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

Kidney Renal Papillary Cell Carcinoma (Primary solid tumor)

28 January 2016 | analyses__2016_01_28

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 (2016): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1Z31Z2N

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 74 arm-level events and 10 molecular subtypes across 288 patients, 362 significant findings detected with P value < 0.05 and Q value < 0.25.

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

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 74 arm-level events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 362 significant findings detected.


		Clinical Features	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
7p gain	171 (59%)	117	1e-05 (8.41e-05)	1e-05 (8.41e-05)	0.0101 (0.0279)	1e-05 (8.41e-05)	1e-05 (8.41e-05)	1e-05 (8.41e-05)	0.00012 (0.000663)	0.00012 (0.000663)	2e-05 (0.000151)	2e-05 (0.000151)
7q gain	172 (60%)	116	1e-05 (8.41e-05)	1e-05 (8.41e-05)	0.018 (0.0442)	2e-05 (0.000151)	1e-05 (8.41e-05)	1e-05 (8.41e-05)	0.00017 (0.000892)	0.00017 (0.000892)	6e-05 (0.000383)	1e-05 (8.41e-05)
17p gain	172 (60%)	116	1e-05 (8.41e-05)	1e-05 (8.41e-05)	6e-05 (0.000383)	1e-05 (8.41e-05)	1e-05 (8.41e-05)	1e-05 (8.41e-05)	0.00011 (0.000631)	0.00014 (0.000762)	1e-05 (8.41e-05)	1e-05 (8.41e-05)
17q gain	191 (66%)	97	1e-05 (8.41e-05)	1e-05 (8.41e-05)	0.00083 (0.00353)	1e-05 (8.41e-05)	1e-05 (8.41e-05)	1e-05 (8.41e-05)	0.00786 (0.0225)	0.00097 (0.00388)	3e-05 (0.000213)	2e-05 (0.000151)
18p loss	42 (15%)	246	0.0206 (0.0499)	1e-05 (8.41e-05)	0.00213 (0.00761)	0.00461 (0.0148)	1e-05 (8.41e-05)	1e-05 (8.41e-05)	0.00141 (0.00532)	0.00094 (0.00388)	0.0249 (0.0575)	0.0231 (0.0536)
18q loss	44 (15%)	244	0.00109 (0.00427)	1e-05 (8.41e-05)	0.00622 (0.0186)	0.00046 (0.00213)	1e-05 (8.41e-05)	1e-05 (8.41e-05)	0.00136 (0.00519)	0.00037 (0.00177)	0.0222 (0.0525)	0.00492 (0.0154)
16p gain	153 (53%)	135	1e-05 (8.41e-05)	1e-05 (8.41e-05)	0.912 (0.953)	0.00076 (0.00331)	1e-05 (8.41e-05)	4e-05 (0.000269)	5e-05 (0.000327)	1e-05 (8.41e-05)	0.00019 (0.00097)	3e-05 (0.000213)
16q gain	148 (51%)	140	1e-05 (8.41e-05)	1e-05 (8.41e-05)	0.954 (0.985)	0.00187 (0.00682)	1e-05 (8.41e-05)	0.00011 (0.000631)	2e-05 (0.000151)	1e-05 (8.41e-05)	0.00011 (0.000631)	1e-05 (8.41e-05)
20p gain	99 (34%)	189	1e-05 (8.41e-05)	0.00021 (0.00104)	0.0259 (0.0592)	0.00265 (0.00929)	0.00114 (0.00444)	0.0218 (0.0519)	0.00551 (0.0167)	0.0031 (0.0106)	0.0718 (0.136)	0.043 (0.0902)
xp gain	88 (31%)	200	1e-05 (8.41e-05)	1e-05 (8.41e-05)	0.109 (0.184)	0.00202 (0.00729)	1e-05 (8.41e-05)	1e-05 (8.41e-05)	7e-05 (0.000432)	0.00019 (0.00097)	0.0002 (0.00101)	0.00069 (0.00304)
xq gain	92 (32%)	196	1e-05 (8.41e-05)	1e-05 (8.41e-05)	0.125 (0.207)	0.00707 (0.0208)	1e-05 (8.41e-05)	3e-05 (0.000213)	0.00039 (0.00185)	0.00019 (0.00097)	0.00097 (0.00388)	0.00302 (0.0104)
13q loss	24 (8%)	264	0.00061 (0.00272)	1e-05 (8.41e-05)	0.478 (0.592)	0.00139 (0.00527)	1e-05 (8.41e-05)	1e-05 (8.41e-05)	0.0367 (0.0793)	0.0104 (0.028)	0.00763 (0.0219)	0.00508 (0.0158)
14q loss	47 (16%)	241	4e-05 (0.000269)	5e-05 (0.000327)	0.00563 (0.017)	7e-05 (0.000432)	1e-05 (8.41e-05)	1e-05 (8.41e-05)	0.0405 (0.0856)	0.861 (0.923)	0.019 (0.0463)	0.00273 (0.00948)
3p gain	75 (26%)	213	1e-05 (8.41e-05)	1e-05 (8.41e-05)	0.214 (0.317)	0.00017 (0.000892)	1e-05 (8.41e-05)	0.00279 (0.00965)	0.0108 (0.0289)	0.00077 (0.00333)	0.122 (0.203)	0.0168 (0.0417)
3q gain	95 (33%)	193	1e-05 (8.41e-05)	2e-05 (0.000151)	0.262 (0.376)	0.00467 (0.015)	1e-05 (8.41e-05)	0.00469 (0.015)	0.00132 (0.00506)	0.00088 (0.00368)	0.734 (0.82)	0.00796 (0.0227)
4q loss	26 (9%)	262	0.00034 (0.00163)	1e-05 (8.41e-05)	0.477 (0.592)	0.00359 (0.012)	1e-05 (8.41e-05)	1e-05 (8.41e-05)	0.0364 (0.0787)	0.201 (0.303)	0.0165 (0.0413)	0.0031 (0.0106)
9p loss	33 (11%)	255	0.00033 (0.00161)	1e-05 (8.41e-05)	0.334 (0.459)	0.0158 (0.04)	1e-05 (8.41e-05)	1e-05 (8.41e-05)	0.0181 (0.0443)	0.143 (0.23)	0.0256 (0.0586)	0.00095 (0.00388)
9q loss	34 (12%)	254	0.00148 (0.00553)	1e-05 (8.41e-05)	0.0571 (0.113)	0.00479 (0.0152)	1e-05 (8.41e-05)	1e-05 (8.41e-05)	0.0423 (0.0889)	0.0641 (0.124)	0.00915 (0.0255)	0.00041 (0.00192)
xp loss	33 (11%)	255	0.00607 (0.0183)	1e-05 (8.41e-05)	0.216 (0.318)	0.00242 (0.00856)	1e-05 (8.41e-05)	3e-05 (0.000213)	0.023 (0.0536)	0.413 (0.534)	0.0266 (0.0602)	0.00398 (0.013)
3p loss	21 (7%)	267	4e-05 (0.000269)	4e-05 (0.000269)	0.159 (0.25)	0.0326 (0.0716)	1e-05 (8.41e-05)	1e-05 (8.41e-05)	0.0386 (0.0824)	0.107 (0.182)	0.089 (0.157)	0.0187 (0.0457)
4p loss	25 (9%)	263	0.00081 (0.00346)	1e-05 (8.41e-05)	0.207 (0.308)	0.00069 (0.00304)	1e-05 (8.41e-05)	1e-05 (8.41e-05)	0.0764 (0.142)	0.0681 (0.13)	0.0165 (0.0413)	0.00539 (0.0165)
10q loss	18 (6%)	270	0.0974 (0.169)	0.00016 (0.000864)	0.608 (0.716)	0.0234 (0.0542)	3e-05 (0.000213)	0.00104 (0.00409)	0.0122 (0.0324)	0.612 (0.719)	0.0225 (0.0528)	0.00094 (0.00388)
15q loss	31 (11%)	257	0.0223 (0.0527)	2e-05 (0.000151)	0.0915 (0.161)	0.0288 (0.0643)	8e-05 (0.00047)	1e-05 (8.41e-05)	0.0208 (0.0501)	0.0603 (0.119)	0.124 (0.205)	0.0252 (0.058)
22q loss	60 (21%)	228	0.001 (0.00396)	1e-05 (8.41e-05)	0.435 (0.553)	0.0146 (0.0375)	1e-05 (8.41e-05)	1e-05 (8.41e-05)	8e-05 (0.00047)	0.695 (0.783)	0.147 (0.235)	0.00861 (0.0241)
1p gain	10 (3%)	278	0.0159 (0.04)	1e-05 (8.41e-05)	0.282 (0.398)	0.0104 (0.028)	8e-05 (0.00047)	0.00374 (0.0124)	0.867 (0.924)	0.039 (0.0828)	0.143 (0.23)	0.161 (0.252)
1q gain	17 (6%)	271	0.00034 (0.00163)	1e-05 (8.41e-05)	0.605 (0.716)	0.0494 (0.101)	1e-05 (8.41e-05)	0.00021 (0.00104)	0.696 (0.783)	0.0102 (0.0279)	0.084 (0.151)	0.0554 (0.112)
20q gain	101 (35%)	187	1e-05 (8.41e-05)	0.00056 (0.00254)	0.0719 (0.136)	0.00762 (0.0219)	0.00745 (0.0216)	0.0502 (0.102)	0.0127 (0.0334)	0.00523 (0.0161)	0.152 (0.241)	0.0966 (0.168)
5q loss	8 (3%)	280	0.0395 (0.0837)	4e-05 (0.000269)	0.581 (0.691)	0.0751 (0.14)	0.00668 (0.0199)	0.00028 (0.00137)	0.0709 (0.135)	0.0231 (0.0536)	0.022 (0.0523)	0.262 (0.376)
11p loss	17 (6%)	271	0.0125 (0.0331)	0.00748 (0.0216)	0.683 (0.776)	0.274 (0.389)	3e-05 (0.000213)	0.00416 (0.0135)	0.0749 (0.14)	0.207 (0.308)	0.0286 (0.0642)	0.0136 (0.0349)
11q loss	21 (7%)	267	0.0463 (0.0957)	0.00096 (0.00388)	0.0964 (0.168)	0.0122 (0.0324)	2e-05 (0.000151)	0.00206 (0.0074)	0.0609 (0.119)	0.344 (0.471)	0.0738 (0.139)	0.0443 (0.0923)
17p loss	13 (5%)	275	0.00332 (0.0112)	0.00026 (0.00128)	0.252 (0.366)	0.3 (0.42)	0.00012 (0.000663)	0.00021 (0.00104)	0.156 (0.247)	0.424 (0.545)	0.00625 (0.0186)	0.00809 (0.0228)
xq loss	29 (10%)	259	0.00273 (0.00948)	1e-05 (8.41e-05)	0.444 (0.56)	0.0125 (0.033)	1e-05 (8.41e-05)	8e-05 (0.00047)	0.0801 (0.147)	0.684 (0.777)	0.0655 (0.126)	0.0134 (0.0346)
11q gain	10 (3%)	278	0.0453 (0.0943)	8e-05 (0.00047)	0.35 (0.475)	0.0175 (0.0433)	0.061 (0.119)	0.00367 (0.0122)	0.00542 (0.0165)	0.921 (0.96)	0.909 (0.951)	0.557 (0.672)
12p gain	112 (39%)	176	0.0211 (0.0507)	0.566 (0.676)	0.0285 (0.0641)	0.0815 (0.149)	0.00099 (0.00394)	0.116 (0.195)	0.03 (0.0667)	0.0507 (0.103)	0.471 (0.588)	0.0269 (0.0606)
12q gain	112 (39%)	176	0.0213 (0.0507)	0.564 (0.676)	0.0289 (0.0643)	0.0818 (0.149)	0.00076 (0.00331)	0.115 (0.194)	0.0301 (0.0668)	0.0515 (0.104)	0.472 (0.588)	0.0262 (0.0595)
1p loss	30 (10%)	258	0.00718 (0.0211)	0.00058 (0.00262)	0.89 (0.938)	0.632 (0.733)	2e-05 (0.000151)	0.00086 (0.00362)	0.00516 (0.0159)	0.0633 (0.122)	0.956 (0.985)	0.15 (0.239)
6q loss	27 (9%)	261	0.0888 (0.157)	1e-05 (8.41e-05)	1 (1.00)	0.0213 (0.0507)	1e-05 (8.41e-05)	4e-05 (0.000269)	0.0308 (0.068)	0.79 (0.867)	0.0809 (0.149)	0.0991 (0.171)
10p loss	17 (6%)	271	0.0935 (0.163)	0.00012 (0.000663)	0.81 (0.885)	0.0827 (0.15)	8e-05 (0.00047)	0.0016 (0.00589)	0.0127 (0.0334)	0.393 (0.515)	0.087 (0.154)	0.0037 (0.0123)
2q gain	47 (16%)	241	1e-05 (8.41e-05)	1e-05 (8.41e-05)	1 (1.00)	0.0334 (0.0731)	0.46 (0.577)	0.736 (0.821)	0.026 (0.0592)	0.106 (0.181)	0.632 (0.733)	0.445 (0.56)
5p gain	34 (12%)	254	0.00224 (0.00797)	0.00047 (0.00215)	0.763 (0.845)	0.845 (0.917)	0.00673 (0.0199)	0.00013 (0.000713)	0.635 (0.734)	0.169 (0.262)	0.667 (0.764)	0.168 (0.26)
5q gain	31 (11%)	257	7e-05 (0.000432)	0.00131 (0.00505)	0.539 (0.654)	0.781 (0.859)	0.00047 (0.00215)	6e-05 (0.000383)	0.766 (0.847)	0.264 (0.378)	0.665 (0.764)	0.266 (0.38)
11p gain	12 (4%)	276	0.373 (0.495)	7e-05 (0.000432)	0.432 (0.551)	0.0072 (0.0211)	0.0589 (0.117)	0.00019 (0.00097)	0.00172 (0.0063)	0.87 (0.925)	0.772 (0.852)	0.413 (0.534)
3q loss	6 (2%)	282	0.0048 (0.0152)	0.00318 (0.0108)	0.536 (0.653)	0.203 (0.305)	0.00061 (0.00272)	0.00243 (0.00856)	0.381 (0.503)	0.667 (0.764)	0.874 (0.926)	0.621 (0.728)
5p loss	7 (2%)	281	0.192 (0.292)	0.00041 (0.00192)	0.578 (0.689)	0.0756 (0.141)	0.0324 (0.0715)	0.00154 (0.0057)	0.148 (0.238)	0.0499 (0.102)	0.0527 (0.107)	0.43 (0.55)
6p loss	21 (7%)	267	0.0936 (0.163)	5e-05 (0.000327)	0.947 (0.98)	0.0406 (0.0856)	2e-05 (0.000151)	0.00017 (0.000892)	0.826 (0.899)	0.261 (0.376)	0.564 (0.676)	0.289 (0.406)
19p loss	16 (6%)	272	0.00046 (0.00213)	0.00151 (0.00562)	1 (1.00)	0.123 (0.205)	0.00191 (0.00693)	0.0103 (0.0279)	0.129 (0.213)	0.0821 (0.15)	0.16 (0.251)	0.19 (0.292)
19q loss	15 (5%)	273	1e-05 (8.41e-05)	0.00012 (0.000663)	0.796 (0.872)	0.11 (0.186)	0.0008 (0.00344)	0.0358 (0.0781)	0.0571 (0.113)	0.445 (0.56)	0.479 (0.592)	0.327 (0.449)
2p gain	42 (15%)	246	1e-05 (8.41e-05)	1e-05 (8.41e-05)	0.94 (0.975)	0.119 (0.2)	0.312 (0.433)	0.901 (0.945)	0.0128 (0.0335)	0.145 (0.233)	0.94 (0.975)	0.668 (0.764)
6p gain	10 (3%)	278	0.581 (0.691)	0.0226 (0.0529)	0.16 (0.251)	0.136 (0.222)	0.015 (0.0382)	0.0618 (0.12)	0.917 (0.957)	0.0385 (0.0824)	0.14 (0.227)	0.0929 (0.163)
8q gain	25 (9%)	263	0.545 (0.66)	0.00491 (0.0154)	0.277 (0.393)	0.45 (0.565)	0.0152 (0.0385)	0.046 (0.0954)	0.126 (0.208)	0.0672 (0.129)	0.0861 (0.153)	0.198 (0.3)
14q gain	3 (1%)	285	0.326 (0.449)	0.0371 (0.0796)	0.0169 (0.0417)	0.41 (0.533)	0.353 (0.476)	0.0363 (0.0787)	0.436 (0.553)	0.478 (0.592)	0.539 (0.654)	0.364 (0.486)
1q loss	21 (7%)	267	0.0841 (0.151)	0.0478 (0.0986)	0.849 (0.917)	0.375 (0.497)	0.185 (0.286)	0.00808 (0.0228)	0.231 (0.337)	0.0128 (0.0335)	0.533 (0.651)	0.277 (0.393)
2p loss	5 (2%)	283	0.591 (0.701)	0.00805 (0.0228)	0.0167 (0.0417)	0.211 (0.313)	0.0557 (0.112)	0.0745 (0.14)	0.02 (0.0486)	0.739 (0.822)
8q loss	9 (3%)	279	0.112 (0.19)	0.0485 (0.0997)	0.445 (0.56)	0.412 (0.534)	0.00485 (0.0153)	0.00084 (0.00355)	0.0601 (0.119)	0.627 (0.73)	1 (1.00)	0.62 (0.727)
16q loss	7 (2%)	281	0.137 (0.224)	0.0131 (0.034)	0.634 (0.734)	0.0609 (0.119)	0.00145 (0.00545)	0.0131 (0.034)	0.151 (0.24)	0.384 (0.506)	0.13 (0.213)	0.124 (0.205)
13q gain	28 (10%)	260	0.0103 (0.0279)	0.507 (0.624)	0.878 (0.928)	0.69 (0.781)	0.514 (0.63)	0.774 (0.853)	0.0436 (0.0911)	0.554 (0.67)	0.123 (0.205)	0.61 (0.718)
19p gain	5 (2%)	283	0.149 (0.238)	0.00381 (0.0125)	0.854 (0.917)	0.204 (0.305)	0.0565 (0.113)	0.00995 (0.0275)	0.105 (0.18)	0.863 (0.923)	0.846 (0.917)	1 (1.00)
19q gain	5 (2%)	283	0.149 (0.238)	0.00378 (0.0124)	0.851 (0.917)	0.204 (0.305)	0.0556 (0.112)	0.00992 (0.0275)	0.105 (0.18)	0.862 (0.923)	0.847 (0.917)	1 (1.00)
2q loss	3 (1%)	285	0.322 (0.446)	0.184 (0.285)			0.353 (0.476)	0.037 (0.0795)	0.0152 (0.0385)	1 (1.00)
8p loss	16 (6%)	272	0.136 (0.222)	0.141 (0.228)	0.168 (0.261)	0.284 (0.401)	0.00436 (0.0141)	0.00905 (0.0253)	0.0788 (0.146)	0.947 (0.98)	0.932 (0.97)	0.364 (0.486)
16p loss	4 (1%)	284	1 (1.00)	0.00334 (0.0112)	0.19 (0.292)	0.083 (0.15)	0.0566 (0.113)	0.00729 (0.0212)	0.556 (0.671)	0.224 (0.329)	0.223 (0.328)	0.119 (0.2)
6q gain	7 (2%)	281	0.627 (0.73)	0.00515 (0.0159)	0.394 (0.515)	0.357 (0.481)	0.261 (0.376)	0.215 (0.318)	0.968 (0.996)	0.269 (0.383)	0.373 (0.495)	0.431 (0.551)
9p gain	3 (1%)	285	0.681 (0.776)				0.427 (0.548)	0.0363 (0.0787)	0.647 (0.746)	0.482 (0.596)	0.539 (0.654)	0.364 (0.486)
10p gain	8 (3%)	280	0.351 (0.475)	0.00117 (0.00453)	0.853 (0.917)	0.085 (0.152)	0.0614 (0.119)	0.291 (0.409)	0.67 (0.765)	0.346 (0.472)	0.875 (0.926)	0.87 (0.925)
10q gain	8 (3%)	280	0.351 (0.475)	0.00096 (0.00388)	0.852 (0.917)	0.0865 (0.154)	0.061 (0.119)	0.293 (0.411)	0.672 (0.766)	0.346 (0.472)	0.874 (0.926)	0.867 (0.924)
21q gain	19 (7%)	269	0.00097 (0.00388)	0.103 (0.176)	0.607 (0.716)	0.52 (0.636)	0.379 (0.501)	0.948 (0.98)	0.373 (0.495)	0.0843 (0.151)	0.395 (0.516)	0.306 (0.427)
21q loss	43 (15%)	245	0.0102 (0.0279)	0.262 (0.376)	0.0739 (0.139)	0.241 (0.35)	0.694 (0.783)	0.419 (0.541)	0.812 (0.886)	0.194 (0.295)	0.662 (0.762)	0.0981 (0.17)
4p gain	10 (3%)	278	0.0889 (0.157)	0.359 (0.482)	0.894 (0.94)	0.437 (0.554)	0.348 (0.474)	0.686 (0.777)	0.225 (0.33)	0.848 (0.917)	0.705 (0.79)	0.894 (0.94)
4q gain	9 (3%)	279	0.189 (0.29)	0.36 (0.482)	0.895 (0.94)	0.435 (0.553)	0.559 (0.672)	0.741 (0.823)	0.138 (0.224)	0.692 (0.782)	0.403 (0.525)	1 (1.00)
8p gain	20 (7%)	268	0.779 (0.858)	0.0737 (0.139)	0.167 (0.26)	0.56 (0.672)	0.47 (0.588)	0.0823 (0.15)	0.08 (0.147)	0.324 (0.448)	0.518 (0.635)	0.513 (0.63)
15q gain	5 (2%)	283	0.163 (0.255)	0.237 (0.346)	0.31 (0.432)	0.204 (0.305)	0.199 (0.302)	0.261 (0.376)	0.107 (0.182)	0.232 (0.339)
18p gain	12 (4%)	276	0.0746 (0.14)	0.218 (0.322)	0.472 (0.588)	0.794 (0.87)	0.624 (0.729)	0.484 (0.597)	0.818 (0.892)	0.567 (0.676)	0.311 (0.432)	0.403 (0.525)
18q gain	9 (3%)	279	0.0833 (0.15)	0.338 (0.463)	0.267 (0.381)	0.595 (0.705)	0.632 (0.733)	0.159 (0.251)	0.714 (0.799)	0.203 (0.305)	0.2 (0.302)	0.312 (0.433)
22q gain	5 (2%)	283	0.191 (0.292)	0.639 (0.738)	1 (1.00)	0.884 (0.933)	0.397 (0.518)	0.717 (0.802)	0.424 (0.545)	0.391 (0.514)	0.746 (0.828)	0.704 (0.79)

