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

Brain Lower Grade Glioma (Primary solid tumor)

15 July 2014 | analyses__2014_07_15

Maintainer Information

Citation Information

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

Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1348J58

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 79 arm-level events and 12 molecular subtypes across 512 patients, 171 significant findings detected with P value < 0.05 and Q value < 0.25.

1p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
1q gain cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.
5p gain cnv correlated to 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
5q gain cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
7p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
7q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
8p gain cnv correlated to 'CN_CNMF'.
8q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
10p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
10q gain cnv correlated to 'CN_CNMF'.
12p gain cnv correlated to 'CN_CNMF'.
18p gain cnv correlated to 'CN_CNMF'.
18q gain cnv correlated to 'MRNASEQ_CHIERARCHICAL'.
19p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
19q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
20p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
20q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
22q gain cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
xq gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
1p 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'.
2p loss cnv correlated to 'CN_CNMF'.
2q loss cnv correlated to 'CN_CNMF'.
4p loss cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
4q loss cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
5p loss cnv correlated to 'CN_CNMF'.
5q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.
6q loss cnv correlated to 'CN_CNMF'.
8p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
8q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
9p loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
10p 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'.
10q 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'.
11p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
11q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
12q loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
13q loss cnv correlated to 'MRNA_CHIERARCHICAL' and 'CN_CNMF'.
14q loss cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
18q loss cnv correlated to 'METHLYATION_CNMF'.
19q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
21q loss cnv correlated to 'CN_CNMF'.
22q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
xq loss cnv correlated to 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_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 79 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, 171 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	183 (36%)	329	0.0283 (1.00)	0.00028 (0.189)	1e-05 (0.0084)	1e-05 (0.0084)	0.00018 (0.123)	0.373 (1.00)	1e-05 (0.0084)	1e-05 (0.0084)	1e-05 (0.0084)	1e-05 (0.0084)	1e-05 (0.0084)	1e-05 (0.0084)
10p loss	83 (16%)	429	0.271 (1.00)	0.883 (1.00)	1e-05 (0.0084)	1e-05 (0.0084)	1e-05 (0.0084)	0.00088 (0.564)	1e-05 (0.0084)	1e-05 (0.0084)	7e-05 (0.0493)	1e-05 (0.0084)	1e-05 (0.0084)	1e-05 (0.0084)
10q loss	96 (19%)	416	0.271 (1.00)	0.882 (1.00)	1e-05 (0.0084)	1e-05 (0.0084)	1e-05 (0.0084)	0.00052 (0.344)	1e-05 (0.0084)	1e-05 (0.0084)	2e-05 (0.0145)	1e-05 (0.0084)	1e-05 (0.0084)	1e-05 (0.0084)
7p gain	120 (23%)	392	0.743 (1.00)	0.781 (1.00)	1e-05 (0.0084)	1e-05 (0.0084)	0.00037 (0.248)	0.0114 (1.00)	1e-05 (0.0084)	1e-05 (0.0084)	0.00385 (1.00)	1e-05 (0.0084)	1e-05 (0.0084)	1e-05 (0.0084)
19q loss	209 (41%)	303	0.183 (1.00)	0.0134 (1.00)	1e-05 (0.0084)	1e-05 (0.0084)	0.0382 (1.00)	0.33 (1.00)	1e-05 (0.0084)	1e-05 (0.0084)	1e-05 (0.0084)	1e-05 (0.0084)	1e-05 (0.0084)	1e-05 (0.0084)
1p gain	13 (3%)	499			0.00017 (0.116)	0.00012 (0.0832)	0.0246 (1.00)	1 (1.00)	1e-05 (0.0084)	1e-05 (0.0084)	0.008 (1.00)	1e-05 (0.0084)	0.0001 (0.0698)	1e-05 (0.0084)
7q gain	150 (29%)	362	0.766 (1.00)	0.52 (1.00)	1e-05 (0.0084)	1e-05 (0.0084)	0.00412 (1.00)	0.2 (1.00)	1e-05 (0.0084)	1e-05 (0.0084)	0.0107 (1.00)	1e-05 (0.0084)	1e-05 (0.0084)	1e-05 (0.0084)
19q gain	25 (5%)	487			1e-05 (0.0084)	1e-05 (0.0084)	0.0587 (1.00)	0.396 (1.00)	1e-05 (0.0084)	1e-05 (0.0084)	0.00291 (1.00)	1e-05 (0.0084)	1e-05 (0.0084)	1e-05 (0.0084)
20p gain	43 (8%)	469			1e-05 (0.0084)	1e-05 (0.0084)	0.00072 (0.469)	0.175 (1.00)	1e-05 (0.0084)	1e-05 (0.0084)	0.112 (1.00)	1e-05 (0.0084)	1e-05 (0.0084)	1e-05 (0.0084)
20q gain	43 (8%)	469			1e-05 (0.0084)	1e-05 (0.0084)	0.00063 (0.412)	0.145 (1.00)	1e-05 (0.0084)	1e-05 (0.0084)	0.0429 (1.00)	1e-05 (0.0084)	1e-05 (0.0084)	1e-05 (0.0084)
19p gain	101 (20%)	411	0.22 (1.00)	1 (1.00)	1e-05 (0.0084)	1e-05 (0.0084)	0.675 (1.00)	0.424 (1.00)	1e-05 (0.0084)	1e-05 (0.0084)	0.0114 (1.00)	0.00164 (1.00)	1e-05 (0.0084)	2e-05 (0.0145)
4p loss	71 (14%)	441	1 (1.00)	0.782 (1.00)	0.051 (1.00)	1e-05 (0.0084)	0.352 (1.00)	1 (1.00)	5e-05 (0.0356)	1e-05 (0.0084)	2e-05 (0.0145)	2e-05 (0.0145)	0.0205 (1.00)	1e-05 (0.0084)
11p loss	63 (12%)	449	1 (1.00)	0.0312 (1.00)	1e-05 (0.0084)	1e-05 (0.0084)	0.012 (1.00)	0.726 (1.00)	1e-05 (0.0084)	1e-05 (0.0084)	0.00068 (0.443)	0.00024 (0.163)	0.00096 (0.611)	0.00025 (0.169)
