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

Kidney Renal Papillary Cell Carcinoma (Primary solid tumor)

17 October 2014 | analyses__2014_10_17

Maintainer Information

Citation Information

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

Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1D799BT

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 72 arm-level events and 10 molecular subtypes across 288 patients, 157 significant findings detected with P value < 0.05 and Q value < 0.25.

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

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 72 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, 157 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 (0.00708)	1e-05 (0.00708)	0.00313 (1.00)	2e-05 (0.0122)	1e-05 (0.00708)	1e-05 (0.00708)	0.0489 (1.00)	1e-05 (0.00708)	8e-05 (0.0471)	1e-05 (0.00708)
7q gain	173 (60%)	115	1e-05 (0.00708)	1e-05 (0.00708)	0.00659 (1.00)	2e-05 (0.0122)	1e-05 (0.00708)	1e-05 (0.00708)	0.0705 (1.00)	1e-05 (0.00708)	0.00012 (0.0695)	2e-05 (0.0122)
17p gain	174 (60%)	114	1e-05 (0.00708)	1e-05 (0.00708)	0.00215 (1.00)	1e-05 (0.00708)	1e-05 (0.00708)	1e-05 (0.00708)	0.00389 (1.00)	2e-05 (0.0122)	1e-05 (0.00708)	1e-05 (0.00708)
17q gain	191 (66%)	97	1e-05 (0.00708)	1e-05 (0.00708)	0.0241 (1.00)	2e-05 (0.0122)	1e-05 (0.00708)	1e-05 (0.00708)	0.0345 (1.00)	4e-05 (0.0239)	0.00022 (0.125)	5e-05 (0.0298)
3p gain	74 (26%)	214	1e-05 (0.00708)	0.00034 (0.189)	0.2 (1.00)	0.00011 (0.0641)	1e-05 (0.00708)	2e-05 (0.0122)	0.0409 (1.00)	7e-05 (0.0413)	0.0906 (1.00)	0.0158 (1.00)
16q gain	148 (51%)	140	1e-05 (0.00708)	0.0422 (1.00)	0.906 (1.00)	0.0201 (1.00)	1e-05 (0.00708)	1e-05 (0.00708)	1e-05 (0.00708)	1e-05 (0.00708)	0.00223 (1.00)	5e-05 (0.0298)
13q loss	24 (8%)	264	1e-05 (0.00708)	1e-05 (0.00708)	0.583 (1.00)	5e-05 (0.0298)	1e-05 (0.00708)	1e-05 (0.00708)	0.0427 (1.00)	0.00726 (1.00)	0.00395 (1.00)	6e-05 (0.0355)
18q loss	45 (16%)	243	1e-05 (0.00708)	1e-05 (0.00708)	0.0662 (1.00)	8e-05 (0.0471)	1e-05 (0.00708)	1e-05 (0.00708)	0.127 (1.00)	0.00081 (0.44)	0.00718 (1.00)	0.00032 (0.179)
16p gain	153 (53%)	135	1e-05 (0.00708)	0.0851 (1.00)	0.847 (1.00)	0.0211 (1.00)	1e-05 (0.00708)	1e-05 (0.00708)	0.00058 (0.318)	1e-05 (0.00708)	0.0098 (1.00)	0.00011 (0.0641)
xq gain	91 (32%)	197	1e-05 (0.00708)	0.00025 (0.141)	0.283 (1.00)	0.0686 (1.00)	1e-05 (0.00708)	1e-05 (0.00708)	0.011 (1.00)	1e-05 (0.00708)	0.011 (1.00)	0.00394 (1.00)
4p loss	25 (9%)	263	1e-05 (0.00708)	1e-05 (0.00708)	0.307 (1.00)	0.00092 (0.498)	1e-05 (0.00708)	1e-05 (0.00708)	0.261 (1.00)	0.109 (1.00)	0.00635 (1.00)	1e-05 (0.00708)
