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

Kidney Renal Papillary Cell Carcinoma (Primary solid tumor)

21 August 2015 | analyses__2015_08_21

Maintainer Information

Citation Information

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

Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1JS9PN5

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, 376 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_MATURE_CHIERARCHICAL'.
1q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
2p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
2q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'RPPA_CHIERARCHICAL'.
3p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', '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 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
6q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_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_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
8p gain cnv correlated to 'METHLYATION_CNMF'.
8q gain cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
9p gain cnv correlated to 'MRNASEQ_CHIERARCHICAL' and 'MIRSEQ_MATURE_CHIERARCHICAL'.
10p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'RPPA_CHIERARCHICAL'.
10q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'RPPA_CHIERARCHICAL'.
11p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', and 'MRNASEQ_CHIERARCHICAL'.
11q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
12p gain cnv correlated to 'CN_CNMF', 'RPPA_CNMF', and 'MRNASEQ_CNMF'.
12q gain cnv correlated to 'CN_CNMF', 'RPPA_CNMF', and 'MRNASEQ_CNMF'.
14q gain cnv correlated to 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
15q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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'.
18p gain cnv correlated to 'CN_CNMF'.
18q gain cnv correlated to 'CN_CNMF'.
19p gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
19q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
20p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
20q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
22q 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', and 'MRNASEQ_CHIERARCHICAL'.
1q loss cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
2p loss cnv correlated to 'METHLYATION_CNMF', 'RPPA_CNMF', and 'MRNASEQ_CNMF'.
2q loss cnv correlated to 'MRNASEQ_CHIERARCHICAL'.
3p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 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_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
5p loss cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
5q loss cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
6p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
6q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
8p loss cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
8q loss cnv correlated to 'CN_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 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
10q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', '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_CNMF'.
13q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', '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_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
15q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
16p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
16q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_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_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_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
19p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_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', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
xp loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', '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, 376 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	172 (60%)	116	1e-05 (7.25e-05)	1e-05 (7.25e-05)	0.00646 (0.0182)	1e-05 (7.25e-05)	1e-05 (7.25e-05)	1e-05 (7.25e-05)	0.0425 (0.087)	0.00016 (0.000805)	0.00015 (0.000766)	1e-05 (7.25e-05)
17p gain	174 (60%)	114	1e-05 (7.25e-05)	1e-05 (7.25e-05)	6e-05 (0.000347)	1e-05 (7.25e-05)	1e-05 (7.25e-05)	1e-05 (7.25e-05)	0.00283 (0.00965)	0.00031 (0.00142)	1e-05 (7.25e-05)	1e-05 (7.25e-05)
17q gain	191 (66%)	97	1e-05 (7.25e-05)	1e-05 (7.25e-05)	0.00089 (0.00364)	1e-05 (7.25e-05)	1e-05 (7.25e-05)	1e-05 (7.25e-05)	0.032 (0.0699)	0.00118 (0.00457)	0.00031 (0.00142)	2e-05 (0.000135)
7q gain	173 (60%)	115	1e-05 (7.25e-05)	1e-05 (7.25e-05)	0.0118 (0.0302)	1e-05 (7.25e-05)	1e-05 (7.25e-05)	1e-05 (7.25e-05)	0.0575 (0.109)	0.00019 (0.000937)	0.00028 (0.00134)	1e-05 (7.25e-05)
16p gain	153 (53%)	135	1e-05 (7.25e-05)	0.0122 (0.0306)	0.911 (0.963)	0.00064 (0.00274)	1e-05 (7.25e-05)	3e-05 (0.000195)	0.00106 (0.00423)	2e-05 (0.000135)	0.00834 (0.0224)	2e-05 (0.000135)
16q gain	148 (51%)	140	1e-05 (7.25e-05)	0.00626 (0.0179)	0.953 (0.992)	0.00194 (0.00707)	1e-05 (7.25e-05)	0.0001 (0.000544)	5e-05 (0.000301)	1e-05 (7.25e-05)	0.00218 (0.00775)	1e-05 (7.25e-05)
xp gain	87 (30%)	201	1e-05 (7.25e-05)	1e-05 (7.25e-05)	0.16 (0.256)	0.00296 (0.00991)	1e-05 (7.25e-05)	1e-05 (7.25e-05)	0.00978 (0.0258)	6e-05 (0.000347)	0.0019 (0.00696)	0.0039 (0.0123)
xq gain	91 (32%)	197	1e-05 (7.25e-05)	2e-05 (0.000135)	0.158 (0.253)	0.00998 (0.0261)	1e-05 (7.25e-05)	3e-05 (0.000195)	0.0116 (0.0298)	0.00034 (0.00153)	0.00953 (0.0253)	0.0174 (0.0416)
18p loss	42 (15%)	246	1e-05 (7.25e-05)	1e-05 (7.25e-05)	0.00231 (0.00806)	0.00535 (0.0157)	1e-05 (7.25e-05)	1e-05 (7.25e-05)	0.104 (0.178)	0.00107 (0.00423)	0.0195 (0.0455)	0.00039 (0.00172)
18q loss	45 (16%)	243	1e-05 (7.25e-05)	1e-05 (7.25e-05)	0.00478 (0.0144)	0.0001 (0.000544)	1e-05 (7.25e-05)	1e-05 (7.25e-05)	0.0527 (0.102)	0.00038 (0.00168)	0.00686 (0.0191)	0.00013 (0.000673)
1q gain	17 (6%)	271	1e-05 (7.25e-05)	1e-05 (7.25e-05)	0.604 (0.707)	0.0491 (0.0968)	6e-05 (0.000347)	9e-05 (0.000497)	0.341 (0.457)	0.00943 (0.0251)	0.00648 (0.0182)	0.00049 (0.00213)
3q gain	94 (33%)	194	1e-05 (7.25e-05)	0.00469 (0.0142)	0.263 (0.372)	0.00429 (0.0133)	1e-05 (7.25e-05)	0.00356 (0.0115)	0.0151 (0.0368)	0.00074 (0.00311)	0.508 (0.622)	0.00448 (0.0139)
20p gain	99 (34%)	189	3e-05 (0.000195)	0.02 (0.0462)	0.0252 (0.0565)	0.00223 (0.00786)	0.00452 (0.0139)	0.0223 (0.0507)	0.0328 (0.0706)	0.00309 (0.0102)	0.186 (0.286)	0.0934 (0.164)
9p loss	33 (11%)	255	1e-05 (7.25e-05)	1e-05 (7.25e-05)	0.337 (0.454)	0.0159 (0.0385)	1e-05 (7.25e-05)	1e-05 (7.25e-05)	0.00453 (0.0139)	0.142 (0.231)	0.00543 (0.0159)	0.00141 (0.00543)
9q loss	34 (12%)	254	1e-05 (7.25e-05)	1e-05 (7.25e-05)	0.0568 (0.108)	0.0046 (0.0141)	1e-05 (7.25e-05)	1e-05 (7.25e-05)	0.00295 (0.00991)	0.0654 (0.123)	0.00107 (0.00423)	0.0002 (0.000974)
13q loss	24 (8%)	264	1e-05 (7.25e-05)	5e-05 (0.000301)	0.478 (0.592)	0.00117 (0.00456)	1e-05 (7.25e-05)	1e-05 (7.25e-05)	0.0535 (0.104)	0.011 (0.0284)	0.00409 (0.0128)	5e-05 (0.000301)
14q loss	47 (16%)	241	1e-05 (7.25e-05)	0.00011 (0.000586)	0.00558 (0.0162)	0.00011 (0.000586)	1e-05 (7.25e-05)	1e-05 (7.25e-05)	0.213 (0.316)	0.861 (0.928)	0.00391 (0.0123)	0.00306 (0.0102)
3p gain	74 (26%)	214	1e-05 (7.25e-05)	0.0017 (0.00632)	0.21 (0.313)	0.00011 (0.000586)	1e-05 (7.25e-05)	0.0019 (0.00696)	0.0732 (0.134)	0.00086 (0.00354)	0.0867 (0.155)	0.00095 (0.00384)
20q gain	101 (35%)	187	0.00015 (0.000766)	0.0211 (0.0484)	0.0723 (0.133)	0.00794 (0.0215)	0.0106 (0.0276)	0.0496 (0.0975)	0.044 (0.0892)	0.00503 (0.0149)	0.341 (0.457)	0.0549 (0.106)
4p loss	25 (9%)	263	1e-05 (7.25e-05)	1e-05 (7.25e-05)	0.206 (0.309)	0.00084 (0.00347)	1e-05 (7.25e-05)	1e-05 (7.25e-05)	0.149 (0.241)	0.0693 (0.129)	0.0058 (0.0167)	1e-05 (7.25e-05)
4q loss	26 (9%)	262	1e-05 (7.25e-05)	1e-05 (7.25e-05)	0.478 (0.592)	0.00361 (0.0116)	1e-05 (7.25e-05)	1e-05 (7.25e-05)	0.262 (0.372)	0.2 (0.303)	0.00724 (0.0199)	5e-05 (0.000301)
5p loss	8 (3%)	280	0.17 (0.266)	0.0485 (0.0965)	0.58 (0.687)	0.0769 (0.14)	0.0298 (0.0657)	0.00032 (0.00145)	0.0391 (0.0817)	0.0234 (0.0527)	0.0122 (0.0307)	6e-05 (0.000347)
5q loss	8 (3%)	280	0.17 (0.266)	0.0486 (0.0965)	0.581 (0.687)	0.0744 (0.136)	0.0288 (0.064)	0.00031 (0.00142)	0.0393 (0.0819)	0.0234 (0.0527)	0.0119 (0.0303)	1e-05 (7.25e-05)
10q loss	17 (6%)	271	1e-05 (7.25e-05)	0.00013 (0.000673)	0.717 (0.81)	0.0472 (0.0941)	0.00013 (0.000673)	0.00207 (0.00751)	0.174 (0.271)	0.663 (0.763)	0.00154 (0.00587)	0.00698 (0.0193)