22q loss	57 (11%)	455	0.815 (1.00)	0.00655 (1.00)	1e-05 (0.0084)	1e-05 (0.0084)	6e-05 (0.0426)	0.0398 (1.00)	1e-05 (0.0084)	1e-05 (0.0084)	0.501 (1.00)	0.00441 (1.00)	0.00288 (1.00)	0.00019 (0.129)
4q loss	91 (18%)	421	1 (1.00)	0.403 (1.00)	0.0156 (1.00)	1e-05 (0.0084)	0.258 (1.00)	0.932 (1.00)	0.00083 (0.534)	3e-05 (0.0216)	1e-05 (0.0084)	1e-05 (0.0084)	0.065 (1.00)	1e-05 (0.0084)
8p loss	17 (3%)	495	0.614 (1.00)	0.0437 (1.00)	1e-05 (0.0084)	5e-05 (0.0356)	0.0185 (1.00)	0.153 (1.00)	1e-05 (0.0084)	2e-05 (0.0145)	0.0781 (1.00)	0.00088 (0.564)	6e-05 (0.0426)	0.00196 (1.00)
11q loss	21 (4%)	491			0.00012 (0.0832)	0.0001 (0.0698)	0.0177 (1.00)	0.65 (1.00)	1e-05 (0.0084)	1e-05 (0.0084)	0.0627 (1.00)	0.00062 (0.407)	0.0014 (0.882)	0.00015 (0.103)
5q gain	8 (2%)	504			0.00318 (1.00)	0.00015 (0.103)			0.00016 (0.11)	0.00016 (0.11)	0.013 (1.00)	0.00072 (0.469)	0.00016 (0.11)	0.0008 (0.516)
10p gain	56 (11%)	456	1 (1.00)	0.0419 (1.00)	1e-05 (0.0084)	1e-05 (0.0084)	0.0209 (1.00)	0.554 (1.00)	1e-05 (0.0084)	1e-05 (0.0084)	0.0639 (1.00)	0.0925 (1.00)	0.00395 (1.00)	0.0009 (0.574)
xq gain	40 (8%)	472			1e-05 (0.0084)	1e-05 (0.0084)	0.234 (1.00)	0.716 (1.00)	6e-05 (0.0426)	2e-05 (0.0145)	0.0711 (1.00)	0.0224 (1.00)	0.0225 (1.00)	0.00643 (1.00)
8q loss	11 (2%)	501			0.0001 (0.0698)	3e-05 (0.0216)	0.0803 (1.00)	0.366 (1.00)	9e-05 (0.063)	9e-05 (0.063)	0.119 (1.00)	0.00266 (1.00)	0.0006 (0.394)	0.00289 (1.00)
xq loss	69 (13%)	443	0.839 (1.00)	0.266 (1.00)	0.705 (1.00)	0.00496 (1.00)	0.0436 (1.00)	0.0199 (1.00)	5e-05 (0.0356)	1e-05 (0.0084)	0.00078 (0.504)	0.00089 (0.569)	0.00028 (0.189)	6e-05 (0.0426)
5p gain	11 (2%)	501			0.0118 (1.00)	0.00212 (1.00)	0.0218 (1.00)	0.607 (1.00)	8e-05 (0.0562)	0.0001 (0.0698)	0.0236 (1.00)	0.0308 (1.00)	0.00017 (0.116)	0.0082 (1.00)
22q gain	23 (4%)	489			0.0131 (1.00)	1e-05 (0.0084)	1 (1.00)	0.686 (1.00)	0.0014 (0.882)	0.00031 (0.209)	0.305 (1.00)	0.0409 (1.00)	0.0337 (1.00)	0.00013 (0.0898)
5q loss	33 (6%)	479	0.446 (1.00)	0.236 (1.00)	1e-05 (0.0084)	0.00018 (0.123)	0.0198 (1.00)	0.116 (1.00)	0.0265 (1.00)	0.00659 (1.00)	3e-05 (0.0216)	0.0929 (1.00)	0.0618 (1.00)	0.00159 (0.994)
14q loss	80 (16%)	432	0.465 (1.00)	0.268 (1.00)	0.00025 (0.169)	0.00058 (0.382)	0.0456 (1.00)	0.116 (1.00)	2e-05 (0.0145)	2e-05 (0.0145)	0.0106 (1.00)	0.00082 (0.528)	0.00039 (0.261)	0.00046 (0.306)
1q gain	23 (4%)	489			0.00074 (0.48)	0.00031 (0.209)	0.433 (1.00)	0.605 (1.00)	3e-05 (0.0216)	0.00046 (0.306)	0.356 (1.00)	0.00339 (1.00)	0.00145 (0.911)	0.00513 (1.00)
8q gain	55 (11%)	457	0.0527 (1.00)	0.408 (1.00)	1e-05 (0.0084)	0.00016 (0.11)	0.0112 (1.00)	0.0581 (1.00)	0.00125 (0.792)	0.00044 (0.293)	0.215 (1.00)	0.0264 (1.00)	0.0028 (1.00)	0.00219 (1.00)
9p loss	118 (23%)	394	0.383 (1.00)	0.266 (1.00)	1e-05 (0.0084)	6e-05 (0.0426)	0.031 (1.00)	0.0203 (1.00)	0.0928 (1.00)	0.0501 (1.00)	0.856 (1.00)	0.168 (1.00)	0.389 (1.00)	0.0495 (1.00)
12q loss	51 (10%)	461	1 (1.00)	0.582 (1.00)	1e-05 (0.0084)	1e-05 (0.0084)	0.685 (1.00)	0.112 (1.00)	0.00686 (1.00)	0.00265 (1.00)	0.00369 (1.00)	0.302 (1.00)	0.158 (1.00)	0.16 (1.00)
13q loss	115 (22%)	397	0.181 (1.00)	4e-05 (0.0286)	1e-05 (0.0084)	0.0418 (1.00)	0.0243 (1.00)	0.627 (1.00)	0.0139 (1.00)	0.00394 (1.00)	0.107 (1.00)	0.149 (1.00)	0.021 (1.00)	0.0849 (1.00)
8p gain	45 (9%)	467			1e-05 (0.0084)	0.00288 (1.00)	0.0634 (1.00)	0.161 (1.00)	0.0189 (1.00)	0.00535 (1.00)	0.565 (1.00)	0.255 (1.00)	0.0581 (1.00)	0.0367 (1.00)
10q gain	12 (2%)	500			6e-05 (0.0426)	0.0389 (1.00)	0.266 (1.00)	0.517 (1.00)	0.0853 (1.00)	0.037 (1.00)	0.123 (1.00)	0.554 (1.00)	0.0775 (1.00)	0.473 (1.00)
12p gain	32 (6%)	480	0.754 (1.00)	0.583 (1.00)	8e-05 (0.0562)	0.0479 (1.00)	0.26 (1.00)	0.31 (1.00)	0.0195 (1.00)	0.0569 (1.00)	0.0358 (1.00)	0.018 (1.00)	0.00413 (1.00)	0.0231 (1.00)
18p gain	16 (3%)	496			7e-05 (0.0493)	0.00805 (1.00)	0.0225 (1.00)	0.442 (1.00)	0.0264 (1.00)	0.00956 (1.00)	0.643 (1.00)	0.334 (1.00)	0.313 (1.00)	0.205 (1.00)
18q gain	13 (3%)	499			0.00077 (0.498)	0.0103 (1.00)	0.082 (1.00)	0.598 (1.00)	0.00149 (0.934)	0.0003 (0.202)	0.634 (1.00)	0.0597 (1.00)	0.0836 (1.00)	0.0155 (1.00)
2p loss	21 (4%)	491			4e-05 (0.0286)	0.0568 (1.00)	0.331 (1.00)	1 (1.00)	0.165 (1.00)	0.0307 (1.00)	0.151 (1.00)	0.259 (1.00)	0.379 (1.00)	0.151 (1.00)
2q loss	18 (4%)	494			0.00011 (0.0763)	0.00871 (1.00)	0.0685 (1.00)	0.606 (1.00)	0.426 (1.00)	0.125 (1.00)	0.0284 (1.00)	0.4 (1.00)	0.438 (1.00)	0.242 (1.00)
5p loss	34 (7%)	478	0.742 (1.00)	0.0669 (1.00)	1e-05 (0.0084)	0.00047 (0.312)	0.917 (1.00)	0.953 (1.00)	0.172 (1.00)	0.0439 (1.00)	0.0709 (1.00)	0.366 (1.00)	0.366 (1.00)	0.132 (1.00)
6q loss	63 (12%)	449			1e-05 (0.0084)	0.00178 (1.00)	0.253 (1.00)	0.565 (1.00)	0.0787 (1.00)	0.0195 (1.00)	0.00499 (1.00)	0.0115 (1.00)	0.0163 (1.00)	0.00681 (1.00)
18q loss	62 (12%)	450	0.341 (1.00)	0.152 (1.00)	0.176 (1.00)	0.00035 (0.235)	0.284 (1.00)	0.0973 (1.00)	0.0319 (1.00)	0.00347 (1.00)	0.0505 (1.00)	0.346 (1.00)	0.122 (1.00)	0.436 (1.00)
21q loss	36 (7%)	476	0.616 (1.00)	0.0424 (1.00)	1e-05 (0.0084)	0.00047 (0.312)	0.463 (1.00)	0.654 (1.00)	0.00091 (0.58)	0.00064 (0.418)	0.378 (1.00)	0.114 (1.00)	0.0186 (1.00)	0.00465 (1.00)
2p gain	14 (3%)	498			0.0602 (1.00)	0.0284 (1.00)	0.311 (1.00)	0.345 (1.00)	0.0132 (1.00)	0.00085 (0.546)	0.426 (1.00)	0.136 (1.00)	0.11 (1.00)	0.17 (1.00)
2q gain	13 (3%)	499			0.138 (1.00)	0.023 (1.00)	0.311 (1.00)	0.346 (1.00)	0.035 (1.00)	0.00057 (0.376)	0.375 (1.00)	0.0343 (1.00)	0.0912 (1.00)	0.105 (1.00)
