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

Brain Lower Grade Glioma (Primary solid tumor)

17 October 2014 | analyses__2014_10_17

Maintainer Information

Citation Information

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

Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1ZP451P

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 513 patients, 164 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', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
1q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
5p gain cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
5q gain cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
7p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
7q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 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'.
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', and 'MIRSEQ_CNMF'.
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', 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'.
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'.
4p loss cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
4q loss cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
5p loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
5q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.
6q loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.
8p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
8q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_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_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
11q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_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 'METHLYATION_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' and 'METHLYATION_CNMF'.
22q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
xq loss cnv correlated to 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 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, 164 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	0.0295 (1.00)	0.00019 (0.131)	1e-05 (0.00836)	1e-05 (0.00836)	0.00027 (0.183)	0.458 (1.00)	1e-05 (0.00836)	1e-05 (0.00836)	1e-05 (0.00836)	1e-05 (0.00836)	1e-05 (0.00836)	1e-05 (0.00836)
10p loss	83 (16%)	430	0.269 (1.00)	0.881 (1.00)	1e-05 (0.00836)	1e-05 (0.00836)	1e-05 (0.00836)	0.00111 (0.712)	1e-05 (0.00836)	1e-05 (0.00836)	2e-05 (0.0147)	1e-05 (0.00836)	1e-05 (0.00836)	1e-05 (0.00836)
10q loss	96 (19%)	417	0.273 (1.00)	0.883 (1.00)	1e-05 (0.00836)	1e-05 (0.00836)	1e-05 (0.00836)	0.00042 (0.281)	1e-05 (0.00836)	1e-05 (0.00836)	1e-05 (0.00836)	1e-05 (0.00836)	1e-05 (0.00836)	1e-05 (0.00836)
19q loss	209 (41%)	304	0.186 (1.00)	0.0126 (1.00)	1e-05 (0.00836)	1e-05 (0.00836)	0.0384 (1.00)	0.335 (1.00)	1e-05 (0.00836)	1e-05 (0.00836)	1e-05 (0.00836)	1e-05 (0.00836)	1e-05 (0.00836)	1e-05 (0.00836)
19q gain	25 (5%)	488			1e-05 (0.00836)	1e-05 (0.00836)	0.0566 (1.00)	0.399 (1.00)	1e-05 (0.00836)	1e-05 (0.00836)	0.00243 (1.00)	1e-05 (0.00836)	1e-05 (0.00836)	1e-05 (0.00836)