'1p gain' versus 'CN_CNMF'

P value = 0.0159 (Fisher's exact test), Q value = 0.04

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	73	49	60
1P GAIN MUTATED	3	0	1	6
1P GAIN WILD-TYPE	103	73	48	54

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

'1p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S2. Gene #1: '1p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
1P GAIN MUTATED	1	0	0	0	3	6
1P GAIN WILD-TYPE	55	42	59	57	26	23

Figure S2. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0104 (Fisher's exact test), Q value = 0.028

Table S3. Gene #1: '1p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
1P GAIN MUTATED	2	0	6	0
1P GAIN WILD-TYPE	37	66	59	43

Figure S3. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'1p gain' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00047

Table S4. Gene #1: '1p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
1P GAIN MUTATED	0	0	1	0	9
1P GAIN WILD-TYPE	32	90	69	32	55

Figure S4. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'1p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00374 (Fisher's exact test), Q value = 0.012

Table S5. Gene #1: '1p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
1P GAIN MUTATED	6	0	4
1P GAIN WILD-TYPE	112	123	43

Figure S5. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'1p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.039 (Fisher's exact test), Q value = 0.083

Table S6. Gene #1: '1p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	80	88
1P GAIN MUTATED	4	0	6
1P GAIN WILD-TYPE	116	80	82

Figure S6. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'1q gain' versus 'CN_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.0016

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	73	49	60
1Q GAIN MUTATED	6	0	1	10
1Q GAIN WILD-TYPE	100	73	48	50

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

'1q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
1Q GAIN MUTATED	1	1	0	0	6	8
1Q GAIN WILD-TYPE	55	41	59	57	23	21

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

'1q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0494 (Fisher's exact test), Q value = 0.1

Table S9. Gene #2: '1q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
1Q GAIN MUTATED	2	1	8	1
1Q GAIN WILD-TYPE	37	65	57	42

Figure S9. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'1q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S10. Gene #2: '1q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
1Q GAIN MUTATED	0	0	3	1	13
1Q GAIN WILD-TYPE	32	90	67	31	51

Figure S10. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'1q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.001

Table S11. Gene #2: '1q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
1Q GAIN MUTATED	12	0	5
1Q GAIN WILD-TYPE	106	123	42

Figure S11. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0102 (Fisher's exact test), Q value = 0.028

Table S12. Gene #2: '1q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	80	88
1Q GAIN MUTATED	9	0	8
1Q GAIN WILD-TYPE	111	80	80

Figure S12. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S13. Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	73	49	60
2P GAIN MUTATED	2	3	28	9
2P GAIN WILD-TYPE	104	70	21	51

Figure S13. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

'2p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
2P GAIN MUTATED	4	3	2	19	3	8
2P GAIN WILD-TYPE	52	39	57	38	26	21

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

'2p gain' versus 'MIRSEQ_CNMF'

P value = 0.0128 (Fisher's exact test), Q value = 0.033

Table S15. Gene #3: '2p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	29	37	66	43	80	33
2P GAIN MUTATED	2	1	17	9	9	4
2P GAIN WILD-TYPE	27	36	49	34	71	29

Figure S15. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'2q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S16. Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	73	49	60
2Q GAIN MUTATED	4	4	30	9
2Q GAIN WILD-TYPE	102	69	19	51

Figure S16. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

'2q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
2Q GAIN MUTATED	5	3	2	22	4	8
2Q GAIN WILD-TYPE	51	39	57	35	25	21

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

'2q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0334 (Fisher's exact test), Q value = 0.073

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
2Q GAIN MUTATED	9	9	15	2
2Q GAIN WILD-TYPE	30	57	50	41

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

'2q gain' versus 'MIRSEQ_CNMF'

P value = 0.026 (Fisher's exact test), Q value = 0.059

Table S19. Gene #4: '2q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	29	37	66	43	80	33
2Q GAIN MUTATED	3	1	17	10	12	4
2Q GAIN WILD-TYPE	26	36	49	33	68	29

Figure S19. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S20. Gene #5: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	73	49	60
3P GAIN MUTATED	16	19	34	6
3P GAIN WILD-TYPE	90	54	15	54

Figure S20. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'

'3p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S21. Gene #5: '3p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
3P GAIN MUTATED	17	6	9	32	0	5
3P GAIN WILD-TYPE	39	36	50	25	29	24

Figure S21. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.00089

Table S22. Gene #5: '3p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
3P GAIN MUTATED	20	18	7	8
3P GAIN WILD-TYPE	19	48	58	35