3p gain	11 (2%)	501			0.354 (1.00)	0.181 (1.00)	0.464 (1.00)	0.202 (1.00)	0.108 (1.00)	0.11 (1.00)	0.151 (1.00)	0.0963 (1.00)	0.2 (1.00)	0.184 (1.00)
3q gain	8 (2%)	504			0.216 (1.00)	0.068 (1.00)	0.0552 (1.00)	0.367 (1.00)	0.0628 (1.00)	0.0037 (1.00)	0.346 (1.00)	0.0836 (1.00)	0.129 (1.00)	0.142 (1.00)
4p gain	13 (3%)	499			0.0115 (1.00)	0.0195 (1.00)	0.0332 (1.00)	0.895 (1.00)	0.00825 (1.00)	0.0016 (0.998)	0.195 (1.00)	0.272 (1.00)	0.0876 (1.00)	0.0681 (1.00)
4q gain	6 (1%)	506			0.0367 (1.00)	0.0432 (1.00)	0.113 (1.00)	0.669 (1.00)	0.0157 (1.00)	0.00357 (1.00)	0.263 (1.00)	0.216 (1.00)	0.05 (1.00)	0.158 (1.00)
6p gain	7 (1%)	505			0.00073 (0.474)	0.0466 (1.00)	0.0375 (1.00)	0.517 (1.00)	0.441 (1.00)	0.0977 (1.00)	0.0264 (1.00)	0.0422 (1.00)	0.02 (1.00)	0.0244 (1.00)
9p gain	17 (3%)	495			0.0113 (1.00)	0.143 (1.00)	0.297 (1.00)	0.531 (1.00)	0.0662 (1.00)	0.0362 (1.00)	0.858 (1.00)	0.0747 (1.00)	0.283 (1.00)	0.0492 (1.00)
9q gain	23 (4%)	489			0.0199 (1.00)	0.132 (1.00)	0.257 (1.00)	0.0546 (1.00)	0.0302 (1.00)	0.013 (1.00)	0.56 (1.00)	0.0656 (1.00)	0.0378 (1.00)	0.0475 (1.00)
11p gain	31 (6%)	481			0.0794 (1.00)	0.00056 (0.37)	0.026 (1.00)	0.108 (1.00)	0.01 (1.00)	0.0033 (1.00)	0.101 (1.00)	0.0203 (1.00)	0.184 (1.00)	0.00153 (0.958)
11q gain	58 (11%)	454	0.614 (1.00)	0.58 (1.00)	0.335 (1.00)	0.0156 (1.00)	0.0814 (1.00)	0.0316 (1.00)	0.0614 (1.00)	0.0381 (1.00)	0.37 (1.00)	0.0277 (1.00)	0.404 (1.00)	0.00377 (1.00)
12q gain	16 (3%)	496			0.00062 (0.407)	0.0459 (1.00)	0.294 (1.00)	0.533 (1.00)	0.00611 (1.00)	0.0865 (1.00)	0.025 (1.00)	0.0607 (1.00)	0.00126 (0.798)	0.0235 (1.00)
13q gain	6 (1%)	506			0.374 (1.00)	0.436 (1.00)	0.794 (1.00)	0.794 (1.00)	0.235 (1.00)	0.474 (1.00)	0.434 (1.00)	0.265 (1.00)	0.876 (1.00)	0.492 (1.00)
14q gain	4 (1%)	508			1 (1.00)	0.892 (1.00)			0.71 (1.00)	0.596 (1.00)	0.497 (1.00)	0.624 (1.00)	0.14 (1.00)	0.324 (1.00)
15q gain	11 (2%)	501			0.00206 (1.00)	0.0208 (1.00)	0.045 (1.00)	0.216 (1.00)	0.0495 (1.00)	0.0132 (1.00)	0.11 (1.00)	0.142 (1.00)	0.0329 (1.00)	0.108 (1.00)
16p gain	16 (3%)	496			0.519 (1.00)	0.535 (1.00)	0.562 (1.00)	0.698 (1.00)	0.151 (1.00)	0.0919 (1.00)	0.178 (1.00)	0.341 (1.00)	0.404 (1.00)	0.14 (1.00)
16q gain	19 (4%)	493			0.0448 (1.00)	0.233 (1.00)	0.473 (1.00)	0.516 (1.00)	0.155 (1.00)	0.0338 (1.00)	0.0577 (1.00)	0.977 (1.00)	0.249 (1.00)	0.491 (1.00)
17p gain	20 (4%)	492			0.298 (1.00)	0.302 (1.00)	0.345 (1.00)	0.886 (1.00)	0.188 (1.00)	0.0465 (1.00)	0.15 (1.00)	0.348 (1.00)	0.0855 (1.00)	0.193 (1.00)
17q gain	23 (4%)	489			0.603 (1.00)	0.182 (1.00)	0.346 (1.00)	0.885 (1.00)	0.348 (1.00)	0.121 (1.00)	0.0743 (1.00)	0.309 (1.00)	0.312 (1.00)	0.127 (1.00)
21q gain	24 (5%)	488			0.0105 (1.00)	0.00275 (1.00)	0.108 (1.00)	0.392 (1.00)	0.425 (1.00)	0.211 (1.00)	0.723 (1.00)	0.103 (1.00)	0.329 (1.00)	0.208 (1.00)
1q loss	23 (4%)	489	0.345 (1.00)	0.152 (1.00)	0.735 (1.00)	0.0366 (1.00)	0.676 (1.00)	0.544 (1.00)	0.391 (1.00)	0.201 (1.00)	0.165 (1.00)	0.26 (1.00)	0.293 (1.00)	0.296 (1.00)
3p loss	30 (6%)	482			0.00039 (0.261)	0.164 (1.00)	0.00634 (1.00)	0.268 (1.00)	0.0393 (1.00)	0.0218 (1.00)	0.00849 (1.00)	0.0148 (1.00)	0.0139 (1.00)	0.0123 (1.00)
3q loss	28 (5%)	484	0.173 (1.00)	0.882 (1.00)	0.00138 (0.871)	0.151 (1.00)	0.257 (1.00)	0.768 (1.00)	0.0735 (1.00)	0.0631 (1.00)	0.157 (1.00)	0.17 (1.00)	0.143 (1.00)	0.0207 (1.00)
6p loss	30 (6%)	482			0.00135 (0.853)	0.123 (1.00)	0.187 (1.00)	0.688 (1.00)	0.379 (1.00)	0.46 (1.00)	0.675 (1.00)	0.177 (1.00)	0.674 (1.00)	0.00752 (1.00)
7p loss	3 (1%)	509			0.605 (1.00)	0.326 (1.00)			1 (1.00)	0.896 (1.00)	1 (1.00)	0.709 (1.00)	1 (1.00)	0.635 (1.00)
7q loss	3 (1%)	509			0.0477 (1.00)	0.325 (1.00)			0.373 (1.00)	0.176 (1.00)	1 (1.00)	0.889 (1.00)	0.599 (1.00)	0.634 (1.00)
9q loss	51 (10%)	461			0.0535 (1.00)	0.241 (1.00)	0.621 (1.00)	0.341 (1.00)	0.474 (1.00)	0.139 (1.00)	0.36 (1.00)	0.924 (1.00)	0.873 (1.00)	0.338 (1.00)
12p loss	26 (5%)	486			0.00974 (1.00)	0.011 (1.00)	0.605 (1.00)	1 (1.00)	0.401 (1.00)	0.326 (1.00)	0.0555 (1.00)	0.469 (1.00)	0.349 (1.00)	0.381 (1.00)
15q loss	51 (10%)	461	1 (1.00)	0.707 (1.00)	0.24 (1.00)	0.00047 (0.312)	0.272 (1.00)	0.0462 (1.00)	0.00122 (0.775)	0.00166 (1.00)	0.395 (1.00)	0.341 (1.00)	0.0762 (1.00)	0.0449 (1.00)
16p loss	14 (3%)	498			0.00337 (1.00)	0.126 (1.00)	0.866 (1.00)	0.202 (1.00)	0.0284 (1.00)	0.118 (1.00)	0.592 (1.00)	0.752 (1.00)	0.529 (1.00)	0.777 (1.00)
16q loss	22 (4%)	490			0.00359 (1.00)	0.00644 (1.00)	0.375 (1.00)	0.0657 (1.00)	0.0174 (1.00)	0.0924 (1.00)	0.647 (1.00)	0.169 (1.00)	0.548 (1.00)	0.0551 (1.00)
17p loss	13 (3%)	499			0.0148 (1.00)	0.214 (1.00)	1 (1.00)	0.783 (1.00)	0.0137 (1.00)	0.0639 (1.00)	0.269 (1.00)	0.00694 (1.00)	0.0718 (1.00)	0.0244 (1.00)
17q loss	8 (2%)	504			0.112 (1.00)	0.258 (1.00)	0.835 (1.00)	0.509 (1.00)	0.277 (1.00)	0.532 (1.00)	0.159 (1.00)	0.148 (1.00)	0.172 (1.00)	0.152 (1.00)
18p loss	68 (13%)	444	0.32 (1.00)	0.0309 (1.00)	0.56 (1.00)	0.026 (1.00)	0.58 (1.00)	0.106 (1.00)	0.138 (1.00)	0.0311 (1.00)	0.484 (1.00)	0.558 (1.00)	0.214 (1.00)	0.711 (1.00)
19p loss	23 (4%)	489	0.846 (1.00)	0.431 (1.00)	0.539 (1.00)	0.822 (1.00)	0.101 (1.00)	0.81 (1.00)	0.735 (1.00)	0.65 (1.00)	0.439 (1.00)	0.155 (1.00)	0.531 (1.00)	0.172 (1.00)
20p loss	7 (1%)	505			0.221 (1.00)	0.227 (1.00)	0.793 (1.00)	1 (1.00)	0.267 (1.00)	0.392 (1.00)	1 (1.00)	0.32 (1.00)	0.317 (1.00)	0.178 (1.00)
20q loss	3 (1%)	509			0.241 (1.00)	0.491 (1.00)			0.0232 (1.00)	0.138 (1.00)	0.216 (1.00)	0.705 (1.00)	0.569 (1.00)	0.634 (1.00)