xp loss	34 (12%)	254	1e-05 (7.25e-05)	1e-05 (7.25e-05)	0.226 (0.329)	0.00321 (0.0105)	1e-05 (7.25e-05)	7e-05 (0.000398)	0.178 (0.277)	0.357 (0.474)	0.0179 (0.0424)	0.00077 (0.00322)
1p gain	9 (3%)	279	4e-05 (0.000255)	2e-05 (0.000135)	0.0706 (0.131)	0.0286 (0.0638)	0.00352 (0.0114)	0.0033 (0.0108)	0.481 (0.594)	0.105 (0.178)	0.0539 (0.104)	0.00591 (0.017)
3p loss	22 (8%)	266	1e-05 (7.25e-05)	1e-05 (7.25e-05)	0.159 (0.254)	0.0319 (0.0699)	1e-05 (7.25e-05)	1e-05 (7.25e-05)	0.273 (0.385)	0.0944 (0.164)	0.0524 (0.102)	0.00094 (0.00382)
6p loss	21 (7%)	267	1e-05 (7.25e-05)	0.0444 (0.0892)	0.946 (0.989)	0.0414 (0.0851)	0.00635 (0.018)	0.00019 (0.000937)	0.0189 (0.0442)	0.261 (0.372)	0.448 (0.564)	0.0974 (0.169)
10p loss	16 (6%)	272	1e-05 (7.25e-05)	5e-05 (0.000301)	0.925 (0.972)	0.154 (0.248)	0.00049 (0.00213)	0.00296 (0.00991)	0.59 (0.695)	0.55 (0.66)	0.0186 (0.0436)	0.0351 (0.0747)
11p loss	18 (6%)	270	2e-05 (0.000135)	0.00073 (0.0031)	0.523 (0.635)	0.149 (0.241)	6e-05 (0.000347)	0.00264 (0.00909)	0.462 (0.578)	0.194 (0.295)	0.0194 (0.0452)	0.0139 (0.0342)
11q loss	21 (7%)	267	1e-05 (7.25e-05)	4e-05 (0.000255)	0.0978 (0.169)	0.0112 (0.0288)	0.00013 (0.000673)	0.00209 (0.00754)	0.779 (0.862)	0.342 (0.457)	0.0368 (0.0772)	0.0773 (0.14)
15q loss	31 (11%)	257	1e-05 (7.25e-05)	0.00219 (0.00775)	0.0916 (0.163)	0.029 (0.0642)	5e-05 (0.000301)	1e-05 (7.25e-05)	0.0939 (0.164)	0.0611 (0.116)	0.0711 (0.131)	0.0023 (0.00806)
16q loss	7 (2%)	281	0.00036 (0.00161)	0.00738 (0.0202)	0.635 (0.734)	0.0622 (0.117)	0.00215 (0.00772)	0.0128 (0.0318)	0.391 (0.508)	0.38 (0.499)	0.0327 (0.0706)	0.0364 (0.0765)
17p loss	12 (4%)	276	0.00412 (0.0129)	0.00032 (0.00145)	0.434 (0.551)	0.548 (0.658)	1e-05 (7.25e-05)	0.0003 (0.00141)	0.429 (0.545)	0.653 (0.754)	0.00649 (0.0182)	0.00074 (0.00311)
22q loss	60 (21%)	228	1e-05 (7.25e-05)	1e-05 (7.25e-05)	0.437 (0.551)	0.014 (0.0344)	1e-05 (7.25e-05)	1e-05 (7.25e-05)	0.95 (0.99)	0.694 (0.786)	0.0544 (0.105)	0.00519 (0.0153)
xq loss	30 (10%)	258	1e-05 (7.25e-05)	2e-05 (0.000135)	0.459 (0.574)	0.0141 (0.0344)	1e-05 (7.25e-05)	9e-05 (0.000497)	0.144 (0.235)	0.629 (0.729)	0.0522 (0.102)	0.0032 (0.0105)
6p gain	10 (3%)	278	0.049 (0.0968)	0.00363 (0.0116)	0.163 (0.258)	0.134 (0.219)	0.00156 (0.00592)	0.0624 (0.118)	0.162 (0.257)	0.04 (0.0832)	0.104 (0.177)	0.0403 (0.0836)
11q gain	10 (3%)	278	1e-05 (7.25e-05)	0.00343 (0.0111)	0.349 (0.465)	0.0171 (0.041)	0.0218 (0.05)	0.00385 (0.0122)	0.92 (0.968)	0.919 (0.968)	0.819 (0.896)	0.177 (0.276)
6q loss	26 (9%)	262	1e-05 (7.25e-05)	0.00241 (0.00837)	0.878 (0.939)	0.0416 (0.0853)	0.00016 (0.000805)	3e-05 (0.000195)	0.274 (0.385)	0.754 (0.842)	0.0987 (0.17)	0.201 (0.303)
16p loss	4 (1%)	284	0.0429 (0.0876)	0.0333 (0.0714)	0.188 (0.288)	0.0843 (0.151)	0.0443 (0.0892)	0.00767 (0.0209)	0.832 (0.906)	0.224 (0.327)	0.114 (0.191)	0.0097 (0.0256)
19p loss	17 (6%)	271	8e-05 (0.000452)	0.00217 (0.00775)	1 (1.00)	0.124 (0.206)	0.00492 (0.0147)	0.00636 (0.018)	0.423 (0.538)	0.0566 (0.108)	0.089 (0.159)	0.013 (0.032)
5p gain	33 (11%)	255	1e-05 (7.25e-05)	0.00685 (0.0191)	0.762 (0.848)	0.843 (0.915)	0.0184 (0.0434)	0.00017 (0.00085)	0.589 (0.695)	0.211 (0.314)	0.331 (0.447)	0.118 (0.196)
5q gain	31 (11%)	257	1e-05 (7.25e-05)	0.00112 (0.00439)	0.538 (0.647)	0.779 (0.862)	0.00564 (0.0163)	5e-05 (0.000301)	0.381 (0.5)	0.263 (0.372)	0.47 (0.585)	0.254 (0.363)
8q gain	25 (9%)	263	0.126 (0.208)	9e-05 (0.000497)	0.279 (0.39)	0.449 (0.565)	0.0128 (0.0318)	0.0441 (0.0892)	0.107 (0.182)	0.0668 (0.124)	0.0435 (0.0885)	0.0971 (0.169)
11p gain	11 (4%)	277	0.00038 (0.00168)	0.02 (0.0462)	0.575 (0.683)	0.017 (0.0409)	0.187 (0.286)	0.00029 (0.00138)	1 (1.00)	1 (1.00)	0.82 (0.896)	0.177 (0.276)
14q gain	3 (1%)	285	0.241 (0.347)	0.0175 (0.0416)	0.0176 (0.0416)	0.407 (0.524)	0.492 (0.605)	0.0357 (0.0758)	1 (1.00)	0.479 (0.593)	0.303 (0.417)	0.012 (0.0304)
1p loss	30 (10%)	258	1e-05 (7.25e-05)	0.0313 (0.0687)	0.891 (0.948)	0.632 (0.732)	7e-05 (0.000398)	0.00084 (0.00347)	0.275 (0.386)	0.0636 (0.119)	0.838 (0.91)	0.125 (0.206)
3q loss	7 (2%)	281	1e-05 (7.25e-05)	0.00183 (0.00677)	0.533 (0.643)	0.203 (0.306)	0.0219 (0.05)	0.00298 (0.00993)	0.389 (0.507)	0.723 (0.816)	0.393 (0.51)	0.294 (0.407)
19q loss	16 (6%)	272	2e-05 (0.000135)	0.00467 (0.0142)	0.796 (0.875)	0.111 (0.186)	0.0049 (0.0147)	0.0226 (0.0511)	0.59 (0.695)	0.414 (0.529)	0.0894 (0.159)	0.108 (0.183)
2q gain	47 (16%)	241	1e-05 (7.25e-05)	0.00744 (0.0203)	1 (1.00)	0.0328 (0.0706)	0.603 (0.707)	0.738 (0.828)	0.25 (0.359)	0.109 (0.184)	0.409 (0.524)	0.276 (0.386)
6q gain	8 (3%)	280	0.0225 (0.0511)	0.0017 (0.00632)	0.627 (0.729)	0.175 (0.273)	0.0123 (0.0308)	0.132 (0.216)	0.22 (0.323)	0.161 (0.257)	0.128 (0.21)	0.0618 (0.117)
10p gain	9 (3%)	279	0.00099 (0.00398)	0.0334 (0.0714)	1 (1.00)	0.0342 (0.0729)	0.0923 (0.163)	0.357 (0.474)	0.22 (0.323)	0.628 (0.729)	0.894 (0.948)	0.185 (0.286)
10q gain	9 (3%)	279	0.00108 (0.00425)	0.0323 (0.0702)	1 (1.00)	0.0327 (0.0706)	0.092 (0.163)	0.357 (0.474)	0.224 (0.327)	0.625 (0.728)	0.892 (0.948)	0.186 (0.286)
12p gain	112 (39%)	176	0.00557 (0.0162)	0.299 (0.413)	0.0295 (0.0651)	0.0789 (0.143)	0.0002 (0.000974)	0.117 (0.194)	0.215 (0.317)	0.0509 (0.1)	0.675 (0.774)	0.0936 (0.164)
12q gain	112 (39%)	176	0.0052 (0.0153)	0.302 (0.416)	0.0282 (0.063)	0.0802 (0.145)	0.00023 (0.00111)	0.115 (0.193)	0.215 (0.317)	0.0519 (0.102)	0.677 (0.775)	0.0931 (0.164)
19p gain	4 (1%)	284	0.0016 (0.00601)	0.69 (0.784)	0.31 (0.425)	0.383 (0.5)	0.0456 (0.0911)	0.041 (0.0845)	1 (1.00)	1 (1.00)	1 (1.00)	0.316 (0.43)
19q gain	4 (1%)	284	0.0016 (0.00601)	0.691 (0.784)	0.31 (0.425)	0.383 (0.5)	0.0453 (0.0908)	0.041 (0.0845)	1 (1.00)	1 (1.00)	1 (1.00)	0.314 (0.428)
1q loss	21 (7%)	267	0.00026 (0.00125)	0.729 (0.82)	0.849 (0.919)	0.378 (0.499)	0.0559 (0.107)	0.00814 (0.022)	0.201 (0.303)	0.013 (0.032)	0.567 (0.676)	0.216 (0.317)
2p loss	5 (2%)	283	0.275 (0.386)	0.00992 (0.026)	0.017 (0.0409)	0.208 (0.311)	0.0162 (0.0392)	0.0747 (0.137)	0.28 (0.391)	0.74 (0.828)
8p loss	16 (6%)	272	0.00154 (0.00587)	0.318 (0.431)	0.169 (0.266)	0.287 (0.399)	0.00462 (0.0141)	0.00919 (0.0246)	0.855 (0.924)	0.947 (0.989)	0.369 (0.488)	0.229 (0.332)
8q loss	9 (3%)	279	0.00248 (0.00858)	0.382 (0.5)	0.444 (0.56)	0.411 (0.527)	0.0121 (0.0306)	0.00059 (0.00255)	0.915 (0.966)	0.623 (0.727)	0.685 (0.782)	0.533 (0.643)
2p gain	42 (15%)	246	1e-05 (7.25e-05)	0.00695 (0.0193)	0.941 (0.987)	0.12 (0.199)	0.134 (0.219)	0.901 (0.954)	0.254 (0.363)	0.147 (0.239)	0.781 (0.863)	0.199 (0.302)
9p gain	3 (1%)	285	0.875 (0.939)				0.0993 (0.171)	0.0363 (0.0765)	0.291 (0.403)	0.48 (0.593)	0.301 (0.416)	0.0116 (0.0298)
15q gain	5 (2%)	283	0.00031 (0.00142)	0.0199 (0.0462)	0.311 (0.425)	0.205 (0.307)	0.221 (0.323)	0.263 (0.372)	0.527 (0.639)	0.231 (0.334)
8p gain	20 (7%)	268	0.746 (0.834)	0.0105 (0.0274)	0.167 (0.264)	0.56 (0.669)	0.0998 (0.171)	0.0803 (0.145)	0.359 (0.476)	0.325 (0.439)	0.408 (0.524)	0.379 (0.499)
18p gain	12 (4%)	276	0.00285 (0.00967)	0.204 (0.307)	0.471 (0.585)	0.793 (0.873)	0.555 (0.664)	0.486 (0.599)	0.168 (0.265)	0.571 (0.679)	0.465 (0.58)	0.761 (0.848)
18q gain	9 (3%)	279	0.0027 (0.00925)	0.0929 (0.164)	0.263 (0.372)	0.593 (0.696)	0.579 (0.687)	0.163 (0.258)	0.405 (0.522)	0.208 (0.311)	0.324 (0.439)	0.395 (0.511)
22q gain	5 (2%)	283	0.00871 (0.0234)	0.727 (0.819)	1 (1.00)	0.883 (0.943)	0.862 (0.928)	0.716 (0.81)	0.53 (0.641)	0.391 (0.508)	0.869 (0.934)	1 (1.00)
2q loss	3 (1%)	285	0.661 (0.762)	0.105 (0.178)			0.1 (0.171)	0.0361 (0.0763)	0.778 (0.862)	1 (1.00)
21q loss	43 (15%)	245	0.00062 (0.00267)	0.456 (0.572)	0.073 (0.134)	0.238 (0.343)	0.188 (0.288)	0.421 (0.537)	0.876 (0.939)	0.194 (0.295)	0.787 (0.868)	0.0662 (0.124)
4p gain	10 (3%)	278	0.241 (0.347)	0.812 (0.891)	0.893 (0.948)	0.435 (0.551)	0.326 (0.44)	0.684 (0.782)	0.673 (0.773)	0.848 (0.919)	0.838 (0.91)	0.945 (0.989)
4q gain	9 (3%)	279	0.517 (0.63)	0.813 (0.891)	0.893 (0.948)	0.435 (0.551)	0.53 (0.641)	0.739 (0.828)	0.402 (0.52)	0.69 (0.784)	0.495 (0.607)	1 (1.00)
13q gain	28 (10%)	260	0.225 (0.327)	0.966 (1.00)	0.877 (0.939)	0.689 (0.784)	0.185 (0.286)	0.774 (0.86)	0.824 (0.899)	0.552 (0.661)	0.347 (0.463)	0.312 (0.426)
21q gain	19 (7%)	269	0.515 (0.628)	0.151 (0.244)	0.607 (0.709)	0.517 (0.63)	0.11 (0.185)	0.949 (0.99)	0.214 (0.317)	0.085 (0.152)	0.508 (0.622)	0.0836 (0.151)