20q gain	43 (8%)	470			1e-05 (0.00836)	1e-05 (0.00836)	0.00073 (0.477)	0.144 (1.00)	1e-05 (0.00836)	1e-05 (0.00836)	0.0491 (1.00)	1e-05 (0.00836)	4e-05 (0.029)	1e-05 (0.00836)
4p loss	71 (14%)	442	1 (1.00)	0.783 (1.00)	0.0033 (1.00)	1e-05 (0.00836)	0.351 (1.00)	1 (1.00)	4e-05 (0.029)	1e-05 (0.00836)	5e-05 (0.0359)	0.00034 (0.229)	4e-05 (0.029)	1e-05 (0.00836)
22q loss	57 (11%)	456	0.818 (1.00)	0.00687 (1.00)	1e-05 (0.00836)	1e-05 (0.00836)	4e-05 (0.029)	0.0402 (1.00)	1e-05 (0.00836)	1e-05 (0.00836)	0.453 (1.00)	0.00033 (0.222)	0.0116 (1.00)	0.00015 (0.104)
1p gain	13 (3%)	500			6e-05 (0.0427)	0.00016 (0.111)	0.0242 (1.00)	1 (1.00)	1e-05 (0.00836)	1e-05 (0.00836)	0.00558 (1.00)	2e-05 (0.0147)	0.0123 (1.00)	0.00014 (0.0974)
7p gain	121 (24%)	392	0.745 (1.00)	0.781 (1.00)	1e-05 (0.00836)	1e-05 (0.00836)	0.00044 (0.293)	0.0116 (1.00)	1e-05 (0.00836)	1e-05 (0.00836)	0.00263 (1.00)	1e-05 (0.00836)	0.00039 (0.262)	1e-05 (0.00836)
7q gain	151 (29%)	362	0.762 (1.00)	0.52 (1.00)	1e-05 (0.00836)	1e-05 (0.00836)	0.00403 (1.00)	0.2 (1.00)	1e-05 (0.00836)	1e-05 (0.00836)	0.00328 (1.00)	1e-05 (0.00836)	0.00079 (0.516)	1e-05 (0.00836)
20p gain	43 (8%)	470			1e-05 (0.00836)	1e-05 (0.00836)	0.00067 (0.441)	0.175 (1.00)	1e-05 (0.00836)	1e-05 (0.00836)	0.16 (1.00)	1e-05 (0.00836)	0.00095 (0.617)	1e-05 (0.00836)
11p loss	63 (12%)	450	1 (1.00)	0.0315 (1.00)	1e-05 (0.00836)	1e-05 (0.00836)	0.0122 (1.00)	0.726 (1.00)	1e-05 (0.00836)	1e-05 (0.00836)	2e-05 (0.0147)	5e-05 (0.0359)	0.434 (1.00)	0.0165 (1.00)
19p gain	100 (19%)	413	0.22 (1.00)	1 (1.00)	1e-05 (0.00836)	1e-05 (0.00836)	0.677 (1.00)	0.424 (1.00)	1e-05 (0.00836)	1e-05 (0.00836)	0.00018 (0.124)	0.0385 (1.00)	0.235 (1.00)	0.00254 (1.00)
4q loss	92 (18%)	421	1 (1.00)	0.404 (1.00)	0.0066 (1.00)	1e-05 (0.00836)	0.258 (1.00)	0.931 (1.00)	0.00071 (0.465)	1e-05 (0.00836)	0.00021 (0.144)	0.00148 (0.937)	2e-05 (0.0147)	2e-05 (0.0147)
8p loss	17 (3%)	496	0.616 (1.00)	0.0426 (1.00)	2e-05 (0.0147)	5e-05 (0.0359)	0.019 (1.00)	0.152 (1.00)	1e-05 (0.00836)	1e-05 (0.00836)	0.117 (1.00)	0.00145 (0.919)	0.816 (1.00)	0.00027 (0.183)
8q loss	11 (2%)	502			0.0002 (0.137)	2e-05 (0.0147)	0.0823 (1.00)	0.364 (1.00)	8e-05 (0.0566)	7e-05 (0.0497)	0.0524 (1.00)	0.00068 (0.447)	0.373 (1.00)	9e-05 (0.0634)
11q loss	21 (4%)	492			0.00017 (0.118)	7e-05 (0.0497)	0.0175 (1.00)	0.652 (1.00)	1e-05 (0.00836)	1e-05 (0.00836)	0.0248 (1.00)	7e-05 (0.0497)	0.492 (1.00)	0.0004 (0.268)
10p gain	57 (11%)	456	1 (1.00)	0.0418 (1.00)	1e-05 (0.00836)	1e-05 (0.00836)	0.0211 (1.00)	0.553 (1.00)	1e-05 (0.00836)	1e-05 (0.00836)	0.0543 (1.00)	0.295 (1.00)	0.474 (1.00)	0.00565 (1.00)
xq gain	41 (8%)	472			1e-05 (0.00836)	1e-05 (0.00836)	0.236 (1.00)	0.714 (1.00)	0.0001 (0.07)	1e-05 (0.00836)	0.0177 (1.00)	0.559 (1.00)	0.67 (1.00)	0.0134 (1.00)
5q gain	8 (2%)	505			0.00469 (1.00)	0.00025 (0.17)			0.00022 (0.15)	0.00018 (0.124)	0.0125 (1.00)	0.00098 (0.634)	0.00855 (1.00)	0.00059 (0.389)
5q loss	33 (6%)	480	0.447 (1.00)	0.239 (1.00)	1e-05 (0.00836)	0.00017 (0.118)	0.0193 (1.00)	0.119 (1.00)	0.0272 (1.00)	0.00649 (1.00)	9e-05 (0.0634)	0.162 (1.00)	0.811 (1.00)	0.61 (1.00)
