039 (0.00217)	0.032 (0.0879)	0.259 (0.432)	0.31 (0.49)	0.0894 (0.19)	0.0308 (0.086)	0.0865 (0.186)	0.0209 (0.0634)	0.188 (0.34)	0.553 (0.739)
15q gain	11 (2%)	502			0.00256 (0.0112)	0.0204 (0.0622)	0.0438 (0.11)	0.218 (0.382)	0.0372 (0.0981)	0.0626 (0.145)	0.177 (0.325)	0.287 (0.461)	0.475 (0.661)	0.0974 (0.205)
xp gain	21 (4%)	492			1e-05 (9.08e-05)	0.00015 (0.000953)	0.731 (0.905)	0.641 (0.823)	0.0469 (0.116)	0.0372 (0.0981)	0.467 (0.655)	0.578 (0.767)	0.688 (0.867)	0.257 (0.432)
2q loss	18 (4%)	495			0.0004 (0.0022)	0.00528 (0.0209)	0.0703 (0.157)	0.608 (0.791)	0.385 (0.578)	0.00148 (0.00679)	0.0263 (0.0763)	0.813 (0.979)	0.692 (0.87)	0.382 (0.576)
3q loss	28 (5%)	485	0.175 (0.322)	0.882 (1.00)	0.00714 (0.0266)	0.134 (0.262)	0.254 (0.428)	0.768 (0.938)	0.0557 (0.133)	0.031 (0.0864)	0.0886 (0.189)	0.0164 (0.0525)	0.268 (0.438)	0.0346 (0.0922)
5p loss	34 (7%)	479	0.743 (0.916)	0.0672 (0.152)	2e-05 (0.000174)	9e-05 (0.000639)	0.915 (1.00)	0.954 (1.00)	0.0401 (0.104)	0.0032 (0.0135)	0.106 (0.217)	0.388 (0.58)	0.735 (0.909)	0.324 (0.509)
18q loss	62 (12%)	451	0.343 (0.53)	0.151 (0.287)	0.045 (0.113)	0.0003 (0.00177)	0.287 (0.461)	0.097 (0.205)	0.018 (0.0563)	0.0157 (0.0509)	0.0578 (0.136)	0.711 (0.886)	0.423 (0.615)	0.533 (0.716)
2p loss	21 (4%)	492			0.00024 (0.00146)	0.0426 (0.109)	0.331 (0.517)	1 (1.00)	0.141 (0.272)	0.0418 (0.108)	0.0728 (0.161)	0.4 (0.592)	0.729 (0.904)	0.261 (0.434)
6p loss	30 (6%)	483			0.033 (0.0892)	0.0572 (0.136)	0.185 (0.337)	0.685 (0.866)	0.401 (0.592)	0.155 (0.292)	0.403 (0.593)	0.404 (0.593)	0.0125 (0.0423)	0.00274 (0.0118)
16p loss	14 (3%)	499			0.00543 (0.0213)	0.0429 (0.109)	0.866 (1.00)	0.203 (0.36)	0.108 (0.221)	0.023 (0.0689)	0.828 (0.991)	0.357 (0.544)	0.706 (0.884)	0.137 (0.265)
17p loss	13 (3%)	500			0.093 (0.197)	0.134 (0.262)	1 (1.00)	0.784 (0.954)	0.0123 (0.0419)	0.126 (0.248)	0.16 (0.299)	0.00615 (0.0236)	0.712 (0.886)	0.0114 (0.0404)
3q gain	8 (2%)	505			0.00198 (0.00883)	0.102 (0.212)	0.0564 (0.134)	0.368 (0.559)	0.0576 (0.136)	0.0046 (0.0186)	0.339 (0.526)	0.135 (0.262)	0.329 (0.515)	0.149 (0.284)
9p gain	17 (3%)	496			0.0161 (0.0517)	0.15 (0.285)	0.295 (0.47)	0.532 (0.716)	0.0553 (0.133)	0.0808 (0.175)	0.839 (0.999)	0.0278 (0.079)	0.861 (1.00)	0.205 (0.362)
12q gain	16 (3%)	497			0.00537 (0.0211)	0.102 (0.212)	0.295 (0.47)	0.533 (0.716)	0.015 (0.0491)	0.124 (0.245)	0.164 (0.305)	0.0589 (0.137)	0.12 (0.237)	0.0884 (0.189)
21q gain	24 (5%)	489			0.00642 (0.0246)	0.0121 (0.0415)	0.11 (0.224)	0.392 (0.584)	0.419 (0.61)	0.247 (0.42)	0.621 (0.8)	0.1 (0.209)	0.727 (0.903)	0.0812 (0.176)
9q loss	51 (10%)	462			0.155 (0.292)	0.461 (0.652)	0.62 (0.799)	0.339 (0.526)	0.456 (0.647)	0.0427 (0.109)	0.396 (0.589)	0.823 (0.988)	0.596 (0.782)	0.0339 (0.0912)
12p loss	26 (5%)	487			0.00414 (0.0169)	0.0634 (0.146)	0.602 (0.787)	1 (1.00)	0.145 (0.278)	0.00672 (0.0252)	0.0805 (0.175)	0.153 (0.289)	0.554 (0.739)	0.93 (1.00)
18p loss	68 (13%)	445	0.32 (0.504)	0.0306 (0.0859)	0.202 (0.358)	0.00154 (0.00699)	0.585 (0.771)	0.103 (0.214)	0.232 (0.401)	0.127 (0.249)	0.601 (0.786)	0.915 (1.00)	0.466 (0.655)	0.516 (0.701)
3p gain	11 (2%)	502			0.0665 (0.151)	0.324 (0.508)	0.464 (0.654)	0.202 (0.358)	0.321 (0.505)	0.0355 (0.0943)	0.119 (0.237)	0.29 (0.465)	0.742 (0.916)	0.197 (0.352)
16p gain	17 (3%)	496			0.491 (0.676)	0.745 (0.917)	0.562 (0.749)	0.698 (0.877)	0.0557 (0.133)	0.00039 (0.00217)	0.117 (0.234)	0.0595 (0.138)	0.11 (0.224)	0.516 (0.701)
16q gain	19 (4%)	494			0.267 (0.438)	0.317 (0.5)	0.466 (0.655)	0.515 (0.701)	0.249 (0.423)	0.00047 (0.00248)	0.0567 (0.135)	0.103 (0.214)	0.141 (0.272)	0.533 (0.716)
1q loss	25 (5%)	488	0.341 (0.527)	0.149 (0.285)	0.452 (0.643)	0.0626 (0.145)	0.474 (0.661)	0.462 (0.653)	0.267 (0.438)	0.0171 (0.0543)	0.0755 (0.167)	0.413 (0.604)	0.162 (0.302)	0.138 (0.268)
7p loss	3 (1%)	510			0.05 (0.123)	0.246 (0.42)			1 (1.00)	0.79 (0.96)	1 (1.00)	1 (1.00)
17q loss	8 (2%)	505			0.113 (0.228)	0.199 (0.356)	0.835 (0.998)	0.509 (0.697)	0.127 (0.249)	0.445 (0.637)	0.164 (0.304)	0.265 (0.438)	1 (1.00)	0.0234 (0.0694)
19p loss	25 (5%)	488	0.847 (1.00)	0.43 (0.621)	0.525 (0.711)	0.876 (1.00)	0.102 (0.212)	0.811 (0.978)	0.492 (0.676)	0.195 (0.351)	0.13 (0.254)	0.116 (0.233)	0.0265 (0.0767)	0.0555 (0.133)
20q loss	3 (1%)	510			0.254 (0.428)	0.443 (0.637)			0.0257 (0.0749)	0.0781 (0.172)	0.233 (0.402)	1 (1.00)	0.305 (0.484)	0.889 (1.00)
13q gain	6 (1%)	507			0.382 (0.576)	0.398 (0.59)	0.793 (0.961)	0.796 (0.964)	0.279 (0.451)	0.479 (0.665)	0.351 (0.537)	0.584 (0.77)	0.454 (0.645)	0.469 (0.656)
14q gain	4 (1%)	509			0.824 (0.988)	0.76 (0.932)			1 (1.00)	0.709 (0.886)	0.216 (0.379)	0.681 (0.863)	0.27 (0.439)	0.76 (0.932)
17p gain	20 (4%)	493			0.491 (0.676)	0.594 (0.781)	0.347 (0.533)	0.885 (1.00)	0.257 (0.432)	0.0641 (0.146)	0.19 (0.343)	0.483 (0.669)	0.687 (0.866)	0.654 (0.836)
17q gain	23 (4%)	490			0.681 (0.863)	0.449 (0.641)	0.345 (0.531)	0.887 (1.00)	0.391 (0.584)	0.256 (0.43)	0.107 (0.22)	0.699 (0.877)	0.424 (0.615)	0.362 (0.551)
7q loss	3 (1%)	510			0.0501 (0.123)	0.244 (0.416)			0.378 (0.571)	0.181 (0.331)	1 (1.00)	1 (1.00)
20p loss	7 (1%)	506			0.226 (0.393)	0.156 (0.294)	0.791 (0.96)	1 (1.00)	0.254 (0.428)	0.216 (0.379)	0.446 (0.637)	0.484 (0.67)	0.711 (0.886)	0.482 (0.668)

'1p gain' versus 'CN_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 9e-04

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
1P GAIN MUTATED	4	9	0
1P GAIN WILD-TYPE	168	111	221

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

'1p gain' versus 'METHLYATION_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 9e-04

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
1P GAIN MUTATED	5	8	0	0
1P GAIN WILD-TYPE	220	73	167	40

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

'1p gain' versus 'RPPA_CNMF'

P value = 0.0236 (Fisher's exact test), Q value = 0.07

Table S3. Gene #1: '1p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
1P GAIN MUTATED	1	5	1	0
1P GAIN WILD-TYPE	51	57	67	74

Figure S3. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'1p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S4. Gene #1: '1p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
1P GAIN MUTATED	0	13	0	0	0
1P GAIN WILD-TYPE	134	96	108	132	30

Figure S4. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S5. Gene #1: '1p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
1P GAIN MUTATED	0	8	0	0	0	5	0
1P GAIN WILD-TYPE	135	63	36	68	90	36	72

Figure S5. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p gain' versus 'MIRSEQ_CNMF'

P value = 0.00549 (Fisher's exact test), Q value = 0.021

Table S6. Gene #1: '1p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
1P GAIN MUTATED	8	4	1	0
1P GAIN WILD-TYPE	129	103	182	82

Figure S6. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S7. Gene #1: '1p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
1P GAIN MUTATED	3	0	10
1P GAIN WILD-TYPE	219	184	93

Figure S7. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0123 (Fisher's exact test), Q value = 0.042

Table S8. Gene #1: '1p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
1P GAIN MUTATED	10	1	2
1P GAIN WILD-TYPE	175	160	157

Figure S8. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'1p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 8e-04

Table S9. Gene #1: '1p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
1P GAIN MUTATED	1	2	1	9
1P GAIN WILD-TYPE	90	135	187	80

Figure S9. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1q gain' versus 'CN_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 8e-04

Table S10. Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
1Q GAIN MUTATED	6	14	3
1Q GAIN WILD-TYPE	166	106	218

Figure S10. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

'1q gain' versus 'METHLYATION_CNMF'

P value = 0.00059 (Fisher's exact test), Q value = 0.003

Table S11. Gene #2: '1q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
1Q GAIN MUTATED	9	11	2	1
1Q GAIN WILD-TYPE	216	70	165	39

Figure S11. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1q gain' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 5e-04

Table S12. Gene #2: '1q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
1Q GAIN MUTATED	2	14	0	5	2
1Q GAIN WILD-TYPE	132	95	108	127	28

Figure S12. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00304 (Fisher's exact test), Q value = 0.013

Table S13. Gene #2: '1q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
1Q GAIN MUTATED	3	9	1	2	1	5	2
1Q GAIN WILD-TYPE	132	62	35	66	89	36	70

Figure S13. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.032 (Fisher's exact test), Q value = 0.088

Table S14. Gene #2: '1q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
1Q GAIN MUTATED	7	6	10
1Q GAIN WILD-TYPE	215	178	93

Figure S14. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0314 (Fisher's exact test), Q value = 0.087