Figure S22. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'3p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S23. Gene #5: '3p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
3P GAIN MUTATED	16	30	21	4	4
3P GAIN WILD-TYPE	16	60	49	28	60

Figure S23. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00279 (Fisher's exact test), Q value = 0.0096

Table S24. Gene #5: '3p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
3P GAIN MUTATED	27	43	5
3P GAIN WILD-TYPE	91	80	42

Figure S24. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3p gain' versus 'MIRSEQ_CNMF'

P value = 0.0108 (Fisher's exact test), Q value = 0.029

Table S25. Gene #5: '3p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	29	37	66	43	80	33
3P GAIN MUTATED	9	10	27	5	15	9
3P GAIN WILD-TYPE	20	27	39	38	65	24

Figure S25. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00077 (Fisher's exact test), Q value = 0.0033

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	80	88
3P GAIN MUTATED	32	31	12
3P GAIN WILD-TYPE	88	49	76

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

'3p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0168 (Fisher's exact test), Q value = 0.042

Table S27. Gene #5: '3p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	99	31
3P GAIN MUTATED	30	15	7
3P GAIN WILD-TYPE	62	84	24

Figure S27. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S28. Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	73	49	60
3Q GAIN MUTATED	24	24	36	11
3Q GAIN WILD-TYPE	82	49	13	49

Figure S28. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

'3q gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00015

Table S29. Gene #6: '3q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
3Q GAIN MUTATED	20	8	15	36	5	5
3Q GAIN WILD-TYPE	36	34	44	21	24	24

Figure S29. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00467 (Fisher's exact test), Q value = 0.015

Table S30. Gene #6: '3q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
3Q GAIN MUTATED	21	23	14	10
3Q GAIN WILD-TYPE	18	43	51	33

Figure S30. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'3q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S31. Gene #6: '3q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
3Q GAIN MUTATED	20	35	27	7	6
3Q GAIN WILD-TYPE	12	55	43	25	58

Figure S31. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00469 (Fisher's exact test), Q value = 0.015

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
3Q GAIN MUTATED	35	52	8
3Q GAIN WILD-TYPE	83	71	39

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

'3q gain' versus 'MIRSEQ_CNMF'

P value = 0.00132 (Fisher's exact test), Q value = 0.0051

Table S33. Gene #6: '3q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	29	37	66	43	80	33
3Q GAIN MUTATED	11	11	31	6	20	16
3Q GAIN WILD-TYPE	18	26	35	37	60	17

Figure S33. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00088 (Fisher's exact test), Q value = 0.0037

Table S34. Gene #6: '3q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	80	88
3Q GAIN MUTATED	41	37	17
3Q GAIN WILD-TYPE	79	43	71

Figure S34. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00796 (Fisher's exact test), Q value = 0.023

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	99	31
3Q GAIN MUTATED	39	24	6
3Q GAIN WILD-TYPE	53	75	25

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

'5p gain' versus 'CN_CNMF'

P value = 0.00224 (Fisher's exact test), Q value = 0.008

Table S36. Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	73	49	60
5P GAIN MUTATED	14	2	4	14
5P GAIN WILD-TYPE	92	71	45	46

Figure S36. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'METHLYATION_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.0021

Table S37. Gene #9: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
5P GAIN MUTATED	8	5	4	0	7	7
5P GAIN WILD-TYPE	48	37	55	57	22	22

Figure S37. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p gain' versus 'MRNASEQ_CNMF'

P value = 0.00673 (Fisher's exact test), Q value = 0.02

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
5P GAIN MUTATED	5	5	8	1	15
5P GAIN WILD-TYPE	27	85	62	31	49

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

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.00071

Table S39. Gene #9: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
5P GAIN MUTATED	23	4	7
5P GAIN WILD-TYPE	95	119	40

Figure S39. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5q gain' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00043

Table S40. Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	73	49	60
5Q GAIN MUTATED	14	0	4	13
5Q GAIN WILD-TYPE	92	73	45	47

Figure S40. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

'5q gain' versus 'METHLYATION_CNMF'

P value = 0.00131 (Fisher's exact test), Q value = 0.005

Table S41. Gene #10: '5q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
5Q GAIN MUTATED	8	4	2	1	7	6
5Q GAIN WILD-TYPE	48	38	57	56	22	23

Figure S41. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q gain' versus 'MRNASEQ_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.0021

Table S42. Gene #10: '5q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
5Q GAIN MUTATED	5	3	9	0	14
5Q GAIN WILD-TYPE	27	87	61	32	50

Figure S42. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00038

Table S43. Gene #10: '5q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
5Q GAIN MUTATED	23	3	5
5Q GAIN WILD-TYPE	95	120	42

Figure S43. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6p gain' versus 'METHLYATION_CNMF'

P value = 0.0226 (Fisher's exact test), Q value = 0.053

Table S44. Gene #11: '6p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
6P GAIN MUTATED	1	1	1	0	3	3
6P GAIN WILD-TYPE	55	41	58	57	26	26

Figure S44. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p gain' versus 'MRNASEQ_CNMF'

P value = 0.015 (Fisher's exact test), Q value = 0.038

Table S45. Gene #11: '6p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
6P GAIN MUTATED	0	1	1	1	7
6P GAIN WILD-TYPE	32	89	69	31	57

Figure S45. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'6p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0385 (Fisher's exact test), Q value = 0.082

Table S46. Gene #11: '6p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	80	88
6P GAIN MUTATED	4	0	6
6P GAIN WILD-TYPE	116	80	82

Figure S46. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6q gain' versus 'METHLYATION_CNMF'

P value = 0.00515 (Fisher's exact test), Q value = 0.016

Table S47. Gene #12: '6q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
6Q GAIN MUTATED	0	0	1	0	2	3
6Q GAIN WILD-TYPE	56	42	58	57	27	26

Figure S47. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S48. Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	73	49	60
7P GAIN MUTATED	29	71	38	33
7P GAIN WILD-TYPE	77	2	11	27

Figure S48. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S49. Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
7P GAIN MUTATED	28	20	45	50	7	11
7P GAIN WILD-TYPE	28	22	14	7	22	18

Figure S49. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p gain' versus 'RPPA_CNMF'

P value = 0.0101 (Fisher's exact test), Q value = 0.028

Table S50. Gene #13: '7p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	82	56
7P GAIN MUTATED	45	59	26
7P GAIN WILD-TYPE	30	23	30

Figure S50. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'7p gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S51. Gene #13: '7p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
7P GAIN MUTATED	31	52	27	20
7P GAIN WILD-TYPE	8	14	38	23

Figure S51. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S52. Gene #13: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
7P GAIN MUTATED	28	77	38	13	15
7P GAIN WILD-TYPE	4	13	32	19	49

Figure S52. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S53. Gene #13: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
7P GAIN MUTATED	53	102	16
7P GAIN WILD-TYPE	65	21	31

Figure S53. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00066

Table S54. Gene #13: '7p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	29	37	66	43	80	33
7P GAIN MUTATED	18	19	52	14	47	21
7P GAIN WILD-TYPE	11	18	14	29	33	12

Figure S54. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'7p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.00066

Table S55. Gene #13: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	80	88
7P GAIN MUTATED	62	63	46
7P GAIN WILD-TYPE	58	17	42

Figure S55. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00015

Table S56. Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	75	76
7P GAIN MUTATED	32	59	37
7P GAIN WILD-TYPE	39	16	39

Figure S56. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'7p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00015

Table S57. Gene #13: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	99	31
7P GAIN MUTATED	59	42	27
7P GAIN WILD-TYPE	33	57	4

Figure S57. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S58. Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	73	49	60
7Q GAIN MUTATED	29	71	38	34
7Q GAIN WILD-TYPE	77	2	11	26

Figure S58. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S59. Gene #14: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
7Q GAIN MUTATED	28	21	45	50	7	11
7Q GAIN WILD-TYPE	28	21	14	7	22	18

Figure S59. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q gain' versus 'RPPA_CNMF'

P value = 0.018 (Fisher's exact test), Q value = 0.044

Table S60. Gene #14: '7q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	82	56
7Q GAIN MUTATED	45	59	27
7Q GAIN WILD-TYPE	30	23	29

Figure S60. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'7q gain' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00015

Table S61. Gene #14: '7q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
7Q GAIN MUTATED	31	52	28	20
7Q GAIN WILD-TYPE	8	14	37	23

Figure S61. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S62. Gene #14: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
7Q GAIN MUTATED	28	77	39	13	15
7Q GAIN WILD-TYPE	4	13	31	19	49

Figure S62. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S63. Gene #14: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
7Q GAIN MUTATED	54	102	16
7Q GAIN WILD-TYPE	64	21	31

Figure S63. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.00089

Table S64. Gene #14: '7q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	29	37	66	43	80	33
7Q GAIN MUTATED	18	20	52	14	47	21
7Q GAIN WILD-TYPE	11	17	14	29	33	12

Figure S64. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'7q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.00089

Table S65. Gene #14: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	80	88
7Q GAIN MUTATED	63	63	46
7Q GAIN WILD-TYPE	57	17	42

Figure S65. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00038

Table S66. Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	75	76
7Q GAIN MUTATED	33	59	37
7Q GAIN WILD-TYPE	38	16	39

Figure S66. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'7q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S67. Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	99	31
7Q GAIN MUTATED	59	43	27
7Q GAIN WILD-TYPE	33	56	4

Figure S67. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q gain' versus 'METHLYATION_CNMF'

P value = 0.00491 (Fisher's exact test), Q value = 0.015

Table S68. Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
8Q GAIN MUTATED	3	2	2	3	6	7
8Q GAIN WILD-TYPE	53	40	57	54	23	22

Figure S68. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 0.0152 (Fisher's exact test), Q value = 0.039

Table S69. Gene #16: '8q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
8Q GAIN MUTATED	1	6	4	1	13
8Q GAIN WILD-TYPE	31	84	66	31	51

Figure S69. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.046 (Fisher's exact test), Q value = 0.095

Table S70. Gene #16: '8q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
8Q GAIN MUTATED	14	5	6
8Q GAIN WILD-TYPE	104	118	41

Figure S70. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0363 (Fisher's exact test), Q value = 0.079

Table S71. Gene #17: '9p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
9P GAIN MUTATED	1	0	2
9P GAIN WILD-TYPE	117	123	45

Figure S71. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10p gain' versus 'METHLYATION_CNMF'

P value = 0.00117 (Fisher's exact test), Q value = 0.0045

Table S72. Gene #18: '10p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
10P GAIN MUTATED	0	0	0	1	1	4
10P GAIN WILD-TYPE	56	42	59	56	28	25

Figure S72. Get High-res Image Gene #18: '10p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10q gain' versus 'METHLYATION_CNMF'

P value = 0.00096 (Fisher's exact test), Q value = 0.0039

Table S73. Gene #19: '10q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
10Q GAIN MUTATED	0	0	0	1	1	4
10Q GAIN WILD-TYPE	56	42	59	56	28	25

Figure S73. Get High-res Image Gene #19: '10q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11p gain' versus 'METHLYATION_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00043

Table S74. Gene #20: '11p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
11P GAIN MUTATED	1	3	0	0	1	6
11P GAIN WILD-TYPE	55	39	59	57	28	23

Figure S74. Get High-res Image Gene #20: '11p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0072 (Fisher's exact test), Q value = 0.021

Table S75. Gene #20: '11p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
11P GAIN MUTATED	0	2	8	0
11P GAIN WILD-TYPE	39	64	57	43

Figure S75. Get High-res Image Gene #20: '11p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'11p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.00097

Table S76. Gene #20: '11p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
11P GAIN MUTATED	6	0	6
11P GAIN WILD-TYPE	112	123	41

Figure S76. Get High-res Image Gene #20: '11p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11p gain' versus 'MIRSEQ_CNMF'

P value = 0.00172 (Fisher's exact test), Q value = 0.0063

Table S77. Gene #20: '11p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	29	37	66	43	80	33
11P GAIN MUTATED	0	1	0	7	4	0
11P GAIN WILD-TYPE	29	36	66	36	76	33

Figure S77. Get High-res Image Gene #20: '11p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'11q gain' versus 'CN_CNMF'

P value = 0.0453 (Fisher's exact test), Q value = 0.094

Table S78. Gene #21: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	73	49	60
11Q GAIN MUTATED	3	0	2	5
11Q GAIN WILD-TYPE	103	73	47	55

Figure S78. Get High-res Image Gene #21: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

'11q gain' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00047

Table S79. Gene #21: '11q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
11Q GAIN MUTATED	0	3	0	0	1	5
11Q GAIN WILD-TYPE	56	39	59	57	28	24

Figure S79. Get High-res Image Gene #21: '11q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0175 (Fisher's exact test), Q value = 0.043

Table S80. Gene #21: '11q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
11Q GAIN MUTATED	0	2	7	0
11Q GAIN WILD-TYPE	39	64	58	43

Figure S80. Get High-res Image Gene #21: '11q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'11q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00367 (Fisher's exact test), Q value = 0.012

Table S81. Gene #21: '11q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
11Q GAIN MUTATED	6	0	4
11Q GAIN WILD-TYPE	112	123	43

Figure S81. Get High-res Image Gene #21: '11q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_CNMF'

P value = 0.00542 (Fisher's exact test), Q value = 0.017

Table S82. Gene #21: '11q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	29	37	66	43	80	33
11Q GAIN MUTATED	0	1	0	6	3	0
11Q GAIN WILD-TYPE	29	36	66	37	77	33

Figure S82. Get High-res Image Gene #21: '11q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 0.0211 (Fisher's exact test), Q value = 0.051

Table S83. Gene #22: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	73	49	60
12P GAIN MUTATED	29	33	23	27
12P GAIN WILD-TYPE	77	40	26	33