'1p gain' versus 'CN_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.12

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
1P GAIN MUTATED	5	8	0
1P GAIN WILD-TYPE	163	110	226

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

'1p gain' versus 'METHLYATION_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.083

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	223	72	57	155
1P GAIN MUTATED	5	8	0	0
1P GAIN WILD-TYPE	218	64	57	155

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

'1p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	135	112	108	127	28
1P GAIN MUTATED	0	13	0	0	0
1P GAIN WILD-TYPE	135	99	108	127	28

Figure S3. 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 = 0.0084

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	137
1P GAIN MUTATED	0	13	0	0
1P GAIN WILD-TYPE	135	100	125	137

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

'1p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	107	137	100
1P GAIN MUTATED	3	0	0	10
1P GAIN WILD-TYPE	152	107	137	90

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

'1p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.07

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	113	94	69	146	34	18	25
1P GAIN MUTATED	2	8	0	0	0	3	0
1P GAIN WILD-TYPE	111	86	69	146	34	15	25

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

'1p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S7. Gene #1: '1p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	141	112	98
1P GAIN MUTATED	3	0	0	10
1P GAIN WILD-TYPE	145	141	112	88

Figure S7. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1q gain' versus 'METHLYATION_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.21

Table S8. Gene #2: '1q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	223	72	57	155
1Q GAIN MUTATED	9	11	1	2
1Q GAIN WILD-TYPE	214	61	56	153

Figure S8. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1q gain' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.022

Table S9. Gene #2: '1q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	135	112	108	127	28
1Q GAIN MUTATED	2	14	0	5	2
1Q GAIN WILD-TYPE	133	98	108	122	26

Figure S9. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5p gain' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.056

Table S10. Gene #9: '5p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	135	112	108	127	28
5P GAIN MUTATED	0	9	0	1	1
5P GAIN WILD-TYPE	135	103	108	126	27

Figure S10. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.07

Table S11. Gene #9: '5p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	137
5P GAIN MUTATED	1	9	0	1
5P GAIN WILD-TYPE	134	104	125	136

Figure S11. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.12

Table S12. Gene #9: '5p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	113	94	69	146	34	18	25
5P GAIN MUTATED	0	9	0	1	0	1	0
5P GAIN WILD-TYPE	113	85	69	145	34	17	25

Figure S12. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5q gain' versus 'METHLYATION_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.1

Table S13. Gene #10: '5q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	223	72	57	155
5Q GAIN MUTATED	1	6	1	0
5Q GAIN WILD-TYPE	222	66	56	155

Figure S13. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5q gain' versus 'MRNASEQ_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.11

Table S14. Gene #10: '5q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	135	112	108	127	28
5Q GAIN MUTATED	0	7	0	0	1
5Q GAIN WILD-TYPE	135	105	108	127	27

Figure S14. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.11

Table S15. Gene #10: '5q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	137
5Q GAIN MUTATED	1	7	0	0
5Q GAIN WILD-TYPE	134	106	125	137

Figure S15. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.11

Table S16. Gene #10: '5q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	113	94	69	146	34	18	25
5Q GAIN MUTATED	0	8	0	0	0	0	0
5Q GAIN WILD-TYPE	113	86	69	146	34	18	25

Figure S16. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S17. Gene #12: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
7P GAIN MUTATED	21	90	9
7P GAIN WILD-TYPE	147	28	217

Figure S17. 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 = 0.0084

Table S18. Gene #12: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	223	72	57	155
7P GAIN MUTATED	38	54	11	15
7P GAIN WILD-TYPE	185	18	46	140

Figure S18. Get High-res Image Gene #12: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p gain' versus 'RPPA_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.25

Table S19. 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 S19. Get High-res Image Gene #12: '7p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S20. Gene #12: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	135	112	108	127	28
7P GAIN MUTATED	22	59	9	22	6
7P GAIN WILD-TYPE	113	53	99	105	22