4q loss	26 (9%)	262	1e-05 (0.00708)	1e-05 (0.00708)	0.51 (1.00)	0.0027 (1.00)	1e-05 (0.00708)	3e-05 (0.0181)	0.379 (1.00)	0.17 (1.00)	0.0065 (1.00)	6e-05 (0.0355)
9q loss	34 (12%)	254	1e-05 (0.00708)	1e-05 (0.00708)	0.0806 (1.00)	0.0158 (1.00)	1e-05 (0.00708)	1e-05 (0.00708)	0.00401 (1.00)	0.134 (1.00)	0.00124 (0.661)	0.00011 (0.0641)
1q gain	17 (6%)	271	1e-05 (0.00708)	1e-05 (0.00708)	0.932 (1.00)	0.0619 (1.00)	1e-05 (0.00708)	0.00191 (0.993)	0.517 (1.00)	0.00025 (0.141)	0.00635 (1.00)	0.0114 (1.00)
3q gain	94 (33%)	194	1e-05 (0.00708)	0.0123 (1.00)	0.232 (1.00)	0.0169 (1.00)	1e-05 (0.00708)	0.00014 (0.0805)	0.00943 (1.00)	0.00016 (0.0915)	0.521 (1.00)	0.0133 (1.00)
3p loss	22 (8%)	266	1e-05 (0.00708)	3e-05 (0.0181)	0.269 (1.00)	0.00536 (1.00)	1e-05 (0.00708)	0.0001 (0.0586)	0.431 (1.00)	0.0272 (1.00)	0.0471 (1.00)	0.0151 (1.00)
9p loss	33 (11%)	255	1e-05 (0.00708)	2e-05 (0.0122)	0.481 (1.00)	0.0115 (1.00)	1e-05 (0.00708)	1e-05 (0.00708)	0.00649 (1.00)	0.252 (1.00)	0.00594 (1.00)	0.00067 (0.365)
14q loss	47 (16%)	241	1e-05 (0.00708)	0.00218 (1.00)	0.0086 (1.00)	0.00028 (0.157)	1e-05 (0.00708)	1e-05 (0.00708)	0.207 (1.00)	0.775 (1.00)	0.0041 (1.00)	0.00644 (1.00)
18p loss	42 (15%)	246	1e-05 (0.00708)	1e-05 (0.00708)	0.0219 (1.00)	0.00169 (0.891)	1e-05 (0.00708)	1e-05 (0.00708)	0.234 (1.00)	0.00105 (0.565)	0.0201 (1.00)	0.00063 (0.345)
22q loss	60 (21%)	228	1e-05 (0.00708)	1e-05 (0.00708)	0.781 (1.00)	0.00874 (1.00)	1e-05 (0.00708)	1e-05 (0.00708)	0.983 (1.00)	0.451 (1.00)	0.0555 (1.00)	0.0109 (1.00)
6q loss	26 (9%)	262	1e-05 (0.00708)	0.0161 (1.00)	0.955 (1.00)	0.204 (1.00)	0.00015 (0.0861)	0.00011 (0.0641)	0.307 (1.00)	0.278 (1.00)	0.101 (1.00)	0.0925 (1.00)
10p loss	16 (6%)	272	1e-05 (0.00708)	0.00012 (0.0695)	0.654 (1.00)	0.0666 (1.00)	0.00017 (0.0971)	0.00264 (1.00)	0.398 (1.00)	0.915 (1.00)	0.019 (1.00)	0.00615 (1.00)
11p loss	18 (6%)	270	1e-05 (0.00708)	0.00043 (0.237)	0.692 (1.00)	0.625 (1.00)	0.00021 (0.119)	0.00232 (1.00)	0.296 (1.00)	0.0638 (1.00)	0.0192 (1.00)	0.00674 (1.00)
15q loss	31 (11%)	257	1e-05 (0.00708)	0.00056 (0.307)	0.115 (1.00)	0.00604 (1.00)	3e-05 (0.0181)	1e-05 (0.00708)	0.0938 (1.00)	0.636 (1.00)	0.0668 (1.00)	0.00267 (1.00)
16q loss	7 (2%)	281	0.00041 (0.227)	0.00025 (0.141)	1 (1.00)	0.327 (1.00)	0.00036 (0.2)	0.0951 (1.00)	0.404 (1.00)	0.235 (1.00)	0.0327 (1.00)	0.0529 (1.00)
xq loss	30 (10%)	258	1e-05 (0.00708)	9e-05 (0.0528)	0.596 (1.00)	0.0099 (1.00)	1e-05 (0.00708)	0.00101 (0.544)	0.271 (1.00)	0.45 (1.00)	0.0494 (1.00)	0.0211 (1.00)