Figure S83. Get High-res Image Gene #22: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

'12p gain' versus 'RPPA_CNMF'

P value = 0.0285 (Fisher's exact test), Q value = 0.064

Table S84. Gene #22: '12p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	82	56
12P GAIN MUTATED	38	27	17
12P GAIN WILD-TYPE	37	55	39

Figure S84. Get High-res Image Gene #22: '12p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 0.00099 (Fisher's exact test), Q value = 0.0039

Table S85. Gene #22: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
12P GAIN MUTATED	18	42	29	4	19
12P GAIN WILD-TYPE	14	48	41	28	45

Figure S85. Get High-res Image Gene #22: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12p gain' versus 'MIRSEQ_CNMF'

P value = 0.03 (Fisher's exact test), Q value = 0.067

Table S86. Gene #22: '12p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	29	37	66	43	80	33
12P GAIN MUTATED	8	15	32	12	26	19
12P GAIN WILD-TYPE	21	22	34	31	54	14

Figure S86. Get High-res Image Gene #22: '12p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'12p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0269 (Fisher's exact test), Q value = 0.061

Table S87. Gene #22: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	99	31
12P GAIN MUTATED	45	31	9
12P GAIN WILD-TYPE	47	68	22

Figure S87. Get High-res Image Gene #22: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q gain' versus 'CN_CNMF'

P value = 0.0213 (Fisher's exact test), Q value = 0.051

Table S88. Gene #23: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	73	49	60
12Q GAIN MUTATED	29	33	23	27
12Q GAIN WILD-TYPE	77	40	26	33

Figure S88. Get High-res Image Gene #23: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

'12q gain' versus 'RPPA_CNMF'

P value = 0.0289 (Fisher's exact test), Q value = 0.064

Table S89. Gene #23: '12q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	82	56
12Q GAIN MUTATED	38	27	17
12Q GAIN WILD-TYPE	37	55	39

Figure S89. Get High-res Image Gene #23: '12q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'12q gain' versus 'MRNASEQ_CNMF'

P value = 0.00076 (Fisher's exact test), Q value = 0.0033

Table S90. Gene #23: '12q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
12Q GAIN MUTATED	18	42	29	4	19
12Q GAIN WILD-TYPE	14	48	41	28	45

Figure S90. Get High-res Image Gene #23: '12q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12q gain' versus 'MIRSEQ_CNMF'

P value = 0.0301 (Fisher's exact test), Q value = 0.067

Table S91. Gene #23: '12q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	29	37	66	43	80	33
12Q GAIN MUTATED	8	15	32	12	26	19
12Q GAIN WILD-TYPE	21	22	34	31	54	14

Figure S91. Get High-res Image Gene #23: '12q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'12q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0262 (Fisher's exact test), Q value = 0.059

Table S92. Gene #23: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	99	31
12Q GAIN MUTATED	45	31	9
12Q GAIN WILD-TYPE	47	68	22

Figure S92. Get High-res Image Gene #23: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q gain' versus 'CN_CNMF'

P value = 0.0103 (Fisher's exact test), Q value = 0.028

Table S93. Gene #24: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	73	49	60
13Q GAIN MUTATED	11	6	10	1
13Q GAIN WILD-TYPE	95	67	39	59

Figure S93. Get High-res Image Gene #24: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

'13q gain' versus 'MIRSEQ_CNMF'

P value = 0.0436 (Fisher's exact test), Q value = 0.091

Table S94. Gene #24: '13q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	29	37	66	43	80	33
13Q GAIN MUTATED	8	1	7	4	6	2
13Q GAIN WILD-TYPE	21	36	59	39	74	31

Figure S94. Get High-res Image Gene #24: '13q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'14q gain' versus 'METHLYATION_CNMF'

P value = 0.0371 (Fisher's exact test), Q value = 0.08

Table S95. Gene #25: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
14Q GAIN MUTATED	1	0	0	0	0	2
14Q GAIN WILD-TYPE	55	42	59	57	29	27

Figure S95. Get High-res Image Gene #25: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'14q gain' versus 'RPPA_CNMF'

P value = 0.0169 (Fisher's exact test), Q value = 0.042

Table S96. Gene #25: '14q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	82	56
14Q GAIN MUTATED	0	0	3
14Q GAIN WILD-TYPE	75	82	53

Figure S96. Get High-res Image Gene #25: '14q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0363 (Fisher's exact test), Q value = 0.079

Table S97. Gene #25: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
14Q GAIN MUTATED	1	0	2
14Q GAIN WILD-TYPE	117	123	45

Figure S97. Get High-res Image Gene #25: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S98. Gene #27: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	73	49	60
16P GAIN MUTATED	36	35	43	39
16P GAIN WILD-TYPE	70	38	6	21

Figure S98. Get High-res Image Gene #27: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

'16p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S99. Gene #27: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
16P GAIN MUTATED	28	24	18	52	13	11
16P GAIN WILD-TYPE	28	18	41	5	16	18

Figure S99. Get High-res Image Gene #27: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00076 (Fisher's exact test), Q value = 0.0033

Table S100. Gene #27: '16p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
16P GAIN MUTATED	27	35	23	30
16P GAIN WILD-TYPE	12	31	42	13

Figure S100. Get High-res Image Gene #27: '16p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S101. Gene #27: '16p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
16P GAIN MUTATED	26	54	47	6	20
16P GAIN WILD-TYPE	6	36	23	26	44

Figure S101. Get High-res Image Gene #27: '16p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00027

Table S102. Gene #27: '16p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
16P GAIN MUTATED	68	74	11
16P GAIN WILD-TYPE	50	49	36

Figure S102. Get High-res Image Gene #27: '16p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00033

Table S103. Gene #27: '16p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	29	37	66	43	80	33
16P GAIN MUTATED	19	23	49	16	31	15
16P GAIN WILD-TYPE	10	14	17	27	49	18

Figure S103. Get High-res Image Gene #27: '16p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S104. Gene #27: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	80	88
16P GAIN MUTATED	66	58	29
16P GAIN WILD-TYPE	54	22	59

Figure S104. Get High-res Image Gene #27: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.00097

Table S105. Gene #27: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	75	76
16P GAIN MUTATED	45	45	25
16P GAIN WILD-TYPE	26	30	51

Figure S105. Get High-res Image Gene #27: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00021

Table S106. Gene #27: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	99	31
16P GAIN MUTATED	65	37	13
16P GAIN WILD-TYPE	27	62	18

Figure S106. Get High-res Image Gene #27: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S107. Gene #28: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	73	49	60
16Q GAIN MUTATED	37	35	43	33
16Q GAIN WILD-TYPE	69	38	6	27

Figure S107. Get High-res Image Gene #28: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S108. Gene #28: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
16Q GAIN MUTATED	28	24	18	51	11	10
16Q GAIN WILD-TYPE	28	18	41	6	18	19

Figure S108. Get High-res Image Gene #28: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00187 (Fisher's exact test), Q value = 0.0068

Table S109. Gene #28: '16q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
16Q GAIN MUTATED	27	35	23	28
16Q GAIN WILD-TYPE	12	31	42	15

Figure S109. Get High-res Image Gene #28: '16q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'16q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S110. Gene #28: '16q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
16Q GAIN MUTATED	26	53	46	6	17
16Q GAIN WILD-TYPE	6	37	24	26	47

Figure S110. Get High-res Image Gene #28: '16q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.00063

Table S111. Gene #28: '16q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
16Q GAIN MUTATED	64	73	11
16Q GAIN WILD-TYPE	54	50	36

Figure S111. Get High-res Image Gene #28: '16q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00015

Table S112. Gene #28: '16q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	29	37	66	43	80	33
16Q GAIN MUTATED	18	22	49	16	29	14
16Q GAIN WILD-TYPE	11	15	17	27	51	19

Figure S112. Get High-res Image Gene #28: '16q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S113. Gene #28: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	80	88
16Q GAIN MUTATED	62	58	28
16Q GAIN WILD-TYPE	58	22	60

Figure S113. Get High-res Image Gene #28: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00063

Table S114. Gene #28: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	75	76
16Q GAIN MUTATED	43	44	23
16Q GAIN WILD-TYPE	28	31	53

Figure S114. Get High-res Image Gene #28: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S115. Gene #28: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	99	31
16Q GAIN MUTATED	65	33	12
16Q GAIN WILD-TYPE	27	66	19

Figure S115. Get High-res Image Gene #28: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S116. Gene #29: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	73	49	60
17P GAIN MUTATED	22	69	41	40
17P GAIN WILD-TYPE	84	4	8	20

Figure S116. Get High-res Image Gene #29: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

'17p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S117. Gene #29: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
17P GAIN MUTATED	27	17	48	53	7	10
17P GAIN WILD-TYPE	29	25	11	4	22	19

Figure S117. Get High-res Image Gene #29: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p gain' versus 'RPPA_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00038

Table S118. Gene #29: '17p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	82	56
17P GAIN MUTATED	48	60	20
17P GAIN WILD-TYPE	27	22	36

Figure S118. Get High-res Image Gene #29: '17p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'17p gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S119. Gene #29: '17p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
17P GAIN MUTATED	31	51	28	18
17P GAIN WILD-TYPE	8	15	37	25

Figure S119. Get High-res Image Gene #29: '17p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'17p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S120. Gene #29: '17p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
17P GAIN MUTATED	26	80	35	12	19
17P GAIN WILD-TYPE	6	10	35	20	45

Figure S120. Get High-res Image Gene #29: '17p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S121. Gene #29: '17p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
17P GAIN MUTATED	54	108	10
17P GAIN WILD-TYPE	64	15	37

Figure S121. Get High-res Image Gene #29: '17p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00063

Table S122. Gene #29: '17p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	29	37	66	43	80	33
17P GAIN MUTATED	18	18	55	18	44	19
17P GAIN WILD-TYPE	11	19	11	25	36	14

Figure S122. Get High-res Image Gene #29: '17p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.00076

Table S123. Gene #29: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	80	88
17P GAIN MUTATED	62	63	47
17P GAIN WILD-TYPE	58	17	41

Figure S123. Get High-res Image Gene #29: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S124. Gene #29: '17p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	75	76
17P GAIN MUTATED	34	63	30
17P GAIN WILD-TYPE	37	12	46

Figure S124. Get High-res Image Gene #29: '17p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S125. Gene #29: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	99	31
17P GAIN MUTATED	62	37	28
17P GAIN WILD-TYPE	30	62	3

Figure S125. Get High-res Image Gene #29: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S126. Gene #30: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	73	49	60
17Q GAIN MUTATED	27	71	43	50
17Q GAIN WILD-TYPE	79	2	6	10

Figure S126. Get High-res Image Gene #30: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S127. Gene #30: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
17Q GAIN MUTATED	31	22	49	53	12	13
17Q GAIN WILD-TYPE	25	20	10	4	17	16

Figure S127. Get High-res Image Gene #30: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q gain' versus 'RPPA_CNMF'

P value = 0.00083 (Fisher's exact test), Q value = 0.0035

Table S128. Gene #30: '17q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	82	56
17Q GAIN MUTATED	53	63	26
17Q GAIN WILD-TYPE	22	19	30

Figure S128. Get High-res Image Gene #30: '17q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'17q gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S129. Gene #30: '17q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
17Q GAIN MUTATED	35	53	33	21
17Q GAIN WILD-TYPE	4	13	32	22

Figure S129. Get High-res Image Gene #30: '17q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S130. Gene #30: '17q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
17Q GAIN MUTATED	28	81	41	13	28
17Q GAIN WILD-TYPE	4	9	29	19	36

Figure S130. Get High-res Image Gene #30: '17q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S131. Gene #30: '17q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
17Q GAIN MUTATED	68	108	15
17Q GAIN WILD-TYPE	50	15	32

Figure S131. Get High-res Image Gene #30: '17q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_CNMF'

P value = 0.00786 (Fisher's exact test), Q value = 0.022

Table S132. Gene #30: '17q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	29	37	66	43	80	33
17Q GAIN MUTATED	21	22	55	22	51	20
17Q GAIN WILD-TYPE	8	15	11	21	29	13

Figure S132. Get High-res Image Gene #30: '17q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00097 (Fisher's exact test), Q value = 0.0039

Table S133. Gene #30: '17q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	80	88
17Q GAIN MUTATED	72	66	53
17Q GAIN WILD-TYPE	48	14	35

Figure S133. Get High-res Image Gene #30: '17q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00021

Table S134. Gene #30: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	75	76
17Q GAIN MUTATED	40	63	40
17Q GAIN WILD-TYPE	31	12	36

Figure S134. Get High-res Image Gene #30: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00015

Table S135. Gene #30: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	99	31
17Q GAIN MUTATED	66	49	28
17Q GAIN WILD-TYPE	26	50	3

Figure S135. Get High-res Image Gene #30: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p gain' versus 'METHLYATION_CNMF'

P value = 0.00381 (Fisher's exact test), Q value = 0.012

Table S136. Gene #33: '19p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
19P GAIN MUTATED	0	1	0	0	1	3
19P GAIN WILD-TYPE	56	41	59	57	28	26

Figure S136. Get High-res Image Gene #33: '19p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00995 (Fisher's exact test), Q value = 0.027

Table S137. Gene #33: '19p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
19P GAIN MUTATED	2	0	3
19P GAIN WILD-TYPE	116	123	44

Figure S137. Get High-res Image Gene #33: '19p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'METHLYATION_CNMF'

P value = 0.00378 (Fisher's exact test), Q value = 0.012

Table S138. Gene #34: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
19Q GAIN MUTATED	0	1	0	0	1	3
19Q GAIN WILD-TYPE	56	41	59	57	28	26

Figure S138. Get High-res Image Gene #34: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00992 (Fisher's exact test), Q value = 0.027