Figure S20. 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 = 0.0084

Table S21. Gene #12: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	137
7P GAIN MUTATED	19	58	11	30
7P GAIN WILD-TYPE	116	55	114	107

Figure S21. Get High-res Image Gene #12: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S22. Gene #12: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	107	137	100
7P GAIN MUTATED	29	18	16	55
7P GAIN WILD-TYPE	126	89	121	45

Figure S22. Get High-res Image Gene #12: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S23. Gene #12: '7p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	113	94	69	146	34	18	25
7P GAIN MUTATED	22	49	6	24	8	6	3
7P GAIN WILD-TYPE	91	45	63	122	26	12	22

Figure S23. 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 = 0.0084

Table S24. Gene #12: '7p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	141	112	98
7P GAIN MUTATED	26	25	12	55
7P GAIN WILD-TYPE	122	116	100	43

Figure S24. 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 = 0.0084

Table S25. Gene #13: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
7Q GAIN MUTATED	36	97	17
7Q GAIN WILD-TYPE	132	21	209

Figure S25. 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 = 0.0084

Table S26. Gene #13: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	223	72	57	155
7Q GAIN MUTATED	56	56	13	23
7Q GAIN WILD-TYPE	167	16	44	132

Figure S26. Get High-res Image Gene #13: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S27. Gene #13: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	135	112	108	127	28
7Q GAIN MUTATED	36	62	12	30	8
7Q GAIN WILD-TYPE	99	50	96	97	20

Figure S27. 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 = 0.0084

Table S28. Gene #13: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	137
7Q GAIN MUTATED	32	60	16	40
7Q GAIN WILD-TYPE	103	53	109	97

Figure S28. Get High-res Image Gene #13: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S29. Gene #13: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	107	137	100
7Q GAIN MUTATED	40	24	24	60
7Q GAIN WILD-TYPE	115	83	113	40

Figure S29. Get High-res Image Gene #13: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S30. Gene #13: '7q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	113	94	69	146	34	18	25
7Q GAIN MUTATED	30	52	7	34	14	6	5
7Q GAIN WILD-TYPE	83	42	62	112	20	12	20

Figure S30. 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 = 0.0084

Table S31. Gene #13: '7q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	141	112	98
7Q GAIN MUTATED	38	32	18	60
7Q GAIN WILD-TYPE	110	109	94	38

Figure S31. Get High-res Image Gene #13: '7q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S32. Gene #14: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
8P GAIN MUTATED	29	10	6
8P GAIN WILD-TYPE	139	108	220

Figure S32. Get High-res Image Gene #14: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S33. Gene #15: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
8Q GAIN MUTATED	35	13	7
8Q GAIN WILD-TYPE	133	105	219

Figure S33. Get High-res Image Gene #15: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.11

Table S34. Gene #15: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	223	72	57	155
8Q GAIN MUTATED	40	3	4	8
8Q GAIN WILD-TYPE	183	69	53	147

Figure S34. Get High-res Image Gene #15: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S35. Gene #18: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
10P GAIN MUTATED	48	2	6
10P GAIN WILD-TYPE	120	116	220

Figure S35. 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 = 0.0084

Table S36. Gene #18: '10p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	223	72	57	155
10P GAIN MUTATED	52	2	2	0
10P GAIN WILD-TYPE	171	70	55	155

Figure S36. Get High-res Image Gene #18: '10p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S37. Gene #18: '10p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	135	112	108	127	28
10P GAIN MUTATED	29	14	0	12	1
10P GAIN WILD-TYPE	106	98	108	115	27

Figure S37. 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 = 0.0084

Table S38. Gene #18: '10p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	137
10P GAIN MUTATED	29	14	0	13
10P GAIN WILD-TYPE	106	99	125	124

Figure S38. Get High-res Image Gene #18: '10p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q gain' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.043

Table S39. Gene #19: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
10Q GAIN MUTATED	11	0	1
10Q GAIN WILD-TYPE	157	118	225

Figure S39. Get High-res Image Gene #19: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.056

Table S40. Gene #22: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
12P GAIN MUTATED	19	10	3
12P GAIN WILD-TYPE	149	108	223

Figure S40. Get High-res Image Gene #22: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

'18p gain' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.049

Table S41. Gene #31: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
18P GAIN MUTATED	11	5	0
18P GAIN WILD-TYPE	157	113	226

Figure S41. Get High-res Image Gene #31: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

'18q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.2

Table S42. Gene #32: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	137
18Q GAIN MUTATED	2	9	0	1
18Q GAIN WILD-TYPE	133	104	125	136

Figure S42. Get High-res Image Gene #32: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S43. Gene #33: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
19P GAIN MUTATED	7	37	57
19P GAIN WILD-TYPE	161	81	169

Figure S43. 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 = 0.0084

Table S44. Gene #33: '19p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	223	72	57	155
19P GAIN MUTATED	10	27	5	57
19P GAIN WILD-TYPE	213	45	52	98

Figure S44. 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 = 0.0084

Table S45. Gene #33: '19p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	135	112	108	127	28
19P GAIN MUTATED	5	30	45	20	1
19P GAIN WILD-TYPE	130	82	63	107	27

Figure S45. 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 = 0.0084

Table S46. Gene #33: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	137
19P GAIN MUTATED	6	28	45	22
19P GAIN WILD-TYPE	129	85	80	115

Figure S46. Get High-res Image Gene #33: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S47. Gene #33: '19p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	113	94	69	146	34	18	25
19P GAIN MUTATED	4	26	30	27	8	2	2
19P GAIN WILD-TYPE	109	68	39	119	26	16	23

Figure S47. Get High-res Image Gene #33: '19p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S48. Gene #33: '19p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	141	112	98
19P GAIN MUTATED	12	40	19	28
19P GAIN WILD-TYPE	136	101	93	70

Figure S48. 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 = 0.0084

Table S49. Gene #34: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
19Q GAIN MUTATED	1	23	1
19Q GAIN WILD-TYPE	167	95	225

Figure S49. 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 = 0.0084

Table S50. Gene #34: '19q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	223	72	57	155
19Q GAIN MUTATED	2	20	2	0
19Q GAIN WILD-TYPE	221	52	55	155

Figure S50. 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 = 0.0084

Table S51. Gene #34: '19q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	135	112	108	127	28
19Q GAIN MUTATED	1	19	0	4	1
19Q GAIN WILD-TYPE	134	93	108	123	27

Figure S51. 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 = 0.0084

Table S52. Gene #34: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	137
19Q GAIN MUTATED	2	19	0	4
19Q GAIN WILD-TYPE	133	94	125	133

Figure S52. Get High-res Image Gene #34: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S53. Gene #34: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	107	137	100
19Q GAIN MUTATED	3	0	2	20
19Q GAIN WILD-TYPE	152	107	135	80

Figure S53. 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 = 0.0084

Table S54. Gene #34: '19q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	113	94	69	146	34	18	25
19Q GAIN MUTATED	0	19	0	5	1	0	0
19Q GAIN WILD-TYPE	113	75	69	141	33	18	25

Figure S54. 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 = 0.0084

Table S55. Gene #34: '19q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	141	112	98
19Q GAIN MUTATED	2	1	1	21
19Q GAIN WILD-TYPE	146	140	111	77

Figure S55. 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 = 0.0084

Table S56. Gene #35: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
20P GAIN MUTATED	8	31	4
20P GAIN WILD-TYPE	160	87	222

Figure S56. 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 = 0.0084

Table S57. Gene #35: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	223	72	57	155
20P GAIN MUTATED	7	26	4	6
20P GAIN WILD-TYPE	216	46	53	149