1p gain	9 (3%)	279	1e-05 (0.00708)	0.0001 (0.0586)	0.611 (1.00)	0.0822 (1.00)	0.00066 (0.36)	0.0257 (1.00)	0.479 (1.00)	0.0839 (1.00)	0.0471 (1.00)	0.0288 (1.00)
1p loss	30 (10%)	258	1e-05 (0.00708)	0.0696 (1.00)	0.478 (1.00)	0.168 (1.00)	0.00026 (0.146)	0.0016 (0.848)	0.355 (1.00)	0.177 (1.00)	0.836 (1.00)	0.0883 (1.00)
5p loss	8 (3%)	280	0.17 (1.00)	0.0124 (1.00)	0.442 (1.00)	0.0153 (1.00)	0.00867 (1.00)	0.00023 (0.13)	0.0723 (1.00)	0.0394 (1.00)	0.0129 (1.00)	0.00017 (0.0971)
5q loss	8 (3%)	280	0.169 (1.00)	0.0121 (1.00)	0.875 (1.00)	0.0154 (1.00)	0.00876 (1.00)	0.00037 (0.205)	0.0717 (1.00)	0.0398 (1.00)	0.0123 (1.00)	1e-05 (0.00708)
6p loss	21 (7%)	267	1e-05 (0.00708)	0.0937 (1.00)	0.549 (1.00)	0.316 (1.00)	0.00601 (1.00)	0.00013 (0.0749)	0.0195 (1.00)	0.0516 (1.00)	0.472 (1.00)	0.11 (1.00)
10q loss	17 (6%)	271	1e-05 (0.00708)	0.00094 (0.508)	0.516 (1.00)	0.0119 (1.00)	3e-05 (0.0181)	0.00172 (0.901)	0.0835 (1.00)	0.862 (1.00)	0.002 (1.00)	0.00107 (0.575)
11q loss	21 (7%)	267	1e-05 (0.00708)	0.00055 (0.302)	0.161 (1.00)	0.119 (1.00)	0.00012 (0.0695)	0.00135 (0.718)	0.659 (1.00)	0.101 (1.00)	0.0364 (1.00)	0.0397 (1.00)
17p loss	12 (4%)	276	0.0038 (1.00)	5e-05 (0.0298)	0.485 (1.00)	0.11 (1.00)	0.00021 (0.119)	0.00307 (1.00)	0.536 (1.00)	0.267 (1.00)	0.00652 (1.00)	0.00117 (0.625)
2p gain	42 (15%)	246	1e-05 (0.00708)	0.0207 (1.00)	0.822 (1.00)	0.1 (1.00)	0.617 (1.00)	0.064 (1.00)	0.123 (1.00)	0.0729 (1.00)	0.783 (1.00)	0.169 (1.00)
2q gain	47 (16%)	241	1e-05 (0.00708)	0.0298 (1.00)	0.971 (1.00)	0.0164 (1.00)	0.729 (1.00)	0.0278 (1.00)	0.219 (1.00)	0.0539 (1.00)	0.418 (1.00)	0.407 (1.00)
5p gain	33 (11%)	255	1e-05 (0.00708)	0.00217 (1.00)	0.649 (1.00)	0.447 (1.00)	0.00751 (1.00)	0.00242 (1.00)	0.572 (1.00)	0.118 (1.00)	0.31 (1.00)	0.256 (1.00)
5q gain	31 (11%)	257	1e-05 (0.00708)	0.00084 (0.455)	0.574 (1.00)	0.281 (1.00)	0.00162 (0.857)	0.00074 (0.403)	0.314 (1.00)	0.154 (1.00)	0.454 (1.00)	0.374 (1.00)
8q gain	25 (9%)	263	0.126 (1.00)	3e-05 (0.0181)	0.227 (1.00)	0.652 (1.00)	0.0179 (1.00)	0.146 (1.00)	0.151 (1.00)	0.11 (1.00)	0.0467 (1.00)	0.135 (1.00)
11p gain	11 (4%)	277	0.00033 (0.184)	0.0153 (1.00)	0.911 (1.00)	0.0244 (1.00)	0.121 (1.00)	0.00288 (1.00)	0.928 (1.00)	0.95 (1.00)	0.819 (1.00)	0.224 (1.00)
11q gain	10 (3%)	278	1e-05 (0.00708)	0.00242 (1.00)	0.754 (1.00)	0.0423 (1.00)	0.0343 (1.00)	0.0262 (1.00)	0.849 (1.00)	1 (1.00)	0.818 (1.00)	0.226 (1.00)
15q gain	5 (2%)	283	0.00017 (0.0971)	0.0263 (1.00)	0.207 (1.00)	0.383 (1.00)	0.532 (1.00)	0.376 (1.00)	0.448 (1.00)	0.77 (1.00)