'1p gain' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00026

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
1P GAIN MUTATED	1	0	0	8
1P GAIN WILD-TYPE	113	76	46	44

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

'1p gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00013

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
1P GAIN MUTATED	1	8	0
1P GAIN WILD-TYPE	81	63	119

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

'1p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0286 (Fisher's exact test), Q value = 0.064

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	5	0
1P GAIN WILD-TYPE	37	66	60	43

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

'1p gain' versus 'MRNASEQ_CNMF'

P value = 0.00352 (Fisher's exact test), Q value = 0.011

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
1P GAIN MUTATED	0	0	1	8
1P GAIN WILD-TYPE	34	96	65	84

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

'1p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0033 (Fisher's exact test), Q value = 0.011

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	5	0	4
1P GAIN WILD-TYPE	113	123	43

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

'1p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00591 (Fisher's exact test), Q value = 0.017

Table S6. Gene #1: '1p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	103	75	15	29
1P GAIN MUTATED	1	4	3	0
1P GAIN WILD-TYPE	102	71	12	29

Figure S6. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.3e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
1Q GAIN MUTATED	4	1	0	12
1Q GAIN WILD-TYPE	110	75	46	40

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 = 7.3e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
1Q GAIN MUTATED	3	13	0
1Q GAIN WILD-TYPE	79	58	119

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

'1q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0491 (Fisher's exact test), Q value = 0.097

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 = 6e-05 (Fisher's exact test), Q value = 0.00035

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
1Q GAIN MUTATED	0	0	3	14
1Q GAIN WILD-TYPE	34	96	63	78

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

'1q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 5e-04

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 = 0.00943 (Fisher's exact test), Q value = 0.025

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'

'1q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00648 (Fisher's exact test), Q value = 0.018

Table S13. Gene #2: '1q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	81	71
1Q GAIN MUTATED	4	1	10
1Q GAIN WILD-TYPE	66	80	61

Figure S13. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'1q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00049 (Fisher's exact test), Q value = 0.0021

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	103	75	15	29
1Q GAIN MUTATED	2	9	4	0
1Q GAIN WILD-TYPE	101	66	11	29

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

'2p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.3e-05

Table S15. Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
2P GAIN MUTATED	1	3	14	24
2P GAIN WILD-TYPE	113	73	32	28

Figure S15. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

'2p gain' versus 'METHLYATION_CNMF'

P value = 0.00695 (Fisher's exact test), Q value = 0.019

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
2P GAIN MUTATED	4	14	21
2P GAIN WILD-TYPE	78	57	98

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

'2q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.3e-05

Table S17. Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
2Q GAIN MUTATED	1	4	15	27
2Q GAIN WILD-TYPE	113	72	31	25

Figure S17. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

'2q gain' versus 'METHLYATION_CNMF'

P value = 0.00744 (Fisher's exact test), Q value = 0.02

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
2Q GAIN MUTATED	5	15	24
2Q GAIN WILD-TYPE	77	56	95

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

'2q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0328 (Fisher's exact test), Q value = 0.071

Table S19. 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 S19. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'3p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.3e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
3P GAIN MUTATED	11	8	45	10
3P GAIN WILD-TYPE	103	68	1	42

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

'3p gain' versus 'METHLYATION_CNMF'

P value = 0.0017 (Fisher's exact test), Q value = 0.0063

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
3P GAIN MUTATED	20	8	40
3P GAIN WILD-TYPE	62	63	79

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

'3p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.00059

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 = 7.3e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
3P GAIN MUTATED	13	30	25	6
3P GAIN WILD-TYPE	21	66	41	86

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

'3p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0019 (Fisher's exact test), Q value = 0.007

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	26	43	5
3P GAIN WILD-TYPE	92	80	42

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

'3p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00086 (Fisher's exact test), Q value = 0.0035

Table S25. Gene #5: '3p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	80	88
3P GAIN MUTATED	31	31	12
3P GAIN WILD-TYPE	89	49	76

Figure S25. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00095 (Fisher's exact test), Q value = 0.0038

Table S26. Gene #5: '3p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	103	75	15	29
3P GAIN MUTATED	35	7	3	6
3P GAIN WILD-TYPE	68	68	12	23

Figure S26. 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 = 7.3e-05

Table S27. Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
3Q GAIN MUTATED	20	14	45	15
3Q GAIN WILD-TYPE	94	62	1	37

Figure S27. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

'3q gain' versus 'METHLYATION_CNMF'

P value = 0.00469 (Fisher's exact test), Q value = 0.014

Table S28. Gene #6: '3q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
3Q GAIN MUTATED	24	14	50
3Q GAIN WILD-TYPE	58	57	69

Figure S28. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00429 (Fisher's exact test), Q value = 0.013

Table S29. 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 S29. 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 = 7.3e-05

Table S30. Gene #6: '3q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
3Q GAIN MUTATED	18	35	31	10
3Q GAIN WILD-TYPE	16	61	35	82

Figure S30. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00356 (Fisher's exact test), Q value = 0.011

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
3Q GAIN MUTATED	34	52	8
3Q GAIN WILD-TYPE	84	71	39

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

'3q gain' versus 'MIRSEQ_CNMF'

P value = 0.0151 (Fisher's exact test), Q value = 0.037

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	110	89
3Q GAIN MUTATED	38	36	20
3Q GAIN WILD-TYPE	51	74	69

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

'3q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00074 (Fisher's exact test), Q value = 0.0031

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	80	88
3Q GAIN MUTATED	40	37	17
3Q GAIN WILD-TYPE	80	43	71

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

'3q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00448 (Fisher's exact test), Q value = 0.014

Table S34. Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	103	75	15	29
3Q GAIN MUTATED	44	16	3	5
3Q GAIN WILD-TYPE	59	59	12	24

Figure S34. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.3e-05

Table S35. Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
5P GAIN MUTATED	13	3	0	17
5P GAIN WILD-TYPE	101	73	46	35

Figure S35. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'METHLYATION_CNMF'

P value = 0.00685 (Fisher's exact test), Q value = 0.019

Table S36. Gene #9: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
5P GAIN MUTATED	10	14	6
5P GAIN WILD-TYPE	72	57	113

Figure S36. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p gain' versus 'MRNASEQ_CNMF'

P value = 0.0184 (Fisher's exact test), Q value = 0.043

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
5P GAIN MUTATED	4	5	6	18
5P GAIN WILD-TYPE	30	91	60	74

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

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.00085

Table S38. 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	6
5P GAIN WILD-TYPE	95	119	41

Figure S38. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.3e-05

Table S39. Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
5Q GAIN MUTATED	14	1	0	16
5Q GAIN WILD-TYPE	100	75	46	36

Figure S39. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

'5q gain' versus 'METHLYATION_CNMF'

P value = 0.00112 (Fisher's exact test), Q value = 0.0044

Table S40. Gene #10: '5q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
5Q GAIN MUTATED	10	14	4
5Q GAIN WILD-TYPE	72	57	115

Figure S40. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q gain' versus 'MRNASEQ_CNMF'

P value = 0.00564 (Fisher's exact test), Q value = 0.016

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
5Q GAIN MUTATED	4	3	7	17
5Q GAIN WILD-TYPE	30	93	59	75

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

'5q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 3e-04

Table S42. 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 S42. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6p gain' versus 'CN_CNMF'

P value = 0.049 (Fisher's exact test), Q value = 0.097

Table S43. Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
6P GAIN MUTATED	4	1	0	5
6P GAIN WILD-TYPE	110	75	46	47

Figure S43. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

'6p gain' versus 'METHLYATION_CNMF'

P value = 0.00363 (Fisher's exact test), Q value = 0.012

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
6P GAIN MUTATED	1	7	1
6P GAIN WILD-TYPE	81	64	118

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

'6p gain' versus 'MRNASEQ_CNMF'

P value = 0.00156 (Fisher's exact test), Q value = 0.0059

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
6P GAIN MUTATED	0	1	0	9
6P GAIN WILD-TYPE	34	95	66	83

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

'6p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.04 (Fisher's exact test), Q value = 0.083

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'

'6p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0403 (Fisher's exact test), Q value = 0.084

Table S47. Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	103	75	15	29
6P GAIN MUTATED	1	5	2	1
6P GAIN WILD-TYPE	102	70	13	28

Figure S47. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q gain' versus 'CN_CNMF'

P value = 0.0225 (Fisher's exact test), Q value = 0.051

Table S48. Gene #12: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
6Q GAIN MUTATED	2	1	0	5
6Q GAIN WILD-TYPE	112	75	46	47

Figure S48. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

'6q gain' versus 'METHLYATION_CNMF'

P value = 0.0017 (Fisher's exact test), Q value = 0.0063

Table S49. Gene #12: '6q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
6Q GAIN MUTATED	0	6	1
6Q GAIN WILD-TYPE	82	65	118

Figure S49. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q gain' versus 'MRNASEQ_CNMF'

P value = 0.0123 (Fisher's exact test), Q value = 0.031

Table S50. Gene #12: '6q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
6Q GAIN MUTATED	0	1	0	7
6Q GAIN WILD-TYPE	34	95	66	85

Figure S50. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.3e-05

Table S51. Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
7P GAIN MUTATED	32	73	43	24
7P GAIN WILD-TYPE	82	3	3	28

Figure S51. 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 = 7.3e-05

Table S52. Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
7P GAIN MUTATED	38	23	101
7P GAIN WILD-TYPE	44	48	18

Figure S52. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p gain' versus 'RPPA_CNMF'

P value = 0.00646 (Fisher's exact test), Q value = 0.018

Table S53. 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	60	26
7P GAIN WILD-TYPE	30	22	30

Figure S53. 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 = 7.3e-05

Table S54. 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	53	27	20
7P GAIN WILD-TYPE	8	13	38	23

Figure S54. 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 = 7.3e-05

Table S55. Gene #13: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
7P GAIN MUTATED	29	82	39	22
7P GAIN WILD-TYPE	5	14	27	70

Figure S55. 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 = 7.3e-05

Table S56. 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	103	16
7P GAIN WILD-TYPE	65	20	31

Figure S56. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_CNMF'

P value = 0.0425 (Fisher's exact test), Q value = 0.087

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	110	89
7P GAIN MUTATED	45	75	52
7P GAIN WILD-TYPE	44	35	37

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

'7p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.00081

Table S58. Gene #13: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

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

Figure S58. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.00077

Table S59. Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	81	71
7P GAIN MUTATED	33	62	34
7P GAIN WILD-TYPE	37	19	37

Figure S59. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'7p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.3e-05

Table S60. Gene #13: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	103	75	15	29
7P GAIN MUTATED	70	30	4	25
7P GAIN WILD-TYPE	33	45	11	4

Figure S60. 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 = 7.3e-05

Table S61. Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
7Q GAIN MUTATED	32	73	43	25
7Q GAIN WILD-TYPE	82	3	3	27

Figure S61. 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 = 7.3e-05

Table S62. Gene #14: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
7Q GAIN MUTATED	38	24	101
7Q GAIN WILD-TYPE	44	47	18

Figure S62. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q gain' versus 'RPPA_CNMF'

P value = 0.0118 (Fisher's exact test), Q value = 0.03

Table S63. 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	60	27
7Q GAIN WILD-TYPE	30	22	29

Figure S63. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'7q gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.3e-05

Table S64. 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	53	28	20
7Q GAIN WILD-TYPE	8	13	37	23

Figure S64. 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 = 7.3e-05

Table S65. Gene #14: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
7Q GAIN MUTATED	29	82	39	23
7Q GAIN WILD-TYPE	5	14	27	69

Figure S65. 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 = 7.3e-05

Table S66. 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	103	16
7Q GAIN WILD-TYPE	64	20	31

Figure S66. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.00094

Table S67. Gene #14: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	80	88
7Q GAIN MUTATED	64	63	46
7Q GAIN WILD-TYPE	56	17	42

Figure S67. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.0013

Table S68. Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	81	71
7Q GAIN MUTATED	34	62	34
7Q GAIN WILD-TYPE	36	19	37

Figure S68. 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 = 7.3e-05

Table S69. Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	103	75	15	29
7Q GAIN MUTATED	70	31	4	25
7Q GAIN WILD-TYPE	33	44	11	4

Figure S69. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p gain' versus 'METHLYATION_CNMF'

P value = 0.0105 (Fisher's exact test), Q value = 0.027

Table S70. Gene #15: '8p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
8P GAIN MUTATED	3	11	5
8P GAIN WILD-TYPE	79	60	114

Figure S70. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 5e-04

Table S71. Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
8Q GAIN MUTATED	2	15	6
8Q GAIN WILD-TYPE	80	56	113

Figure S71. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 0.0128 (Fisher's exact test), Q value = 0.032

Table S72. Gene #16: '8q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
8Q GAIN MUTATED	0	6	4	15
8Q GAIN WILD-TYPE	34	90	62	77