14q loss	80 (16%)	433	0.466 (1.00)	0.266 (1.00)	0.00104 (0.669)	0.00016 (0.111)	0.0441 (1.00)	0.115 (1.00)	2e-05 (0.0147)	3e-05 (0.0218)	0.0103 (1.00)	0.00083 (0.541)	0.0114 (1.00)	0.00055 (0.364)
xq loss	69 (13%)	444	0.837 (1.00)	0.266 (1.00)	0.254 (1.00)	0.0121 (1.00)	0.0448 (1.00)	0.0209 (1.00)	5e-05 (0.0359)	1e-05 (0.00836)	8e-05 (0.0566)	0.15 (1.00)	0.0314 (1.00)	0.00825 (1.00)
1q gain	23 (4%)	490			0.00023 (0.157)	0.00057 (0.377)	0.434 (1.00)	0.607 (1.00)	6e-05 (0.0427)	0.00045 (0.3)	0.122 (1.00)	0.0316 (1.00)	0.0308 (1.00)	0.0568 (1.00)
5p gain	11 (2%)	502			0.00644 (1.00)	0.00292 (1.00)	0.0214 (1.00)	0.609 (1.00)	4e-05 (0.029)	0.0001 (0.07)	0.0238 (1.00)	0.0268 (1.00)	0.142 (1.00)	0.0159 (1.00)
8q gain	56 (11%)	457	0.0515 (1.00)	0.405 (1.00)	1e-05 (0.00836)	5e-05 (0.0359)	0.0114 (1.00)	0.0558 (1.00)	0.00153 (0.967)	0.00049 (0.325)	0.191 (1.00)	0.12 (1.00)	0.0677 (1.00)	0.0154 (1.00)
5p loss	34 (7%)	479	0.745 (1.00)	0.0663 (1.00)	1e-05 (0.00836)	0.0001 (0.07)	0.915 (1.00)	0.954 (1.00)	0.173 (1.00)	0.0435 (1.00)	0.105 (1.00)	0.392 (1.00)	0.733 (1.00)	0.325 (1.00)
6q loss	63 (12%)	450			8e-05 (0.0566)	0.00134 (0.854)	0.251 (1.00)	0.568 (1.00)	0.0765 (1.00)	0.0192 (1.00)	0.00122 (0.781)	0.173 (1.00)	0.0137 (1.00)	4e-05 (0.029)
9p loss	118 (23%)	395	0.382 (1.00)	0.266 (1.00)	1e-05 (0.00836)	0.0003 (0.203)	0.0319 (1.00)	0.0198 (1.00)	0.0948 (1.00)	0.051 (1.00)	0.894 (1.00)	0.221 (1.00)	0.285 (1.00)	0.0346 (1.00)
12q loss	51 (10%)	462	1 (1.00)	0.579 (1.00)	1e-05 (0.00836)	1e-05 (0.00836)	0.681 (1.00)	0.11 (1.00)	0.00707 (1.00)	0.00288 (1.00)	0.00583 (1.00)	0.332 (1.00)	0.834 (1.00)	0.809 (1.00)
13q loss	116 (23%)	397	0.179 (1.00)	9e-05 (0.0634)	5e-05 (0.0359)	0.00589 (1.00)	0.0262 (1.00)	0.622 (1.00)	0.0159 (1.00)	0.00516 (1.00)	0.0348 (1.00)	0.0132 (1.00)	0.297 (1.00)	0.24 (1.00)
21q loss	36 (7%)	477	0.612 (1.00)	0.0426 (1.00)	1e-05 (0.00836)	0.00021 (0.144)	0.464 (1.00)	0.654 (1.00)	0.00088 (0.573)	0.00046 (0.306)	0.249 (1.00)	0.0264 (1.00)	0.507 (1.00)	0.288 (1.00)
8p gain	46 (9%)	467			9e-05 (0.0634)	0.00133 (0.849)	0.0638 (1.00)	0.16 (1.00)	0.0223 (1.00)	0.00569 (1.00)	0.391 (1.00)	0.413 (1.00)	0.207 (1.00)	0.071 (1.00)
12p gain	33 (6%)	480	0.754 (1.00)	0.58 (1.00)	0.00029 (0.196)	0.0329 (1.00)	0.259 (1.00)	0.309 (1.00)	0.0421 (1.00)	0.0875 (1.00)	0.0873 (1.00)	0.0215 (1.00)	0.191 (1.00)	0.559 (1.00)
18p gain	17 (3%)	496			0.00013 (0.0906)	0.00483 (1.00)	0.0232 (1.00)	0.441 (1.00)	0.0309 (1.00)	0.0116 (1.00)	0.839 (1.00)	0.0926 (1.00)	0.612 (1.00)	0.0372 (1.00)
18q gain	13 (3%)	500			0.00098 (0.634)	0.00355 (1.00)	0.081 (1.00)	0.599 (1.00)	0.00162 (1.00)	0.00023 (0.157)	0.509 (1.00)	0.0172 (1.00)	0.182 (1.00)	0.00453 (1.00)
22q gain	23 (4%)	490			0.012 (1.00)	4e-05 (0.029)	1 (1.00)	0.686 (1.00)	0.00106 (0.681)	0.00038 (0.255)	0.119 (1.00)	0.527 (1.00)	0.0417 (1.00)	0.224 (1.00)
2p loss	21 (4%)	492			0.00024 (0.163)	0.0416 (1.00)	0.333 (1.00)	1 (1.00)	0.161 (1.00)	0.0303 (1.00)	0.0727 (1.00)	0.405 (1.00)	0.729 (1.00)	0.259 (1.00)