Table S139. Gene #34: '19q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
19Q GAIN MUTATED	2	0	3
19Q GAIN WILD-TYPE	116	123	44

Figure S139. Get High-res Image Gene #34: '19q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S140. Gene #35: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	73	49	60
20P GAIN MUTATED	13	27	26	33
20P GAIN WILD-TYPE	93	46	23	27

Figure S140. Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.001

Table S141. Gene #35: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
20P GAIN MUTATED	12	8	17	33	11	11
20P GAIN WILD-TYPE	44	34	42	24	18	18

Figure S141. Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20p gain' versus 'RPPA_CNMF'

P value = 0.0259 (Fisher's exact test), Q value = 0.059

Table S142. Gene #35: '20p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	82	56
20P GAIN MUTATED	22	35	12
20P GAIN WILD-TYPE	53	47	44

Figure S142. Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'20p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00265 (Fisher's exact test), Q value = 0.0093

Table S143. Gene #35: '20p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
20P GAIN MUTATED	14	31	18	6
20P GAIN WILD-TYPE	25	35	47	37

Figure S143. Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 0.00114 (Fisher's exact test), Q value = 0.0044

Table S144. Gene #35: '20p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
20P GAIN MUTATED	10	45	21	4	19
20P GAIN WILD-TYPE	22	45	49	28	45

Figure S144. Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0218 (Fisher's exact test), Q value = 0.052

Table S145. Gene #35: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
20P GAIN MUTATED	35	53	11
20P GAIN WILD-TYPE	83	70	36

Figure S145. Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_CNMF'

P value = 0.00551 (Fisher's exact test), Q value = 0.017

Table S146. Gene #35: '20p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	29	37	66	43	80	33
20P GAIN MUTATED	6	12	36	10	25	10
20P GAIN WILD-TYPE	23	25	30	33	55	23

Figure S146. Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0031 (Fisher's exact test), Q value = 0.011

Table S147. Gene #35: '20p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	80	88
20P GAIN MUTATED	34	40	25
20P GAIN WILD-TYPE	86	40	63

Figure S147. Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.043 (Fisher's exact test), Q value = 0.09

Table S148. Gene #35: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	99	31
20P GAIN MUTATED	36	24	13
20P GAIN WILD-TYPE	56	75	18

Figure S148. Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S149. Gene #36: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	73	49	60
20Q GAIN MUTATED	16	27	25	33
20Q GAIN WILD-TYPE	90	46	24	27

Figure S149. Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 0.00056 (Fisher's exact test), Q value = 0.0025

Table S150. Gene #36: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
20Q GAIN MUTATED	12	8	17	32	12	12
20Q GAIN WILD-TYPE	44	34	42	25	17	17

Figure S150. Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00762 (Fisher's exact test), Q value = 0.022

Table S151. Gene #36: '20q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
20Q GAIN MUTATED	13	31	19	7
20Q GAIN WILD-TYPE	26	35	46	36

Figure S151. Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 0.00745 (Fisher's exact test), Q value = 0.022

Table S152. Gene #36: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
20Q GAIN MUTATED	10	45	21	6	19
20Q GAIN WILD-TYPE	22	45	49	26	45

Figure S152. Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 0.0127 (Fisher's exact test), Q value = 0.033

Table S153. Gene #36: '20q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	29	37	66	43	80	33
20Q GAIN MUTATED	6	13	35	10	27	10
20Q GAIN WILD-TYPE	23	24	31	33	53	23

Figure S153. Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00523 (Fisher's exact test), Q value = 0.016

Table S154. Gene #36: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	80	88
20Q GAIN MUTATED	34	40	27
20Q GAIN WILD-TYPE	86	40	61

Figure S154. Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'21q gain' versus 'CN_CNMF'

P value = 0.00097 (Fisher's exact test), Q value = 0.0039

Table S155. Gene #37: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	73	49	60
21Q GAIN MUTATED	2	2	5	10
21Q GAIN WILD-TYPE	104	71	44	50

Figure S155. Get High-res Image Gene #37: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

'xp gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S156. Gene #39: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	73	49	60
XP GAIN MUTATED	8	36	34	10
XP GAIN WILD-TYPE	98	37	15	50

Figure S156. Get High-res Image Gene #39: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'

'xp gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S157. Gene #39: 'xp gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
XP GAIN MUTATED	12	11	16	37	2	3
XP GAIN WILD-TYPE	44	31	43	20	27	26

Figure S157. Get High-res Image Gene #39: 'xp gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xp gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00202 (Fisher's exact test), Q value = 0.0073

Table S158. Gene #39: 'xp gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
XP GAIN MUTATED	18	26	11	9
XP GAIN WILD-TYPE	21	40	54	34

Figure S158. Get High-res Image Gene #39: 'xp gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'xp gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S159. Gene #39: 'xp gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
XP GAIN MUTATED	14	45	23	1	5
XP GAIN WILD-TYPE	18	45	47	31	59

Figure S159. Get High-res Image Gene #39: 'xp gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xp gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S160. Gene #39: 'xp gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
XP GAIN MUTATED	27	56	5
XP GAIN WILD-TYPE	91	67	42

Figure S160. Get High-res Image Gene #39: 'xp gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xp gain' versus 'MIRSEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00043

Table S161. Gene #39: 'xp gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	29	37	66	43	80	33
XP GAIN MUTATED	10	12	36	8	14	8
XP GAIN WILD-TYPE	19	25	30	35	66	25

Figure S161. Get High-res Image Gene #39: 'xp gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'xp gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.00097

Table S162. Gene #39: 'xp gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	80	88
XP GAIN MUTATED	32	39	17
XP GAIN WILD-TYPE	88	41	71

Figure S162. Get High-res Image Gene #39: 'xp gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'xp gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.001

Table S163. Gene #39: 'xp gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	75	76
XP GAIN MUTATED	21	31	9
XP GAIN WILD-TYPE	50	44	67

Figure S163. Get High-res Image Gene #39: 'xp gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xp gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00069 (Fisher's exact test), Q value = 0.003

Table S164. Gene #39: 'xp gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	99	31
XP GAIN MUTATED	35	15	11
XP GAIN WILD-TYPE	57	84	20

Figure S164. Get High-res Image Gene #39: 'xp gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S165. Gene #40: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	73	49	60
XQ GAIN MUTATED	9	37	35	11
XQ GAIN WILD-TYPE	97	36	14	49

Figure S165. Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

'xq gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S166. Gene #40: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
XQ GAIN MUTATED	12	11	16	37	4	4
XQ GAIN WILD-TYPE	44	31	43	20	25	25

Figure S166. Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00707 (Fisher's exact test), Q value = 0.021

Table S167. Gene #40: 'xq gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
XQ GAIN MUTATED	18	26	13	9
XQ GAIN WILD-TYPE	21	40	52	34

Figure S167. Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'xq gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S168. Gene #40: 'xq gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
XQ GAIN MUTATED	14	46	24	1	7
XQ GAIN WILD-TYPE	18	44	46	31	57

Figure S168. Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xq gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00021

Table S169. Gene #40: 'xq gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
XQ GAIN MUTATED	29	57	6
XQ GAIN WILD-TYPE	89	66	41

Figure S169. Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xq gain' versus 'MIRSEQ_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.0018

Table S170. Gene #40: 'xq gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	29	37	66	43	80	33
XQ GAIN MUTATED	10	12	36	10	15	9
XQ GAIN WILD-TYPE	19	25	30	33	65	24

Figure S170. Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'xq gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.00097

Table S171. Gene #40: 'xq gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	80	88
XQ GAIN MUTATED	35	39	18
XQ GAIN WILD-TYPE	85	41	70

Figure S171. Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'xq gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00097 (Fisher's exact test), Q value = 0.0039

Table S172. Gene #40: 'xq gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	75	76
XQ GAIN MUTATED	21	31	11
XQ GAIN WILD-TYPE	50	44	65

Figure S172. Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xq gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00302 (Fisher's exact test), Q value = 0.01

Table S173. Gene #40: 'xq gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	99	31
XQ GAIN MUTATED	35	17	11
XQ GAIN WILD-TYPE	57	82	20

Figure S173. Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

P value = 0.00718 (Fisher's exact test), Q value = 0.021

Table S174. Gene #41: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	73	49	60
1P LOSS MUTATED	12	1	7	10
1P LOSS WILD-TYPE	94	72	42	50

Figure S174. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 0.00058 (Fisher's exact test), Q value = 0.0026

Table S175. Gene #41: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
1P LOSS MUTATED	7	2	1	4	8	7
1P LOSS WILD-TYPE	49	40	58	53	21	22

Figure S175. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00015

Table S176. Gene #41: '1p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
1P LOSS MUTATED	1	4	3	3	19
1P LOSS WILD-TYPE	31	86	67	29	45

Figure S176. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00086 (Fisher's exact test), Q value = 0.0036

Table S177. Gene #41: '1p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
1P LOSS MUTATED	12	6	12
1P LOSS WILD-TYPE	106	117	35

Figure S177. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_CNMF'

P value = 0.00516 (Fisher's exact test), Q value = 0.016

Table S178. Gene #41: '1p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	29	37	66	43	80	33
1P LOSS MUTATED	2	6	5	11	6	0
1P LOSS WILD-TYPE	27	31	61	32	74	33

Figure S178. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'1q loss' versus 'METHLYATION_CNMF'

P value = 0.0478 (Fisher's exact test), Q value = 0.099

Table S179. Gene #42: '1q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
1Q LOSS MUTATED	5	1	1	4	4	5
1Q LOSS WILD-TYPE	51	41	58	53	25	24

Figure S179. Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00808 (Fisher's exact test), Q value = 0.023

Table S180. Gene #42: '1q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
1Q LOSS MUTATED	6	6	9
1Q LOSS WILD-TYPE	112	117	38

Figure S180. Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'1q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0128 (Fisher's exact test), Q value = 0.033

Table S181. Gene #42: '1q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	80	88
1Q LOSS MUTATED	5	12	4
1Q LOSS WILD-TYPE	115	68	84

Figure S181. Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2p loss' versus 'METHLYATION_CNMF'

P value = 0.00805 (Fisher's exact test), Q value = 0.023

Table S182. Gene #43: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
2P LOSS MUTATED	1	0	0	0	3	1
2P LOSS WILD-TYPE	55	42	59	57	26	28

Figure S182. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2p loss' versus 'RPPA_CNMF'

P value = 0.0167 (Fisher's exact test), Q value = 0.042

Table S183. Gene #43: '2p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	82	56
2P LOSS MUTATED	0	0	3
2P LOSS WILD-TYPE	75	82	53

Figure S183. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'2p loss' versus 'MIRSEQ_CNMF'

P value = 0.02 (Fisher's exact test), Q value = 0.049

Table S184. Gene #43: '2p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	29	37	66	43	80	33
2P LOSS MUTATED	2	2	0	1	0	0
2P LOSS WILD-TYPE	27	35	66	42	80	33

Figure S184. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'2q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.037 (Fisher's exact test), Q value = 0.08

Table S185. Gene #44: '2q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
2Q LOSS MUTATED	1	0	2
2Q LOSS WILD-TYPE	117	123	45

Figure S185. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_CNMF'

P value = 0.0152 (Fisher's exact test), Q value = 0.039

Table S186. Gene #44: '2q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	29	37	66	43	80	33
2Q LOSS MUTATED	2	1	0	0	0	0
2Q LOSS WILD-TYPE	27	36	66	43	80	33

Figure S186. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3p loss' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00027

Table S187. Gene #45: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	73	49	60
3P LOSS MUTATED	8	0	1	12
3P LOSS WILD-TYPE	98	73	48	48

Figure S187. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00027

Table S188. Gene #45: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
3P LOSS MUTATED	5	4	0	0	8	3
3P LOSS WILD-TYPE	51	38	59	57	21	26

Figure S188. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0326 (Fisher's exact test), Q value = 0.072

Table S189. Gene #45: '3p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
3P LOSS MUTATED	3	3	11	1
3P LOSS WILD-TYPE	36	63	54	42

Figure S189. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S190. Gene #45: '3p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
3P LOSS MUTATED	0	0	6	1	14
3P LOSS WILD-TYPE	32	90	64	31	50

Figure S190. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S191. Gene #45: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
3P LOSS MUTATED	17	0	4
3P LOSS WILD-TYPE	101	123	43

Figure S191. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CNMF'

P value = 0.0386 (Fisher's exact test), Q value = 0.082

Table S192. Gene #45: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	29	37	66	43	80	33
3P LOSS MUTATED	1	3	1	8	6	2
3P LOSS WILD-TYPE	28	34	65	35	74	31

Figure S192. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0187 (Fisher's exact test), Q value = 0.046

Table S193. Gene #45: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	99	31
3P LOSS MUTATED	6	15	0
3P LOSS WILD-TYPE	86	84	31

Figure S193. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

P value = 0.0048 (Fisher's exact test), Q value = 0.015

Table S194. Gene #46: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	73	49	60
3Q LOSS MUTATED	1	0	0	5
3Q LOSS WILD-TYPE	105	73	49	55

Figure S194. Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

'3q loss' versus 'METHLYATION_CNMF'

P value = 0.00318 (Fisher's exact test), Q value = 0.011

Table S195. Gene #46: '3q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
3Q LOSS MUTATED	0	1	0	0	2	3
3Q LOSS WILD-TYPE	56	41	59	57	27	26

Figure S195. Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3q loss' versus 'MRNASEQ_CNMF'

P value = 0.00061 (Fisher's exact test), Q value = 0.0027

Table S196. Gene #46: '3q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
3Q LOSS MUTATED	0	0	0	0	6
3Q LOSS WILD-TYPE	32	90	70	32	58

Figure S196. Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00243 (Fisher's exact test), Q value = 0.0086