Figure S72. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0441 (Fisher's exact test), Q value = 0.089

Table S73. 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 S73. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0435 (Fisher's exact test), Q value = 0.089

Table S74. Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	81	71
8Q GAIN MUTATED	4	7	13
8Q GAIN WILD-TYPE	66	74	58

Figure S74. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'9p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0363 (Fisher's exact test), Q value = 0.076

Table S75. 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 S75. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0116 (Fisher's exact test), Q value = 0.03

Table S76. Gene #17: '9p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	103	75	15	29
9P GAIN MUTATED	0	1	2	0
9P GAIN WILD-TYPE	103	74	13	29

Figure S76. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p gain' versus 'CN_CNMF'

P value = 0.00099 (Fisher's exact test), Q value = 0.004

Table S77. Gene #18: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
10P GAIN MUTATED	0	2	1	6
10P GAIN WILD-TYPE	114	74	45	46

Figure S77. Get High-res Image Gene #18: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

'10p gain' versus 'METHLYATION_CNMF'

P value = 0.0334 (Fisher's exact test), Q value = 0.071

Table S78. Gene #18: '10p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
10P GAIN MUTATED	1	5	1
10P GAIN WILD-TYPE	81	66	118

Figure S78. Get High-res Image Gene #18: '10p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0342 (Fisher's exact test), Q value = 0.073

Table S79. Gene #18: '10p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
10P GAIN MUTATED	0	0	5	1
10P GAIN WILD-TYPE	39	66	60	42

Figure S79. Get High-res Image Gene #18: '10p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'10q gain' versus 'CN_CNMF'

P value = 0.00108 (Fisher's exact test), Q value = 0.0043

Table S80. Gene #19: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
10Q GAIN MUTATED	0	2	1	6
10Q GAIN WILD-TYPE	114	74	45	46

Figure S80. Get High-res Image Gene #19: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

'10q gain' versus 'METHLYATION_CNMF'

P value = 0.0323 (Fisher's exact test), Q value = 0.07

Table S81. Gene #19: '10q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
10Q GAIN MUTATED	1	5	1
10Q GAIN WILD-TYPE	81	66	118

Figure S81. Get High-res Image Gene #19: '10q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0327 (Fisher's exact test), Q value = 0.071

Table S82. Gene #19: '10q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	66	65	43
10Q GAIN MUTATED	0	0	5	1
10Q GAIN WILD-TYPE	39	66	60	42

Figure S82. Get High-res Image Gene #19: '10q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'11p gain' versus 'CN_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.0017

Table S83. Gene #20: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
11P GAIN MUTATED	2	1	0	8
11P GAIN WILD-TYPE	112	75	46	44

Figure S83. Get High-res Image Gene #20: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

'11p gain' versus 'METHLYATION_CNMF'

P value = 0.02 (Fisher's exact test), Q value = 0.046

Table S84. Gene #20: '11p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
11P GAIN MUTATED	3	6	1
11P GAIN WILD-TYPE	79	65	118

Figure S84. Get High-res Image Gene #20: '11p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.017 (Fisher's exact test), Q value = 0.041

Table S85. 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	7	0
11P GAIN WILD-TYPE	39	64	58	43

Figure S85. Get High-res Image Gene #20: '11p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'11p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.0014

Table S86. Gene #20: '11p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
11P GAIN MUTATED	5	0	6
11P GAIN WILD-TYPE	113	123	41

Figure S86. Get High-res Image Gene #20: '11p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.3e-05

Table S87. Gene #21: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
11Q GAIN MUTATED	1	0	0	9
11Q GAIN WILD-TYPE	113	76	46	43

Figure S87. Get High-res Image Gene #21: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

'11q gain' versus 'METHLYATION_CNMF'

P value = 0.00343 (Fisher's exact test), Q value = 0.011

Table S88. Gene #21: '11q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
11Q GAIN MUTATED	1	7	1
11Q GAIN WILD-TYPE	81	64	118

Figure S88. Get High-res Image Gene #21: '11q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0171 (Fisher's exact test), Q value = 0.041

Table S89. 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 S89. Get High-res Image Gene #21: '11q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'11q gain' versus 'MRNASEQ_CNMF'

P value = 0.0218 (Fisher's exact test), Q value = 0.05

Table S90. Gene #21: '11q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
11Q GAIN MUTATED	0	1	1	8
11Q GAIN WILD-TYPE	34	95	65	84

Figure S90. Get High-res Image Gene #21: '11q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'11q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00385 (Fisher's exact test), Q value = 0.012

Table S91. 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 S91. Get High-res Image Gene #21: '11q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'CN_CNMF'

P value = 0.00557 (Fisher's exact test), Q value = 0.016

Table S92. Gene #22: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
12P GAIN MUTATED	31	33	25	23
12P GAIN WILD-TYPE	83	43	21	29

Figure S92. Get High-res Image Gene #22: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

'12p gain' versus 'RPPA_CNMF'

P value = 0.0295 (Fisher's exact test), Q value = 0.065

Table S93. 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 S93. Get High-res Image Gene #22: '12p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.00097

Table S94. Gene #22: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
12P GAIN MUTATED	21	40	30	21
12P GAIN WILD-TYPE	13	56	36	71

Figure S94. Get High-res Image Gene #22: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12q gain' versus 'CN_CNMF'

P value = 0.0052 (Fisher's exact test), Q value = 0.015

Table S95. Gene #23: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
12Q GAIN MUTATED	31	33	25	23
12Q GAIN WILD-TYPE	83	43	21	29

Figure S95. Get High-res Image Gene #23: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

'12q gain' versus 'RPPA_CNMF'

P value = 0.0282 (Fisher's exact test), Q value = 0.063

Table S96. 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 S96. Get High-res Image Gene #23: '12q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'12q gain' versus 'MRNASEQ_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.0011

Table S97. Gene #23: '12q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
12Q GAIN MUTATED	21	40	30	21
12Q GAIN WILD-TYPE	13	56	36	71

Figure S97. Get High-res Image Gene #23: '12q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'14q gain' versus 'METHLYATION_CNMF'

P value = 0.0175 (Fisher's exact test), Q value = 0.042

Table S98. Gene #25: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
14Q GAIN MUTATED	0	3	0
14Q GAIN WILD-TYPE	82	68	119

Figure S98. Get High-res Image Gene #25: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'14q gain' versus 'RPPA_CNMF'

P value = 0.0176 (Fisher's exact test), Q value = 0.042

Table S99. 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 S99. Get High-res Image Gene #25: '14q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0357 (Fisher's exact test), Q value = 0.076

Table S100. 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 S100. Get High-res Image Gene #25: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.012 (Fisher's exact test), Q value = 0.03

Table S101. Gene #25: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	103	75	15	29
14Q GAIN MUTATED	0	1	2	0
14Q GAIN WILD-TYPE	103	74	13	29

Figure S101. Get High-res Image Gene #25: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q gain' versus 'CN_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.0014

Table S102. Gene #26: '15q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
15Q GAIN MUTATED	0	0	0	5
15Q GAIN WILD-TYPE	114	76	46	47

Figure S102. Get High-res Image Gene #26: '15q gain' versus Molecular Subtype #1: 'CN_CNMF'

'15q gain' versus 'METHLYATION_CNMF'

P value = 0.0199 (Fisher's exact test), Q value = 0.046

Table S103. Gene #26: '15q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
15Q GAIN MUTATED	0	4	1
15Q GAIN WILD-TYPE	82	67	118

Figure S103. Get High-res Image Gene #26: '15q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.3e-05

Table S104. Gene #27: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
16P GAIN MUTATED	49	36	46	22
16P GAIN WILD-TYPE	65	40	0	30

Figure S104. Get High-res Image Gene #27: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

'16p gain' versus 'METHLYATION_CNMF'

P value = 0.0122 (Fisher's exact test), Q value = 0.031

Table S105. Gene #27: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
16P GAIN MUTATED	37	33	76
16P GAIN WILD-TYPE	45	38	43

Figure S105. Get High-res Image Gene #27: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00064 (Fisher's exact test), Q value = 0.0027

Table S106. 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 S106. 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 = 7.3e-05

Table S107. Gene #27: '16p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
16P GAIN MUTATED	18	57	50	28
16P GAIN WILD-TYPE	16	39	16	64

Figure S107. Get High-res Image Gene #27: '16p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00019

Table S108. 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 S108. Get High-res Image Gene #27: '16p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_CNMF'

P value = 0.00106 (Fisher's exact test), Q value = 0.0042

Table S109. Gene #27: '16p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	110	89
16P GAIN MUTATED	51	69	33
16P GAIN WILD-TYPE	38	41	56

Figure S109. Get High-res Image Gene #27: '16p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00013

Table S110. 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 S110. Get High-res Image Gene #27: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00834 (Fisher's exact test), Q value = 0.022

Table S111. Gene #27: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	81	71
16P GAIN MUTATED	42	47	26
16P GAIN WILD-TYPE	28	34	45

Figure S111. Get High-res Image Gene #27: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00013

Table S112. Gene #27: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	103	75	15	29
16P GAIN MUTATED	71	29	4	11
16P GAIN WILD-TYPE	32	46	11	18

Figure S112. 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 = 7.3e-05

Table S113. Gene #28: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
16Q GAIN MUTATED	49	35	46	18
16Q GAIN WILD-TYPE	65	41	0	34

Figure S113. Get High-res Image Gene #28: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16q gain' versus 'METHLYATION_CNMF'

P value = 0.00626 (Fisher's exact test), Q value = 0.018

Table S114. Gene #28: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
16Q GAIN MUTATED	37	30	75
16Q GAIN WILD-TYPE	45	41	44

Figure S114. Get High-res Image Gene #28: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00194 (Fisher's exact test), Q value = 0.0071

Table S115. 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 S115. 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 = 7.3e-05

Table S116. Gene #28: '16q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
16Q GAIN MUTATED	18	56	50	24
16Q GAIN WILD-TYPE	16	40	16	68

Figure S116. Get High-res Image Gene #28: '16q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00054

Table S117. 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 S117. Get High-res Image Gene #28: '16q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 3e-04

Table S118. Gene #28: '16q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	110	89
16Q GAIN MUTATED	49	70	29
16Q GAIN WILD-TYPE	40	40	60

Figure S118. 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 = 7.3e-05

Table S119. 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 S119. Get High-res Image Gene #28: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00218 (Fisher's exact test), Q value = 0.0078

Table S120. Gene #28: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	81	71
16Q GAIN MUTATED	41	46	23
16Q GAIN WILD-TYPE	29	35	48

Figure S120. 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 = 7.3e-05

Table S121. Gene #28: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	103	75	15	29
16Q GAIN MUTATED	71	25	4	10
16Q GAIN WILD-TYPE	32	50	11	19

Figure S121. 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 = 7.3e-05

Table S122. Gene #29: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
17P GAIN MUTATED	29	75	45	25
17P GAIN WILD-TYPE	85	1	1	27

Figure S122. 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 = 7.3e-05

Table S123. Gene #29: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
17P GAIN MUTATED	37	22	105
17P GAIN WILD-TYPE	45	49	14

Figure S123. 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 = 0.00035

Table S124. 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	61	21
17P GAIN WILD-TYPE	27	21	35

Figure S124. 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 = 7.3e-05

Table S125. 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	52	29	18
17P GAIN WILD-TYPE	8	14	36	25

Figure S125. 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 = 7.3e-05

Table S126. Gene #29: '17p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
17P GAIN MUTATED	23	87	41	23
17P GAIN WILD-TYPE	11	9	25	69

Figure S126. 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 = 7.3e-05

Table S127. Gene #29: '17p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
17P GAIN MUTATED	55	108	11
17P GAIN WILD-TYPE	63	15	36

Figure S127. Get High-res Image Gene #29: '17p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_CNMF'

P value = 0.00283 (Fisher's exact test), Q value = 0.0097

Table S128. Gene #29: '17p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	110	89
17P GAIN MUTATED	45	80	49
17P GAIN WILD-TYPE	44	30	40

Figure S128. Get High-res Image Gene #29: '17p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.0014

Table S129. 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	49
17P GAIN WILD-TYPE	58	17	39

Figure S129. 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 = 7.3e-05

Table S130. Gene #29: '17p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	81	71
17P GAIN MUTATED	33	66	30
17P GAIN WILD-TYPE	37	15	41