18q loss	62 (12%)	451	0.343 (1.00)	0.152 (1.00)	0.0463 (1.00)	0.00031 (0.209)	0.288 (1.00)	0.0978 (1.00)	0.0309 (1.00)	0.00337 (1.00)	0.0581 (1.00)	0.712 (1.00)	0.423 (1.00)	0.53 (1.00)
2p gain	14 (3%)	499			0.0168 (1.00)	0.015 (1.00)	0.309 (1.00)	0.345 (1.00)	0.0124 (1.00)	0.00103 (0.664)	0.603 (1.00)	0.0212 (1.00)	0.89 (1.00)	0.0399 (1.00)
2q gain	13 (3%)	500			0.0381 (1.00)	0.0103 (1.00)	0.308 (1.00)	0.343 (1.00)	0.0349 (1.00)	0.00069 (0.453)	0.512 (1.00)	0.0177 (1.00)	0.684 (1.00)	0.0457 (1.00)
3p gain	11 (2%)	502			0.0647 (1.00)	0.327 (1.00)	0.463 (1.00)	0.203 (1.00)	0.108 (1.00)	0.109 (1.00)	0.119 (1.00)	0.288 (1.00)	0.743 (1.00)	0.199 (1.00)
3q gain	8 (2%)	505			0.00191 (1.00)	0.1 (1.00)	0.0564 (1.00)	0.366 (1.00)	0.0628 (1.00)	0.00369 (1.00)	0.342 (1.00)	0.133 (1.00)	0.33 (1.00)	0.15 (1.00)
4p gain	13 (3%)	500			0.00061 (0.402)	0.00706 (1.00)	0.0324 (1.00)	0.895 (1.00)	0.00844 (1.00)	0.00177 (1.00)	0.191 (1.00)	0.106 (1.00)	0.337 (1.00)	0.275 (1.00)
4q gain	6 (1%)	507			0.0391 (1.00)	0.0176 (1.00)	0.112 (1.00)	0.67 (1.00)	0.0142 (1.00)	0.00355 (1.00)	0.261 (1.00)	0.15 (1.00)	0.382 (1.00)	0.222 (1.00)
6p gain	7 (1%)	506			0.225 (1.00)	0.0466 (1.00)	0.0377 (1.00)	0.518 (1.00)	0.434 (1.00)	0.0979 (1.00)	0.0234 (1.00)	0.0637 (1.00)	0.572 (1.00)	0.033 (1.00)
9p gain	17 (3%)	496			0.0156 (1.00)	0.149 (1.00)	0.292 (1.00)	0.531 (1.00)	0.0648 (1.00)	0.0365 (1.00)	0.839 (1.00)	0.0261 (1.00)	0.861 (1.00)	0.204 (1.00)
9q gain	24 (5%)	489			0.0123 (1.00)	0.105 (1.00)	0.258 (1.00)	0.0543 (1.00)	0.0399 (1.00)	0.0136 (1.00)	0.43 (1.00)	0.0104 (1.00)	0.584 (1.00)	0.173 (1.00)
10q gain	12 (2%)	501			0.00132 (0.843)	0.0203 (1.00)	0.267 (1.00)	0.515 (1.00)	0.0854 (1.00)	0.0362 (1.00)	0.0779 (1.00)	0.0303 (1.00)	0.58 (1.00)	0.208 (1.00)
11p gain	31 (6%)	482			0.0326 (1.00)	0.00089 (0.578)	0.0259 (1.00)	0.11 (1.00)	0.00933 (1.00)	0.00318 (1.00)	0.0937 (1.00)	0.0245 (1.00)	0.407 (1.00)	0.0082 (1.00)
11q gain	58 (11%)	455	0.616 (1.00)	0.582 (1.00)	0.178 (1.00)	0.0106 (1.00)	0.0817 (1.00)	0.0307 (1.00)	0.0623 (1.00)	0.0366 (1.00)	0.546 (1.00)	0.0464 (1.00)	0.648 (1.00)	0.0319 (1.00)
12q gain	16 (3%)	497			0.00546 (1.00)	0.102 (1.00)	0.294 (1.00)	0.532 (1.00)	0.00549 (1.00)	0.0851 (1.00)	0.165 (1.00)	0.0592 (1.00)	0.119 (1.00)	0.091 (1.00)
13q gain	6 (1%)	507			0.382 (1.00)	0.397 (1.00)	0.794 (1.00)	0.795 (1.00)	0.234 (1.00)	0.474 (1.00)	0.352 (1.00)	0.588 (1.00)	0.454 (1.00)	0.469 (1.00)
14q gain	4 (1%)	509			0.826 (1.00)	0.758 (1.00)			0.71 (1.00)	0.59 (1.00)	0.217 (1.00)	0.68 (1.00)	0.27 (1.00)	0.759 (1.00)
15q gain	11 (2%)	502			0.00221 (1.00)	0.0203 (1.00)	0.0449 (1.00)	0.217 (1.00)	0.0478 (1.00)	0.0134 (1.00)	0.176 (1.00)	0.288 (1.00)	0.475 (1.00)	0.0964 (1.00)
16p gain	17 (3%)	496			0.488 (1.00)	0.745 (1.00)	0.56 (1.00)	0.698 (1.00)	0.0749 (1.00)	0.0479 (1.00)	0.12 (1.00)	0.0592 (1.00)	0.11 (1.00)	0.515 (1.00)
16q gain	19 (4%)	494			0.268 (1.00)	0.315 (1.00)	0.47 (1.00)	0.513 (1.00)	0.152 (1.00)	0.034 (1.00)	0.0548 (1.00)	0.0999 (1.00)	0.139 (1.00)	0.53 (1.00)
17p gain	20 (4%)	493			0.489 (1.00)	0.596 (1.00)	0.348 (1.00)	0.888 (1.00)	0.186 (1.00)	0.0455 (1.00)	0.189 (1.00)	0.485 (1.00)	0.687 (1.00)	0.654 (1.00)