Table S197. Gene #46: '3q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
3Q LOSS MUTATED	2	0	4
3Q LOSS WILD-TYPE	116	123	43

Figure S197. Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

P value = 0.00081 (Fisher's exact test), Q value = 0.0035

Table S198. Gene #47: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	73	49	60
4P LOSS MUTATED	9	0	6	10
4P LOSS WILD-TYPE	97	73	43	50

Figure S198. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S199. Gene #47: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
4P LOSS MUTATED	3	2	0	1	6	12
4P LOSS WILD-TYPE	53	40	59	56	23	17

Figure S199. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00069 (Fisher's exact test), Q value = 0.003

Table S200. Gene #47: '4p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
4P LOSS MUTATED	2	3	15	1
4P LOSS WILD-TYPE	37	63	50	42

Figure S200. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S201. Gene #47: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
4P LOSS MUTATED	0	0	2	4	19
4P LOSS WILD-TYPE	32	90	68	28	45

Figure S201. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S202. Gene #47: '4p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
4P LOSS MUTATED	12	1	12
4P LOSS WILD-TYPE	106	122	35

Figure S202. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0165 (Fisher's exact test), Q value = 0.041

Table S203. Gene #47: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	75	76
4P LOSS MUTATED	5	2	12
4P LOSS WILD-TYPE	66	73	64

Figure S203. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00539 (Fisher's exact test), Q value = 0.016

Table S204. Gene #47: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	99	31
4P LOSS MUTATED	4	15	0
4P LOSS WILD-TYPE	88	84	31

Figure S204. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.0016

Table S205. Gene #48: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	73	49	60
4Q LOSS MUTATED	9	0	6	11
4Q LOSS WILD-TYPE	97	73	43	49

Figure S205. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S206. Gene #48: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
4Q LOSS MUTATED	3	4	0	1	6	11
4Q LOSS WILD-TYPE	53	38	59	56	23	18

Figure S206. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00359 (Fisher's exact test), Q value = 0.012

Table S207. Gene #48: '4q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
4Q LOSS MUTATED	2	4	14	1
4Q LOSS WILD-TYPE	37	62	51	42

Figure S207. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S208. Gene #48: '4q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
4Q LOSS MUTATED	0	0	4	3	19
4Q LOSS WILD-TYPE	32	90	66	29	45

Figure S208. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S209. Gene #48: '4q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
4Q LOSS MUTATED	14	1	11
4Q LOSS WILD-TYPE	104	122	36

Figure S209. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_CNMF'

P value = 0.0364 (Fisher's exact test), Q value = 0.079

Table S210. Gene #48: '4q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	29	37	66	43	80	33
4Q LOSS MUTATED	1	2	3	9	10	1
4Q LOSS WILD-TYPE	28	35	63	34	70	32

Figure S210. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'4q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0165 (Fisher's exact test), Q value = 0.041

Table S211. Gene #48: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	75	76
4Q LOSS MUTATED	6	2	12
4Q LOSS WILD-TYPE	65	73	64

Figure S211. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'4q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0031 (Fisher's exact test), Q value = 0.011

Table S212. Gene #48: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	99	31
4Q LOSS MUTATED	4	16	0
4Q LOSS WILD-TYPE	88	83	31

Figure S212. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p loss' versus 'METHLYATION_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.0019

Table S213. Gene #49: '5p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
5P LOSS MUTATED	1	0	1	0	0	5
5P LOSS WILD-TYPE	55	42	58	57	29	24

Figure S213. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p loss' versus 'MRNASEQ_CNMF'

P value = 0.0324 (Fisher's exact test), Q value = 0.071

Table S214. Gene #49: '5p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
5P LOSS MUTATED	1	0	1	3	2
5P LOSS WILD-TYPE	31	90	69	29	62

Figure S214. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00154 (Fisher's exact test), Q value = 0.0057

Table S215. Gene #49: '5p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
5P LOSS MUTATED	1	1	5
5P LOSS WILD-TYPE	117	122	42

Figure S215. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0499 (Fisher's exact test), Q value = 0.1

Table S216. Gene #49: '5p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	80	88
5P LOSS MUTATED	2	0	5
5P LOSS WILD-TYPE	118	80	83

Figure S216. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'CN_CNMF'

P value = 0.0395 (Fisher's exact test), Q value = 0.084

Table S217. Gene #50: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	73	49	60
5Q LOSS MUTATED	5	0	3	0
5Q LOSS WILD-TYPE	101	73	46	60

Figure S217. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00027

Table S218. Gene #50: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
5Q LOSS MUTATED	1	0	1	0	0	6
5Q LOSS WILD-TYPE	55	42	58	57	29	23

Figure S218. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 0.00668 (Fisher's exact test), Q value = 0.02

Table S219. Gene #50: '5q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
5Q LOSS MUTATED	1	0	1	4	2
5Q LOSS WILD-TYPE	31	90	69	28	62

Figure S219. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 0.0014

Table S220. Gene #50: '5q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
5Q LOSS MUTATED	1	1	6
5Q LOSS WILD-TYPE	117	122	41

Figure S220. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0231 (Fisher's exact test), Q value = 0.054

Table S221. Gene #50: '5q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	80	88
5Q LOSS MUTATED	2	0	6
5Q LOSS WILD-TYPE	118	80	82

Figure S221. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.022 (Fisher's exact test), Q value = 0.052

Table S222. Gene #50: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	75	76
5Q LOSS MUTATED	2	0	6
5Q LOSS WILD-TYPE	69	75	70

Figure S222. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'6p loss' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00033

Table S223. Gene #51: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
6P LOSS MUTATED	4	1	0	2	5	8
6P LOSS WILD-TYPE	52	41	59	55	24	21

Figure S223. Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0406 (Fisher's exact test), Q value = 0.086

Table S224. Gene #51: '6p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
6P LOSS MUTATED	2	5	9	0
6P LOSS WILD-TYPE	37	61	56	43

Figure S224. Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'6p loss' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00015

Table S225. Gene #51: '6p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
6P LOSS MUTATED	0	3	2	1	15
6P LOSS WILD-TYPE	32	87	68	31	49

Figure S225. Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.00089

Table S226. Gene #51: '6p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
6P LOSS MUTATED	6	4	11
6P LOSS WILD-TYPE	112	119	36

Figure S226. Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S227. Gene #52: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
6Q LOSS MUTATED	6	2	0	2	8	8
6Q LOSS WILD-TYPE	50	40	59	55	21	21

Figure S227. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0213 (Fisher's exact test), Q value = 0.051

Table S228. Gene #52: '6q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
6Q LOSS MUTATED	3	5	13	1
6Q LOSS WILD-TYPE	36	61	52	42

Figure S228. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'6q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S229. Gene #52: '6q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
6Q LOSS MUTATED	0	2	5	2	18
6Q LOSS WILD-TYPE	32	88	65	30	46

Figure S229. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00027

Table S230. Gene #52: '6q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
6Q LOSS MUTATED	12	3	12
6Q LOSS WILD-TYPE	106	120	35

Figure S230. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_CNMF'

P value = 0.0308 (Fisher's exact test), Q value = 0.068

Table S231. Gene #52: '6q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	29	37	66	43	80	33
6Q LOSS MUTATED	3	5	4	9	6	0
6Q LOSS WILD-TYPE	26	32	62	34	74	33

Figure S231. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 0.00436 (Fisher's exact test), Q value = 0.014

Table S232. Gene #53: '8p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
8P LOSS MUTATED	0	2	2	2	10
8P LOSS WILD-TYPE	32	88	68	30	54

Figure S232. Get High-res Image Gene #53: '8p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00905 (Fisher's exact test), Q value = 0.025

Table S233. Gene #53: '8p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
8P LOSS MUTATED	6	3	7
8P LOSS WILD-TYPE	112	120	40

Figure S233. Get High-res Image Gene #53: '8p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8q loss' versus 'METHLYATION_CNMF'

P value = 0.0485 (Fisher's exact test), Q value = 0.1

Table S234. Gene #54: '8q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
8Q LOSS MUTATED	3	0	0	1	1	3
8Q LOSS WILD-TYPE	53	42	59	56	28	26

Figure S234. Get High-res Image Gene #54: '8q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8q loss' versus 'MRNASEQ_CNMF'

P value = 0.00485 (Fisher's exact test), Q value = 0.015

Table S235. Gene #54: '8q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
8Q LOSS MUTATED	0	0	1	2	6
8Q LOSS WILD-TYPE	32	90	69	30	58

Figure S235. Get High-res Image Gene #54: '8q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00084 (Fisher's exact test), Q value = 0.0036

Table S236. Gene #54: '8q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
8Q LOSS MUTATED	2	1	6
8Q LOSS WILD-TYPE	116	122	41

Figure S236. Get High-res Image Gene #54: '8q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.0016

Table S237. Gene #55: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	73	49	60
9P LOSS MUTATED	16	1	3	13
9P LOSS WILD-TYPE	90	72	46	47

Figure S237. Get High-res Image Gene #55: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S238. Gene #55: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
9P LOSS MUTATED	8	3	0	0	8	11
9P LOSS WILD-TYPE	48	39	59	57	21	18

Figure S238. Get High-res Image Gene #55: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0158 (Fisher's exact test), Q value = 0.04

Table S239. Gene #55: '9p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
9P LOSS MUTATED	3	4	15	3
9P LOSS WILD-TYPE	36	62	50	40

Figure S239. Get High-res Image Gene #55: '9p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S240. Gene #55: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
9P LOSS MUTATED	0	0	4	4	25
9P LOSS WILD-TYPE	32	90	66	28	39

Figure S240. Get High-res Image Gene #55: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S241. Gene #55: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
9P LOSS MUTATED	19	0	14
9P LOSS WILD-TYPE	99	123	33

Figure S241. Get High-res Image Gene #55: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_CNMF'

P value = 0.0181 (Fisher's exact test), Q value = 0.044

Table S242. Gene #55: '9p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	29	37	66	43	80	33
9P LOSS MUTATED	4	4	3	11	10	1
9P LOSS WILD-TYPE	25	33	63	32	70	32

Figure S242. Get High-res Image Gene #55: '9p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'9p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0256 (Fisher's exact test), Q value = 0.059

Table S243. Gene #55: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	75	76
9P LOSS MUTATED	9	4	15
9P LOSS WILD-TYPE	62	71	61

Figure S243. Get High-res Image Gene #55: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'9p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00095 (Fisher's exact test), Q value = 0.0039

Table S244. Gene #55: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	99	31
9P LOSS MUTATED	7	21	0
9P LOSS WILD-TYPE	85	78	31

Figure S244. Get High-res Image Gene #55: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 0.00148 (Fisher's exact test), Q value = 0.0055

Table S245. Gene #56: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	73	49	60
9Q LOSS MUTATED	17	1	5	11
9Q LOSS WILD-TYPE	89	72	44	49

Figure S245. Get High-res Image Gene #56: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S246. Gene #56: '9q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
9Q LOSS MUTATED	8	2	0	0	7	14
9Q LOSS WILD-TYPE	48	40	59	57	22	15

Figure S246. Get High-res Image Gene #56: '9q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00479 (Fisher's exact test), Q value = 0.015

Table S247. Gene #56: '9q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
9Q LOSS MUTATED	3	3	16	4
9Q LOSS WILD-TYPE	36	63	49	39

Figure S247. Get High-res Image Gene #56: '9q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S248. Gene #56: '9q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
9Q LOSS MUTATED	0	0	4	5	25
9Q LOSS WILD-TYPE	32	90	66	27	39

Figure S248. Get High-res Image Gene #56: '9q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S249. Gene #56: '9q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
9Q LOSS MUTATED	17	0	17
9Q LOSS WILD-TYPE	101	123	30

Figure S249. Get High-res Image Gene #56: '9q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_CNMF'

P value = 0.0423 (Fisher's exact test), Q value = 0.089

Table S250. Gene #56: '9q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	29	37	66	43	80	33
9Q LOSS MUTATED	5	4	3	9	12	1
9Q LOSS WILD-TYPE	24	33	63	34	68	32

Figure S250. Get High-res Image Gene #56: '9q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'9q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00915 (Fisher's exact test), Q value = 0.025

Table S251. Gene #56: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	75	76
9Q LOSS MUTATED	9	4	17
9Q LOSS WILD-TYPE	62	71	59

Figure S251. Get High-res Image Gene #56: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'9q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00041 (Fisher's exact test), Q value = 0.0019

Table S252. Gene #56: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	99	31
9Q LOSS MUTATED	7	23	0
9Q LOSS WILD-TYPE	85	76	31

Figure S252. Get High-res Image Gene #56: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p loss' versus 'METHLYATION_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00066

Table S253. Gene #57: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
10P LOSS MUTATED	1	3	0	1	6	4
10P LOSS WILD-TYPE	55	39	59	56	23	25

Figure S253. Get High-res Image Gene #57: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00047

Table S254. Gene #57: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
10P LOSS MUTATED	0	0	4	1	12
10P LOSS WILD-TYPE	32	90	66	31	52

Figure S254. Get High-res Image Gene #57: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0016 (Fisher's exact test), Q value = 0.0059

Table S255. Gene #57: '10p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
10P LOSS MUTATED	11	1	5
10P LOSS WILD-TYPE	107	122	42

Figure S255. Get High-res Image Gene #57: '10p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_CNMF'

P value = 0.0127 (Fisher's exact test), Q value = 0.033

Table S256. Gene #57: '10p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	29	37	66	43	80	33
10P LOSS MUTATED	1	3	0	7	5	1
10P LOSS WILD-TYPE	28	34	66	36	75	32

Figure S256. Get High-res Image Gene #57: '10p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'10p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0037 (Fisher's exact test), Q value = 0.012

Table S257. Gene #57: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	99	31
10P LOSS MUTATED	1	11	0
10P LOSS WILD-TYPE	91	88	31