Figure S130. 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 = 7.3e-05

Table S131. Gene #29: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	103	75	15	29
17P GAIN MUTATED	72	27	4	26
17P GAIN WILD-TYPE	31	48	11	3

Figure S131. 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 = 7.3e-05

Table S132. Gene #30: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
17Q GAIN MUTATED	38	75	45	33
17Q GAIN WILD-TYPE	76	1	1	19

Figure S132. 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 = 7.3e-05

Table S133. Gene #30: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
17Q GAIN MUTATED	42	33	105
17Q GAIN WILD-TYPE	40	38	14

Figure S133. Get High-res Image Gene #30: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q gain' versus 'RPPA_CNMF'

P value = 0.00089 (Fisher's exact test), Q value = 0.0036

Table S134. 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 S134. 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 = 7.3e-05

Table S135. 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 S135. 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 = 7.3e-05

Table S136. Gene #30: '17q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
17Q GAIN MUTATED	24	87	44	36
17Q GAIN WILD-TYPE	10	9	22	56

Figure S136. 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 = 7.3e-05

Table S137. 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 S137. Get High-res Image Gene #30: '17q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_CNMF'

P value = 0.032 (Fisher's exact test), Q value = 0.07

Table S138. Gene #30: '17q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	110	89
17Q GAIN MUTATED	53	83	55
17Q GAIN WILD-TYPE	36	27	34

Figure S138. Get High-res Image Gene #30: '17q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00118 (Fisher's exact test), Q value = 0.0046

Table S139. 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 S139. Get High-res Image Gene #30: '17q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.0014

Table S140. Gene #30: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	81	71
17Q GAIN MUTATED	39	66	38
17Q GAIN WILD-TYPE	31	15	33

Figure S140. 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 = 0.00013

Table S141. Gene #30: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	103	75	15	29
17Q GAIN MUTATED	77	35	5	26
17Q GAIN WILD-TYPE	26	40	10	3

Figure S141. Get High-res Image Gene #30: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p gain' versus 'CN_CNMF'

P value = 0.00285 (Fisher's exact test), Q value = 0.0097

Table S142. Gene #31: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
18P GAIN MUTATED	0	4	5	3
18P GAIN WILD-TYPE	114	72	41	49

Figure S142. Get High-res Image Gene #31: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

'18q gain' versus 'CN_CNMF'

P value = 0.0027 (Fisher's exact test), Q value = 0.0092

Table S143. Gene #32: '18q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
18Q GAIN MUTATED	0	3	5	1
18Q GAIN WILD-TYPE	114	73	41	51

Figure S143. Get High-res Image Gene #32: '18q gain' versus Molecular Subtype #1: 'CN_CNMF'

'19p gain' versus 'CN_CNMF'

P value = 0.0016 (Fisher's exact test), Q value = 0.006

Table S144. Gene #33: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
19P GAIN MUTATED	0	0	0	4
19P GAIN WILD-TYPE	114	76	46	48

Figure S144. Get High-res Image Gene #33: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

'19p gain' versus 'MRNASEQ_CNMF'

P value = 0.0456 (Fisher's exact test), Q value = 0.091

Table S145. Gene #33: '19p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
19P GAIN MUTATED	0	0	0	4
19P GAIN WILD-TYPE	34	96	66	88

Figure S145. Get High-res Image Gene #33: '19p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.041 (Fisher's exact test), Q value = 0.085

Table S146. 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	2
19P GAIN WILD-TYPE	116	123	45

Figure S146. Get High-res Image Gene #33: '19p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'CN_CNMF'

P value = 0.0016 (Fisher's exact test), Q value = 0.006

Table S147. Gene #34: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
19Q GAIN MUTATED	0	0	0	4
19Q GAIN WILD-TYPE	114	76	46	48

Figure S147. Get High-res Image Gene #34: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 0.0453 (Fisher's exact test), Q value = 0.091

Table S148. Gene #34: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
19Q GAIN MUTATED	0	0	0	4
19Q GAIN WILD-TYPE	34	96	66	88

Figure S148. Get High-res Image Gene #34: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.041 (Fisher's exact test), Q value = 0.085

Table S149. 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	2
19Q GAIN WILD-TYPE	116	123	45

Figure S149. Get High-res Image Gene #34: '19q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00019

Table S150. Gene #35: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
20P GAIN MUTATED	21	31	24	23
20P GAIN WILD-TYPE	93	45	22	29

Figure S150. Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 0.02 (Fisher's exact test), Q value = 0.046

Table S151. Gene #35: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
20P GAIN MUTATED	19	23	50
20P GAIN WILD-TYPE	63	48	69

Figure S151. Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20p gain' versus 'RPPA_CNMF'

P value = 0.0252 (Fisher's exact test), Q value = 0.056

Table S152. 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 S152. Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'20p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00223 (Fisher's exact test), Q value = 0.0079

Table S153. 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 S153. Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 0.00452 (Fisher's exact test), Q value = 0.014

Table S154. Gene #35: '20p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
20P GAIN MUTATED	9	46	22	22
20P GAIN WILD-TYPE	25	50	44	70

Figure S154. Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0223 (Fisher's exact test), Q value = 0.051

Table S155. 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 S155. Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_CNMF'

P value = 0.0328 (Fisher's exact test), Q value = 0.071

Table S156. Gene #35: '20p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	110	89
20P GAIN MUTATED	24	48	27
20P GAIN WILD-TYPE	65	62	62

Figure S156. Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00309 (Fisher's exact test), Q value = 0.01

Table S157. 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 S157. Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.00077

Table S158. Gene #36: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
20Q GAIN MUTATED	23	32	23	23
20Q GAIN WILD-TYPE	91	44	23	29

Figure S158. Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 0.0211 (Fisher's exact test), Q value = 0.048

Table S159. Gene #36: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
20Q GAIN MUTATED	19	24	50
20Q GAIN WILD-TYPE	63	47	69

Figure S159. Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00794 (Fisher's exact test), Q value = 0.022

Table S160. 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 S160. Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 0.0106 (Fisher's exact test), Q value = 0.028

Table S161. Gene #36: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
20Q GAIN MUTATED	9	46	22	24
20Q GAIN WILD-TYPE	25	50	44	68

Figure S161. Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0496 (Fisher's exact test), Q value = 0.098

Table S162. Gene #36: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
20Q GAIN MUTATED	35	53	13
20Q GAIN WILD-TYPE	83	70	34

Figure S162. Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 0.044 (Fisher's exact test), Q value = 0.089

Table S163. Gene #36: '20q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	110	89
20Q GAIN MUTATED	24	48	29
20Q GAIN WILD-TYPE	65	62	60

Figure S163. Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00503 (Fisher's exact test), Q value = 0.015

Table S164. 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 S164. Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'22q gain' versus 'CN_CNMF'

P value = 0.00871 (Fisher's exact test), Q value = 0.023

Table S165. Gene #38: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
22Q GAIN MUTATED	0	0	2	3
22Q GAIN WILD-TYPE	114	76	44	49

Figure S165. Get High-res Image Gene #38: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

'xp gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.3e-05

Table S166. Gene #39: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
XP GAIN MUTATED	6	30	39	12
XP GAIN WILD-TYPE	108	46	7	40

Figure S166. 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 = 7.3e-05

Table S167. Gene #39: 'xp gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
XP GAIN MUTATED	14	12	54
XP GAIN WILD-TYPE	68	59	65

Figure S167. Get High-res Image Gene #39: 'xp gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xp gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00296 (Fisher's exact test), Q value = 0.0099

Table S168. 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	25	11	9
XP GAIN WILD-TYPE	21	41	54	34

Figure S168. 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 = 7.3e-05

Table S169. Gene #39: 'xp gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
XP GAIN MUTATED	8	45	28	6
XP GAIN WILD-TYPE	26	51	38	86

Figure S169. 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 = 7.3e-05

Table S170. 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	55	5
XP GAIN WILD-TYPE	91	68	42

Figure S170. Get High-res Image Gene #39: 'xp gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xp gain' versus 'MIRSEQ_CNMF'

P value = 0.00978 (Fisher's exact test), Q value = 0.026

Table S171. Gene #39: 'xp gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	110	89
XP GAIN MUTATED	25	44	18
XP GAIN WILD-TYPE	64	66	71

Figure S171. Get High-res Image Gene #39: 'xp gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'xp gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00035

Table S172. Gene #39: 'xp gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	80	88
XP GAIN MUTATED	31	39	17
XP GAIN WILD-TYPE	89	41	71

Figure S172. Get High-res Image Gene #39: 'xp gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'xp gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0019 (Fisher's exact test), Q value = 0.007

Table S173. Gene #39: 'xp gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	81	71
XP GAIN MUTATED	21	30	9
XP GAIN WILD-TYPE	49	51	62

Figure S173. Get High-res Image Gene #39: 'xp gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xp gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0039 (Fisher's exact test), Q value = 0.012

Table S174. Gene #39: 'xp gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	103	75	15	29
XP GAIN MUTATED	37	10	3	10
XP GAIN WILD-TYPE	66	65	12	19

Figure S174. 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 = 7.3e-05

Table S175. Gene #40: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
XQ GAIN MUTATED	7	31	39	14
XQ GAIN WILD-TYPE	107	45	7	38

Figure S175. Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

'xq gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00013

Table S176. Gene #40: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
XQ GAIN MUTATED	14	14	55
XQ GAIN WILD-TYPE	68	57	64

Figure S176. Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00998 (Fisher's exact test), Q value = 0.026

Table S177. 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	25	13	9
XQ GAIN WILD-TYPE	21	41	52	34

Figure S177. 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 = 7.3e-05

Table S178. Gene #40: 'xq gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
XQ GAIN MUTATED	8	46	28	9
XQ GAIN WILD-TYPE	26	50	38	83

Figure S178. 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 = 0.00019

Table S179. 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	56	6
XQ GAIN WILD-TYPE	89	67	41

Figure S179. Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xq gain' versus 'MIRSEQ_CNMF'

P value = 0.0116 (Fisher's exact test), Q value = 0.03

Table S180. Gene #40: 'xq gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	110	89
XQ GAIN MUTATED	27	45	19
XQ GAIN WILD-TYPE	62	65	70

Figure S180. Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'xq gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00034 (Fisher's exact test), Q value = 0.0015

Table S181. Gene #40: 'xq gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	80	88
XQ GAIN MUTATED	34	39	18
XQ GAIN WILD-TYPE	86	41	70

Figure S181. Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'xq gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00953 (Fisher's exact test), Q value = 0.025

Table S182. Gene #40: 'xq gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	81	71
XQ GAIN MUTATED	21	30	11
XQ GAIN WILD-TYPE	49	51	60

Figure S182. Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xq gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0174 (Fisher's exact test), Q value = 0.042

Table S183. Gene #40: 'xq gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	103	75	15	29
XQ GAIN MUTATED	37	12	3	10
XQ GAIN WILD-TYPE	66	63	12	19

Figure S183. Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.3e-05

Table S184. Gene #41: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
1P LOSS MUTATED	13	0	2	15
1P LOSS WILD-TYPE	101	76	44	37

Figure S184. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 0.0313 (Fisher's exact test), Q value = 0.069

Table S185. Gene #41: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
1P LOSS MUTATED	9	13	7
1P LOSS WILD-TYPE	73	58	112

Figure S185. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 4e-04

Table S186. Gene #41: '1p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
1P LOSS MUTATED	0	4	5	21
1P LOSS WILD-TYPE	34	92	61	71

Figure S186. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00084 (Fisher's exact test), Q value = 0.0035

Table S187. 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 S187. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'1q loss' versus 'CN_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.0012

Table S188. Gene #42: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
1Q LOSS MUTATED	9	0	2	10
1Q LOSS WILD-TYPE	105	76	44	42

Figure S188. Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

'1q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00814 (Fisher's exact test), Q value = 0.022

Table S189. 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 S189. Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'1q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.013 (Fisher's exact test), Q value = 0.032

Table S190. 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 S190. Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2p loss' versus 'METHLYATION_CNMF'

P value = 0.00992 (Fisher's exact test), Q value = 0.026

Table S191. Gene #43: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
2P LOSS MUTATED	1	4	0
2P LOSS WILD-TYPE	81	67	119

Figure S191. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2p loss' versus 'RPPA_CNMF'

P value = 0.017 (Fisher's exact test), Q value = 0.041

Table S192. 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 S192. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'2p loss' versus 'MRNASEQ_CNMF'

P value = 0.0162 (Fisher's exact test), Q value = 0.039

Table S193. Gene #43: '2p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
2P LOSS MUTATED	0	0	0	5
2P LOSS WILD-TYPE	34	96	66	87