Figure S57. Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S58. Gene #35: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	135	112	108	127	28
20P GAIN MUTATED	3	28	3	8	1
20P GAIN WILD-TYPE	132	84	105	119	27

Figure S58. 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 = 0.0084

Table S59. Gene #35: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	137
20P GAIN MUTATED	3	26	4	10
20P GAIN WILD-TYPE	132	87	121	127

Figure S59. 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 = 0.0084

Table S60. Gene #35: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	107	137	100
20P GAIN MUTATED	5	4	8	26
20P GAIN WILD-TYPE	150	103	129	74

Figure S60. Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S61. Gene #35: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	113	94	69	146	34	18	25
20P GAIN MUTATED	2	22	2	10	5	2	0
20P GAIN WILD-TYPE	111	72	67	136	29	16	25

Figure S61. 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 = 0.0084

Table S62. Gene #35: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	141	112	98
20P GAIN MUTATED	7	6	4	26
20P GAIN WILD-TYPE	141	135	108	72

Figure S62. 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 = 0.0084

Table S63. Gene #36: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
20Q GAIN MUTATED	8	31	4
20Q GAIN WILD-TYPE	160	87	222

Figure S63. 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 = 0.0084

Table S64. Gene #36: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	223	72	57	155
20Q GAIN MUTATED	8	27	2	6
20Q GAIN WILD-TYPE	215	45	55	149

Figure S64. Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S65. Gene #36: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	135	112	108	127	28
20Q GAIN MUTATED	4	29	3	6	1
20Q GAIN WILD-TYPE	131	83	105	121	27

Figure S65. 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 = 0.0084

Table S66. Gene #36: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	137
20Q GAIN MUTATED	4	27	4	8
20Q GAIN WILD-TYPE	131	86	121	129

Figure S66. 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 = 0.0084

Table S67. Gene #36: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	107	137	100
20Q GAIN MUTATED	8	4	6	25
20Q GAIN WILD-TYPE	147	103	131	75

Figure S67. Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S68. Gene #36: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	113	94	69	146	34	18	25
20Q GAIN MUTATED	2	23	2	8	6	2	0
20Q GAIN WILD-TYPE	111	71	67	138	28	16	25

Figure S68. 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 = 0.0084

Table S69. Gene #36: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	141	112	98
20Q GAIN MUTATED	9	6	2	26
20Q GAIN WILD-TYPE	139	135	110	72

Figure S69. Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S70. Gene #38: '22q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	223	72	57	155
22Q GAIN MUTATED	2	3	0	18
22Q GAIN WILD-TYPE	221	69	57	137

Figure S70. Get High-res Image Gene #38: '22q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.21

Table S71. Gene #38: '22q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	137
22Q GAIN MUTATED	0	4	13	6
22Q GAIN WILD-TYPE	135	109	112	131

Figure S71. Get High-res Image Gene #38: '22q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.09

Table S72. Gene #38: '22q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	141	112	98
22Q GAIN MUTATED	1	15	2	3
22Q GAIN WILD-TYPE	147	126	110	95

Figure S72. Get High-res Image Gene #38: '22q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S73. Gene #39: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
XQ GAIN MUTATED	32	6	2
XQ GAIN WILD-TYPE	136	112	224

Figure S73. Get High-res Image Gene #39: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

'xq gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S74. Gene #39: 'xq gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	223	72	57	155
XQ GAIN MUTATED	34	3	3	0
XQ GAIN WILD-TYPE	189	69	54	155

Figure S74. Get High-res Image Gene #39: 'xq gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xq gain' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.043

Table S75. Gene #39: 'xq gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	135	112	108	127	28
XQ GAIN MUTATED	19	7	0	10	4
XQ GAIN WILD-TYPE	116	105	108	117	24

Figure S75. Get High-res Image Gene #39: 'xq gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'xq gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S76. Gene #39: 'xq gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	137
XQ GAIN MUTATED	23	7	0	10
XQ GAIN WILD-TYPE	112	106	125	127

Figure S76. Get High-res Image Gene #39: 'xq gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 0.19

Table S77. Gene #40: '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 S77. Get High-res Image Gene #40: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S78. Gene #40: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
1P LOSS MUTATED	6	16	161
1P LOSS WILD-TYPE	162	102	65

Figure S78. Get High-res Image Gene #40: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S79. Gene #40: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	223	72	57	155
1P LOSS MUTATED	4	4	18	154
1P LOSS WILD-TYPE	219	68	39	1

Figure S79. Get High-res Image Gene #40: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1p loss' versus 'RPPA_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.12

Table S80. Gene #40: '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	14	26	36
1P LOSS WILD-TYPE	44	48	42	38

Figure S80. Get High-res Image Gene #40: '1p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S81. Gene #40: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	135	112	108	127	28
1P LOSS MUTATED	3	9	106	55	10
1P LOSS WILD-TYPE	132	103	2	72	18

Figure S81. Get High-res Image Gene #40: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S82. Gene #40: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	137
1P LOSS MUTATED	3	7	122	51
1P LOSS WILD-TYPE	132	106	3	86

Figure S82. Get High-res Image Gene #40: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S83. Gene #40: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	136	104	187	72
1P LOSS MUTATED	27	8	89	57
1P LOSS WILD-TYPE	109	96	98	15

Figure S83. Get High-res Image Gene #40: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S84. Gene #40: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	107	137	100
1P LOSS MUTATED	32	80	62	7
1P LOSS WILD-TYPE	123	27	75	93

Figure S84. Get High-res Image Gene #40: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S85. Gene #40: '1p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	113	94	69	146	34	18	25
1P LOSS MUTATED	4	16	64	70	13	1	13
1P LOSS WILD-TYPE	109	78	5	76	21	17	12

Figure S85. Get High-res Image Gene #40: '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 = 0.0084

Table S86. Gene #40: '1p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	141	112	98
1P LOSS MUTATED	19	99	56	7
1P LOSS WILD-TYPE	129	42	56	91

Figure S86. Get High-res Image Gene #40: '1p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2p loss' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.029

Table S87. Gene #42: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
2P LOSS MUTATED	17	2	2
2P LOSS WILD-TYPE	151	116	224

Figure S87. Get High-res Image Gene #42: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

'2q loss' versus 'CN_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.076

Table S88. Gene #43: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
2Q LOSS MUTATED	15	1	2
2Q LOSS WILD-TYPE	153	117	224

Figure S88. Get High-res Image Gene #43: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S89. Gene #46: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	223	72	57	155
4P LOSS MUTATED	25	1	1	44
4P LOSS WILD-TYPE	198	71	56	111

Figure S89. Get High-res Image Gene #46: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.036

Table S90. Gene #46: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	135	112	108	127	28
4P LOSS MUTATED	15	5	30	17	3
4P LOSS WILD-TYPE	120	107	78	110	25

Figure S90. Get High-res Image Gene #46: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S91. Gene #46: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	137
4P LOSS MUTATED	13	4	37	16
4P LOSS WILD-TYPE	122	109	88	121

Figure S91. Get High-res Image Gene #46: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S92. Gene #46: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	136	104	187	72
4P LOSS MUTATED	10	12	24	24
4P LOSS WILD-TYPE	126	92	163	48

Figure S92. Get High-res Image Gene #46: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S93. Gene #46: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	107	137	100
4P LOSS MUTATED	21	31	13	5
4P LOSS WILD-TYPE	134	76	124	95

Figure S93. Get High-res Image Gene #46: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S94. Gene #46: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	141	112	98
4P LOSS MUTATED	16	39	12	3
4P LOSS WILD-TYPE	132	102	100	95