Figure S257. Get High-res Image Gene #57: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q loss' versus 'METHLYATION_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.00086

Table S258. Gene #58: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
10Q LOSS MUTATED	2	3	0	1	7	4
10Q LOSS WILD-TYPE	54	39	59	56	22	25

Figure S258. Get High-res Image Gene #58: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0234 (Fisher's exact test), Q value = 0.054

Table S259. Gene #58: '10q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
10Q LOSS MUTATED	1	4	9	0
10Q LOSS WILD-TYPE	38	62	56	43

Figure S259. Get High-res Image Gene #58: '10q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00021

Table S260. Gene #58: '10q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
10Q LOSS MUTATED	0	0	4	1	13
10Q LOSS WILD-TYPE	32	90	66	31	51

Figure S260. Get High-res Image Gene #58: '10q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00104 (Fisher's exact test), Q value = 0.0041

Table S261. Gene #58: '10q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
10Q LOSS MUTATED	13	1	4
10Q LOSS WILD-TYPE	105	122	43

Figure S261. Get High-res Image Gene #58: '10q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_CNMF'

P value = 0.0122 (Fisher's exact test), Q value = 0.032

Table S262. Gene #58: '10q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	29	37	66	43	80	33
10Q LOSS MUTATED	1	3	0	7	6	1
10Q LOSS WILD-TYPE	28	34	66	36	74	32

Figure S262. Get High-res Image Gene #58: '10q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'10q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0225 (Fisher's exact test), Q value = 0.053

Table S263. Gene #58: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	75	76
10Q LOSS MUTATED	4	1	9
10Q LOSS WILD-TYPE	67	74	67

Figure S263. Get High-res Image Gene #58: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'10q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00094 (Fisher's exact test), Q value = 0.0039

Table S264. Gene #58: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	99	31
10Q LOSS MUTATED	1	13	0
10Q LOSS WILD-TYPE	91	86	31

Figure S264. Get High-res Image Gene #58: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 0.0125 (Fisher's exact test), Q value = 0.033

Table S265. Gene #59: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	73	49	60
11P LOSS MUTATED	8	0	2	7
11P LOSS WILD-TYPE	98	73	47	53

Figure S265. Get High-res Image Gene #59: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 0.00748 (Fisher's exact test), Q value = 0.022

Table S266. Gene #59: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
11P LOSS MUTATED	3	2	0	2	5	4
11P LOSS WILD-TYPE	53	40	59	55	24	25

Figure S266. Get High-res Image Gene #59: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11p loss' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00021

Table S267. Gene #59: '11p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
11P LOSS MUTATED	0	0	3	3	11
11P LOSS WILD-TYPE	32	90	67	29	53

Figure S267. Get High-res Image Gene #59: '11p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'11p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00416 (Fisher's exact test), Q value = 0.014

Table S268. Gene #59: '11p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
11P LOSS MUTATED	8	2	7
11P LOSS WILD-TYPE	110	121	40

Figure S268. Get High-res Image Gene #59: '11p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0286 (Fisher's exact test), Q value = 0.064

Table S269. Gene #59: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	75	76
11P LOSS MUTATED	3	2	10
11P LOSS WILD-TYPE	68	73	66

Figure S269. Get High-res Image Gene #59: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'11p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0136 (Fisher's exact test), Q value = 0.035

Table S270. Gene #59: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	99	31
11P LOSS MUTATED	3	12	0
11P LOSS WILD-TYPE	89	87	31

Figure S270. Get High-res Image Gene #59: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

P value = 0.0463 (Fisher's exact test), Q value = 0.096

Table S271. Gene #60: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	73	49	60
11Q LOSS MUTATED	9	1	3	8
11Q LOSS WILD-TYPE	97	72	46	52

Figure S271. Get High-res Image Gene #60: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

P value = 0.00096 (Fisher's exact test), Q value = 0.0039

Table S272. Gene #60: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
11Q LOSS MUTATED	5	3	0	2	7	4
11Q LOSS WILD-TYPE	51	39	59	55	22	25

Figure S272. Get High-res Image Gene #60: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0122 (Fisher's exact test), Q value = 0.032

Table S273. Gene #60: '11q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
11Q LOSS MUTATED	3	1	11	3
11Q LOSS WILD-TYPE	36	65	54	40

Figure S273. Get High-res Image Gene #60: '11q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'11q loss' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00015

Table S274. Gene #60: '11q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
11Q LOSS MUTATED	0	0	6	2	13
11Q LOSS WILD-TYPE	32	90	64	30	51

Figure S274. Get High-res Image Gene #60: '11q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'11q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00206 (Fisher's exact test), Q value = 0.0074

Table S275. Gene #60: '11q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
11Q LOSS MUTATED	13	2	6
11Q LOSS WILD-TYPE	105	121	41

Figure S275. Get High-res Image Gene #60: '11q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0443 (Fisher's exact test), Q value = 0.092

Table S276. Gene #60: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	99	31
11Q LOSS MUTATED	6	13	0
11Q LOSS WILD-TYPE	86	86	31

Figure S276. Get High-res Image Gene #60: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 0.00061 (Fisher's exact test), Q value = 0.0027

Table S277. Gene #61: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	73	49	60
13Q LOSS MUTATED	5	1	8	10
13Q LOSS WILD-TYPE	101	72	41	50

Figure S277. Get High-res Image Gene #61: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S278. Gene #61: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
13Q LOSS MUTATED	3	1	0	2	4	13
13Q LOSS WILD-TYPE	53	41	59	55	25	16

Figure S278. Get High-res Image Gene #61: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00139 (Fisher's exact test), Q value = 0.0053

Table S279. Gene #61: '13q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
13Q LOSS MUTATED	4	2	14	1
13Q LOSS WILD-TYPE	35	64	51	42

Figure S279. Get High-res Image Gene #61: '13q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S280. Gene #61: '13q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
13Q LOSS MUTATED	0	1	0	4	19
13Q LOSS WILD-TYPE	32	89	70	28	45

Figure S280. Get High-res Image Gene #61: '13q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S281. Gene #61: '13q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
13Q LOSS MUTATED	8	2	14
13Q LOSS WILD-TYPE	110	121	33

Figure S281. Get High-res Image Gene #61: '13q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_CNMF'

P value = 0.0367 (Fisher's exact test), Q value = 0.079

Table S282. Gene #61: '13q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	29	37	66	43	80	33
13Q LOSS MUTATED	0	1	4	6	12	1
13Q LOSS WILD-TYPE	29	36	62	37	68	32

Figure S282. Get High-res Image Gene #61: '13q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'13q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0104 (Fisher's exact test), Q value = 0.028

Table S283. Gene #61: '13q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	80	88
13Q LOSS MUTATED	4	7	13
13Q LOSS WILD-TYPE	116	73	75

Figure S283. Get High-res Image Gene #61: '13q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00763 (Fisher's exact test), Q value = 0.022

Table S284. Gene #61: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	75	76
13Q LOSS MUTATED	3	3	13
13Q LOSS WILD-TYPE	68	72	63

Figure S284. Get High-res Image Gene #61: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'13q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00508 (Fisher's exact test), Q value = 0.016

Table S285. Gene #61: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	99	31
13Q LOSS MUTATED	4	15	0
13Q LOSS WILD-TYPE	88	84	31

Figure S285. Get High-res Image Gene #61: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00027

Table S286. Gene #62: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	73	49	60
14Q LOSS MUTATED	20	1	8	18
14Q LOSS WILD-TYPE	86	72	41	42

Figure S286. Get High-res Image Gene #62: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00033

Table S287. Gene #62: '14q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
14Q LOSS MUTATED	14	3	2	4	9	11
14Q LOSS WILD-TYPE	42	39	57	53	20	18

Figure S287. Get High-res Image Gene #62: '14q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'14q loss' versus 'RPPA_CNMF'

P value = 0.00563 (Fisher's exact test), Q value = 0.017

Table S288. Gene #62: '14q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	82	56
14Q LOSS MUTATED	20	8	5
14Q LOSS WILD-TYPE	55	74	51

Figure S288. Get High-res Image Gene #62: '14q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'14q loss' versus 'RPPA_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00043

Table S289. Gene #62: '14q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
14Q LOSS MUTATED	7	5	20	1
14Q LOSS WILD-TYPE	32	61	45	42

Figure S289. Get High-res Image Gene #62: '14q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S290. Gene #62: '14q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
14Q LOSS MUTATED	3	3	7	7	27
14Q LOSS WILD-TYPE	29	87	63	25	37

Figure S290. Get High-res Image Gene #62: '14q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S291. Gene #62: '14q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
14Q LOSS MUTATED	22	6	19
14Q LOSS WILD-TYPE	96	117	28

Figure S291. Get High-res Image Gene #62: '14q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_CNMF'

P value = 0.0405 (Fisher's exact test), Q value = 0.086

Table S292. Gene #62: '14q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	29	37	66	43	80	33
14Q LOSS MUTATED	2	5	7	13	17	3
14Q LOSS WILD-TYPE	27	32	59	30	63	30

Figure S292. Get High-res Image Gene #62: '14q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'14q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.019 (Fisher's exact test), Q value = 0.046

Table S293. Gene #62: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	75	76
14Q LOSS MUTATED	11	6	19
14Q LOSS WILD-TYPE	60	69	57

Figure S293. Get High-res Image Gene #62: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'14q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00273 (Fisher's exact test), Q value = 0.0095

Table S294. Gene #62: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	99	31
14Q LOSS MUTATED	10	25	1
14Q LOSS WILD-TYPE	82	74	30

Figure S294. Get High-res Image Gene #62: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 0.0223 (Fisher's exact test), Q value = 0.053

Table S295. Gene #63: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	73	49	60
15Q LOSS MUTATED	13	2	5	11
15Q LOSS WILD-TYPE	93	71	44	49

Figure S295. Get High-res Image Gene #63: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00015

Table S296. Gene #63: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
15Q LOSS MUTATED	10	2	1	3	3	11
15Q LOSS WILD-TYPE	46	40	58	54	26	18

Figure S296. Get High-res Image Gene #63: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'15q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0288 (Fisher's exact test), Q value = 0.064

Table S297. Gene #63: '15q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
15Q LOSS MUTATED	3	5	15	3
15Q LOSS WILD-TYPE	36	61	50	40

Figure S297. Get High-res Image Gene #63: '15q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00047

Table S298. Gene #63: '15q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
15Q LOSS MUTATED	1	3	5	5	17
15Q LOSS WILD-TYPE	31	87	65	27	47

Figure S298. Get High-res Image Gene #63: '15q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S299. Gene #63: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
15Q LOSS MUTATED	12	4	15
15Q LOSS WILD-TYPE	106	119	32

Figure S299. Get High-res Image Gene #63: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_CNMF'

P value = 0.0208 (Fisher's exact test), Q value = 0.05

Table S300. Gene #63: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	29	37	66	43	80	33
15Q LOSS MUTATED	3	4	3	8	13	0
15Q LOSS WILD-TYPE	26	33	63	35	67	33

Figure S300. Get High-res Image Gene #63: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0252 (Fisher's exact test), Q value = 0.058

Table S301. Gene #63: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	99	31
15Q LOSS MUTATED	9	16	0
15Q LOSS WILD-TYPE	83	83	31

Figure S301. Get High-res Image Gene #63: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p loss' versus 'METHLYATION_CNMF'

P value = 0.00334 (Fisher's exact test), Q value = 0.011

Table S302. Gene #64: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
16P LOSS MUTATED	0	1	0	0	0	3
16P LOSS WILD-TYPE	56	41	59	57	29	26

Figure S302. Get High-res Image Gene #64: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00729 (Fisher's exact test), Q value = 0.021

Table S303. Gene #64: '16p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
16P LOSS MUTATED	1	0	3
16P LOSS WILD-TYPE	117	123	44

Figure S303. Get High-res Image Gene #64: '16p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'METHLYATION_CNMF'

P value = 0.0131 (Fisher's exact test), Q value = 0.034

Table S304. Gene #65: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
16Q LOSS MUTATED	1	1	0	0	2	3
16Q LOSS WILD-TYPE	55	41	59	57	27	26

Figure S304. Get High-res Image Gene #65: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 0.00145 (Fisher's exact test), Q value = 0.0054

Table S305. Gene #65: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
16Q LOSS MUTATED	0	0	0	1	6
16Q LOSS WILD-TYPE	32	90	70	31	58

Figure S305. Get High-res Image Gene #65: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0131 (Fisher's exact test), Q value = 0.034

Table S306. Gene #65: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
16Q LOSS MUTATED	4	0	3
16Q LOSS WILD-TYPE	114	123	44

Figure S306. Get High-res Image Gene #65: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 0.00332 (Fisher's exact test), Q value = 0.011

Table S307. Gene #66: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	73	49	60
17P LOSS MUTATED	4	1	0	8
17P LOSS WILD-TYPE	102	72	49	52

Figure S307. Get High-res Image Gene #66: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.0013

Table S308. Gene #66: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
17P LOSS MUTATED	2	2	0	0	2	6
17P LOSS WILD-TYPE	54	40	59	57	27	23

Figure S308. Get High-res Image Gene #66: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00066

Table S309. Gene #66: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
17P LOSS MUTATED	0	0	2	1	10
17P LOSS WILD-TYPE	32	90	68	31	54

Figure S309. Get High-res Image Gene #66: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.001

Table S310. Gene #66: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
17P LOSS MUTATED	7	0	6
17P LOSS WILD-TYPE	111	123	41

Figure S310. Get High-res Image Gene #66: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00625 (Fisher's exact test), Q value = 0.019

Table S311. Gene #66: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	75	76
17P LOSS MUTATED	3	0	8
17P LOSS WILD-TYPE	68	75	68