17q gain	23 (4%)	490			0.682 (1.00)	0.449 (1.00)	0.347 (1.00)	0.885 (1.00)	0.349 (1.00)	0.121 (1.00)	0.109 (1.00)	0.7 (1.00)	0.425 (1.00)	0.358 (1.00)
21q gain	24 (5%)	489			0.00596 (1.00)	0.0119 (1.00)	0.11 (1.00)	0.395 (1.00)	0.428 (1.00)	0.211 (1.00)	0.623 (1.00)	0.0983 (1.00)	0.728 (1.00)	0.0799 (1.00)
1q loss	25 (5%)	488	0.344 (1.00)	0.15 (1.00)	0.455 (1.00)	0.0632 (1.00)	0.475 (1.00)	0.465 (1.00)	0.361 (1.00)	0.282 (1.00)	0.0761 (1.00)	0.413 (1.00)	0.163 (1.00)	0.138 (1.00)
2q loss	18 (4%)	495			0.00041 (0.274)	0.00573 (1.00)	0.0694 (1.00)	0.607 (1.00)	0.423 (1.00)	0.125 (1.00)	0.026 (1.00)	0.811 (1.00)	0.691 (1.00)	0.384 (1.00)
3p loss	30 (6%)	483			0.0048 (1.00)	0.0583 (1.00)	0.00637 (1.00)	0.272 (1.00)	0.038 (1.00)	0.0211 (1.00)	0.00103 (0.664)	0.00047 (0.312)	0.193 (1.00)	0.00293 (1.00)
3q loss	28 (5%)	485	0.176 (1.00)	0.882 (1.00)	0.00723 (1.00)	0.133 (1.00)	0.252 (1.00)	0.769 (1.00)	0.0723 (1.00)	0.0628 (1.00)	0.0903 (1.00)	0.0169 (1.00)	0.269 (1.00)	0.0354 (1.00)
6p loss	30 (6%)	483			0.0333 (1.00)	0.0581 (1.00)	0.187 (1.00)	0.685 (1.00)	0.371 (1.00)	0.462 (1.00)	0.4 (1.00)	0.404 (1.00)	0.0123 (1.00)	0.00304 (1.00)
7p loss	3 (1%)	510			0.0499 (1.00)	0.245 (1.00)			1 (1.00)	0.895 (1.00)	1 (1.00)	1 (1.00)
7q loss	3 (1%)	510			0.0494 (1.00)	0.243 (1.00)			0.374 (1.00)	0.176 (1.00)	1 (1.00)	1 (1.00)
9q loss	51 (10%)	462			0.153 (1.00)	0.461 (1.00)	0.622 (1.00)	0.343 (1.00)	0.467 (1.00)	0.132 (1.00)	0.396 (1.00)	0.824 (1.00)	0.593 (1.00)	0.0334 (1.00)
12p loss	26 (5%)	487			0.00381 (1.00)	0.0632 (1.00)	0.606 (1.00)	1 (1.00)	0.403 (1.00)	0.32 (1.00)	0.0791 (1.00)	0.152 (1.00)	0.553 (1.00)	0.93 (1.00)
15q loss	51 (10%)	462	1 (1.00)	0.706 (1.00)	0.0283 (1.00)	0.00179 (1.00)	0.271 (1.00)	0.0463 (1.00)	0.00095 (0.617)	0.00139 (0.883)	0.235 (1.00)	0.473 (1.00)	0.0574 (1.00)	0.0839 (1.00)
16p loss	14 (3%)	499			0.00495 (1.00)	0.043 (1.00)	0.866 (1.00)	0.201 (1.00)	0.0287 (1.00)	0.12 (1.00)	0.823 (1.00)	0.357 (1.00)	0.706 (1.00)	0.136 (1.00)
16q loss	22 (4%)	491			0.00582 (1.00)	0.00221 (1.00)	0.376 (1.00)	0.0681 (1.00)	0.0168 (1.00)	0.0919 (1.00)	0.664 (1.00)	0.00355 (1.00)	0.295 (1.00)	0.00926 (1.00)
17p loss	13 (3%)	500			0.0941 (1.00)	0.132 (1.00)	1 (1.00)	0.782 (1.00)	0.0139 (1.00)	0.0622 (1.00)	0.158 (1.00)	0.00634 (1.00)	0.714 (1.00)	0.0114 (1.00)
17q loss	8 (2%)	505			0.116 (1.00)	0.2 (1.00)	0.837 (1.00)	0.51 (1.00)	0.27 (1.00)	0.531 (1.00)	0.162 (1.00)	0.265 (1.00)	1 (1.00)	0.0235 (1.00)
18p loss	68 (13%)	445	0.321 (1.00)	0.0298 (1.00)	0.203 (1.00)	0.00138 (0.878)	0.582 (1.00)	0.105 (1.00)	0.134 (1.00)	0.0292 (1.00)	0.597 (1.00)	0.915 (1.00)	0.471 (1.00)	0.512 (1.00)
19p loss	25 (5%)	488	0.847 (1.00)	0.433 (1.00)	0.526 (1.00)	0.875 (1.00)	0.103 (1.00)	0.809 (1.00)	0.562 (1.00)	0.458 (1.00)	0.131 (1.00)	0.116 (1.00)	0.0259 (1.00)	0.0558 (1.00)
20p loss	7 (1%)	506			0.225 (1.00)	0.156 (1.00)	0.793 (1.00)	1 (1.00)	0.26 (1.00)	0.395 (1.00)	0.447 (1.00)	0.482 (1.00)	0.71 (1.00)	0.481 (1.00)
20q loss	3 (1%)	510			0.253 (1.00)	0.446 (1.00)			0.024 (1.00)	0.138 (1.00)	0.234 (1.00)	1 (1.00)	0.301 (1.00)	0.888 (1.00)