Figure S94. Get High-res Image Gene #46: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S95. Gene #47: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	223	72	57	155
4Q LOSS MUTATED	39	1	4	47
4Q LOSS WILD-TYPE	184	71	53	108

Figure S95. Get High-res Image Gene #47: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.022

Table S96. Gene #47: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	137
4Q LOSS MUTATED	18	9	39	24
4Q LOSS WILD-TYPE	117	104	86	113

Figure S96. Get High-res Image Gene #47: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S97. Gene #47: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	136	104	187	72
4Q LOSS MUTATED	11	17	37	25
4Q LOSS WILD-TYPE	125	87	150	47

Figure S97. Get High-res Image Gene #47: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S98. Gene #47: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	107	137	100
4Q LOSS MUTATED	25	37	20	8
4Q LOSS WILD-TYPE	130	70	117	92

Figure S98. Get High-res Image Gene #47: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S99. Gene #47: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	141	112	98
4Q LOSS MUTATED	22	45	19	4
4Q LOSS WILD-TYPE	126	96	93	94

Figure S99. Get High-res Image Gene #47: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S100. Gene #48: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
5P LOSS MUTATED	26	5	3
5P LOSS WILD-TYPE	142	113	223

Figure S100. Get High-res Image Gene #48: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

'5q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S101. Gene #49: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
5Q LOSS MUTATED	27	3	3
5Q LOSS WILD-TYPE	141	115	223

Figure S101. Get High-res Image Gene #49: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.12

Table S102. Gene #49: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	223	72	57	155
5Q LOSS MUTATED	26	3	2	2
5Q LOSS WILD-TYPE	197	69	55	153

Figure S102. Get High-res Image Gene #49: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5q loss' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.022

Table S103. Gene #49: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	136	104	187	72
5Q LOSS MUTATED	6	18	9	0
5Q LOSS WILD-TYPE	130	86	178	72

Figure S103. Get High-res Image Gene #49: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S104. Gene #51: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
6Q LOSS MUTATED	29	26	8
6Q LOSS WILD-TYPE	139	92	218

Figure S104. Get High-res Image Gene #51: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S105. Gene #54: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
8P LOSS MUTATED	7	10	0
8P LOSS WILD-TYPE	161	108	226

Figure S105. Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.036

Table S106. Gene #54: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	223	72	57	155
8P LOSS MUTATED	7	9	1	0
8P LOSS WILD-TYPE	216	63	56	155

Figure S106. Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S107. Gene #54: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	135	112	108	127	28
8P LOSS MUTATED	0	13	0	3	1
8P LOSS WILD-TYPE	135	99	108	124	27

Figure S107. Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S108. Gene #54: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	137
8P LOSS MUTATED	1	13	0	3
8P LOSS WILD-TYPE	134	100	125	134

Figure S108. Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.043

Table S109. Gene #54: '8p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	113	94	69	146	34	18	25
8P LOSS MUTATED	0	12	0	3	0	1	1
8P LOSS WILD-TYPE	113	82	69	143	34	17	24

Figure S109. Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8q loss' versus 'CN_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.07

Table S110. Gene #55: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
8Q LOSS MUTATED	3	8	0
8Q LOSS WILD-TYPE	165	110	226

Figure S110. Get High-res Image Gene #55: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'

'8q loss' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.022

Table S111. Gene #55: '8q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	223	72	57	155
8Q LOSS MUTATED	2	8	1	0
8Q LOSS WILD-TYPE	221	64	56	155

Figure S111. Get High-res Image Gene #55: '8q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8q loss' versus 'MRNASEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.063

Table S112. Gene #55: '8q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	135	112	108	127	28
8Q LOSS MUTATED	0	9	0	1	1
8Q LOSS WILD-TYPE	135	103	108	126	27

Figure S112. Get High-res Image Gene #55: '8q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.063

Table S113. Gene #55: '8q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	137
8Q LOSS MUTATED	1	9	0	1
8Q LOSS WILD-TYPE	134	104	125	136

Figure S113. Get High-res Image Gene #55: '8q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S114. Gene #56: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
9P LOSS MUTATED	47	45	26
9P LOSS WILD-TYPE	121	73	200

Figure S114. Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.043

Table S115. Gene #56: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	223	72	57	155
9P LOSS MUTATED	61	27	7	21
9P LOSS WILD-TYPE	162	45	50	134

Figure S115. Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S116. Gene #58: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
10P LOSS MUTATED	7	71	5
10P LOSS WILD-TYPE	161	47	221

Figure S116. Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S117. Gene #58: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	223	72	57	155
10P LOSS MUTATED	4	62	10	6
10P LOSS WILD-TYPE	219	10	47	149

Figure S117. Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S118. Gene #58: '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 S118. Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S119. Gene #58: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	135	112	108	127	28
10P LOSS MUTATED	1	64	1	12	4
10P LOSS WILD-TYPE	134	48	107	115	24

Figure S119. Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S120. Gene #58: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	137
10P LOSS MUTATED	1	63	6	12
10P LOSS WILD-TYPE	134	50	119	125

Figure S120. Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.049

Table S121. Gene #58: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	136	104	187	72
10P LOSS MUTATED	34	24	19	4
10P LOSS WILD-TYPE	102	80	168	68

Figure S121. Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S122. Gene #58: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	107	137	100
10P LOSS MUTATED	8	5	9	59
10P LOSS WILD-TYPE	147	102	128	41

Figure S122. Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S123. Gene #58: '10p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	113	94	69	146	34	18	25
10P LOSS MUTATED	2	52	2	15	6	2	2
10P LOSS WILD-TYPE	111	42	67	131	28	16	23

Figure S123. Get High-res Image Gene #58: '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 = 0.0084

Table S124. Gene #58: '10p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	141	112	98
10P LOSS MUTATED	8	4	6	63
10P LOSS WILD-TYPE	140	137	106	35

Figure S124. Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S125. Gene #59: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
10Q LOSS MUTATED	18	72	6
10Q LOSS WILD-TYPE	150	46	220

Figure S125. Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S126. Gene #59: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	223	72	57	155
10Q LOSS MUTATED	17	62	10	6
10Q LOSS WILD-TYPE	206	10	47	149

Figure S126. Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S127. Gene #59: '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 S127. Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S128. Gene #59: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	135	112	108	127	28
10Q LOSS MUTATED	5	70	1	15	4
10Q LOSS WILD-TYPE	130	42	107	112	24

Figure S128. Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S129. Gene #59: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	137
10Q LOSS MUTATED	6	68	6	15
10Q LOSS WILD-TYPE	129	45	119	122

Figure S129. Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S130. Gene #59: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	136	104	187	72
10Q LOSS MUTATED	37	30	23	5
10Q LOSS WILD-TYPE	99	74	164	67

Figure S130. Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S131. Gene #59: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	107	137	100
10Q LOSS MUTATED	12	7	11	65
10Q LOSS WILD-TYPE	143	100	126	35

Figure S131. Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S132. Gene #59: '10q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	113	94	69	146	34	18	25
10Q LOSS MUTATED	5	55	2	17	8	5	3
10Q LOSS WILD-TYPE	108	39	67	129	26	13	22

Figure S132. Get High-res Image Gene #59: '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 = 0.0084

Table S133. Gene #59: '10q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	141	112	98
10Q LOSS MUTATED	13	4	8	70
10Q LOSS WILD-TYPE	135	137	104	28

Figure S133. Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S134. Gene #60: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
11P LOSS MUTATED	49	11	3
11P LOSS WILD-TYPE	119	107	223

Figure S134. Get High-res Image Gene #60: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S135. Gene #60: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	223	72	57	155
11P LOSS MUTATED	47	12	4	0
11P LOSS WILD-TYPE	176	60	53	155