Table S15. Gene #2: '1q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
1Q GAIN MUTATED	12	2	9
1Q GAIN WILD-TYPE	173	159	150

Figure S15. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'2p gain' versus 'CN_CNMF'

P value = 0.016 (Fisher's exact test), Q value = 0.052

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
2P GAIN MUTATED	2	8	4
2P GAIN WILD-TYPE	170	112	217

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

'2p gain' versus 'METHLYATION_CNMF'

P value = 0.0145 (Fisher's exact test), Q value = 0.048

Table S17. Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
2P GAIN MUTATED	3	7	4	0
2P GAIN WILD-TYPE	222	74	163	40

Figure S17. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00164 (Fisher's exact test), Q value = 0.0074

Table S18. Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
2P GAIN MUTATED	0	5	1	2	2	4	0
2P GAIN WILD-TYPE	135	66	35	66	88	37	72

Figure S18. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0212 (Fisher's exact test), Q value = 0.064

Table S19. Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
2P GAIN MUTATED	5	2	7
2P GAIN WILD-TYPE	217	182	96

Figure S19. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0403 (Fisher's exact test), Q value = 0.1

Table S20. Gene #3: '2p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
2P GAIN MUTATED	1	5	2	6
2P GAIN WILD-TYPE	90	132	186	83

Figure S20. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q gain' versus 'CN_CNMF'

P value = 0.0383 (Fisher's exact test), Q value = 0.1

Table S21. Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
2Q GAIN MUTATED	2	7	4
2Q GAIN WILD-TYPE	170	113	217

Figure S21. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

'2q gain' versus 'METHLYATION_CNMF'

P value = 0.0105 (Fisher's exact test), Q value = 0.038

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
2Q GAIN MUTATED	3	7	3	0
2Q GAIN WILD-TYPE	222	74	164	40

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

'2q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00082 (Fisher's exact test), Q value = 0.004

Table S23. Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
2Q GAIN MUTATED	0	5	1	2	1	4	0
2Q GAIN WILD-TYPE	135	66	35	66	89	37	72

Figure S23. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0178 (Fisher's exact test), Q value = 0.056

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
2Q GAIN MUTATED	4	2	7
2Q GAIN WILD-TYPE	218	182	96

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

'2q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0457 (Fisher's exact test), Q value = 0.11

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
2Q GAIN MUTATED	1	4	2	6
2Q GAIN WILD-TYPE	90	133	186	83

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

'3p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0355 (Fisher's exact test), Q value = 0.094

Table S26. Gene #5: '3p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
3P GAIN MUTATED	2	4	2	0	0	2	1
3P GAIN WILD-TYPE	133	67	34	68	90	39	71

Figure S26. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3q gain' versus 'CN_CNMF'

P value = 0.00198 (Fisher's exact test), Q value = 0.0088

Table S27. Gene #6: '3q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
3Q GAIN MUTATED	0	6	2
3Q GAIN WILD-TYPE	172	114	219

Figure S27. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #3: 'CN_CNMF'

'3q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0046 (Fisher's exact test), Q value = 0.019

Table S28. Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
3Q GAIN MUTATED	0	4	1	0	0	2	1
3Q GAIN WILD-TYPE	135	67	35	68	90	39	71

Figure S28. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p gain' versus 'CN_CNMF'

P value = 0.00075 (Fisher's exact test), Q value = 0.0037

Table S29. Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
4P GAIN MUTATED	9	4	0
4P GAIN WILD-TYPE	163	116	221

Figure S29. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

'4p gain' versus 'METHLYATION_CNMF'

P value = 0.00663 (Fisher's exact test), Q value = 0.025

Table S30. Gene #7: '4p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
4P GAIN MUTATED	8	5	0	0
4P GAIN WILD-TYPE	217	76	167	40

Figure S30. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p gain' versus 'RPPA_CNMF'

P value = 0.0326 (Fisher's exact test), Q value = 0.089

Table S31. Gene #7: '4p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
4P GAIN MUTATED	2	5	0	1
4P GAIN WILD-TYPE	50	57	68	73

Figure S31. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'4p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0171 (Fisher's exact test), Q value = 0.054

Table S32. Gene #7: '4p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
4P GAIN MUTATED	4	5	0	0	0	3	1
4P GAIN WILD-TYPE	131	66	36	68	90	38	71

Figure S32. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q gain' versus 'CN_CNMF'

P value = 0.0397 (Fisher's exact test), Q value = 0.1

Table S33. Gene #8: '4q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
4Q GAIN MUTATED	3	3	0
4Q GAIN WILD-TYPE	169	117	221

Figure S33. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #3: 'CN_CNMF'

'4q gain' versus 'METHLYATION_CNMF'

P value = 0.0186 (Fisher's exact test), Q value = 0.058

Table S34. Gene #8: '4q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
4Q GAIN MUTATED	2	4	0	0
4Q GAIN WILD-TYPE	223	77	167	40

Figure S34. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q gain' versus 'MRNASEQ_CNMF'

P value = 0.0116 (Fisher's exact test), Q value = 0.041

Table S35. Gene #8: '4q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
4Q GAIN MUTATED	0	5	0	1	0
4Q GAIN WILD-TYPE	134	104	108	131	30

Figure S35. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00943 (Fisher's exact test), Q value = 0.034

Table S36. Gene #8: '4q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
4Q GAIN MUTATED	0	4	0	0	0	1	1
4Q GAIN WILD-TYPE	135	67	36	68	90	40	71

Figure S36. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5p gain' versus 'CN_CNMF'

P value = 0.00595 (Fisher's exact test), Q value = 0.023

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
5P GAIN MUTATED	3	7	1
5P GAIN WILD-TYPE	169	113	220

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

'5p gain' versus 'METHLYATION_CNMF'

P value = 0.0032 (Fisher's exact test), Q value = 0.013

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
5P GAIN MUTATED	4	6	0	1
5P GAIN WILD-TYPE	221	75	167	39

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

'5p gain' versus 'RPPA_CNMF'

P value = 0.0217 (Fisher's exact test), Q value = 0.066

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
5P GAIN MUTATED	0	3	0	0
5P GAIN WILD-TYPE	52	59	68	74

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

'5p gain' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 5e-04

Table S40. Gene #9: '5p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
5P GAIN MUTATED	0	9	0	1	1
5P GAIN WILD-TYPE	134	100	108	131	29

Figure S40. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00043 (Fisher's exact test), Q value = 0.0023

Table S41. Gene #9: '5p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
5P GAIN MUTATED	1	7	0	1	0	2	0
5P GAIN WILD-TYPE	134	64	36	67	90	39	72

Figure S41. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_CNMF'

P value = 0.0249 (Fisher's exact test), Q value = 0.073

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
5P GAIN MUTATED	5	5	1	0
5P GAIN WILD-TYPE	132	102	182	82

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

'5p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0271 (Fisher's exact test), Q value = 0.078

Table S43. Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
5P GAIN MUTATED	3	2	6
5P GAIN WILD-TYPE	219	182	97

Figure S43. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0159 (Fisher's exact test), Q value = 0.052

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
5P GAIN MUTATED	1	3	1	6
5P GAIN WILD-TYPE	90	134	187	83

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

'5q gain' versus 'CN_CNMF'

P value = 0.00486 (Fisher's exact test), Q value = 0.019

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
5Q GAIN MUTATED	1	6	1
5Q GAIN WILD-TYPE	171	114	220

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

'5q gain' versus 'METHLYATION_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.0015

Table S46. Gene #10: '5q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
5Q GAIN MUTATED	1	6	0	1
5Q GAIN WILD-TYPE	224	75	167	39

Figure S46. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5q gain' versus 'MRNASEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00064

Table S47. Gene #10: '5q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
5Q GAIN MUTATED	0	7	0	0	1
5Q GAIN WILD-TYPE	134	102	108	132	29

Figure S47. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 8e-04

Table S48. Gene #10: '5q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
5Q GAIN MUTATED	1	7	0	0	0	0	0
5Q GAIN WILD-TYPE	134	64	36	68	90	41	72

Figure S48. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_CNMF'

P value = 0.0129 (Fisher's exact test), Q value = 0.043

Table S49. Gene #10: '5q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
5Q GAIN MUTATED	5	3	0	0
5Q GAIN WILD-TYPE	132	104	183	82

Figure S49. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00075 (Fisher's exact test), Q value = 0.0037

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
5Q GAIN MUTATED	2	0	6
5Q GAIN WILD-TYPE	220	184	97

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

'5q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00769 (Fisher's exact test), Q value = 0.029

Table S51. Gene #10: '5q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
5Q GAIN MUTATED	7	1	0
5Q GAIN WILD-TYPE	178	160	159

Figure S51. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00045 (Fisher's exact test), Q value = 0.0024

Table S52. Gene #10: '5q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
5Q GAIN MUTATED	1	1	0	6
5Q GAIN WILD-TYPE	90	136	188	83

Figure S52. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p gain' versus 'METHLYATION_CNMF'

P value = 0.0469 (Fisher's exact test), Q value = 0.12

Table S53. Gene #11: '6p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
6P GAIN MUTATED	7	0	0	0
6P GAIN WILD-TYPE	218	81	167	40

Figure S53. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6p gain' versus 'RPPA_CNMF'

P value = 0.0385 (Fisher's exact test), Q value = 0.1

Table S54. Gene #11: '6p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
6P GAIN MUTATED	2	3	0	0
6P GAIN WILD-TYPE	50	59	68	74

Figure S54. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'6p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00482 (Fisher's exact test), Q value = 0.019

Table S55. Gene #11: '6p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
6P GAIN MUTATED	2	0	0	1	0	4	0
6P GAIN WILD-TYPE	133	71	36	67	90	37	72

Figure S55. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_CNMF'

P value = 0.0221 (Fisher's exact test), Q value = 0.067

Table S56. Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
6P GAIN MUTATED	4	3	0	0
6P GAIN WILD-TYPE	133	104	183	82

Figure S56. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0332 (Fisher's exact test), Q value = 0.089

Table S57. Gene #11: '6p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
6P GAIN MUTATED	4	0	2	1
6P GAIN WILD-TYPE	87	137	186	88

Figure S57. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S58. Gene #12: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
7P GAIN MUTATED	20	91	10
7P GAIN WILD-TYPE	152	29	211

Figure S58. Get High-res Image Gene #12: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S59. Gene #12: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
7P GAIN MUTATED	40	57	16	8
7P GAIN WILD-TYPE	185	24	151	32

Figure S59. Get High-res Image Gene #12: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p gain' versus 'RPPA_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.0025

Table S60. Gene #12: '7p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
7P GAIN MUTATED	11	27	12	10
7P GAIN WILD-TYPE	41	35	56	64

Figure S60. Get High-res Image Gene #12: '7p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'7p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0118 (Fisher's exact test), Q value = 0.041

Table S61. Gene #12: '7p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	131	58
7P GAIN MUTATED	15	39	6
7P GAIN WILD-TYPE	52	92	52

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

'7p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S62. Gene #12: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
7P GAIN MUTATED	22	58	11	24	6
7P GAIN WILD-TYPE	112	51	97	108	24

Figure S62. Get High-res Image Gene #12: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S63. Gene #12: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
7P GAIN MUTATED	19	51	3	27	8	8	5
7P GAIN WILD-TYPE	116	20	33	41	82	33	67

Figure S63. Get High-res Image Gene #12: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_CNMF'

P value = 0.00264 (Fisher's exact test), Q value = 0.011

Table S64. Gene #12: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
7P GAIN MUTATED	42	33	30	14
7P GAIN WILD-TYPE	95	74	153	68

Figure S64. Get High-res Image Gene #12: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S65. Gene #12: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
7P GAIN MUTATED	38	26	55
7P GAIN WILD-TYPE	184	158	48

Figure S65. Get High-res Image Gene #12: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.0021

Table S66. Gene #12: '7p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
7P GAIN MUTATED	61	25	32
7P GAIN WILD-TYPE	124	136	127

Figure S66. Get High-res Image Gene #12: '7p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S67. Gene #12: '7p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
7P GAIN MUTATED	13	22	32	51
7P GAIN WILD-TYPE	78	115	156	38

Figure S67. Get High-res Image Gene #12: '7p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S68. Gene #13: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
7Q GAIN MUTATED	33	99	19
7Q GAIN WILD-TYPE	139	21	202