'1p gain' versus 'CN_CNMF'

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

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

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 '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	128	28
1P GAIN MUTATED	0	13	0	0	0
1P GAIN WILD-TYPE	135	99	108	128	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	138
1P GAIN MUTATED	0	13	0	0
1P GAIN WILD-TYPE	135	100	125	138

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

'1p gain' versus 'MIRSEQ_CHIERARCHICAL'

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

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

'1p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.097

Table S6. 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 S6. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1q gain' versus 'CN_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.16

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

'1q gain' versus 'MRNASEQ_CNMF'

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

Table S8. 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	128	28
1Q GAIN MUTATED	2	14	0	5	2
1Q GAIN WILD-TYPE	133	98	108	123	26

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

'5p gain' versus 'MRNASEQ_CNMF'

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

Table S9. 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	128	28
5P GAIN MUTATED	0	9	0	1	1
5P GAIN WILD-TYPE	135	103	108	127	27

Figure S9. 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 S10. Gene #9: '5p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	138
5P GAIN MUTATED	1	9	0	1
5P GAIN WILD-TYPE	134	104	125	137

Figure S10. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q gain' versus 'METHLYATION_CNMF'

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

Table S11. 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 S11. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5q gain' versus 'MRNASEQ_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.15

Table S12. 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	128	28
5Q GAIN MUTATED	0	7	0	0	1
5Q GAIN WILD-TYPE	135	105	108	128	27

Figure S12. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5q gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S13. Gene #10: '5q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	138
5Q GAIN MUTATED	1	7	0	0
5Q GAIN WILD-TYPE	134	106	125	138

Figure S13. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

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

Table S14. 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 S14. 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 S15. 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 S15. Get High-res Image Gene #12: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

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

Table S16. 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	128	28
7P GAIN MUTATED	22	59	9	23	6
7P GAIN WILD-TYPE	113	53	99	105	22

Figure S16. 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 S17. Gene #12: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	138
7P GAIN MUTATED	19	58	11	31
7P GAIN WILD-TYPE	116	55	114	107

Figure S17. 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 S18. 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 S18. Get High-res Image Gene #12: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S19. 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 S19. 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 S20. 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 S20. 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 S21. 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 S21. 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 S22. 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	128	28
7Q GAIN MUTATED	36	62	12	31	8
7Q GAIN WILD-TYPE	99	50	96	97	20

Figure S22. 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 S23. Gene #13: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	138
7Q GAIN MUTATED	32	60	16	41
7Q GAIN WILD-TYPE	103	53	109	97

Figure S23. 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 S24. 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 S24. Get High-res Image Gene #13: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S25. 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 S25. Get High-res Image Gene #13: '7q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

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

Table S26. 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 S26. 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 S27. 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 S27. Get High-res Image Gene #15: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

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

Table S28. 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 S28. 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 S29. 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 S29. 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 S30. 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 S30. 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 S31. 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	128	28
10P GAIN MUTATED	29	14	0	13	1
10P GAIN WILD-TYPE	106	98	108	115	27

Figure S31. 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 S32. Gene #18: '10p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	138
10P GAIN MUTATED	29	14	0	14
10P GAIN WILD-TYPE	106	99	125	124

Figure S32. Get High-res Image Gene #18: '10p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'CN_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.2

Table S33. 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 S33. Get High-res Image Gene #22: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

'18p gain' versus 'CN_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.091

Table S34. 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 S34. Get High-res Image Gene #31: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

'18q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.16

Table S35. Gene #32: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	138
18Q GAIN MUTATED	2	9	0	1
18Q GAIN WILD-TYPE	133	104	125	137

Figure S35. 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 S36. 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 S36. 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 S37. 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 S37. 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 S38. 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	128	28
19P GAIN MUTATED	5	30	44	20	1
19P GAIN WILD-TYPE	130	82	64	108	27

Figure S38. 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 S39. Gene #33: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	138
19P GAIN MUTATED	6	28	44	22
19P GAIN WILD-TYPE	129	85	81	116

Figure S39. Get High-res Image Gene #33: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_CNMF'

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

Table S40. 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 S40. Get High-res Image Gene #33: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q gain' versus 'CN_CNMF'

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

Table S41. 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 S41. 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 S42. 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 S42. 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 S43. 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	128	28
19Q GAIN MUTATED	1	19	0	4	1
19Q GAIN WILD-TYPE	134	93	108	124	27

Figure S43. 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 S44. Gene #34: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	138
19Q GAIN MUTATED	2	19	0	4
19Q GAIN WILD-TYPE	133	94	125	134

Figure S44. 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 S45. 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 S45. 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 S46. 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 S46. 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 S47. 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 S47. 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 S48. 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 S48. 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 S49. 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 S49. 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 S50. 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	128	28
20P GAIN MUTATED	3	28	3	8	1
20P GAIN WILD-TYPE	132	84	105	120	27

Figure S50. 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 S51. Gene #35: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	138
20P GAIN MUTATED	3	26	4	10
20P GAIN WILD-TYPE	132	87	121	128

Figure S51. 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 S52. 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 S52. Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S53. 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 S53. 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 S54. 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 S54. 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 S55. 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 S55. 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 S56. 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	128	28
20Q GAIN MUTATED	4	29	3	6	1
20Q GAIN WILD-TYPE	131	83	105	122	27

Figure S56. 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 S57. Gene #36: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	138
20Q GAIN MUTATED	4	27	4	8
20Q GAIN WILD-TYPE	131	86	121	130

Figure S57. 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 S58. 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 S58. Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

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

Table S59. 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 S59. 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 S60. 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 S60. Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q gain' versus 'METHLYATION_CNMF'

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

Table S61. 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 S61. Get High-res Image Gene #38: '22q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xq gain' versus 'CN_CNMF'

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

Table S62. Gene #39: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	120	221
XQ GAIN MUTATED	31	7	3
XQ GAIN WILD-TYPE	141	113	218

Figure S62. 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 S63. Gene #39: '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	35	4	0	2
XQ GAIN WILD-TYPE	190	77	167	38

Figure S63. Get High-res Image Gene #39: 'xq gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xq gain' versus 'MRNASEQ_CNMF'