Figure S135. Get High-res Image Gene #60: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S136. Gene #60: '11p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	135	112	108	127	28
11P LOSS MUTATED	14	31	0	11	6
11P LOSS WILD-TYPE	121	81	108	116	22

Figure S136. Get High-res Image Gene #60: '11p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S137. Gene #60: '11p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	137
11P LOSS MUTATED	17	34	0	11
11P LOSS WILD-TYPE	118	79	125	126

Figure S137. Get High-res Image Gene #60: '11p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.16

Table S138. Gene #60: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	107	137	100
11P LOSS MUTATED	18	5	12	24
11P LOSS WILD-TYPE	137	102	125	76

Figure S138. Get High-res Image Gene #60: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00025 (Fisher's exact test), Q value = 0.17

Table S139. Gene #60: '11p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	141	112	98
11P LOSS MUTATED	22	6	10	21
11P LOSS WILD-TYPE	126	135	102	77

Figure S139. Get High-res Image Gene #60: '11p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.083

Table S140. Gene #61: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
11Q LOSS MUTATED	11	9	1
11Q LOSS WILD-TYPE	157	109	225

Figure S140. Get High-res Image Gene #61: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.07

Table S141. Gene #61: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	223	72	57	155
11Q LOSS MUTATED	9	9	3	0
11Q LOSS WILD-TYPE	214	63	54	155

Figure S141. Get High-res Image Gene #61: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S142. Gene #61: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	135	112	108	127	28
11Q LOSS MUTATED	1	16	0	3	1
11Q LOSS WILD-TYPE	134	96	108	124	27

Figure S142. Get High-res Image Gene #61: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S143. Gene #61: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	137
11Q LOSS MUTATED	2	16	0	3
11Q LOSS WILD-TYPE	133	97	125	134

Figure S143. Get High-res Image Gene #61: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.1

Table S144. Gene #61: '11q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	141	112	98
11Q LOSS MUTATED	5	1	2	12
11Q LOSS WILD-TYPE	143	140	110	86

Figure S144. Get High-res Image Gene #61: '11q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S145. Gene #63: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
12Q LOSS MUTATED	40	3	8
12Q LOSS WILD-TYPE	128	115	218

Figure S145. Get High-res Image Gene #63: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

'12q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S146. Gene #63: '12q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	223	72	57	155
12Q LOSS MUTATED	41	0	5	5
12Q LOSS WILD-TYPE	182	72	52	150

Figure S146. Get High-res Image Gene #63: '12q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q loss' versus 'MRNA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.029

Table S147. Gene #64: '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 S147. Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S148. Gene #64: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
13Q LOSS MUTATED	62	26	27
13Q LOSS WILD-TYPE	106	92	199

Figure S148. Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

'14q loss' versus 'CN_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.17

Table S149. Gene #65: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
14Q LOSS MUTATED	26	32	22
14Q LOSS WILD-TYPE	142	86	204

Figure S149. Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S150. Gene #65: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	135	112	108	127	28
14Q LOSS MUTATED	10	35	11	16	7
14Q LOSS WILD-TYPE	125	77	97	111	21

Figure S150. Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S151. Gene #65: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	137
14Q LOSS MUTATED	15	35	13	16
14Q LOSS WILD-TYPE	120	78	112	121

Figure S151. Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'METHLYATION_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.23

Table S152. Gene #72: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	223	72	57	155
18Q LOSS MUTATED	19	8	2	33
18Q LOSS WILD-TYPE	204	64	55	122

Figure S152. Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S153. Gene #74: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
19Q LOSS MUTATED	28	19	162
19Q LOSS WILD-TYPE	140	99	64

Figure S153. Get High-res Image Gene #74: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S154. Gene #74: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	223	72	57	155
19Q LOSS MUTATED	30	4	18	154
19Q LOSS WILD-TYPE	193	68	39	1

Figure S154. Get High-res Image Gene #74: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S155. Gene #74: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	135	112	108	127	28
19Q LOSS MUTATED	18	15	106	59	10
19Q LOSS WILD-TYPE	117	97	2	68	18

Figure S155. Get High-res Image Gene #74: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S156. Gene #74: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	137
19Q LOSS MUTATED	16	14	122	56
19Q LOSS WILD-TYPE	119	99	3	81

Figure S156. Get High-res Image Gene #74: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S157. Gene #74: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	136	104	187	72
19Q LOSS MUTATED	32	22	94	57
19Q LOSS WILD-TYPE	104	82	93	15

Figure S157. Get High-res Image Gene #74: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S158. Gene #74: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	107	137	100
19Q LOSS MUTATED	45	85	65	10
19Q LOSS WILD-TYPE	110	22	72	90

Figure S158. Get High-res Image Gene #74: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S159. Gene #74: '19q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	113	94	69	146	34	18	25
19Q LOSS MUTATED	16	18	63	75	15	4	14
19Q LOSS WILD-TYPE	97	76	6	71	19	14	11

Figure S159. Get High-res Image Gene #74: '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 = 0.0084

Table S160. Gene #74: '19q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	141	112	98
19Q LOSS MUTATED	36	101	60	8
19Q LOSS WILD-TYPE	112	40	52	90

Figure S160. Get High-res Image Gene #74: '19q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S161. Gene #77: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
21Q LOSS MUTATED	26	5	5
21Q LOSS WILD-TYPE	142	113	221

Figure S161. Get High-res Image Gene #77: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S162. Gene #78: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
22Q LOSS MUTATED	28	27	2
22Q LOSS WILD-TYPE	140	91	224

Figure S162. Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S163. Gene #78: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	223	72	57	155
22Q LOSS MUTATED	24	21	8	4
22Q LOSS WILD-TYPE	199	51	49	151

Figure S163. Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q loss' versus 'RPPA_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.043

Table S164. Gene #78: '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 S164. Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S165. Gene #78: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	135	112	108	127	28
22Q LOSS MUTATED	9	31	2	10	4
22Q LOSS WILD-TYPE	126	81	106	117	24

Figure S165. Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S166. Gene #78: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	137
22Q LOSS MUTATED	11	29	4	12
22Q LOSS WILD-TYPE	124	84	121	125

Figure S166. Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.13

Table S167. Gene #78: '22q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	141	112	98
22Q LOSS MUTATED	13	9	8	24
22Q LOSS WILD-TYPE	135	132	104	74

Figure S167. Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq loss' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.036

Table S168. Gene #79: 'xq loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	135	112	108	127	28
XQ LOSS MUTATED	11	23	25	10	0
XQ LOSS WILD-TYPE	124	89	83	117	28

Figure S168. Get High-res Image Gene #79: 'xq loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'xq loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0084

Table S169. Gene #79: 'xq loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	137
XQ LOSS MUTATED	10	23	29	7
XQ LOSS WILD-TYPE	125	90	96	130

Figure S169. Get High-res Image Gene #79: 'xq loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.19

Table S170. Gene #79: 'xq loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	113	94	69	146	34	18	25
XQ LOSS MUTATED	8	16	19	11	7	4	1
XQ LOSS WILD-TYPE	105	78	50	135	27	14	24

Figure S170. Get High-res Image Gene #79: 'xq loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'xq loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.043

Table S171. Gene #79: 'xq loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	141	112	98
XQ LOSS MUTATED	21	27	2	16
XQ LOSS WILD-TYPE	127	114	110	82

Figure S171. Get High-res Image Gene #79: 'xq loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtypes file = LGG-TP.transferedmergedcluster.txt
Number of patients = 512
Number of significantly arm-level cnvs = 79
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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