Figure S193. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0361 (Fisher's exact test), Q value = 0.076

Table S194. 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 S194. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.3e-05

Table S195. Gene #45: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
3P LOSS MUTATED	5	0	0	17
3P LOSS WILD-TYPE	109	76	46	35

Figure S195. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.3e-05

Table S196. Gene #45: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
3P LOSS MUTATED	5	15	1
3P LOSS WILD-TYPE	77	56	118

Figure S196. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0319 (Fisher's exact test), Q value = 0.07

Table S197. 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 S197. 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 = 7.3e-05

Table S198. Gene #45: '3p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
3P LOSS MUTATED	0	0	4	18
3P LOSS WILD-TYPE	34	96	62	74

Figure S198. 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 = 7.3e-05

Table S199. Gene #45: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
3P LOSS MUTATED	18	0	4
3P LOSS WILD-TYPE	100	123	43

Figure S199. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00094 (Fisher's exact test), Q value = 0.0038

Table S200. Gene #45: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	103	75	15	29
3P LOSS MUTATED	5	16	1	0
3P LOSS WILD-TYPE	98	59	14	29

Figure S200. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.3e-05

Table S201. Gene #46: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
3Q LOSS MUTATED	0	0	0	7
3Q LOSS WILD-TYPE	114	76	46	45

Figure S201. Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

'3q loss' versus 'METHLYATION_CNMF'

P value = 0.00183 (Fisher's exact test), Q value = 0.0068

Table S202. Gene #46: '3q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
3Q LOSS MUTATED	0	6	1
3Q LOSS WILD-TYPE	82	65	118

Figure S202. Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3q loss' versus 'MRNASEQ_CNMF'

P value = 0.0219 (Fisher's exact test), Q value = 0.05

Table S203. Gene #46: '3q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
3Q LOSS MUTATED	0	0	1	6
3Q LOSS WILD-TYPE	34	96	65	86

Figure S203. Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00298 (Fisher's exact test), Q value = 0.0099

Table S204. Gene #46: '3q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
3Q LOSS MUTATED	3	0	4
3Q LOSS WILD-TYPE	115	123	43

Figure S204. Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.3e-05

Table S205. Gene #47: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
4P LOSS MUTATED	6	0	0	19
4P LOSS WILD-TYPE	108	76	46	33

Figure S205. 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 = 7.3e-05

Table S206. Gene #47: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
4P LOSS MUTATED	5	18	1
4P LOSS WILD-TYPE	77	53	118

Figure S206. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00084 (Fisher's exact test), Q value = 0.0035

Table S207. 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 S207. 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 = 7.3e-05

Table S208. Gene #47: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
4P LOSS MUTATED	0	0	1	24
4P LOSS WILD-TYPE	34	96	65	68

Figure S208. 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 = 7.3e-05

Table S209. 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 S209. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0058 (Fisher's exact test), Q value = 0.017

Table S210. Gene #47: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	81	71
4P LOSS MUTATED	5	2	12
4P LOSS WILD-TYPE	65	79	59

Figure S210. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.3e-05

Table S211. Gene #47: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	103	75	15	29
4P LOSS MUTATED	4	7	8	0
4P LOSS WILD-TYPE	99	68	7	29

Figure S211. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.3e-05

Table S212. Gene #48: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
4Q LOSS MUTATED	6	0	0	20
4Q LOSS WILD-TYPE	108	76	46	32

Figure S212. 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 = 7.3e-05

Table S213. Gene #48: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
4Q LOSS MUTATED	5	19	1
4Q LOSS WILD-TYPE	77	52	118

Figure S213. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00361 (Fisher's exact test), Q value = 0.012

Table S214. 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 S214. 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 = 7.3e-05

Table S215. Gene #48: '4q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
4Q LOSS MUTATED	0	0	1	25
4Q LOSS WILD-TYPE	34	96	65	67

Figure S215. 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 = 7.3e-05

Table S216. 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 S216. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00724 (Fisher's exact test), Q value = 0.02

Table S217. Gene #48: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	81	71
4Q LOSS MUTATED	6	2	12
4Q LOSS WILD-TYPE	64	79	59

Figure S217. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'4q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 3e-04

Table S218. Gene #48: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	103	75	15	29
4Q LOSS MUTATED	4	9	7	0
4Q LOSS WILD-TYPE	99	66	8	29

Figure S218. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p loss' versus 'METHLYATION_CNMF'

P value = 0.0485 (Fisher's exact test), Q value = 0.096

Table S219. Gene #49: '5p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
5P LOSS MUTATED	2	5	1
5P LOSS WILD-TYPE	80	66	118

Figure S219. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p loss' versus 'MRNASEQ_CNMF'

P value = 0.0298 (Fisher's exact test), Q value = 0.066

Table S220. Gene #49: '5p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
5P LOSS MUTATED	1	0	1	6
5P LOSS WILD-TYPE	33	96	65	86

Figure S220. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00032 (Fisher's exact test), Q value = 0.0015

Table S221. 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	6
5P LOSS WILD-TYPE	117	122	41

Figure S221. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_CNMF'

P value = 0.0391 (Fisher's exact test), Q value = 0.082

Table S222. Gene #49: '5p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	110	89
5P LOSS MUTATED	1	1	6
5P LOSS WILD-TYPE	88	109	83

Figure S222. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'5p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0234 (Fisher's exact test), Q value = 0.053

Table S223. 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	6
5P LOSS WILD-TYPE	118	80	82

Figure S223. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0122 (Fisher's exact test), Q value = 0.031

Table S224. Gene #49: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	81	71
5P LOSS MUTATED	2	0	6
5P LOSS WILD-TYPE	68	81	65

Figure S224. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'5p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00035

Table S225. Gene #49: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	103	75	15	29
5P LOSS MUTATED	1	2	5	0
5P LOSS WILD-TYPE	102	73	10	29

Figure S225. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q loss' versus 'METHLYATION_CNMF'

P value = 0.0486 (Fisher's exact test), Q value = 0.096

Table S226. Gene #50: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
5Q LOSS MUTATED	2	5	1
5Q LOSS WILD-TYPE	80	66	118

Figure S226. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 0.0288 (Fisher's exact test), Q value = 0.064

Table S227. Gene #50: '5q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
5Q LOSS MUTATED	1	0	1	6
5Q LOSS WILD-TYPE	33	96	65	86

Figure S227. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.0014

Table S228. 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 S228. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CNMF'

P value = 0.0393 (Fisher's exact test), Q value = 0.082

Table S229. Gene #50: '5q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	110	89
5Q LOSS MUTATED	1	1	6
5Q LOSS WILD-TYPE	88	109	83

Figure S229. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0234 (Fisher's exact test), Q value = 0.053

Table S230. 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 S230. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0119 (Fisher's exact test), Q value = 0.03

Table S231. Gene #50: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	81	71
5Q LOSS MUTATED	2	0	6
5Q LOSS WILD-TYPE	68	81	65

Figure S231. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'5q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.3e-05

Table S232. Gene #50: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	103	75	15	29
5Q LOSS MUTATED	1	1	6	0
5Q LOSS WILD-TYPE	102	74	9	29

Figure S232. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.3e-05

Table S233. Gene #51: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
6P LOSS MUTATED	6	0	1	14
6P LOSS WILD-TYPE	108	76	45	38

Figure S233. Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

'6p loss' versus 'METHLYATION_CNMF'

P value = 0.0444 (Fisher's exact test), Q value = 0.089

Table S234. Gene #51: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
6P LOSS MUTATED	5	10	5
6P LOSS WILD-TYPE	77	61	114

Figure S234. Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0414 (Fisher's exact test), Q value = 0.085

Table S235. 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 S235. Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'6p loss' versus 'MRNASEQ_CNMF'

P value = 0.00635 (Fisher's exact test), Q value = 0.018

Table S236. Gene #51: '6p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
6P LOSS MUTATED	0	4	3	14
6P LOSS WILD-TYPE	34	92	63	78

Figure S236. Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.00094

Table S237. 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 S237. Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_CNMF'

P value = 0.0189 (Fisher's exact test), Q value = 0.044

Table S238. Gene #51: '6p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	110	89
6P LOSS MUTATED	2	14	5
6P LOSS WILD-TYPE	87	96	84

Figure S238. Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'6q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.3e-05

Table S239. Gene #52: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
6Q LOSS MUTATED	7	0	1	18
6Q LOSS WILD-TYPE	107	76	45	34

Figure S239. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

'6q loss' versus 'METHLYATION_CNMF'

P value = 0.00241 (Fisher's exact test), Q value = 0.0084

Table S240. Gene #52: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
6Q LOSS MUTATED	8	13	4
6Q LOSS WILD-TYPE	74	58	115

Figure S240. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0416 (Fisher's exact test), Q value = 0.085

Table S241. 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	12	1
6Q LOSS WILD-TYPE	36	61	53	42

Figure S241. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'6q loss' versus 'MRNASEQ_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.00081

Table S242. Gene #52: '6q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
6Q LOSS MUTATED	0	3	5	18
6Q LOSS WILD-TYPE	34	93	61	74

Figure S242. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00019

Table S243. Gene #52: '6q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
6Q LOSS MUTATED	11	3	12
6Q LOSS WILD-TYPE	107	120	35

Figure S243. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

P value = 0.00154 (Fisher's exact test), Q value = 0.0059

Table S244. Gene #53: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
8P LOSS MUTATED	5	2	0	9
8P LOSS WILD-TYPE	109	74	46	43

Figure S244. Get High-res Image Gene #53: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 0.00462 (Fisher's exact test), Q value = 0.014

Table S245. Gene #53: '8p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
8P LOSS MUTATED	1	2	1	12
8P LOSS WILD-TYPE	33	94	65	80

Figure S245. Get High-res Image Gene #53: '8p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00919 (Fisher's exact test), Q value = 0.025

Table S246. 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 S246. Get High-res Image Gene #53: '8p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8q loss' versus 'CN_CNMF'

P value = 0.00248 (Fisher's exact test), Q value = 0.0086

Table S247. Gene #54: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
8Q LOSS MUTATED	3	0	0	6
8Q LOSS WILD-TYPE	111	76	46	46

Figure S247. Get High-res Image Gene #54: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

'8q loss' versus 'MRNASEQ_CNMF'

P value = 0.0121 (Fisher's exact test), Q value = 0.031

Table S248. Gene #54: '8q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
8Q LOSS MUTATED	1	0	1	7
8Q LOSS WILD-TYPE	33	96	65	85

Figure S248. Get High-res Image Gene #54: '8q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00059 (Fisher's exact test), Q value = 0.0026

Table S249. 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 S249. Get High-res Image Gene #54: '8q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.3e-05

Table S250. Gene #55: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
9P LOSS MUTATED	9	0	1	23
9P LOSS WILD-TYPE	105	76	45	29

Figure S250. 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 = 7.3e-05

Table S251. Gene #55: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
9P LOSS MUTATED	11	18	1
9P LOSS WILD-TYPE	71	53	118

Figure S251. Get High-res Image Gene #55: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0159 (Fisher's exact test), Q value = 0.038

Table S252. 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 S252. 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 = 7.3e-05

Table S253. Gene #55: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
9P LOSS MUTATED	1	0	3	29
9P LOSS WILD-TYPE	33	96	63	63

Figure S253. 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 = 7.3e-05

Table S254. 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 S254. Get High-res Image Gene #55: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_CNMF'

P value = 0.00453 (Fisher's exact test), Q value = 0.014

Table S255. Gene #55: '9p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	110	89
9P LOSS MUTATED	3	14	16
9P LOSS WILD-TYPE	86	96	73

Figure S255. Get High-res Image Gene #55: '9p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'9p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00543 (Fisher's exact test), Q value = 0.016

Table S256. Gene #55: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	81	71
9P LOSS MUTATED	8	4	16
9P LOSS WILD-TYPE	62	77	55

Figure S256. Get High-res Image Gene #55: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'9p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00141 (Fisher's exact test), Q value = 0.0054

Table S257. Gene #55: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	103	75	15	29
9P LOSS MUTATED	8	17	3	0
9P LOSS WILD-TYPE	95	58	12	29

Figure S257. Get High-res Image Gene #55: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.3e-05

Table S258. Gene #56: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
9Q LOSS MUTATED	11	1	1	21
9Q LOSS WILD-TYPE	103	75	45	31

Figure S258. 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 = 7.3e-05

Table S259. Gene #56: '9q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
9Q LOSS MUTATED	12	18	1
9Q LOSS WILD-TYPE	70	53	118