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

Table S64. 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	128	28
XQ GAIN MUTATED	19	7	0	11	4
XQ GAIN WILD-TYPE	116	105	108	117	24

Figure S64. Get High-res Image Gene #39: 'xq gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'xq gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S65. Gene #39: 'xq gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	138
XQ GAIN MUTATED	23	7	0	11
XQ GAIN WILD-TYPE	112	106	125	127

Figure S65. Get High-res Image Gene #39: 'xq gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MRNA_CHIERARCHICAL'

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

Table S66. 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 S66. 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 S67. Gene #40: '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 S67. 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 S68. Gene #40: '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 S68. Get High-res Image Gene #40: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1p loss' versus 'RPPA_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.18

Table S69. 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	15	26	36
1P LOSS WILD-TYPE	44	47	42	38

Figure S69. 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 S70. 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	128	28
1P LOSS MUTATED	3	10	106	55	10
1P LOSS WILD-TYPE	132	102	2	73	18

Figure S70. 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 S71. Gene #40: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	138
1P LOSS MUTATED	3	8	122	51
1P LOSS WILD-TYPE	132	105	3	87

Figure S71. 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 S72. Gene #40: '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 S72. 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 S73. Gene #40: '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 S73. 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 S74. Gene #40: '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 S74. 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 S75. Gene #40: '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 S75. Get High-res Image Gene #40: '1p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2p loss' versus 'CN_CNMF'

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

Table S76. Gene #42: '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 S76. Get High-res Image Gene #42: '2p 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 S77. Gene #46: '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 S77. Get High-res Image Gene #46: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

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

Table S78. 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	128	28
4P LOSS MUTATED	15	5	30	17	3
4P LOSS WILD-TYPE	120	107	78	111	25

Figure S78. 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 S79. Gene #46: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	138
4P LOSS MUTATED	13	4	37	16
4P LOSS WILD-TYPE	122	109	88	122

Figure S79. Get High-res Image Gene #46: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_CNMF'

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

Table S80. Gene #46: '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 S80. Get High-res Image Gene #46: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00034 (Fisher's exact test), Q value = 0.23

Table S81. Gene #46: '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 S81. Get High-res Image Gene #46: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CNMF'

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

Table S82. Gene #46: '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 S82. Get High-res Image Gene #46: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S83. Gene #46: '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 S83. 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 S84. Gene #47: '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 S84. Get High-res Image Gene #47: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S85. Gene #47: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	138
4Q LOSS MUTATED	18	9	39	25
4Q LOSS WILD-TYPE	117	104	86	113

Figure S85. Get High-res Image Gene #47: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.14

Table S86. Gene #47: '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 S86. Get High-res Image Gene #47: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4q loss' versus 'MIRSEQ_MATURE_CNMF'

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

Table S87. Gene #47: '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 S87. Get High-res Image Gene #47: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S88. Gene #47: '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 S88. 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 S89. Gene #48: '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 S89. Get High-res Image Gene #48: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

'5p loss' versus 'METHLYATION_CNMF'

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

Table S90. Gene #48: '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 S90. Get High-res Image Gene #48: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5q loss' versus 'CN_CNMF'

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

Table S91. Gene #49: '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 S91. Get High-res Image Gene #49: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

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

Table S92. Gene #49: '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 S92. Get High-res Image Gene #49: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5q loss' versus 'MIRSEQ_CNMF'

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

Table S93. Gene #49: '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 S93. Get High-res Image Gene #49: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6q loss' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.057

Table S94. Gene #51: '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 S94. Get High-res Image Gene #51: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

'6q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S95. Gene #51: '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 S95. Get High-res Image Gene #51: '6q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

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

Table S96. Gene #54: '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 S96. 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 S97. Gene #54: '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 S97. 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 S98. 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	128	28
8P LOSS MUTATED	0	13	0	3	1
8P LOSS WILD-TYPE	135	99	108	125	27

Figure S98. Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S99. Gene #54: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	138
8P LOSS MUTATED	1	13	0	3
8P LOSS WILD-TYPE	134	100	125	135

Figure S99. Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 0.18

Table S100. Gene #54: '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 S100. Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q loss' versus 'CN_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.14

Table S101. Gene #55: '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 S101. Get High-res Image Gene #55: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'

'8q loss' versus 'METHLYATION_CNMF'

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

Table S102. Gene #55: '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 S102. Get High-res Image Gene #55: '8q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8q loss' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.057

Table S103. 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	128	28
8Q LOSS MUTATED	0	9	0	1	1
8Q LOSS WILD-TYPE	135	103	108	127	27

Figure S103. Get High-res Image Gene #55: '8q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.05

Table S104. Gene #55: '8q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	138
8Q LOSS MUTATED	1	9	0	1
8Q LOSS WILD-TYPE	134	104	125	137

Figure S104. Get High-res Image Gene #55: '8q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S105. Gene #55: '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 S105. Get High-res Image Gene #55: '8q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

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

Table S106. Gene #56: '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 S106. Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

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

Table S107. Gene #56: '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 S107. 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 S108. Gene #58: '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 S108. 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 S109. Gene #58: '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 S109. 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 S110. 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 S110. 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 S111. 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	128	28
10P LOSS MUTATED	1	64	1	12	4
10P LOSS WILD-TYPE	134	48	107	116	24