20p gain	99 (34%)	189	3e-05 (0.0181)	0.097 (1.00)	0.0167 (1.00)	0.0061 (1.00)	0.00726 (1.00)	0.00181 (0.943)	0.0122 (1.00)	0.00359 (1.00)	0.178 (1.00)	0.0611 (1.00)
20q gain	101 (35%)	187	0.00015 (0.0861)	0.113 (1.00)	0.0272 (1.00)	0.0108 (1.00)	0.0289 (1.00)	0.00449 (1.00)	0.019 (1.00)	0.00523 (1.00)	0.339 (1.00)	0.0434 (1.00)
1q loss	21 (7%)	267	0.0003 (0.168)	0.619 (1.00)	1 (1.00)	0.0658 (1.00)	0.224 (1.00)	0.0148 (1.00)	0.293 (1.00)	0.0849 (1.00)	0.57 (1.00)	0.199 (1.00)
3q loss	7 (2%)	281	2e-05 (0.0122)	0.0257 (1.00)	0.37 (1.00)	0.0882 (1.00)	0.00647 (1.00)	0.0268 (1.00)	0.402 (1.00)	0.839 (1.00)	0.396 (1.00)	0.357 (1.00)
19p loss	17 (6%)	271	0.0001 (0.0586)	0.00593 (1.00)	0.917 (1.00)	0.106 (1.00)	0.0221 (1.00)	0.00426 (1.00)	0.226 (1.00)	0.103 (1.00)	0.0891 (1.00)	0.0578 (1.00)
19q loss	16 (6%)	272	1e-05 (0.00708)	0.0158 (1.00)	0.62 (1.00)	0.0357 (1.00)	0.0092 (1.00)	0.0139 (1.00)	0.401 (1.00)	0.15 (1.00)	0.0913 (1.00)	0.278 (1.00)
4p gain	10 (3%)	278	0.245 (1.00)	0.552 (1.00)	0.791 (1.00)	0.366 (1.00)	0.192 (1.00)	0.572 (1.00)	0.614 (1.00)	0.921 (1.00)	0.835 (1.00)	0.949 (1.00)
4q gain	9 (3%)	279	0.518 (1.00)	0.552 (1.00)	0.791 (1.00)	0.366 (1.00)	0.361 (1.00)	0.65 (1.00)	0.278 (1.00)	0.856 (1.00)	0.493 (1.00)	1 (1.00)
6p gain	10 (3%)	278	0.0482 (1.00)	0.0122 (1.00)	0.0716 (1.00)	0.342 (1.00)	0.00745 (1.00)	0.284 (1.00)	0.166 (1.00)	0.251 (1.00)	0.102 (1.00)	0.0598 (1.00)
6q gain	8 (3%)	280	0.0221 (1.00)	0.00793 (1.00)	0.543 (1.00)	0.29 (1.00)	0.0478 (1.00)	0.484 (1.00)	0.226 (1.00)	0.649 (1.00)	0.127 (1.00)	0.0864 (1.00)
8p gain	20 (7%)	268	0.748 (1.00)	0.00331 (1.00)	0.163 (1.00)	0.584 (1.00)	0.111 (1.00)	0.137 (1.00)	0.455 (1.00)	0.539 (1.00)	0.405 (1.00)	0.241 (1.00)
9p gain	3 (1%)	285	0.876 (1.00)				0.365 (1.00)	0.204 (1.00)	0.41 (1.00)	0.372 (1.00)	0.298 (1.00)	0.0144 (1.00)
10p gain	9 (3%)	279	0.00107 (0.575)	0.0702 (1.00)	1 (1.00)	0.43 (1.00)	0.0582 (1.00)	0.306 (1.00)	0.143 (1.00)	0.684 (1.00)	0.892 (1.00)	0.186 (1.00)
10q gain	9 (3%)	279	0.00111 (0.594)	0.0705 (1.00)	1 (1.00)	0.43 (1.00)	0.058 (1.00)	0.307 (1.00)	0.141 (1.00)	0.685 (1.00)	0.894 (1.00)	0.186 (1.00)
12p gain	112 (39%)	176	0.00522 (1.00)	0.153 (1.00)	0.0242 (1.00)	0.18 (1.00)	0.0152 (1.00)	0.00249 (1.00)	0.0922 (1.00)	0.0167 (1.00)	0.662 (1.00)	0.0704 (1.00)
12q gain	112 (39%)	176	0.00567 (1.00)	0.151 (1.00)	0.0241 (1.00)	0.181 (1.00)	0.0151 (1.00)	0.00209 (1.00)	0.0917 (1.00)	0.0169 (1.00)	0.664 (1.00)	0.0689 (1.00)