Figure S68. Get High-res Image Gene #13: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S69. Gene #13: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
7Q GAIN MUTATED	58	60	24	9
7Q GAIN WILD-TYPE	167	21	143	31

Figure S69. Get High-res Image Gene #13: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7q gain' versus 'RPPA_CNMF'

P value = 0.00403 (Fisher's exact test), Q value = 0.017

Table S70. Gene #13: '7q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
7Q GAIN MUTATED	16	30	14	18
7Q GAIN WILD-TYPE	36	32	54	56

Figure S70. Get High-res Image Gene #13: '7q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S71. Gene #13: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
7Q GAIN MUTATED	37	60	14	32	8
7Q GAIN WILD-TYPE	97	49	94	100	22

Figure S71. Get High-res Image Gene #13: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S72. Gene #13: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
7Q GAIN MUTATED	32	54	4	30	12	7	12
7Q GAIN WILD-TYPE	103	17	32	38	78	34	60

Figure S72. Get High-res Image Gene #13: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_CNMF'

P value = 0.00332 (Fisher's exact test), Q value = 0.014

Table S73. Gene #13: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
7Q GAIN MUTATED	49	41	43	16
7Q GAIN WILD-TYPE	88	66	140	66

Figure S73. Get High-res Image Gene #13: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S74. Gene #13: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
7Q GAIN MUTATED	51	39	59
7Q GAIN WILD-TYPE	171	145	44

Figure S74. Get High-res Image Gene #13: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00056 (Fisher's exact test), Q value = 0.0029

Table S75. Gene #13: '7q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
7Q GAIN MUTATED	71	32	45
7Q GAIN WILD-TYPE	114	129	114

Figure S75. Get High-res Image Gene #13: '7q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S76. Gene #13: '7q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
7Q GAIN MUTATED	19	29	45	55
7Q GAIN WILD-TYPE	72	108	143	34

Figure S76. Get High-res Image Gene #13: '7q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00038

Table S77. Gene #14: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
8P GAIN MUTATED	28	10	8
8P GAIN WILD-TYPE	144	110	213

Figure S77. Get High-res Image Gene #14: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

'8p gain' versus 'METHLYATION_CNMF'

P value = 0.00141 (Fisher's exact test), Q value = 0.0065

Table S78. Gene #14: '8p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
8P GAIN MUTATED	33	4	8	1
8P GAIN WILD-TYPE	192	77	159	39

Figure S78. Get High-res Image Gene #14: '8p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p gain' versus 'MRNASEQ_CNMF'

P value = 0.033 (Fisher's exact test), Q value = 0.089

Table S79. Gene #14: '8p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
8P GAIN MUTATED	21	7	5	10	3
8P GAIN WILD-TYPE	113	102	103	122	27

Figure S79. Get High-res Image Gene #14: '8p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0133 (Fisher's exact test), Q value = 0.044

Table S80. Gene #14: '8p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
8P GAIN MUTATED	22	3	2	7	3	5	4
8P GAIN WILD-TYPE	113	68	34	61	87	36	68

Figure S80. Get High-res Image Gene #14: '8p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S81. Gene #15: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
8Q GAIN MUTATED	35	13	8
8Q GAIN WILD-TYPE	137	107	213

Figure S81. Get High-res Image Gene #15: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 5e-04

Table S82. Gene #15: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
8Q GAIN MUTATED	41	4	8	3
8Q GAIN WILD-TYPE	184	77	159	37

Figure S82. Get High-res Image Gene #15: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8q gain' versus 'RPPA_CNMF'

P value = 0.0119 (Fisher's exact test), Q value = 0.041

Table S83. Gene #15: '8q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
8Q GAIN MUTATED	10	8	10	2
8Q GAIN WILD-TYPE	42	54	58	72

Figure S83. Get High-res Image Gene #15: '8q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 0.00205 (Fisher's exact test), Q value = 0.0091

Table S84. Gene #15: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
8Q GAIN MUTATED	27	8	5	13	3
8Q GAIN WILD-TYPE	107	101	103	119	27

Figure S84. Get High-res Image Gene #15: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00053 (Fisher's exact test), Q value = 0.0028

Table S85. Gene #15: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
8Q GAIN MUTATED	27	3	2	10	3	6	5
8Q GAIN WILD-TYPE	108	68	34	58	87	35	67

Figure S85. Get High-res Image Gene #15: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0148 (Fisher's exact test), Q value = 0.049

Table S86. Gene #15: '8q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
8Q GAIN MUTATED	19	12	18	6
8Q GAIN WILD-TYPE	72	125	170	83

Figure S86. Get High-res Image Gene #15: '8q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p gain' versus 'CN_CNMF'

P value = 0.0161 (Fisher's exact test), Q value = 0.052

Table S87. Gene #16: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
9P GAIN MUTATED	9	6	2
9P GAIN WILD-TYPE	163	114	219

Figure S87. Get High-res Image Gene #16: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'

'9p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0278 (Fisher's exact test), Q value = 0.079

Table S88. Gene #16: '9p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
9P GAIN MUTATED	4	5	8
9P GAIN WILD-TYPE	218	179	95

Figure S88. Get High-res Image Gene #16: '9p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9q gain' versus 'CN_CNMF'

P value = 0.0119 (Fisher's exact test), Q value = 0.041

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
9Q GAIN MUTATED	10	10	4
9Q GAIN WILD-TYPE	162	110	217

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

'9q gain' versus 'MRNASEQ_CNMF'

P value = 0.0276 (Fisher's exact test), Q value = 0.079

Table S90. Gene #17: '9q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
9Q GAIN MUTATED	3	12	3	5	1
9Q GAIN WILD-TYPE	131	97	105	127	29

Figure S90. Get High-res Image Gene #17: '9q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00434 (Fisher's exact test), Q value = 0.018

Table S91. Gene #17: '9q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
9Q GAIN MUTATED	3	5	1	5	2	7	1
9Q GAIN WILD-TYPE	132	66	35	63	88	34	71

Figure S91. Get High-res Image Gene #17: '9q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0104 (Fisher's exact test), Q value = 0.038

Table S92. Gene #17: '9q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
9Q GAIN MUTATED	6	7	11
9Q GAIN WILD-TYPE	216	177	92

Figure S92. Get High-res Image Gene #17: '9q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0419 (Fisher's exact test), Q value = 0.11

Table S93. Gene #18: '10p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	7	7	6
10P GAIN MUTATED	0	3	0	0
10P GAIN WILD-TYPE	7	4	7	6

Figure S93. Get High-res Image Gene #18: '10p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'10p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S94. Gene #18: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
10P GAIN MUTATED	46	6	5
10P GAIN WILD-TYPE	126	114	216

Figure S94. Get High-res Image Gene #18: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

'10p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S95. Gene #18: '10p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
10P GAIN MUTATED	53	3	0	1
10P GAIN WILD-TYPE	172	78	167	39

Figure S95. Get High-res Image Gene #18: '10p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p gain' versus 'RPPA_CNMF'

P value = 0.0204 (Fisher's exact test), Q value = 0.062

Table S96. Gene #18: '10p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
10P GAIN MUTATED	11	5	8	3
10P GAIN WILD-TYPE	41	57	60	71

Figure S96. Get High-res Image Gene #18: '10p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'10p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S97. Gene #18: '10p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
10P GAIN MUTATED	29	12	1	13	2
10P GAIN WILD-TYPE	105	97	107	119	28

Figure S97. Get High-res Image Gene #18: '10p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S98. Gene #18: '10p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
10P GAIN MUTATED	29	0	0	11	0	14	3
10P GAIN WILD-TYPE	106	71	36	57	90	27	69

Figure S98. Get High-res Image Gene #18: '10p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00516 (Fisher's exact test), Q value = 0.02

Table S99. Gene #18: '10p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
10P GAIN MUTATED	20	15	14	7
10P GAIN WILD-TYPE	71	122	174	82

Figure S99. Get High-res Image Gene #18: '10p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q gain' versus 'CN_CNMF'

P value = 0.00164 (Fisher's exact test), Q value = 0.0074

Table S100. Gene #19: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
10Q GAIN MUTATED	10	1	1
10Q GAIN WILD-TYPE	162	119	220

Figure S100. Get High-res Image Gene #19: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

'10q gain' versus 'METHLYATION_CNMF'

P value = 0.0195 (Fisher's exact test), Q value = 0.06

Table S101. Gene #19: '10q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
10Q GAIN MUTATED	9	3	0	0
10Q GAIN WILD-TYPE	216	78	167	40

Figure S101. Get High-res Image Gene #19: '10q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00038

Table S102. Gene #19: '10q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
10Q GAIN MUTATED	2	0	0	4	0	6	0
10Q GAIN WILD-TYPE	133	71	36	64	90	35	72

Figure S102. Get High-res Image Gene #19: '10q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0323 (Fisher's exact test), Q value = 0.088

Table S103. Gene #19: '10q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
10Q GAIN MUTATED	2	4	6
10Q GAIN WILD-TYPE	220	180	97

Figure S103. Get High-res Image Gene #19: '10q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11p gain' versus 'CN_CNMF'

P value = 0.0326 (Fisher's exact test), Q value = 0.089

Table S104. Gene #20: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
11P GAIN MUTATED	5	6	20
11P GAIN WILD-TYPE	167	114	201

Figure S104. Get High-res Image Gene #20: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

'11p gain' versus 'METHLYATION_CNMF'

P value = 0.00096 (Fisher's exact test), Q value = 0.0047

Table S105. Gene #20: '11p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
11P GAIN MUTATED	10	1	20	0
11P GAIN WILD-TYPE	215	80	147	40

Figure S105. Get High-res Image Gene #20: '11p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p gain' versus 'RPPA_CNMF'

P value = 0.026 (Fisher's exact test), Q value = 0.076

Table S106. Gene #20: '11p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
11P GAIN MUTATED	0	3	9	5
11P GAIN WILD-TYPE	52	59	59	69

Figure S106. Get High-res Image Gene #20: '11p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'11p gain' versus 'MRNASEQ_CNMF'

P value = 0.0115 (Fisher's exact test), Q value = 0.041

Table S107. Gene #20: '11p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
11P GAIN MUTATED	8	1	13	7	2
11P GAIN WILD-TYPE	126	108	95	125	28

Figure S107. Get High-res Image Gene #20: '11p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0121 (Fisher's exact test), Q value = 0.041

Table S108. Gene #20: '11p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
11P GAIN MUTATED	7	0	6	3	9	1	5
11P GAIN WILD-TYPE	128	71	30	65	81	40	67

Figure S108. Get High-res Image Gene #20: '11p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0243 (Fisher's exact test), Q value = 0.072

Table S109. Gene #20: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
11P GAIN MUTATED	15	15	1
11P GAIN WILD-TYPE	207	169	102

Figure S109. Get High-res Image Gene #20: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00785 (Fisher's exact test), Q value = 0.029

Table S110. Gene #20: '11p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
11P GAIN MUTATED	4	10	17	0
11P GAIN WILD-TYPE	87	127	171	89

Figure S110. Get High-res Image Gene #20: '11p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q gain' versus 'METHLYATION_CNMF'

P value = 0.0103 (Fisher's exact test), Q value = 0.037

Table S111. Gene #21: '11q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
11Q GAIN MUTATED	30	3	24	1
11Q GAIN WILD-TYPE	195	78	143	39

Figure S111. Get High-res Image Gene #21: '11q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0307 (Fisher's exact test), Q value = 0.086

Table S112. Gene #21: '11q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	131	58
11Q GAIN MUTATED	2	19	7
11Q GAIN WILD-TYPE	65	112	51

Figure S112. Get High-res Image Gene #21: '11q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0463 (Fisher's exact test), Q value = 0.12

Table S113. Gene #21: '11q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
11Q GAIN MUTATED	30	23	5
11Q GAIN WILD-TYPE	192	161	98

Figure S113. Get High-res Image Gene #21: '11q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0317 (Fisher's exact test), Q value = 0.088

Table S114. Gene #21: '11q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
11Q GAIN MUTATED	10	18	27	3
11Q GAIN WILD-TYPE	81	119	161	86

Figure S114. Get High-res Image Gene #21: '11q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12p gain' versus 'CN_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.0022