Figure S259. Get High-res Image Gene #56: '9q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0046 (Fisher's exact test), Q value = 0.014

Table S260. 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 S260. 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 = 7.3e-05

Table S261. Gene #56: '9q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
9Q LOSS MUTATED	1	0	3	30
9Q LOSS WILD-TYPE	33	96	63	62

Figure S261. 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 = 7.3e-05

Table S262. 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 S262. Get High-res Image Gene #56: '9q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_CNMF'

P value = 0.00295 (Fisher's exact test), Q value = 0.0099

Table S263. Gene #56: '9q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	110	89
9Q LOSS MUTATED	3	14	17
9Q LOSS WILD-TYPE	86	96	72

Figure S263. Get High-res Image Gene #56: '9q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'9q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00107 (Fisher's exact test), Q value = 0.0042

Table S264. Gene #56: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	81	71
9Q LOSS MUTATED	8	4	18
9Q LOSS WILD-TYPE	62	77	53

Figure S264. Get High-res Image Gene #56: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'9q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.00097

Table S265. Gene #56: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	103	75	15	29
9Q LOSS MUTATED	8	16	6	0
9Q LOSS WILD-TYPE	95	59	9	29

Figure S265. Get High-res Image Gene #56: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.3e-05

Table S266. Gene #57: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
10P LOSS MUTATED	3	0	0	13
10P LOSS WILD-TYPE	111	76	46	39

Figure S266. Get High-res Image Gene #57: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 3e-04

Table S267. Gene #57: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
10P LOSS MUTATED	1	11	2
10P LOSS WILD-TYPE	81	60	117

Figure S267. Get High-res Image Gene #57: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.0021

Table S268. Gene #57: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
10P LOSS MUTATED	0	1	2	13
10P LOSS WILD-TYPE	34	95	64	79

Figure S268. Get High-res Image Gene #57: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00296 (Fisher's exact test), Q value = 0.0099

Table S269. Gene #57: '10p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
10P LOSS MUTATED	10	1	5
10P LOSS WILD-TYPE	108	122	42

Figure S269. Get High-res Image Gene #57: '10p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0186 (Fisher's exact test), Q value = 0.044

Table S270. Gene #57: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	81	71
10P LOSS MUTATED	2	1	8
10P LOSS WILD-TYPE	68	80	63

Figure S270. Get High-res Image Gene #57: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'10p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0351 (Fisher's exact test), Q value = 0.075

Table S271. Gene #57: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	103	75	15	29
10P LOSS MUTATED	2	8	1	0
10P LOSS WILD-TYPE	101	67	14	29

Figure S271. Get High-res Image Gene #57: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.3e-05

Table S272. Gene #58: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
10Q LOSS MUTATED	3	0	0	14
10Q LOSS WILD-TYPE	111	76	46	38

Figure S272. Get High-res Image Gene #58: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00067

Table S273. Gene #58: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
10Q LOSS MUTATED	2	12	2
10Q LOSS WILD-TYPE	80	59	117

Figure S273. Get High-res Image Gene #58: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0472 (Fisher's exact test), Q value = 0.094

Table S274. 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	8	0
10Q LOSS WILD-TYPE	38	62	57	43

Figure S274. Get High-res Image Gene #58: '10q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00067

Table S275. Gene #58: '10q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
10Q LOSS MUTATED	0	1	2	14
10Q LOSS WILD-TYPE	34	95	64	78

Figure S275. Get High-res Image Gene #58: '10q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00207 (Fisher's exact test), Q value = 0.0075

Table S276. Gene #58: '10q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
10Q LOSS MUTATED	12	1	4
10Q LOSS WILD-TYPE	106	122	43

Figure S276. Get High-res Image Gene #58: '10q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00154 (Fisher's exact test), Q value = 0.0059

Table S277. Gene #58: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	81	71
10Q LOSS MUTATED	2	1	10
10Q LOSS WILD-TYPE	68	80	61

Figure S277. Get High-res Image Gene #58: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'10q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00698 (Fisher's exact test), Q value = 0.019

Table S278. Gene #58: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	103	75	15	29
10Q LOSS MUTATED	2	10	1	0
10Q LOSS WILD-TYPE	101	65	14	29

Figure S278. Get High-res Image Gene #58: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00013

Table S279. Gene #59: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
11P LOSS MUTATED	5	1	0	12
11P LOSS WILD-TYPE	109	75	46	40

Figure S279. Get High-res Image Gene #59: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 0.00073 (Fisher's exact test), Q value = 0.0031

Table S280. Gene #59: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
11P LOSS MUTATED	4	11	2
11P LOSS WILD-TYPE	78	60	117

Figure S280. Get High-res Image Gene #59: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11p loss' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00035

Table S281. Gene #59: '11p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
11P LOSS MUTATED	0	1	2	15
11P LOSS WILD-TYPE	34	95	64	77

Figure S281. Get High-res Image Gene #59: '11p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'11p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00264 (Fisher's exact test), Q value = 0.0091

Table S282. Gene #59: '11p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
11P LOSS MUTATED	9	2	7
11P LOSS WILD-TYPE	109	121	40

Figure S282. Get High-res Image Gene #59: '11p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0194 (Fisher's exact test), Q value = 0.045

Table S283. Gene #59: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	81	71
11P LOSS MUTATED	4	2	10
11P LOSS WILD-TYPE	66	79	61

Figure S283. Get High-res Image Gene #59: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'11p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0139 (Fisher's exact test), Q value = 0.034

Table S284. Gene #59: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	103	75	15	29
11P LOSS MUTATED	4	9	3	0
11P LOSS WILD-TYPE	99	66	12	29

Figure S284. Get High-res Image Gene #59: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.3e-05

Table S285. Gene #60: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
11Q LOSS MUTATED	5	0	0	16
11Q LOSS WILD-TYPE	109	76	46	36

Figure S285. Get High-res Image Gene #60: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00026

Table S286. Gene #60: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
11Q LOSS MUTATED	5	14	2
11Q LOSS WILD-TYPE	77	57	117

Figure S286. Get High-res Image Gene #60: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0112 (Fisher's exact test), Q value = 0.029

Table S287. 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 S287. Get High-res Image Gene #60: '11q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'11q loss' versus 'MRNASEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00067

Table S288. Gene #60: '11q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
11Q LOSS MUTATED	1	1	3	16
11Q LOSS WILD-TYPE	33	95	63	76

Figure S288. Get High-res Image Gene #60: '11q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'11q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00209 (Fisher's exact test), Q value = 0.0075

Table S289. 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 S289. Get High-res Image Gene #60: '11q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0368 (Fisher's exact test), Q value = 0.077

Table S290. Gene #60: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	81	71
11Q LOSS MUTATED	5	3	11
11Q LOSS WILD-TYPE	65	78	60

Figure S290. Get High-res Image Gene #60: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'13q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.3e-05

Table S291. Gene #61: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
13Q LOSS MUTATED	6	0	1	17
13Q LOSS WILD-TYPE	108	76	45	35

Figure S291. Get High-res Image Gene #61: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 3e-04

Table S292. Gene #61: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
13Q LOSS MUTATED	5	15	3
13Q LOSS WILD-TYPE	77	56	116

Figure S292. Get High-res Image Gene #61: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00117 (Fisher's exact test), Q value = 0.0046

Table S293. 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 S293. 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 = 7.3e-05

Table S294. Gene #61: '13q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
13Q LOSS MUTATED	0	2	0	22
13Q LOSS WILD-TYPE	34	94	66	70

Figure S294. 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 = 7.3e-05

Table S295. 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 S295. Get High-res Image Gene #61: '13q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.011 (Fisher's exact test), Q value = 0.028

Table S296. 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 S296. Get High-res Image Gene #61: '13q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00409 (Fisher's exact test), Q value = 0.013

Table S297. Gene #61: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	81	71
13Q LOSS MUTATED	3	3	13
13Q LOSS WILD-TYPE	67	78	58

Figure S297. Get High-res Image Gene #61: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'13q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 3e-04

Table S298. Gene #61: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	103	75	15	29
13Q LOSS MUTATED	5	7	7	0
13Q LOSS WILD-TYPE	98	68	8	29

Figure S298. Get High-res Image Gene #61: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.3e-05

Table S299. Gene #62: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
14Q LOSS MUTATED	18	0	1	28
14Q LOSS WILD-TYPE	96	76	45	24

Figure S299. Get High-res Image Gene #62: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00059

Table S300. Gene #62: '14q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
14Q LOSS MUTATED	18	18	7
14Q LOSS WILD-TYPE	64	53	112

Figure S300. Get High-res Image Gene #62: '14q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'14q loss' versus 'RPPA_CNMF'

P value = 0.00558 (Fisher's exact test), Q value = 0.016

Table S301. 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 S301. Get High-res Image Gene #62: '14q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'14q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.00059

Table S302. 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 S302. 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 = 7.3e-05

Table S303. Gene #62: '14q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
14Q LOSS MUTATED	3	4	9	31
14Q LOSS WILD-TYPE	31	92	57	61

Figure S303. 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 = 7.3e-05

Table S304. 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 S304. Get High-res Image Gene #62: '14q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00391 (Fisher's exact test), Q value = 0.012

Table S305. Gene #62: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	81	71
14Q LOSS MUTATED	9	7	20
14Q LOSS WILD-TYPE	61	74	51

Figure S305. Get High-res Image Gene #62: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'14q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00306 (Fisher's exact test), Q value = 0.01

Table S306. Gene #62: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	103	75	15	29
14Q LOSS MUTATED	11	20	4	1
14Q LOSS WILD-TYPE	92	55	11	28

Figure S306. Get High-res Image Gene #62: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.3e-05

Table S307. Gene #63: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
15Q LOSS MUTATED	11	0	3	17
15Q LOSS WILD-TYPE	103	76	43	35

Figure S307. Get High-res Image Gene #63: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 0.00219 (Fisher's exact test), Q value = 0.0078

Table S308. Gene #63: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
15Q LOSS MUTATED	11	14	5
15Q LOSS WILD-TYPE	71	57	114

Figure S308. Get High-res Image Gene #63: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'15q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.029 (Fisher's exact test), Q value = 0.064

Table S309. 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 S309. Get High-res Image Gene #63: '15q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 3e-04

Table S310. Gene #63: '15q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
15Q LOSS MUTATED	1	3	6	21
15Q LOSS WILD-TYPE	33	93	60	71

Figure S310. 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 = 7.3e-05

Table S311. 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 S311. Get High-res Image Gene #63: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0023 (Fisher's exact test), Q value = 0.0081

Table S312. Gene #63: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	103	75	15	29
15Q LOSS MUTATED	10	9	6	0
15Q LOSS WILD-TYPE	93	66	9	29

Figure S312. Get High-res Image Gene #63: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p loss' versus 'CN_CNMF'

P value = 0.0429 (Fisher's exact test), Q value = 0.088

Table S313. Gene #64: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
16P LOSS MUTATED	1	0	0	3
16P LOSS WILD-TYPE	113	76	46	49

Figure S313. Get High-res Image Gene #64: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

'16p loss' versus 'METHLYATION_CNMF'

P value = 0.0333 (Fisher's exact test), Q value = 0.071

Table S314. Gene #64: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
16P LOSS MUTATED	1	3	0
16P LOSS WILD-TYPE	81	68	119

Figure S314. Get High-res Image Gene #64: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p loss' versus 'MRNASEQ_CNMF'

P value = 0.0443 (Fisher's exact test), Q value = 0.089

Table S315. Gene #64: '16p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
16P LOSS MUTATED	0	0	0	4
16P LOSS WILD-TYPE	34	96	66	88

Figure S315. Get High-res Image Gene #64: '16p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00767 (Fisher's exact test), Q value = 0.021

Table S316. 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 S316. Get High-res Image Gene #64: '16p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0097 (Fisher's exact test), Q value = 0.026

Table S317. Gene #64: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	103	75	15	29
16P LOSS MUTATED	0	2	2	0
16P LOSS WILD-TYPE	103	73	13	29

Figure S317. Get High-res Image Gene #64: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q loss' versus 'CN_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.0016

Table S318. Gene #65: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
16Q LOSS MUTATED	1	0	0	6
16Q LOSS WILD-TYPE	113	76	46	46

Figure S318. Get High-res Image Gene #65: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 0.00738 (Fisher's exact test), Q value = 0.02

Table S319. Gene #65: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
16Q LOSS MUTATED	2	5	0
16Q LOSS WILD-TYPE	80	66	119