Figure S311. Get High-res Image Gene #66: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00809 (Fisher's exact test), Q value = 0.023

Table S312. Gene #66: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	99	31
17P LOSS MUTATED	1	10	0
17P LOSS WILD-TYPE	91	89	31

Figure S312. Get High-res Image Gene #66: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 0.0206 (Fisher's exact test), Q value = 0.05

Table S313. Gene #67: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	73	49	60
18P LOSS MUTATED	18	4	6	14
18P LOSS WILD-TYPE	88	69	43	46

Figure S313. Get High-res Image Gene #67: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S314. Gene #67: '18p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
18P LOSS MUTATED	5	9	4	2	7	13
18P LOSS WILD-TYPE	51	33	55	55	22	16

Figure S314. Get High-res Image Gene #67: '18p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18p loss' versus 'RPPA_CNMF'

P value = 0.00213 (Fisher's exact test), Q value = 0.0076

Table S315. Gene #67: '18p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	82	56
18P LOSS MUTATED	15	4	13
18P LOSS WILD-TYPE	60	78	43

Figure S315. Get High-res Image Gene #67: '18p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'18p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00461 (Fisher's exact test), Q value = 0.015

Table S316. Gene #67: '18p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
18P LOSS MUTATED	5	3	17	7
18P LOSS WILD-TYPE	34	63	48	36

Figure S316. Get High-res Image Gene #67: '18p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'18p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S317. Gene #67: '18p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
18P LOSS MUTATED	1	2	11	7	21
18P LOSS WILD-TYPE	31	88	59	25	43

Figure S317. Get High-res Image Gene #67: '18p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'18p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S318. Gene #67: '18p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
18P LOSS MUTATED	24	3	15
18P LOSS WILD-TYPE	94	120	32

Figure S318. Get High-res Image Gene #67: '18p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_CNMF'

P value = 0.00141 (Fisher's exact test), Q value = 0.0053

Table S319. Gene #67: '18p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	29	37	66	43	80	33
18P LOSS MUTATED	1	7	3	10	19	2
18P LOSS WILD-TYPE	28	30	63	33	61	31

Figure S319. Get High-res Image Gene #67: '18p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'18p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00094 (Fisher's exact test), Q value = 0.0039

Table S320. Gene #67: '18p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	80	88
18P LOSS MUTATED	19	3	20
18P LOSS WILD-TYPE	101	77	68

Figure S320. Get High-res Image Gene #67: '18p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0249 (Fisher's exact test), Q value = 0.057

Table S321. Gene #67: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	75	76
18P LOSS MUTATED	9	8	20
18P LOSS WILD-TYPE	62	67	56

Figure S321. Get High-res Image Gene #67: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'18p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0231 (Fisher's exact test), Q value = 0.054

Table S322. Gene #67: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	99	31
18P LOSS MUTATED	11	24	2
18P LOSS WILD-TYPE	81	75	29

Figure S322. Get High-res Image Gene #67: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q loss' versus 'CN_CNMF'

P value = 0.00109 (Fisher's exact test), Q value = 0.0043

Table S323. Gene #68: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	73	49	60
18Q LOSS MUTATED	20	3	5	16
18Q LOSS WILD-TYPE	86	70	44	44

Figure S323. Get High-res Image Gene #68: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S324. Gene #68: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
18Q LOSS MUTATED	6	9	3	2	10	12
18Q LOSS WILD-TYPE	50	33	56	55	19	17

Figure S324. Get High-res Image Gene #68: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18q loss' versus 'RPPA_CNMF'

P value = 0.00622 (Fisher's exact test), Q value = 0.019

Table S325. Gene #68: '18q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	82	56
18Q LOSS MUTATED	15	5	13
18Q LOSS WILD-TYPE	60	77	43

Figure S325. Get High-res Image Gene #68: '18q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'18q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00046 (Fisher's exact test), Q value = 0.0021

Table S326. Gene #68: '18q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
18Q LOSS MUTATED	5	2	19	7
18Q LOSS WILD-TYPE	34	64	46	36

Figure S326. Get High-res Image Gene #68: '18q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S327. Gene #68: '18q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
18Q LOSS MUTATED	1	1	12	7	23
18Q LOSS WILD-TYPE	31	89	58	25	41

Figure S327. Get High-res Image Gene #68: '18q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S328. Gene #68: '18q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
18Q LOSS MUTATED	27	3	14
18Q LOSS WILD-TYPE	91	120	33

Figure S328. Get High-res Image Gene #68: '18q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_CNMF'

P value = 0.00136 (Fisher's exact test), Q value = 0.0052

Table S329. Gene #68: '18q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	29	37	66	43	80	33
18Q LOSS MUTATED	1	7	3	11	19	3
18Q LOSS WILD-TYPE	28	30	63	32	61	30

Figure S329. Get High-res Image Gene #68: '18q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'18q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00037 (Fisher's exact test), Q value = 0.0018

Table S330. Gene #68: '18q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	80	88
18Q LOSS MUTATED	20	3	21
18Q LOSS WILD-TYPE	100	77	67

Figure S330. Get High-res Image Gene #68: '18q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0222 (Fisher's exact test), Q value = 0.053

Table S331. Gene #68: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	75	76
18Q LOSS MUTATED	11	8	21
18Q LOSS WILD-TYPE	60	67	55

Figure S331. Get High-res Image Gene #68: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'18q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00492 (Fisher's exact test), Q value = 0.015

Table S332. Gene #68: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	99	31
18Q LOSS MUTATED	11	27	2
18Q LOSS WILD-TYPE	81	72	29

Figure S332. Get High-res Image Gene #68: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.0021

Table S333. Gene #69: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	73	49	60
19P LOSS MUTATED	3	0	4	9
19P LOSS WILD-TYPE	103	73	45	51

Figure S333. Get High-res Image Gene #69: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

P value = 0.00151 (Fisher's exact test), Q value = 0.0056

Table S334. Gene #69: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
19P LOSS MUTATED	2	3	0	3	7	1
19P LOSS WILD-TYPE	54	39	59	54	22	28

Figure S334. Get High-res Image Gene #69: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19p loss' versus 'MRNASEQ_CNMF'

P value = 0.00191 (Fisher's exact test), Q value = 0.0069

Table S335. Gene #69: '19p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
19P LOSS MUTATED	0	0	7	2	7
19P LOSS WILD-TYPE	32	90	63	30	57

Figure S335. Get High-res Image Gene #69: '19p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0103 (Fisher's exact test), Q value = 0.028

Table S336. Gene #69: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
19P LOSS MUTATED	12	2	2
19P LOSS WILD-TYPE	106	121	45

Figure S336. Get High-res Image Gene #69: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S337. Gene #70: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	73	49	60
19Q LOSS MUTATED	0	0	5	10
19Q LOSS WILD-TYPE	106	73	44	50

Figure S337. Get High-res Image Gene #70: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00066

Table S338. Gene #70: '19q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
19Q LOSS MUTATED	3	0	0	3	7	2
19Q LOSS WILD-TYPE	53	42	59	54	22	27

Figure S338. Get High-res Image Gene #70: '19q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19q loss' versus 'MRNASEQ_CNMF'

P value = 8e-04 (Fisher's exact test), Q value = 0.0034

Table S339. Gene #70: '19q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
19Q LOSS MUTATED	0	0	4	2	9
19Q LOSS WILD-TYPE	32	90	66	30	55

Figure S339. Get High-res Image Gene #70: '19q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0358 (Fisher's exact test), Q value = 0.078

Table S340. Gene #70: '19q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
19Q LOSS MUTATED	10	2	3
19Q LOSS WILD-TYPE	108	121	44

Figure S340. Get High-res Image Gene #70: '19q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'21q loss' versus 'CN_CNMF'

P value = 0.0102 (Fisher's exact test), Q value = 0.028

Table S341. Gene #71: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	73	49	60
21Q LOSS MUTATED	10	7	13	13
21Q LOSS WILD-TYPE	96	66	36	47

Figure S341. Get High-res Image Gene #71: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 0.001 (Fisher's exact test), Q value = 0.004

Table S342. Gene #72: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	73	49	60
22Q LOSS MUTATED	23	5	12	20
22Q LOSS WILD-TYPE	83	68	37	40

Figure S342. Get High-res Image Gene #72: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S343. Gene #72: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
22Q LOSS MUTATED	9	7	1	5	22	13
22Q LOSS WILD-TYPE	47	35	58	52	7	16

Figure S343. Get High-res Image Gene #72: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0146 (Fisher's exact test), Q value = 0.037

Table S344. Gene #72: '22q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
22Q LOSS MUTATED	4	11	23	10
22Q LOSS WILD-TYPE	35	55	42	33

Figure S344. Get High-res Image Gene #72: '22q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S345. Gene #72: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
22Q LOSS MUTATED	2	4	15	7	32
22Q LOSS WILD-TYPE	30	86	55	25	32

Figure S345. Get High-res Image Gene #72: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S346. Gene #72: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
22Q LOSS MUTATED	35	8	17
22Q LOSS WILD-TYPE	83	115	30

Figure S346. Get High-res Image Gene #72: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00047

Table S347. Gene #72: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	29	37	66	43	80	33
22Q LOSS MUTATED	3	14	7	19	14	3
22Q LOSS WILD-TYPE	26	23	59	24	66	30

Figure S347. Get High-res Image Gene #72: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'22q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00861 (Fisher's exact test), Q value = 0.024

Table S348. Gene #72: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	99	31
22Q LOSS MUTATED	21	27	1
22Q LOSS WILD-TYPE	71	72	30

Figure S348. Get High-res Image Gene #72: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xp loss' versus 'CN_CNMF'

P value = 0.00607 (Fisher's exact test), Q value = 0.018

Table S349. Gene #73: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	73	49	60
XP LOSS MUTATED	12	2	6	13
XP LOSS WILD-TYPE	94	71	43	47

Figure S349. Get High-res Image Gene #73: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'

'xp loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S350. Gene #73: 'xp loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
XP LOSS MUTATED	6	3	0	2	12	7
XP LOSS WILD-TYPE	50	39	59	55	17	22

Figure S350. Get High-res Image Gene #73: 'xp loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xp loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00242 (Fisher's exact test), Q value = 0.0086

Table S351. Gene #73: 'xp loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
XP LOSS MUTATED	1	5	14	1
XP LOSS WILD-TYPE	38	61	51	42

Figure S351. Get High-res Image Gene #73: 'xp loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'xp loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S352. Gene #73: 'xp loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
XP LOSS MUTATED	0	2	7	2	22
XP LOSS WILD-TYPE	32	88	63	30	42

Figure S352. Get High-res Image Gene #73: 'xp loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xp loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00021

Table S353. Gene #73: 'xp loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
XP LOSS MUTATED	19	3	11
XP LOSS WILD-TYPE	99	120	36

Figure S353. Get High-res Image Gene #73: 'xp loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_CNMF'

P value = 0.023 (Fisher's exact test), Q value = 0.054

Table S354. Gene #73: 'xp loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	29	37	66	43	80	33
XP LOSS MUTATED	1	5	3	11	10	3
XP LOSS WILD-TYPE	28	32	63	32	70	30

Figure S354. Get High-res Image Gene #73: 'xp loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'xp loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0266 (Fisher's exact test), Q value = 0.06

Table S355. Gene #73: 'xp loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	75	76
XP LOSS MUTATED	9	3	13
XP LOSS WILD-TYPE	62	72	63

Figure S355. Get High-res Image Gene #73: 'xp loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xp loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00398 (Fisher's exact test), Q value = 0.013

Table S356. Gene #73: 'xp loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	99	31
XP LOSS MUTATED	5	19	1
XP LOSS WILD-TYPE	87	80	30

Figure S356. Get High-res Image Gene #73: 'xp loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq loss' versus 'CN_CNMF'

P value = 0.00273 (Fisher's exact test), Q value = 0.0095

Table S357. Gene #74: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	73	49	60
XQ LOSS MUTATED	11	1	5	12
XQ LOSS WILD-TYPE	95	72	44	48

Figure S357. Get High-res Image Gene #74: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S358. Gene #74: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	56	42	59	57	29	29
XQ LOSS MUTATED	6	3	0	2	10	6
XQ LOSS WILD-TYPE	50	39	59	55	19	23

Figure S358. Get High-res Image Gene #74: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0125 (Fisher's exact test), Q value = 0.033

Table S359. Gene #74: 'xq loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
XQ LOSS MUTATED	1	5	12	1
XQ LOSS WILD-TYPE	38	61	53	42

Figure S359. Get High-res Image Gene #74: 'xq loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'xq loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S360. Gene #74: 'xq loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	90	70	32	64
XQ LOSS MUTATED	0	1	6	2	20
XQ LOSS WILD-TYPE	32	89	64	30	44

Figure S360. Get High-res Image Gene #74: 'xq loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xq loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00047

Table S361. Gene #74: 'xq loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
XQ LOSS MUTATED	17	2	10
XQ LOSS WILD-TYPE	101	121	37

Figure S361. Get High-res Image Gene #74: 'xq loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0134 (Fisher's exact test), Q value = 0.035

Table S362. Gene #74: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	92	99	31
XQ LOSS MUTATED	5	17	1
XQ LOSS WILD-TYPE	87	82	30

Figure S362. Get High-res Image Gene #74: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data

Input

Copy number data file = broad_values_by_arm.txt from GISTIC pipeline
Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/KIRP-TP/22533934/transformed.cor.cli.txt
Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/KIRP-TP/22542911/KIRP-TP.transferedmergedcluster.txt
Number of patients = 288
Number of significantly arm-level cnvs = 74
Number of molecular subtypes = 10
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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