Table S115. Gene #22: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
12P GAIN MUTATED	18	11	4
12P GAIN WILD-TYPE	154	109	217

Figure S115. Get High-res Image Gene #22: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 0.032 (Fisher's exact test), Q value = 0.088

Table S116. Gene #22: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
12P GAIN MUTATED	21	6	4	2
12P GAIN WILD-TYPE	204	75	163	38

Figure S116. Get High-res Image Gene #22: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0308 (Fisher's exact test), Q value = 0.086

Table S117. Gene #22: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
12P GAIN MUTATED	13	6	1	6	3	4	0
12P GAIN WILD-TYPE	122	65	35	62	87	37	72

Figure S117. Get High-res Image Gene #22: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0209 (Fisher's exact test), Q value = 0.063

Table S118. Gene #22: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
12P GAIN MUTATED	18	5	10
12P GAIN WILD-TYPE	204	179	93

Figure S118. Get High-res Image Gene #22: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12q gain' versus 'CN_CNMF'

P value = 0.00537 (Fisher's exact test), Q value = 0.021

Table S119. Gene #23: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
12Q GAIN MUTATED	5	9	2
12Q GAIN WILD-TYPE	167	111	219

Figure S119. Get High-res Image Gene #23: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

'12q gain' versus 'MRNASEQ_CNMF'

P value = 0.015 (Fisher's exact test), Q value = 0.049

Table S120. Gene #23: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
12Q GAIN MUTATED	4	8	3	0	1
12Q GAIN WILD-TYPE	130	101	105	132	29

Figure S120. Get High-res Image Gene #23: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q gain' versus 'CN_CNMF'

P value = 0.00256 (Fisher's exact test), Q value = 0.011

Table S121. Gene #26: '15q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
15Q GAIN MUTATED	6	5	0
15Q GAIN WILD-TYPE	166	115	221

Figure S121. Get High-res Image Gene #26: '15q gain' versus Molecular Subtype #3: 'CN_CNMF'

'15q gain' versus 'METHLYATION_CNMF'

P value = 0.0204 (Fisher's exact test), Q value = 0.062

Table S122. Gene #26: '15q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
15Q GAIN MUTATED	7	4	0	0
15Q GAIN WILD-TYPE	218	77	167	40

Figure S122. Get High-res Image Gene #26: '15q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'15q gain' versus 'RPPA_CNMF'

P value = 0.0438 (Fisher's exact test), Q value = 0.11

Table S123. Gene #26: '15q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
15Q GAIN MUTATED	0	4	2	0
15Q GAIN WILD-TYPE	52	58	66	74

Figure S123. Get High-res Image Gene #26: '15q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'15q gain' versus 'MRNASEQ_CNMF'

P value = 0.0372 (Fisher's exact test), Q value = 0.098

Table S124. Gene #26: '15q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
15Q GAIN MUTATED	4	6	0	1	0
15Q GAIN WILD-TYPE	130	103	108	131	30

Figure S124. Get High-res Image Gene #26: '15q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00039 (Fisher's exact test), Q value = 0.0022

Table S125. Gene #27: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
16P GAIN MUTATED	1	1	2	3	1	7	2
16P GAIN WILD-TYPE	134	70	34	65	89	34	70

Figure S125. Get High-res Image Gene #27: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00047 (Fisher's exact test), Q value = 0.0025

Table S126. Gene #28: '16q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
16Q GAIN MUTATED	2	1	1	3	1	8	3
16Q GAIN WILD-TYPE	133	70	35	65	89	33	69

Figure S126. Get High-res Image Gene #28: '16q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p gain' versus 'CN_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 8e-04

Table S127. Gene #31: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
18P GAIN MUTATED	10	7	0
18P GAIN WILD-TYPE	162	113	221

Figure S127. Get High-res Image Gene #31: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 0.00433 (Fisher's exact test), Q value = 0.018

Table S128. Gene #31: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
18P GAIN MUTATED	11	5	0	1
18P GAIN WILD-TYPE	214	76	167	39

Figure S128. Get High-res Image Gene #31: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p gain' versus 'RPPA_CNMF'

P value = 0.0232 (Fisher's exact test), Q value = 0.069

Table S129. Gene #31: '18p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
18P GAIN MUTATED	3	5	1	0
18P GAIN WILD-TYPE	49	57	67	74

Figure S129. Get High-res Image Gene #31: '18p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'18p gain' versus 'MRNASEQ_CNMF'

P value = 0.0124 (Fisher's exact test), Q value = 0.042

Table S130. Gene #31: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
18P GAIN MUTATED	3	9	0	4	1
18P GAIN WILD-TYPE	131	100	108	128	29

Figure S130. Get High-res Image Gene #31: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0132 (Fisher's exact test), Q value = 0.044

Table S131. Gene #31: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
18P GAIN MUTATED	4	4	0	3	0	5	1
18P GAIN WILD-TYPE	131	67	36	65	90	36	71

Figure S131. Get High-res Image Gene #31: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0367 (Fisher's exact test), Q value = 0.097

Table S132. Gene #31: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
18P GAIN MUTATED	2	7	2	6
18P GAIN WILD-TYPE	89	130	186	83

Figure S132. Get High-res Image Gene #31: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q gain' versus 'CN_CNMF'

P value = 0.00085 (Fisher's exact test), Q value = 0.0042

Table S133. Gene #32: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
18Q GAIN MUTATED	7	6	0
18Q GAIN WILD-TYPE	165	114	221

Figure S133. Get High-res Image Gene #32: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

'18q gain' versus 'METHLYATION_CNMF'

P value = 0.00337 (Fisher's exact test), Q value = 0.014

Table S134. Gene #32: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
18Q GAIN MUTATED	6	6	0	1
18Q GAIN WILD-TYPE	219	75	167	39

Figure S134. Get High-res Image Gene #32: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q gain' versus 'MRNASEQ_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.0016

Table S135. Gene #32: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
18Q GAIN MUTATED	2	10	0	1	0
18Q GAIN WILD-TYPE	132	99	108	131	30

Figure S135. Get High-res Image Gene #32: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00043 (Fisher's exact test), Q value = 0.0023

Table S136. Gene #32: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
18Q GAIN MUTATED	2	5	0	0	0	5	1
18Q GAIN WILD-TYPE	133	66	36	68	90	36	71

Figure S136. Get High-res Image Gene #32: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0172 (Fisher's exact test), Q value = 0.054

Table S137. Gene #32: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
18Q GAIN MUTATED	4	2	7
18Q GAIN WILD-TYPE	218	182	96

Figure S137. Get High-res Image Gene #32: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00413 (Fisher's exact test), Q value = 0.017

Table S138. Gene #32: '18q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
18Q GAIN MUTATED	1	4	1	7
18Q GAIN WILD-TYPE	90	133	187	82

Figure S138. Get High-res Image Gene #32: '18q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S139. Gene #33: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
19P GAIN MUTATED	6	37	57
19P GAIN WILD-TYPE	166	83	164

Figure S139. Get High-res Image Gene #33: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

'19p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S140. Gene #33: '19p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
19P GAIN MUTATED	10	27	60	3
19P GAIN WILD-TYPE	215	54	107	37

Figure S140. Get High-res Image Gene #33: '19p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S141. Gene #33: '19p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
19P GAIN MUTATED	5	29	43	22	1
19P GAIN WILD-TYPE	129	80	65	110	29

Figure S141. Get High-res Image Gene #33: '19p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S142. Gene #33: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
19P GAIN MUTATED	6	25	15	7	29	3	15
19P GAIN WILD-TYPE	129	46	21	61	61	38	57

Figure S142. Get High-res Image Gene #33: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.0016

Table S143. Gene #33: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
19P GAIN MUTATED	18	18	33	31
19P GAIN WILD-TYPE	119	89	150	51

Figure S143. Get High-res Image Gene #33: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0396 (Fisher's exact test), Q value = 0.1

Table S144. Gene #33: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
19P GAIN MUTATED	34	38	28
19P GAIN WILD-TYPE	188	146	75

Figure S144. Get High-res Image Gene #33: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00314 (Fisher's exact test), Q value = 0.013

Table S145. Gene #33: '19p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
19P GAIN MUTATED	8	32	34	26
19P GAIN WILD-TYPE	83	105	154	63

Figure S145. Get High-res Image Gene #33: '19p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S146. Gene #34: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
19Q GAIN MUTATED	2	23	0
19Q GAIN WILD-TYPE	170	97	221

Figure S146. Get High-res Image Gene #34: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

'19q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S147. Gene #34: '19q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
19Q GAIN MUTATED	2	21	0	2
19Q GAIN WILD-TYPE	223	60	167	38

Figure S147. Get High-res Image Gene #34: '19q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S148. Gene #34: '19q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
19Q GAIN MUTATED	1	19	0	4	1
19Q GAIN WILD-TYPE	133	90	108	128	29

Figure S148. Get High-res Image Gene #34: '19q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S149. Gene #34: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
19Q GAIN MUTATED	2	19	0	4	0	0	0
19Q GAIN WILD-TYPE	133	52	36	64	90	41	72

Figure S149. Get High-res Image Gene #34: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_CNMF'

P value = 0.00235 (Fisher's exact test), Q value = 0.01

Table S150. Gene #34: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
19Q GAIN MUTATED	7	12	6	0
19Q GAIN WILD-TYPE	130	95	177	82

Figure S150. Get High-res Image Gene #34: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S151. Gene #34: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
19Q GAIN MUTATED	3	2	20
19Q GAIN WILD-TYPE	219	182	83

Figure S151. Get High-res Image Gene #34: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S152. Gene #34: '19q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
19Q GAIN MUTATED	20	0	5
19Q GAIN WILD-TYPE	165	161	154

Figure S152. Get High-res Image Gene #34: '19q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S153. Gene #34: '19q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
19Q GAIN MUTATED	2	0	2	21
19Q GAIN WILD-TYPE	89	137	186	68

Figure S153. Get High-res Image Gene #34: '19q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S154. Gene #35: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
20P GAIN MUTATED	7	31	5
20P GAIN WILD-TYPE	165	89	216

Figure S154. Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S155. Gene #35: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
20P GAIN MUTATED	8	27	6	2
20P GAIN WILD-TYPE	217	54	161	38

Figure S155. Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p gain' versus 'RPPA_CNMF'

P value = 6e-04 (Fisher's exact test), Q value = 0.0031

Table S156. Gene #35: '20p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
20P GAIN MUTATED	2	14	2	5
20P GAIN WILD-TYPE	50	48	66	69

Figure S156. Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S157. Gene #35: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
20P GAIN MUTATED	3	27	4	8	1
20P GAIN WILD-TYPE	131	82	104	124	29

Figure S157. Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S158. Gene #35: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
20P GAIN MUTATED	3	22	2	8	2	4	2
20P GAIN WILD-TYPE	132	49	34	60	88	37	70

Figure S158. Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S159. Gene #35: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
20P GAIN MUTATED	8	10	25
20P GAIN WILD-TYPE	214	174	78

Figure S159. Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00105 (Fisher's exact test), Q value = 0.005

Table S160. Gene #35: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
20P GAIN MUTATED	26	5	12
20P GAIN WILD-TYPE	159	156	147

Figure S160. Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S161. Gene #35: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
20P GAIN MUTATED	3	5	10	25
20P GAIN WILD-TYPE	88	132	178	64

Figure S161. Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S162. Gene #36: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
20Q GAIN MUTATED	7	31	5
20Q GAIN WILD-TYPE	165	89	216

Figure S162. Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S163. Gene #36: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
20Q GAIN MUTATED	8	28	6	1
20Q GAIN WILD-TYPE	217	53	161	39

Figure S163. Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q gain' versus 'RPPA_CNMF'

P value = 0.00066 (Fisher's exact test), Q value = 0.0033

Table S164. Gene #36: '20q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
20Q GAIN MUTATED	5	14	2	3
20Q GAIN WILD-TYPE	47	48	66	71

Figure S164. Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S165. Gene #36: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
20Q GAIN MUTATED	4	28	4	6	1
20Q GAIN WILD-TYPE	130	81	104	126	29

Figure S165. Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S166. Gene #36: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
20Q GAIN MUTATED	4	23	2	7	2	4	1
20Q GAIN WILD-TYPE	131	48	34	61	88	37	71