Figure S319. Get High-res Image Gene #65: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 0.00215 (Fisher's exact test), Q value = 0.0077

Table S320. Gene #65: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
16Q LOSS MUTATED	0	0	0	7
16Q LOSS WILD-TYPE	34	96	66	85

Figure S320. Get High-res Image Gene #65: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0128 (Fisher's exact test), Q value = 0.032

Table S321. 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 S321. Get High-res Image Gene #65: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0327 (Fisher's exact test), Q value = 0.071

Table S322. Gene #65: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	81	71
16Q LOSS MUTATED	2	0	5
16Q LOSS WILD-TYPE	68	81	66

Figure S322. Get High-res Image Gene #65: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0364 (Fisher's exact test), Q value = 0.076

Table S323. Gene #65: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	103	75	15	29
16Q LOSS MUTATED	1	4	2	0
16Q LOSS WILD-TYPE	102	71	13	29

Figure S323. Get High-res Image Gene #65: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 0.00412 (Fisher's exact test), Q value = 0.013

Table S324. Gene #66: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
17P LOSS MUTATED	6	0	0	6
17P LOSS WILD-TYPE	108	76	46	46

Figure S324. Get High-res Image Gene #66: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.0015

Table S325. Gene #66: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
17P LOSS MUTATED	3	8	0
17P LOSS WILD-TYPE	79	63	119

Figure S325. Get High-res Image Gene #66: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.3e-05

Table S326. Gene #66: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
17P LOSS MUTATED	0	0	0	12
17P LOSS WILD-TYPE	34	96	66	80

Figure S326. Get High-res Image Gene #66: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.0014

Table S327. Gene #66: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
17P LOSS MUTATED	6	0	6
17P LOSS WILD-TYPE	112	123	41

Figure S327. Get High-res Image Gene #66: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00649 (Fisher's exact test), Q value = 0.018

Table S328. Gene #66: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	81	71
17P LOSS MUTATED	3	0	7
17P LOSS WILD-TYPE	67	81	64

Figure S328. Get High-res Image Gene #66: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00074 (Fisher's exact test), Q value = 0.0031

Table S329. Gene #66: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	103	75	15	29
17P LOSS MUTATED	1	5	4	0
17P LOSS WILD-TYPE	102	70	11	29

Figure S329. Get High-res Image Gene #66: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.3e-05

Table S330. Gene #67: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
18P LOSS MUTATED	17	5	1	19
18P LOSS WILD-TYPE	97	71	45	33

Figure S330. 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 = 7.3e-05

Table S331. Gene #67: '18p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
18P LOSS MUTATED	11	23	6
18P LOSS WILD-TYPE	71	48	113

Figure S331. Get High-res Image Gene #67: '18p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18p loss' versus 'RPPA_CNMF'

P value = 0.00231 (Fisher's exact test), Q value = 0.0081

Table S332. 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 S332. Get High-res Image Gene #67: '18p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'18p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00535 (Fisher's exact test), Q value = 0.016

Table S333. 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 S333. 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 = 7.3e-05

Table S334. Gene #67: '18p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
18P LOSS MUTATED	2	2	7	31
18P LOSS WILD-TYPE	32	94	59	61

Figure S334. 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 = 7.3e-05

Table S335. 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 S335. Get High-res Image Gene #67: '18p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00107 (Fisher's exact test), Q value = 0.0042

Table S336. 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 S336. Get High-res Image Gene #67: '18p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0195 (Fisher's exact test), Q value = 0.045

Table S337. Gene #67: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	81	71
18P LOSS MUTATED	10	8	19
18P LOSS WILD-TYPE	60	73	52

Figure S337. Get High-res Image Gene #67: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'18p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00039 (Fisher's exact test), Q value = 0.0017

Table S338. Gene #67: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	103	75	15	29
18P LOSS MUTATED	11	18	7	1
18P LOSS WILD-TYPE	92	57	8	28

Figure S338. Get High-res Image Gene #67: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.3e-05

Table S339. Gene #68: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
18Q LOSS MUTATED	18	4	1	22
18Q LOSS WILD-TYPE	96	72	45	30

Figure S339. 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 = 7.3e-05

Table S340. Gene #68: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
18Q LOSS MUTATED	12	26	5
18Q LOSS WILD-TYPE	70	45	114

Figure S340. Get High-res Image Gene #68: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18q loss' versus 'RPPA_CNMF'

P value = 0.00478 (Fisher's exact test), Q value = 0.014

Table S341. Gene #68: '18q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	82	56
18Q LOSS MUTATED	16	5	13
18Q LOSS WILD-TYPE	59	77	43

Figure S341. Get High-res Image Gene #68: '18q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'18q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00054

Table S342. 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	20	7
18Q LOSS WILD-TYPE	34	64	45	36

Figure S342. 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 = 7.3e-05

Table S343. Gene #68: '18q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
18Q LOSS MUTATED	2	1	7	35
18Q LOSS WILD-TYPE	32	95	59	57

Figure S343. 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 = 7.3e-05

Table S344. Gene #68: '18q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
18Q LOSS MUTATED	28	3	14
18Q LOSS WILD-TYPE	90	120	33

Figure S344. Get High-res Image Gene #68: '18q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00038 (Fisher's exact test), Q value = 0.0017

Table S345. Gene #68: '18q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	80	88
18Q LOSS MUTATED	21	3	21
18Q LOSS WILD-TYPE	99	77	67

Figure S345. Get High-res Image Gene #68: '18q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00686 (Fisher's exact test), Q value = 0.019

Table S346. Gene #68: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	81	71
18Q LOSS MUTATED	11	8	21
18Q LOSS WILD-TYPE	59	73	50

Figure S346. Get High-res Image Gene #68: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'18q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.00067

Table S347. Gene #68: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	103	75	15	29
18Q LOSS MUTATED	11	21	7	1
18Q LOSS WILD-TYPE	92	54	8	28

Figure S347. Get High-res Image Gene #68: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00045

Table S348. Gene #69: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
19P LOSS MUTATED	3	2	1	11
19P LOSS WILD-TYPE	111	74	45	41

Figure S348. Get High-res Image Gene #69: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

P value = 0.00217 (Fisher's exact test), Q value = 0.0078

Table S349. Gene #69: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
19P LOSS MUTATED	3	11	3
19P LOSS WILD-TYPE	79	60	116

Figure S349. Get High-res Image Gene #69: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19p loss' versus 'MRNASEQ_CNMF'

P value = 0.00492 (Fisher's exact test), Q value = 0.015

Table S350. Gene #69: '19p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
19P LOSS MUTATED	0	1	6	10
19P LOSS WILD-TYPE	34	95	60	82

Figure S350. Get High-res Image Gene #69: '19p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00636 (Fisher's exact test), Q value = 0.018

Table S351. Gene #69: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
19P LOSS MUTATED	13	2	2
19P LOSS WILD-TYPE	105	121	45

Figure S351. Get High-res Image Gene #69: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.013 (Fisher's exact test), Q value = 0.032

Table S352. Gene #69: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	103	75	15	29
19P LOSS MUTATED	4	11	0	0
19P LOSS WILD-TYPE	99	64	15	29

Figure S352. Get High-res Image Gene #69: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00013

Table S353. Gene #70: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
19Q LOSS MUTATED	1	2	1	12
19Q LOSS WILD-TYPE	113	74	45	40

Figure S353. Get High-res Image Gene #70: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

P value = 0.00467 (Fisher's exact test), Q value = 0.014

Table S354. Gene #70: '19q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
19Q LOSS MUTATED	3	10	3
19Q LOSS WILD-TYPE	79	61	116

Figure S354. Get High-res Image Gene #70: '19q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19q loss' versus 'MRNASEQ_CNMF'

P value = 0.0049 (Fisher's exact test), Q value = 0.015

Table S355. Gene #70: '19q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
19Q LOSS MUTATED	0	1	4	11
19Q LOSS WILD-TYPE	34	95	62	81

Figure S355. Get High-res Image Gene #70: '19q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0226 (Fisher's exact test), Q value = 0.051

Table S356. Gene #70: '19q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	123	47
19Q LOSS MUTATED	11	2	3
19Q LOSS WILD-TYPE	107	121	44

Figure S356. Get High-res Image Gene #70: '19q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'21q loss' versus 'CN_CNMF'

P value = 0.00062 (Fisher's exact test), Q value = 0.0027

Table S357. Gene #71: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
21Q LOSS MUTATED	12	6	7	18
21Q LOSS WILD-TYPE	102	70	39	34

Figure S357. Get High-res Image Gene #71: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.3e-05

Table S358. Gene #72: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
22Q LOSS MUTATED	22	5	2	31
22Q LOSS WILD-TYPE	92	71	44	21

Figure S358. 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 = 7.3e-05

Table S359. Gene #72: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
22Q LOSS MUTATED	13	34	10
22Q LOSS WILD-TYPE	69	37	109

Figure S359. Get High-res Image Gene #72: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.014 (Fisher's exact test), Q value = 0.034

Table S360. 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 S360. 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 = 7.3e-05

Table S361. Gene #72: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
22Q LOSS MUTATED	0	6	12	42
22Q LOSS WILD-TYPE	34	90	54	50

Figure S361. 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 = 7.3e-05

Table S362. 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 S362. Get High-res Image Gene #72: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00519 (Fisher's exact test), Q value = 0.015

Table S363. Gene #72: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	103	75	15	29
22Q LOSS MUTATED	20	22	6	1
22Q LOSS WILD-TYPE	83	53	9	28

Figure S363. Get High-res Image Gene #72: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xp loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.3e-05

Table S364. Gene #73: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
XP LOSS MUTATED	10	2	2	20
XP LOSS WILD-TYPE	104	74	44	32

Figure S364. 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 = 7.3e-05

Table S365. Gene #73: 'xp loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
XP LOSS MUTATED	8	19	4
XP LOSS WILD-TYPE	74	52	115

Figure S365. Get High-res Image Gene #73: 'xp loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xp loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00321 (Fisher's exact test), Q value = 0.011

Table S366. 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	6	14	1
XP LOSS WILD-TYPE	38	60	51	42

Figure S366. 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 = 7.3e-05

Table S367. Gene #73: 'xp loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
XP LOSS MUTATED	0	3	4	27
XP LOSS WILD-TYPE	34	93	62	65

Figure S367. Get High-res Image Gene #73: 'xp loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xp loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 4e-04

Table S368. 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	4	11
XP LOSS WILD-TYPE	99	119	36

Figure S368. Get High-res Image Gene #73: 'xp loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0179 (Fisher's exact test), Q value = 0.042

Table S369. Gene #73: 'xp loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	81	71
XP LOSS MUTATED	8	4	14
XP LOSS WILD-TYPE	62	77	57

Figure S369. Get High-res Image Gene #73: 'xp loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xp loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00077 (Fisher's exact test), Q value = 0.0032

Table S370. Gene #73: 'xp loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	103	75	15	29
XP LOSS MUTATED	5	17	3	1
XP LOSS WILD-TYPE	98	58	12	28

Figure S370. Get High-res Image Gene #73: 'xp loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.3e-05

Table S371. Gene #74: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	114	76	46	52
XQ LOSS MUTATED	9	1	2	18
XQ LOSS WILD-TYPE	105	75	44	34

Figure S371. Get High-res Image Gene #74: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00013

Table S372. Gene #74: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	71	119
XQ LOSS MUTATED	8	17	3
XQ LOSS WILD-TYPE	74	54	116

Figure S372. Get High-res Image Gene #74: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0141 (Fisher's exact test), Q value = 0.034

Table S373. 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	6	12	1
XQ LOSS WILD-TYPE	38	60	53	42

Figure S373. 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 = 7.3e-05

Table S374. Gene #74: 'xq loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	96	66	92
XQ LOSS MUTATED	0	2	4	24
XQ LOSS WILD-TYPE	34	94	62	68

Figure S374. Get High-res Image Gene #74: 'xq loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xq loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 5e-04

Table S375. 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	3	10
XQ LOSS WILD-TYPE	101	120	37

Figure S375. Get High-res Image Gene #74: 'xq loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0032 (Fisher's exact test), Q value = 0.011

Table S376. Gene #74: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	103	75	15	29
XQ LOSS MUTATED	5	15	3	1
XQ LOSS WILD-TYPE	98	60	12	28

Figure S376. 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/19781623/transformed.cor.cli.txt
Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/KIRP-TP/20139337/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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