Figure S111. 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 S112. Gene #58: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	138
10P LOSS MUTATED	1	63	6	12
10P LOSS WILD-TYPE	134	50	119	126

Figure S112. Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_CNMF'

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

Table S113. Gene #58: '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 S113. 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 S114. Gene #58: '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 S114. 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 S115. Gene #58: '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 S115. 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 S116. Gene #58: '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 S116. 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 S117. Gene #59: '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 S117. 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 S118. Gene #59: '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 S118. 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 S119. 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 S119. 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 S120. 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	128	28
10Q LOSS MUTATED	5	70	1	15	4
10Q LOSS WILD-TYPE	130	42	107	113	24

Figure S120. 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 S121. Gene #59: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	138
10Q LOSS MUTATED	6	68	6	15
10Q LOSS WILD-TYPE	129	45	119	123

Figure S121. Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_CNMF'

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

Table S122. Gene #59: '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 S122. 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 S123. Gene #59: '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 S123. 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 S124. Gene #59: '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 S124. 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 S125. Gene #59: '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 S125. 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 S126. Gene #60: '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 S126. 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 S127. Gene #60: '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 S127. 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 S128. 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	128	28
11P LOSS MUTATED	14	31	0	11	6
11P LOSS WILD-TYPE	121	81	108	117	22

Figure S128. 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 S129. Gene #60: '11p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	138
11P LOSS MUTATED	17	34	0	11
11P LOSS WILD-TYPE	118	79	125	127

Figure S129. Get High-res Image Gene #60: '11p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_CNMF'

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

Table S130. Gene #60: '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 S130. Get High-res Image Gene #60: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11p loss' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S131. Gene #60: '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 S131. Get High-res Image Gene #60: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

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

Table S132. Gene #61: '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 S132. Get High-res Image Gene #61: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.05

Table S133. Gene #61: '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 S133. 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 S134. 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	128	28
11Q LOSS MUTATED	1	16	0	3	1
11Q LOSS WILD-TYPE	134	96	108	125	27

Figure S134. 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 S135. Gene #61: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	138
11Q LOSS MUTATED	2	16	0	3
11Q LOSS WILD-TYPE	133	97	125	135

Figure S135. Get High-res Image Gene #61: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.05

Table S136. Gene #61: '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 S136. Get High-res Image Gene #61: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12q loss' versus 'CN_CNMF'

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

Table S137. Gene #63: '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 S137. 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 S138. Gene #63: '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 S138. Get High-res Image Gene #63: '12q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q loss' versus 'MRNA_CHIERARCHICAL'

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

Table S139. 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 S139. Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

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

Table S140. Gene #64: '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 S140. Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

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

Table S141. Gene #65: '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 S141. Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q loss' versus 'MRNASEQ_CNMF'

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

Table S142. 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	128	28
14Q LOSS MUTATED	10	35	11	16	7
14Q LOSS WILD-TYPE	125	77	97	112	21

Figure S142. Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S143. Gene #65: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	138
14Q LOSS MUTATED	15	35	13	16
14Q LOSS WILD-TYPE	120	78	112	122

Figure S143. Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'METHLYATION_CNMF'

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

Table S144. Gene #72: '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 S144. 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 S145. Gene #74: '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 S145. 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 S146. Gene #74: '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 S146. 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 S147. 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	128	28
19Q LOSS MUTATED	18	15	106	59	10
19Q LOSS WILD-TYPE	117	97	2	69	18

Figure S147. 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 S148. Gene #74: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	138
19Q LOSS MUTATED	16	14	122	56
19Q LOSS WILD-TYPE	119	99	3	82

Figure S148. 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 S149. Gene #74: '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 S149. 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 S150. Gene #74: '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 S150. 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 S151. Gene #74: '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 S151. 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 S152. Gene #74: '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 S152. 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 S153. Gene #77: '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 S153. Get High-res Image Gene #77: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

'21q loss' versus 'METHLYATION_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.14

Table S154. Gene #77: '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 S154. Get High-res Image Gene #77: '21q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q loss' versus 'CN_CNMF'

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

Table S155. Gene #78: '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 S155. 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 S156. Gene #78: '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 S156. Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q loss' versus 'RPPA_CNMF'

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

Table S157. 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 S157. 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 S158. 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	128	28
22Q LOSS MUTATED	9	31	2	10	4
22Q LOSS WILD-TYPE	126	81	106	118	24

Figure S158. 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 S159. Gene #78: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	138
22Q LOSS MUTATED	11	29	4	12
22Q LOSS WILD-TYPE	124	84	121	126

Figure S159. Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00033 (Fisher's exact test), Q value = 0.22

Table S160. Gene #78: '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 S160. Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S161. Gene #78: '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 S161. 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 S162. 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	128	28
XQ LOSS MUTATED	11	23	25	10	0
XQ LOSS WILD-TYPE	124	89	83	118	28

Figure S162. 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 S163. Gene #79: 'xq loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	138
XQ LOSS MUTATED	10	23	29	7
XQ LOSS WILD-TYPE	125	90	96	131

Figure S163. Get High-res Image Gene #79: 'xq loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.057

Table S164. Gene #79: '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	16	16	25
XQ LOSS WILD-TYPE	125	91	167	57

Figure S164. Get High-res Image Gene #79: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtypes file = LGG-TP.transferedmergedcluster.txt
Number of patients = 513
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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