Figure S166. Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S167. Gene #36: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
20Q GAIN MUTATED	10	8	25
20Q GAIN WILD-TYPE	212	176	78

Figure S167. Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00025

Table S168. Gene #36: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
20Q GAIN MUTATED	29	4	10
20Q GAIN WILD-TYPE	156	157	149

Figure S168. Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S169. Gene #36: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
20Q GAIN MUTATED	6	4	8	25
20Q GAIN WILD-TYPE	85	133	180	64

Figure S169. Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q gain' versus 'CN_CNMF'

P value = 0.00642 (Fisher's exact test), Q value = 0.025

Table S170. Gene #37: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
21Q GAIN MUTATED	3	12	9
21Q GAIN WILD-TYPE	169	108	212

Figure S170. Get High-res Image Gene #37: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

'21q gain' versus 'METHLYATION_CNMF'

P value = 0.0121 (Fisher's exact test), Q value = 0.041

Table S171. Gene #37: '21q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
21Q GAIN MUTATED	6	9	9	0
21Q GAIN WILD-TYPE	219	72	158	40

Figure S171. Get High-res Image Gene #37: '21q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q gain' versus 'CN_CNMF'

P value = 0.0111 (Fisher's exact test), Q value = 0.04

Table S172. Gene #38: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
22Q GAIN MUTATED	3	3	17
22Q GAIN WILD-TYPE	169	117	204

Figure S172. Get High-res Image Gene #38: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

'22q gain' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00025

Table S173. Gene #38: '22q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
22Q GAIN MUTATED	2	3	18	0
22Q GAIN WILD-TYPE	223	78	149	40

Figure S173. Get High-res Image Gene #38: '22q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q gain' versus 'MRNASEQ_CNMF'

P value = 0.001 (Fisher's exact test), Q value = 0.0048

Table S174. Gene #38: '22q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
22Q GAIN MUTATED	1	4	13	5	0
22Q GAIN WILD-TYPE	133	105	95	127	30

Figure S174. Get High-res Image Gene #38: '22q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-04 (Fisher's exact test), Q value = 0.0022

Table S175. Gene #38: '22q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
22Q GAIN MUTATED	0	2	6	2	7	2	4
22Q GAIN WILD-TYPE	135	69	30	66	83	39	68

Figure S175. Get High-res Image Gene #38: '22q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0423 (Fisher's exact test), Q value = 0.11

Table S176. Gene #38: '22q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
22Q GAIN MUTATED	3	10	10
22Q GAIN WILD-TYPE	182	151	149

Figure S176. Get High-res Image Gene #38: '22q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'xp gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S177. Gene #39: 'xp gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
XP GAIN MUTATED	15	6	0
XP GAIN WILD-TYPE	157	114	221

Figure S177. Get High-res Image Gene #39: 'xp gain' versus Molecular Subtype #3: 'CN_CNMF'

'xp gain' versus 'METHLYATION_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.00095

Table S178. Gene #39: 'xp gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
XP GAIN MUTATED	18	3	0	0
XP GAIN WILD-TYPE	207	78	167	40

Figure S178. Get High-res Image Gene #39: 'xp gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xp gain' versus 'MRNASEQ_CNMF'

P value = 0.0469 (Fisher's exact test), Q value = 0.12

Table S179. Gene #39: 'xp gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
XP GAIN MUTATED	9	4	0	7	1
XP GAIN WILD-TYPE	125	105	108	125	29

Figure S179. Get High-res Image Gene #39: 'xp gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'xp gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0372 (Fisher's exact test), Q value = 0.098

Table S180. Gene #39: 'xp gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
XP GAIN MUTATED	9	2	0	6	0	2	2
XP GAIN WILD-TYPE	126	69	36	62	90	39	70

Figure S180. Get High-res Image Gene #39: 'xp gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xq gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S181. Gene #40: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
XQ GAIN MUTATED	30	7	3
XQ GAIN WILD-TYPE	142	113	218

Figure S181. Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

'xq gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S182. Gene #40: 'xq gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
XQ GAIN MUTATED	34	4	0	2
XQ GAIN WILD-TYPE	191	77	167	38

Figure S182. Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xq gain' versus 'MRNASEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00077

Table S183. Gene #40: 'xq gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
XQ GAIN MUTATED	18	7	0	10	5
XQ GAIN WILD-TYPE	116	102	108	122	25

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

'xq gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00025

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
XQ GAIN MUTATED	23	3	0	7	0	4	3
XQ GAIN WILD-TYPE	112	68	36	61	90	37	69

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

'xq gain' versus 'MIRSEQ_CNMF'

P value = 0.0153 (Fisher's exact test), Q value = 0.05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
XQ GAIN MUTATED	17	9	12	1
XQ GAIN WILD-TYPE	120	98	171	81

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

'xq gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0113 (Fisher's exact test), Q value = 0.04

Table S186. Gene #40: 'xq gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
XQ GAIN MUTATED	15	6	13	5
XQ GAIN WILD-TYPE	76	131	175	84

Figure S186. Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1p loss' versus 'MRNA_CNMF'

P value = 0.0285 (Fisher's exact test), Q value = 0.081

Table S187. Gene #41: '1p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	9	10	8
1P LOSS MUTATED	1	7	2
1P LOSS WILD-TYPE	8	3	6

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

'1p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 9e-04

Table S188. Gene #41: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	7	7	6
1P LOSS MUTATED	0	1	7	2
1P LOSS WILD-TYPE	7	6	0	4

Figure S188. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S189. Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
1P LOSS MUTATED	6	13	165
1P LOSS WILD-TYPE	166	107	56

Figure S189. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S190. Gene #41: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
1P LOSS MUTATED	5	5	165	9
1P LOSS WILD-TYPE	220	76	2	31

Figure S190. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1p loss' versus 'RPPA_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.0019

Table S191. Gene #41: '1p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
1P LOSS MUTATED	8	15	26	36
1P LOSS WILD-TYPE	44	47	42	38

Figure S191. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S192. Gene #41: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
1P LOSS MUTATED	3	8	105	58	10
1P LOSS WILD-TYPE	131	101	3	74	20

Figure S192. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S193. Gene #41: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
1P LOSS MUTATED	3	6	35	1	88	1	50
1P LOSS WILD-TYPE	132	65	1	67	2	40	22

Figure S193. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S194. Gene #41: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
1P LOSS MUTATED	25	9	84	66
1P LOSS WILD-TYPE	112	98	99	16

Figure S194. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S195. Gene #41: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
1P LOSS MUTATED	80	97	7
1P LOSS WILD-TYPE	142	87	96

Figure S195. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S196. Gene #41: '1p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
1P LOSS MUTATED	29	82	73
1P LOSS WILD-TYPE	156	79	86

Figure S196. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'1p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S197. Gene #41: '1p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
1P LOSS MUTATED	6	82	89	7
1P LOSS WILD-TYPE	85	55	99	82

Figure S197. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0171 (Fisher's exact test), Q value = 0.054

Table S198. Gene #42: '1q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
1Q LOSS MUTATED	4	3	5	0	5	1	7
1Q LOSS WILD-TYPE	131	68	31	68	85	40	65

Figure S198. Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p loss' versus 'CN_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.0015

Table S199. Gene #43: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
2P LOSS MUTATED	16	2	3
2P LOSS WILD-TYPE	156	118	218

Figure S199. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

'2p loss' versus 'METHLYATION_CNMF'

P value = 0.0426 (Fisher's exact test), Q value = 0.11

Table S200. Gene #43: '2p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
2P LOSS MUTATED	15	3	2	1
2P LOSS WILD-TYPE	210	78	165	39

Figure S200. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0418 (Fisher's exact test), Q value = 0.11

Table S201. Gene #43: '2p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
2P LOSS MUTATED	6	4	0	2	2	6	1
2P LOSS WILD-TYPE	129	67	36	66	88	35	71

Figure S201. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'CN_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.0022

Table S202. Gene #44: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
2Q LOSS MUTATED	14	1	3
2Q LOSS WILD-TYPE	158	119	218

Figure S202. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

'2q loss' versus 'METHLYATION_CNMF'

P value = 0.00528 (Fisher's exact test), Q value = 0.021

Table S203. Gene #44: '2q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
2Q LOSS MUTATED	15	0	2	1
2Q LOSS WILD-TYPE	210	81	165	39

Figure S203. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00148 (Fisher's exact test), Q value = 0.0068

Table S204. Gene #44: '2q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
2Q LOSS MUTATED	5	1	0	3	2	7	0
2Q LOSS WILD-TYPE	130	70	36	65	88	34	72

Figure S204. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_CNMF'

P value = 0.0263 (Fisher's exact test), Q value = 0.076

Table S205. Gene #44: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
2Q LOSS MUTATED	3	9	3	2
2Q LOSS WILD-TYPE	134	98	180	80

Figure S205. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3p loss' versus 'CN_CNMF'

P value = 0.00504 (Fisher's exact test), Q value = 0.02

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
3P LOSS MUTATED	16	9	5
3P LOSS WILD-TYPE	156	111	216

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

'3p loss' versus 'RPPA_CNMF'

P value = 0.00659 (Fisher's exact test), Q value = 0.025

Table S207. Gene #45: '3p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
3P LOSS MUTATED	2	8	0	3
3P LOSS WILD-TYPE	50	54	68	71

Figure S207. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 0.0268 (Fisher's exact test), Q value = 0.077

Table S208. Gene #45: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
3P LOSS MUTATED	9	13	3	5	0
3P LOSS WILD-TYPE	125	96	105	127	30

Figure S208. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3p loss' versus 'MIRSEQ_CNMF'

P value = 0.00109 (Fisher's exact test), Q value = 0.0052

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
3P LOSS MUTATED	9	14	3	4
3P LOSS WILD-TYPE	128	93	180	78

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

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00044 (Fisher's exact test), Q value = 0.0024

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
3P LOSS MUTATED	18	2	10
3P LOSS WILD-TYPE	204	182	93

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

'3p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00311 (Fisher's exact test), Q value = 0.013

Table S211. Gene #45: '3p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
3P LOSS MUTATED	11	6	4	8
3P LOSS WILD-TYPE	80	131	184	81

Figure S211. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

P value = 0.00714 (Fisher's exact test), Q value = 0.027

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
3Q LOSS MUTATED	17	5	6
3Q LOSS WILD-TYPE	155	115	215

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

'3q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.031 (Fisher's exact test), Q value = 0.086

Table S213. Gene #46: '3q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
3Q LOSS MUTATED	9	4	1	4	2	7	1
3Q LOSS WILD-TYPE	126	67	35	64	88	34	71

Figure S213. Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0164 (Fisher's exact test), Q value = 0.053

Table S214. Gene #46: '3q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
3Q LOSS MUTATED	14	4	10
3Q LOSS WILD-TYPE	208	180	93

Figure S214. Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0346 (Fisher's exact test), Q value = 0.092

Table S215. Gene #46: '3q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
3Q LOSS MUTATED	9	8	4	6
3Q LOSS WILD-TYPE	82	129	184	83

Figure S215. Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

P value = 0.00302 (Fisher's exact test), Q value = 0.013

Table S216. Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
4P LOSS MUTATED	15	12	44
4P LOSS WILD-TYPE	157	108	177

Figure S216. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S217. Gene #47: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
4P LOSS MUTATED	25	1	45	0
4P LOSS WILD-TYPE	200	80	122	40

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

'4p loss' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00025

Table S218. Gene #47: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
4P LOSS MUTATED	15	4	30	19	3
4P LOSS WILD-TYPE	119	105	78	113	27

Figure S218. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S219. Gene #47: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
4P LOSS MUTATED	13	1	14	7	23	3	10
4P LOSS WILD-TYPE	122	70	22	61	67	38	62

Figure S219. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00032

Table S220. Gene #47: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
4P LOSS MUTATED	11	12	22	26
4P LOSS WILD-TYPE	126	95	161	56

Figure S220. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00032 (Fisher's exact test), Q value = 0.0019

Table S221. Gene #47: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
4P LOSS MUTATED	38	30	3
4P LOSS WILD-TYPE	184	154	100

Figure S221. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00038

Table S222. Gene #47: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
4P LOSS MUTATED	10	35	26
4P LOSS WILD-TYPE	175	126	133

Figure S222. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00017

Table S223. Gene #47: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
4P LOSS MUTATED	6	34	29	2
4P LOSS WILD-TYPE	85	103	159	87

Figure S223. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 0.00692 (Fisher's exact test), Q value = 0.026

Table S224. Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
4Q LOSS MUTATED	31	11	50
4Q LOSS WILD-TYPE	141	109	171

Figure S224. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S225. Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
4Q LOSS MUTATED	40	1	48	3
4Q LOSS WILD-TYPE	185	80	119	37

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

'4q loss' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 5e-04

Table S226. Gene #48: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
4Q LOSS MUTATED	21	8	33	28	2
4Q LOSS WILD-TYPE	113	101	75	104	28

Figure S226. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S227. Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
4Q LOSS MUTATED	18	1	15	11	24	8	15
4Q LOSS WILD-TYPE	117	70	21	57	66	33	57

Figure S227. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.0011

Table S228. Gene #48: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
4Q LOSS MUTATED	12	18	35	27
4Q LOSS WILD-TYPE	125	89	148	55

Figure S228. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00126 (Fisher's exact test), Q value = 0.0059

Table S229. Gene #48: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
4Q LOSS MUTATED	44	41	7
4Q LOSS WILD-TYPE	178	143	96

Figure S229. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S230. Gene #48: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
4Q LOSS MUTATED	14	42	36
4Q LOSS WILD-TYPE	171	119	123

Figure S230. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S231. Gene #48: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
4Q LOSS MUTATED	9	39	39	5
4Q LOSS WILD-TYPE	82	98	149	84

Figure S231. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00017

Table S232. Gene #49: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
5P LOSS MUTATED	24	7	3
5P LOSS WILD-TYPE	148	113	218

Figure S232. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

'5p loss' versus 'METHLYATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00064

Table S233. Gene #49: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
5P LOSS MUTATED	27	4	2	1
5P LOSS WILD-TYPE	198	77	165	39

Figure S233. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5p loss' versus 'MRNASEQ_CNMF'

P value = 0.0401 (Fisher's exact test), Q value = 0.1

Table S234. Gene #49: '5p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
5P LOSS MUTATED	10	10	1	11	2
5P LOSS WILD-TYPE	124	99	107	121	28

Figure S234. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0032 (Fisher's exact test), Q value = 0.013

Table S235. Gene #49: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
5P LOSS MUTATED	10	2	0	8	2	8	4
5P LOSS WILD-TYPE	125	69	36	60	88	33	68

Figure S235. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S236. Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
5Q LOSS MUTATED	26	4	3
5Q LOSS WILD-TYPE	146	116	218

Figure S236. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 8e-04

Table S237. Gene #50: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
5Q LOSS MUTATED	26	4	2	1
5Q LOSS WILD-TYPE	199	77	165	39

Figure S237. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5q loss' versus 'RPPA_CNMF'

P value = 0.02 (Fisher's exact test), Q value = 0.062

Table S238. Gene #50: '5q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
5Q LOSS MUTATED	5	9	4	1
5Q LOSS WILD-TYPE	47	53	64	73

Figure S238. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 0.0114 (Fisher's exact test), Q value = 0.04

Table S239. Gene #50: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
5Q LOSS MUTATED	10	13	1	7	2
5Q LOSS WILD-TYPE	124	96	107	125	28

Figure S239. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S240. Gene #50: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
5Q LOSS MUTATED	9	2	0	7	2	12	1
5Q LOSS WILD-TYPE	126	69	36	61	88	29	71

Figure S240. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00085

Table S241. Gene #50: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
5Q LOSS MUTATED	6	18	8	1
5Q LOSS WILD-TYPE	131	89	175	81

Figure S241. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6p loss' versus 'CN_CNMF'

P value = 0.033 (Fisher's exact test), Q value = 0.089

Table S242. Gene #51: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
6P LOSS MUTATED	11	12	7
6P LOSS WILD-TYPE	161	108	214

Figure S242. Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

'6p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0125 (Fisher's exact test), Q value = 0.042

Table S243. Gene #51: '6p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
6P LOSS MUTATED	18	4	7
6P LOSS WILD-TYPE	167	157	152

Figure S243. Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'6p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00274 (Fisher's exact test), Q value = 0.012

Table S244. Gene #51: '6p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
6P LOSS MUTATED	7	5	5	12
6P LOSS WILD-TYPE	84	132	183	77

Figure S244. Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q loss' versus 'CN_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00085

Table S245. Gene #52: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
6Q LOSS MUTATED	22	27	14
6Q LOSS WILD-TYPE	150	93	207

Figure S245. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

'6q loss' versus 'METHLYATION_CNMF'

P value = 0.00153 (Fisher's exact test), Q value = 0.007

Table S246. Gene #52: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
6Q LOSS MUTATED	36	14	8	5
6Q LOSS WILD-TYPE	189	67	159	35

Figure S246. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6q loss' versus 'MIRSEQ_CNMF'

P value = 0.00134 (Fisher's exact test), Q value = 0.0063

Table S247. Gene #52: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
6Q LOSS MUTATED	29	14	16	4
6Q LOSS WILD-TYPE	108	93	167	78

Figure S247. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0129 (Fisher's exact test), Q value = 0.043

Table S248. Gene #52: '6q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
6Q LOSS MUTATED	33	14	14
6Q LOSS WILD-TYPE	152	147	145

Figure S248. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'6q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.00085

Table S249. Gene #52: '6q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
6Q LOSS MUTATED	20	8	15	18
6Q LOSS WILD-TYPE	71	129	173	71

Figure S249. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7p loss' versus 'CN_CNMF'

P value = 0.05 (Fisher's exact test), Q value = 0.12

Table S250. Gene #53: '7p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
7P LOSS MUTATED	3	0	0
7P LOSS WILD-TYPE	169	120	221

Figure S250. Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.043 (Fisher's exact test), Q value = 0.11

Table S251. Gene #55: '8p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	7	7	6
8P LOSS MUTATED	0	3	0	0
8P LOSS WILD-TYPE	7	4	7	6

Figure S251. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00032

Table S252. Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
8P LOSS MUTATED	7	10	0
8P LOSS WILD-TYPE	165	110	221

Figure S252. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 8e-04

Table S253. Gene #55: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
8P LOSS MUTATED	6	10	0	1
8P LOSS WILD-TYPE	219	71	167	39

Figure S253. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p loss' versus 'RPPA_CNMF'

P value = 0.0187 (Fisher's exact test), Q value = 0.058

Table S254. Gene #55: '8p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
8P LOSS MUTATED	1	6	0	2
8P LOSS WILD-TYPE	51	56	68	72

Figure S254. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S255. Gene #55: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
8P LOSS MUTATED	0	13	0	3	1
8P LOSS WILD-TYPE	134	96	108	129	29

Figure S255. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00032

Table S256. Gene #55: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
8P LOSS MUTATED	1	8	0	2	0	5	1
8P LOSS WILD-TYPE	134	63	36	66	90	36	71

Figure S256. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00115 (Fisher's exact test), Q value = 0.0054

Table S257. Gene #55: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
8P LOSS MUTATED	7	1	9
8P LOSS WILD-TYPE	215	183	94

Figure S257. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00033 (Fisher's exact test), Q value = 0.0019

Table S258. Gene #55: '8p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
8P LOSS MUTATED	1	5	1	9
8P LOSS WILD-TYPE	90	132	187	80

Figure S258. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q loss' versus 'CN_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.0011

Table S259. Gene #56: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
8Q LOSS MUTATED	3	8	0
8Q LOSS WILD-TYPE	169	112	221

Figure S259. Get High-res Image Gene #56: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'

'8q loss' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00017

Table S260. Gene #56: '8q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
8Q LOSS MUTATED	2	8	0	1
8Q LOSS WILD-TYPE	223	73	167	39

Figure S260. Get High-res Image Gene #56: '8q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8q loss' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00038

Table S261. Gene #56: '8q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
8Q LOSS MUTATED	0	9	0	1	1
8Q LOSS WILD-TYPE	134	100	108	131	29

Figure S261. Get High-res Image Gene #56: '8q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00052 (Fisher's exact test), Q value = 0.0027

Table S262. Gene #56: '8q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
8Q LOSS MUTATED	1	7	0	1	0	2	0
8Q LOSS WILD-TYPE	134	64	36	67	90	39	72

Figure S262. Get High-res Image Gene #56: '8q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00073 (Fisher's exact test), Q value = 0.0037

Table S263. Gene #56: '8q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
8Q LOSS MUTATED	4	0	7
8Q LOSS WILD-TYPE	218	184	96

Figure S263. Get High-res Image Gene #56: '8q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 7e-04

Table S264. Gene #56: '8q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
8Q LOSS MUTATED	0	3	0	7
8Q LOSS WILD-TYPE	91	134	188	82

Figure S264. Get High-res Image Gene #56: '8q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S265. Gene #57: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
9P LOSS MUTATED	41	47	30
9P LOSS WILD-TYPE	131	73	191

Figure S265. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 0.00042 (Fisher's exact test), Q value = 0.0023

Table S266. Gene #57: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
9P LOSS MUTATED	61	28	22	7
9P LOSS WILD-TYPE	164	53	145	33

Figure S266. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p loss' versus 'RPPA_CNMF'

P value = 0.0326 (Fisher's exact test), Q value = 0.089

Table S267. Gene #57: '9p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
9P LOSS MUTATED	9	24	17	14
9P LOSS WILD-TYPE	43	38	51	60

Figure S267. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'9p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0195 (Fisher's exact test), Q value = 0.06

Table S268. Gene #57: '9p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	131	58
9P LOSS MUTATED	9	41	14
9P LOSS WILD-TYPE	58	90	44

Figure S268. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.0012

Table S269. Gene #57: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
9P LOSS MUTATED	33	21	9	25	10	13	7
9P LOSS WILD-TYPE	102	50	27	43	80	28	65

Figure S269. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0341 (Fisher's exact test), Q value = 0.091

Table S270. Gene #57: '9p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
9P LOSS MUTATED	22	23	42	30
9P LOSS WILD-TYPE	69	114	146	59

Figure S270. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0427 (Fisher's exact test), Q value = 0.11

Table S271. Gene #58: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
9Q LOSS MUTATED	11	11	7	7	7	6	2
9Q LOSS WILD-TYPE	124	60	29	61	83	35	70

Figure S271. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0339 (Fisher's exact test), Q value = 0.091

Table S272. Gene #58: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
9Q LOSS MUTATED	10	7	17	15
9Q LOSS WILD-TYPE	81	130	171	74

Figure S272. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S273. Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
10P LOSS MUTATED	8	70	5
10P LOSS WILD-TYPE	164	50	216

Figure S273. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S274. Gene #59: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
10P LOSS MUTATED	4	68	6	5
10P LOSS WILD-TYPE	221	13	161	35

Figure S274. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S275. Gene #59: '10p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
10P LOSS MUTATED	4	24	3	6
10P LOSS WILD-TYPE	48	38	65	68

Figure S275. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'10p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00104 (Fisher's exact test), Q value = 0.005

Table S276. Gene #59: '10p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	131	58
10P LOSS MUTATED	3	29	5
10P LOSS WILD-TYPE	64	102	53

Figure S276. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S277. Gene #59: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
10P LOSS MUTATED	1	64	2	12	4
10P LOSS WILD-TYPE	133	45	106	120	26

Figure S277. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S278. Gene #59: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
10P LOSS MUTATED	1	60	3	12	3	4	0
10P LOSS WILD-TYPE	134	11	33	56	87	37	72

Figure S278. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00032

Table S279. Gene #59: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
10P LOSS MUTATED	33	26	20	4
10P LOSS WILD-TYPE	104	81	163	78

Figure S279. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S280. Gene #59: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
10P LOSS MUTATED	11	12	60
10P LOSS WILD-TYPE	211	172	43

Figure S280. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S281. Gene #59: '10p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
10P LOSS MUTATED	62	3	18
10P LOSS WILD-TYPE	123	158	141

Figure S281. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S282. Gene #59: '10p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
10P LOSS MUTATED	4	5	11	63
10P LOSS WILD-TYPE	87	132	177	26

Figure S282. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S283. Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
10Q LOSS MUTATED	17	72	7
10Q LOSS WILD-TYPE	155	48	214

Figure S283. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S284. Gene #60: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
10Q LOSS MUTATED	16	69	6	5
10Q LOSS WILD-TYPE	209	12	161	35

Figure S284. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q loss' versus 'RPPA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00017

Table S285. Gene #60: '10q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
10Q LOSS MUTATED	6	27	7	7
10Q LOSS WILD-TYPE	46	35	61	67

Figure S285. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'10q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00055 (Fisher's exact test), Q value = 0.0029

Table S286. Gene #60: '10q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	131	58
10Q LOSS MUTATED	5	36	6
10Q LOSS WILD-TYPE	62	95	52

Figure S286. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S287. Gene #60: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
10Q LOSS MUTATED	6	69	2	15	4
10Q LOSS WILD-TYPE	128	40	106	117	26

Figure S287. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S288. Gene #60: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
10Q LOSS MUTATED	6	60	3	14	3	9	1
10Q LOSS WILD-TYPE	129	11	33	54	87	32	71

Figure S288. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S289. Gene #60: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
10Q LOSS MUTATED	36	31	24	5
10Q LOSS WILD-TYPE	101	76	159	77

Figure S289. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S290. Gene #60: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
10Q LOSS MUTATED	15	15	66
10Q LOSS WILD-TYPE	207	169	37

Figure S290. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S291. Gene #60: '10q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
10Q LOSS MUTATED	67	7	22
10Q LOSS WILD-TYPE	118	154	137

Figure S291. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S292. Gene #60: '10q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
10Q LOSS MUTATED	7	7	16	66
10Q LOSS WILD-TYPE	84	130	172	23

Figure S292. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0294 (Fisher's exact test), Q value = 0.083

Table S293. Gene #61: '11p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	7	7	6
11P LOSS MUTATED	1	4	0	0
11P LOSS WILD-TYPE	6	3	7	6

Figure S293. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S294. Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
11P LOSS MUTATED	47	12	4
11P LOSS WILD-TYPE	125	108	217

Figure S294. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S295. Gene #61: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
11P LOSS MUTATED	46	14	0	3
11P LOSS WILD-TYPE	179	67	167	37

Figure S295. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p loss' versus 'RPPA_CNMF'

P value = 0.0117 (Fisher's exact test), Q value = 0.041

Table S296. Gene #61: '11p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
11P LOSS MUTATED	10	15	5	6
11P LOSS WILD-TYPE	42	47	63	68

Figure S296. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'11p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S297. Gene #61: '11p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
11P LOSS MUTATED	14	31	0	12	6
11P LOSS WILD-TYPE	120	78	108	120	24

Figure S297. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S298. Gene #61: '11p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
11P LOSS MUTATED	17	9	0	6	0	25	6
11P LOSS WILD-TYPE	118	62	36	62	90	16	66

Figure S298. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S299. Gene #61: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
11P LOSS MUTATED	13	29	17	4
11P LOSS WILD-TYPE	124	78	166	78

Figure S299. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 5e-04

Table S300. Gene #61: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
11P LOSS MUTATED	22	14	27
11P LOSS WILD-TYPE	200	170	76

Figure S300. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0161 (Fisher's exact test), Q value = 0.052

Table S301. Gene #61: '11p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
11P LOSS MUTATED	10	16	16	20
11P LOSS WILD-TYPE	81	121	172	69

Figure S301. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.0015

Table S302. Gene #62: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
11Q LOSS MUTATED	11	9	1
11Q LOSS WILD-TYPE	161	111	220

Figure S302. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00032

Table S303. Gene #62: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
11Q LOSS MUTATED	9	10	0	2
11Q LOSS WILD-TYPE	216	71	167	38

Figure S303. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11q loss' versus 'RPPA_CNMF'

P value = 0.0179 (Fisher's exact test), Q value = 0.056

Table S304. Gene #62: '11q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
11Q LOSS MUTATED	3	7	0	3
11Q LOSS WILD-TYPE	49	55	68	71

Figure S304. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'11q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S305. Gene #62: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
11Q LOSS MUTATED	1	16	0	3	1
11Q LOSS WILD-TYPE	133	93	108	129	29

Figure S305. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S306. Gene #62: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
11Q LOSS MUTATED	2	9	0	2	0	7	1
11Q LOSS WILD-TYPE	133	62	36	66	90	34	71

Figure S306. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_CNMF'

P value = 0.027 (Fisher's exact test), Q value = 0.078

Table S307. Gene #62: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
11Q LOSS MUTATED	6	9	6	0
11Q LOSS WILD-TYPE	131	98	177	82

Figure S307. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 5e-04

Table S308. Gene #62: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
11Q LOSS MUTATED	5	3	13
11Q LOSS WILD-TYPE	217	181	90

Figure S308. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00033 (Fisher's exact test), Q value = 0.0019

Table S309. Gene #62: '11q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
11Q LOSS MUTATED	1	5	3	11
11Q LOSS WILD-TYPE	90	132	185	78

Figure S309. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12p loss' versus 'CN_CNMF'

P value = 0.00414 (Fisher's exact test), Q value = 0.017

Table S310. Gene #63: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
12P LOSS MUTATED	17	3	6
12P LOSS WILD-TYPE	155	117	215

Figure S310. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

'12p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00672 (Fisher's exact test), Q value = 0.025

Table S311. Gene #63: '12p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
12P LOSS MUTATED	8	1	1	1	3	8	4
12P LOSS WILD-TYPE	127	70	35	67	87	33	68

Figure S311. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S312. Gene #64: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
12Q LOSS MUTATED	42	2	7
12Q LOSS WILD-TYPE	130	118	214

Figure S312. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

'12q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S313. Gene #64: '12q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
12Q LOSS MUTATED	41	3	5	2
12Q LOSS WILD-TYPE	184	78	162	38

Figure S313. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12q loss' versus 'MRNASEQ_CNMF'

P value = 0.00142 (Fisher's exact test), Q value = 0.0065

Table S314. Gene #64: '12q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
12Q LOSS MUTATED	18	14	1	14	4
12Q LOSS WILD-TYPE	116	95	107	118	26

Figure S314. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S315. Gene #64: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
12Q LOSS MUTATED	21	1	1	5	3	14	6
12Q LOSS WILD-TYPE	114	70	35	63	87	27	66

Figure S315. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q loss' versus 'MIRSEQ_CNMF'

P value = 0.00655 (Fisher's exact test), Q value = 0.025

Table S316. Gene #64: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
12Q LOSS MUTATED	10	21	15	5
12Q LOSS WILD-TYPE	127	86	168	77

Figure S316. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'13q loss' versus 'MRNA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00025

Table S317. Gene #65: '13q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	7	7	6
13Q LOSS MUTATED	2	7	0	0
13Q LOSS WILD-TYPE	5	0	7	6

Figure S317. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00017

Table S318. Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
13Q LOSS MUTATED	57	29	30
13Q LOSS WILD-TYPE	115	91	191

Figure S318. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 0.00566 (Fisher's exact test), Q value = 0.022

Table S319. Gene #65: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
13Q LOSS MUTATED	60	25	26	5
13Q LOSS WILD-TYPE	165	56	141	35

Figure S319. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q loss' versus 'RPPA_CNMF'

P value = 0.0249 (Fisher's exact test), Q value = 0.073

Table S320. Gene #65: '13q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
13Q LOSS MUTATED	7	23	16	15
13Q LOSS WILD-TYPE	45	39	52	59

Figure S320. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0014 (Fisher's exact test), Q value = 0.0065

Table S321. Gene #65: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
13Q LOSS MUTATED	33	19	2	12	17	19	14
13Q LOSS WILD-TYPE	102	52	34	56	73	22	58

Figure S321. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_CNMF'

P value = 0.0342 (Fisher's exact test), Q value = 0.091

Table S322. Gene #65: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
13Q LOSS MUTATED	30	34	31	20
13Q LOSS WILD-TYPE	107	73	152	62

Figure S322. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'13q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0132 (Fisher's exact test), Q value = 0.044

Table S323. Gene #65: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
13Q LOSS MUTATED	53	30	32
13Q LOSS WILD-TYPE	169	154	71

Figure S323. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 0.00111 (Fisher's exact test), Q value = 0.0053

Table S324. Gene #66: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
14Q LOSS MUTATED	23	32	25
14Q LOSS WILD-TYPE	149	88	196

Figure S324. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.0012

Table S325. Gene #66: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
14Q LOSS MUTATED	29	27	20	4
14Q LOSS WILD-TYPE	196	54	147	36

Figure S325. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q loss' versus 'RPPA_CNMF'

P value = 0.0449 (Fisher's exact test), Q value = 0.11

Table S326. Gene #66: '14q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
14Q LOSS MUTATED	5	16	11	7
14Q LOSS WILD-TYPE	47	46	57	67

Figure S326. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S327. Gene #66: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
14Q LOSS MUTATED	11	34	12	16	7
14Q LOSS WILD-TYPE	123	75	96	116	23

Figure S327. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.0015

Table S328. Gene #66: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
14Q LOSS MUTATED	15	25	6	9	8	10	7
14Q LOSS WILD-TYPE	120	46	30	59	82	31	65

Figure S328. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_CNMF'

P value = 0.0101 (Fisher's exact test), Q value = 0.037

Table S329. Gene #66: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
14Q LOSS MUTATED	34	13	22	10
14Q LOSS WILD-TYPE	103	94	161	72

Figure S329. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'14q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00095 (Fisher's exact test), Q value = 0.0046

Table S330. Gene #66: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
14Q LOSS MUTATED	27	23	29
14Q LOSS WILD-TYPE	195	161	74

Figure S330. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0115 (Fisher's exact test), Q value = 0.041

Table S331. Gene #66: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
14Q LOSS MUTATED	41	19	19
14Q LOSS WILD-TYPE	144	142	140

Figure S331. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'14q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00037 (Fisher's exact test), Q value = 0.0021

Table S332. Gene #66: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
14Q LOSS MUTATED	13	16	22	28
14Q LOSS WILD-TYPE	78	121	166	61

Figure S332. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 0.0288 (Fisher's exact test), Q value = 0.081

Table S333. Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
15Q LOSS MUTATED	13	7	31
15Q LOSS WILD-TYPE	159	113	190

Figure S333. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 0.00215 (Fisher's exact test), Q value = 0.0095

Table S334. Gene #67: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
15Q LOSS MUTATED	19	3	28	1
15Q LOSS WILD-TYPE	206	78	139	39

Figure S334. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'15q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0456 (Fisher's exact test), Q value = 0.11

Table S335. Gene #67: '15q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	131	58
15Q LOSS MUTATED	3	17	2
15Q LOSS WILD-TYPE	64	114	56

Figure S335. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 0.00165 (Fisher's exact test), Q value = 0.0074

Table S336. Gene #67: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
15Q LOSS MUTATED	6	10	22	10	3
15Q LOSS WILD-TYPE	128	99	86	122	27

Figure S336. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S337. Gene #67: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
15Q LOSS MUTATED	7	2	6	2	18	10	6
15Q LOSS WILD-TYPE	128	69	30	66	72	31	66

Figure S337. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16p loss' versus 'CN_CNMF'

P value = 0.00543 (Fisher's exact test), Q value = 0.021

Table S338. Gene #68: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
16P LOSS MUTATED	6	7	1
16P LOSS WILD-TYPE	166	113	220

Figure S338. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

'16p loss' versus 'METHLYATION_CNMF'

P value = 0.0429 (Fisher's exact test), Q value = 0.11

Table S339. Gene #68: '16p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
16P LOSS MUTATED	6	6	2	0
16P LOSS WILD-TYPE	219	75	165	40

Figure S339. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.023 (Fisher's exact test), Q value = 0.069

Table S340. Gene #68: '16p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
16P LOSS MUTATED	1	4	0	5	2	2	0
16P LOSS WILD-TYPE	134	67	36	63	88	39	72

Figure S340. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'CN_CNMF'

P value = 0.00602 (Fisher's exact test), Q value = 0.023

Table S341. Gene #69: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
16Q LOSS MUTATED	9	10	3
16Q LOSS WILD-TYPE	163	110	218

Figure S341. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 0.00264 (Fisher's exact test), Q value = 0.011

Table S342. Gene #69: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
16Q LOSS MUTATED	9	10	3	0
16Q LOSS WILD-TYPE	216	71	164	40

Figure S342. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 0.0485 (Fisher's exact test), Q value = 0.12

Table S343. Gene #69: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
16Q LOSS MUTATED	4	11	3	4	0
16Q LOSS WILD-TYPE	130	98	105	128	30

Figure S343. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0197 (Fisher's exact test), Q value = 0.061

Table S344. Gene #69: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
16Q LOSS MUTATED	4	8	1	5	2	2	0
16Q LOSS WILD-TYPE	131	63	35	63	88	39	72

Figure S344. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00365 (Fisher's exact test), Q value = 0.015

Table S345. Gene #69: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
16Q LOSS MUTATED	7	4	11
16Q LOSS WILD-TYPE	215	180	92

Figure S345. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00899 (Fisher's exact test), Q value = 0.033

Table S346. Gene #69: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
16Q LOSS MUTATED	3	4	4	10
16Q LOSS WILD-TYPE	88	133	184	79

Figure S346. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 0.0123 (Fisher's exact test), Q value = 0.042

Table S347. Gene #70: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
17P LOSS MUTATED	1	7	2	1	2
17P LOSS WILD-TYPE	133	102	106	131	28

Figure S347. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00615 (Fisher's exact test), Q value = 0.024

Table S348. Gene #70: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
17P LOSS MUTATED	5	1	7
17P LOSS WILD-TYPE	217	183	96

Figure S348. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0114 (Fisher's exact test), Q value = 0.04

Table S349. Gene #70: '17p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
17P LOSS MUTATED	3	2	1	6
17P LOSS WILD-TYPE	88	135	187	83

Figure S349. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0234 (Fisher's exact test), Q value = 0.069

Table S350. Gene #71: '17q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
17Q LOSS MUTATED	3	0	1	3
17Q LOSS WILD-TYPE	88	137	187	86

Figure S350. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0306 (Fisher's exact test), Q value = 0.086

Table S351. Gene #72: '18p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	7	7	6
18P LOSS MUTATED	0	4	1	0
18P LOSS WILD-TYPE	7	3	6	6

Figure S351. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18p loss' versus 'METHLYATION_CNMF'

P value = 0.00154 (Fisher's exact test), Q value = 0.007

Table S352. Gene #72: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
18P LOSS MUTATED	23	14	31	0
18P LOSS WILD-TYPE	202	67	136	40

Figure S352. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 0.045 (Fisher's exact test), Q value = 0.11

Table S353. Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
18Q LOSS MUTATED	15	11	36
18Q LOSS WILD-TYPE	157	109	185

Figure S353. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.0018

Table S354. Gene #73: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
18Q LOSS MUTATED	19	10	33	0
18Q LOSS WILD-TYPE	206	71	134	40

Figure S354. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 0.018 (Fisher's exact test), Q value = 0.056

Table S355. Gene #73: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
18Q LOSS MUTATED	9	12	23	15	3
18Q LOSS WILD-TYPE	125	97	85	117	27

Figure S355. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0157 (Fisher's exact test), Q value = 0.051

Table S356. Gene #73: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
18Q LOSS MUTATED	9	8	7	6	20	6	6
18Q LOSS WILD-TYPE	126	63	29	62	70	35	66

Figure S356. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0265 (Fisher's exact test), Q value = 0.077

Table S357. Gene #74: '19p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
19P LOSS MUTATED	6	14	4
19P LOSS WILD-TYPE	179	147	155

Figure S357. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0132 (Fisher's exact test), Q value = 0.044

Table S358. Gene #75: '19q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	7	7	6
19Q LOSS MUTATED	1	6	6	2
19Q LOSS WILD-TYPE	6	1	1	4

Figure S358. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S359. Gene #75: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
19Q LOSS MUTATED	22	17	170
19Q LOSS WILD-TYPE	150	103	51

Figure S359. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S360. Gene #75: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
19Q LOSS MUTATED	30	5	165	9
19Q LOSS WILD-TYPE	195	76	2	31

Figure S360. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q loss' versus 'RPPA_CNMF'

P value = 0.0399 (Fisher's exact test), Q value = 0.1

Table S361. Gene #75: '19q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
19Q LOSS MUTATED	13	22	25	37
19Q LOSS WILD-TYPE	39	40	43	37

Figure S361. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'19q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S362. Gene #75: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
19Q LOSS MUTATED	18	13	105	63	10
19Q LOSS WILD-TYPE	116	96	3	69	20

Figure S362. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S363. Gene #75: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
19Q LOSS MUTATED	16	5	36	8	87	8	49
19Q LOSS WILD-TYPE	119	66	0	60	3	33	23

Figure S363. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S364. Gene #75: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
19Q LOSS MUTATED	31	22	88	68
19Q LOSS WILD-TYPE	106	85	95	14

Figure S364. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S365. Gene #75: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
19Q LOSS MUTATED	97	103	9
19Q LOSS WILD-TYPE	125	81	94

Figure S365. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S366. Gene #75: '19q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
19Q LOSS MUTATED	34	96	78
19Q LOSS WILD-TYPE	151	65	81

Figure S366. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S367. Gene #75: '19q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
19Q LOSS MUTATED	11	92	97	8
19Q LOSS WILD-TYPE	80	45	91	81

Figure S367. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q loss' versus 'MRNASEQ_CNMF'

P value = 0.0257 (Fisher's exact test), Q value = 0.075

Table S368. Gene #77: '20q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
20Q LOSS MUTATED	0	2	0	0	1
20Q LOSS WILD-TYPE	134	107	108	132	29

Figure S368. Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.043 (Fisher's exact test), Q value = 0.11

Table S369. Gene #78: '21q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	7	7	6
21Q LOSS MUTATED	0	3	0	0
21Q LOSS WILD-TYPE	7	4	7	6

Figure S369. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'21q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S370. Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
21Q LOSS MUTATED	26	4	6
21Q LOSS WILD-TYPE	146	116	215

Figure S370. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

'21q loss' versus 'METHLYATION_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.0019

Table S371. Gene #78: '21q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
21Q LOSS MUTATED	26	6	2	2
21Q LOSS WILD-TYPE	199	75	165	38

Figure S371. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'21q loss' versus 'MRNASEQ_CNMF'

P value = 0.00068 (Fisher's exact test), Q value = 0.0034

Table S372. Gene #78: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
21Q LOSS MUTATED	14	11	1	5	5
21Q LOSS WILD-TYPE	120	98	107	127	25

Figure S372. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00025

Table S373. Gene #78: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
21Q LOSS MUTATED	16	3	2	4	0	10	1
21Q LOSS WILD-TYPE	119	68	34	64	90	31	71

Figure S373. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0272 (Fisher's exact test), Q value = 0.078

Table S374. Gene #78: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
21Q LOSS MUTATED	20	6	10
21Q LOSS WILD-TYPE	202	178	93

Figure S374. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00659 (Fisher's exact test), Q value = 0.025

Table S375. Gene #79: '22q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	7	7	6
22Q LOSS MUTATED	0	4	0	0
22Q LOSS WILD-TYPE	7	3	7	6

Figure S375. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S376. Gene #79: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
22Q LOSS MUTATED	25	28	4
22Q LOSS WILD-TYPE	147	92	217

Figure S376. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S377. Gene #79: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
22Q LOSS MUTATED	24	24	4	5
22Q LOSS WILD-TYPE	201	57	163	35

Figure S377. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q loss' versus 'RPPA_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00038

Table S378. Gene #79: '22q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
22Q LOSS MUTATED	2	18	5	4
22Q LOSS WILD-TYPE	50	44	63	70

Figure S378. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'22q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0392 (Fisher's exact test), Q value = 0.1

Table S379. Gene #79: '22q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	131	58
22Q LOSS MUTATED	3	21	5
22Q LOSS WILD-TYPE	64	110	53

Figure S379. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S380. Gene #79: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
22Q LOSS MUTATED	8	30	4	10	5
22Q LOSS WILD-TYPE	126	79	104	122	25

Figure S380. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S381. Gene #79: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
22Q LOSS MUTATED	11	21	2	11	2	9	1
22Q LOSS WILD-TYPE	124	50	34	57	88	32	71

Figure S381. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.0018

Table S382. Gene #79: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
22Q LOSS MUTATED	18	15	24
22Q LOSS WILD-TYPE	204	169	79

Figure S382. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0112 (Fisher's exact test), Q value = 0.04

Table S383. Gene #79: '22q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
22Q LOSS MUTATED	31	13	12
22Q LOSS WILD-TYPE	154	148	147

Figure S383. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'22q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 8e-04

Table S384. Gene #79: '22q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
22Q LOSS MUTATED	5	13	15	23
22Q LOSS WILD-TYPE	86	124	173	66

Figure S384. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xp loss' versus 'CN_CNMF'

P value = 0.00056 (Fisher's exact test), Q value = 0.0029

Table S385. Gene #80: 'xp loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
XP LOSS MUTATED	48	12	40
XP LOSS WILD-TYPE	124	108	181

Figure S385. Get High-res Image Gene #80: 'xp loss' versus Molecular Subtype #3: 'CN_CNMF'

'xp loss' versus 'RPPA_CNMF'

P value = 0.00803 (Fisher's exact test), Q value = 0.03

Table S386. Gene #80: 'xp loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
XP LOSS MUTATED	6	19	17	8
XP LOSS WILD-TYPE	46	43	51	66

Figure S386. Get High-res Image Gene #80: 'xp loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'xp loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00366 (Fisher's exact test), Q value = 0.015

Table S387. Gene #80: 'xp loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	131	58
XP LOSS MUTATED	6	36	8
XP LOSS WILD-TYPE	61	95	50

Figure S387. Get High-res Image Gene #80: 'xp loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'xp loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S388. Gene #80: 'xp loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
XP LOSS MUTATED	29	10	10	10	20	18	3
XP LOSS WILD-TYPE	106	61	26	58	70	23	69

Figure S388. Get High-res Image Gene #80: 'xp loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_CNMF'

P value = 0.0244 (Fisher's exact test), Q value = 0.072

Table S389. Gene #80: 'xp loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
XP LOSS MUTATED	22	26	28	24
XP LOSS WILD-TYPE	115	81	155	58

Figure S389. Get High-res Image Gene #80: 'xp loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 0.0201 (Fisher's exact test), Q value = 0.062

Table S390. Gene #81: 'xq loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	225	81	167	40
XQ LOSS MUTATED	26	12	32	1
XQ LOSS WILD-TYPE	199	69	135	39

Figure S390. Get High-res Image Gene #81: 'xq loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xq loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0319 (Fisher's exact test), Q value = 0.088

Table S391. Gene #81: 'xq loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	131	58
XQ LOSS MUTATED	4	25	6
XQ LOSS WILD-TYPE	63	106	52

Figure S391. Get High-res Image Gene #81: 'xq loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'xq loss' versus 'MRNASEQ_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.0022

Table S392. Gene #81: 'xq loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	134	109	108	132	30
XQ LOSS MUTATED	12	21	25	13	0
XQ LOSS WILD-TYPE	122	88	83	119	30

Figure S392. Get High-res Image Gene #81: 'xq loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'xq loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.1e-05

Table S393. Gene #81: 'xq loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
XQ LOSS MUTATED	10	9	10	7	20	13	2
XQ LOSS WILD-TYPE	125	62	26	61	70	28	70

Figure S393. Get High-res Image Gene #81: 'xq loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00045

Table S394. Gene #81: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
XQ LOSS MUTATED	12	17	17	25
XQ LOSS WILD-TYPE	125	90	166	57

Figure S394. Get High-res Image Gene #81: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xq loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0228 (Fisher's exact test), Q value = 0.068

Table S395. Gene #81: 'xq loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
XQ LOSS MUTATED	10	27	17	16
XQ LOSS WILD-TYPE	81	110	171	73

Figure S395. Get High-res Image Gene #81: 'xq loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data

Input

Copy number data file = broad_values_by_arm.txt from GISTIC pipeline
Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LGG-TP/15087637/transformed.cor.cli.txt
Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LGG-TP/15115118/LGG-TP.transferedmergedcluster.txt
Number of patients = 513
Number of significantly arm-level cnvs = 81
Number of molecular subtypes = 12
Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References

[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)

[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)

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