13q gain	28 (10%)	260	0.223 (1.00)	0.854 (1.00)	1 (1.00)	0.608 (1.00)	0.14 (1.00)	0.785 (1.00)	0.879 (1.00)	0.462 (1.00)	0.317 (1.00)	0.523 (1.00)
14q gain	3 (1%)	285	0.242 (1.00)	0.0163 (1.00)	0.45 (1.00)	0.852 (1.00)	0.0554 (1.00)	0.203 (1.00)	1 (1.00)	0.37 (1.00)	0.3 (1.00)	0.0137 (1.00)
18p gain	12 (4%)	276	0.00247 (1.00)	0.244 (1.00)	0.526 (1.00)	0.134 (1.00)	0.655 (1.00)	0.475 (1.00)	0.19 (1.00)	0.512 (1.00)	0.465 (1.00)	0.604 (1.00)
18q gain	9 (3%)	279	0.00316 (1.00)	0.107 (1.00)	0.262 (1.00)	0.0576 (1.00)	0.694 (1.00)	0.0729 (1.00)	0.4 (1.00)	0.447 (1.00)	0.322 (1.00)	0.0837 (1.00)
19p gain	4 (1%)	284	0.00168 (0.887)	0.282 (1.00)	0.277 (1.00)	0.243 (1.00)	0.136 (1.00)	0.236 (1.00)	1 (1.00)	0.479 (1.00)	1 (1.00)	0.339 (1.00)
19q gain	4 (1%)	284	0.00175 (0.915)	0.281 (1.00)	0.279 (1.00)	0.244 (1.00)	0.139 (1.00)	0.234 (1.00)	1 (1.00)	0.476 (1.00)	1 (1.00)	0.337 (1.00)
21q gain	19 (7%)	269	0.516 (1.00)	0.403 (1.00)	0.78 (1.00)	0.452 (1.00)	0.222 (1.00)	0.307 (1.00)	0.149 (1.00)	0.218 (1.00)	0.507 (1.00)	0.141 (1.00)
22q gain	5 (2%)	283	0.00898 (1.00)	1 (1.00)	1 (1.00)	0.311 (1.00)	1 (1.00)	0.681 (1.00)	0.451 (1.00)	0.299 (1.00)	0.868 (1.00)	1 (1.00)
2p loss	5 (2%)	283	0.28 (1.00)	0.0169 (1.00)	0.178 (1.00)	0.567 (1.00)	0.0496 (1.00)	0.209 (1.00)	0.237 (1.00)	0.87 (1.00)
2q loss	3 (1%)	285	0.66 (1.00)				0.366 (1.00)	0.203 (1.00)	0.529 (1.00)	1 (1.00)
8p loss	16 (6%)	272	0.0017 (0.894)	0.383 (1.00)	0.233 (1.00)	0.177 (1.00)	0.0017 (0.894)	0.00334 (1.00)	0.899 (1.00)	0.756 (1.00)	0.37 (1.00)	0.315 (1.00)
8q loss	9 (3%)	279	0.00265 (1.00)	0.766 (1.00)	0.546 (1.00)	0.0136 (1.00)	0.00156 (0.828)	0.00175 (0.915)	0.912 (1.00)	0.784 (1.00)	0.686 (1.00)	0.553 (1.00)
16p loss	4 (1%)	284	0.0423 (1.00)	0.00428 (1.00)	1 (1.00)	0.487 (1.00)	0.0169 (1.00)	0.0332 (1.00)	0.84 (1.00)	0.204 (1.00)	0.114 (1.00)	0.0125 (1.00)
21q loss	43 (15%)	245	0.00047 (0.259)	0.354 (1.00)	0.247 (1.00)	0.268 (1.00)	0.16 (1.00)	0.236 (1.00)	0.623 (1.00)	0.222 (1.00)	0.808 (1.00)	0.0859 (1.00)

'1p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

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 = 1e-04 (Fisher's exact test), Q value = 0.059

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	58	103
1P GAIN MUTATED	1	7	0
1P GAIN WILD-TYPE	62	51	103

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

'1q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S3. 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 S3. 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 = 0.0071

Table S4. Gene #2: '1q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	58	103
1Q GAIN MUTATED	1	13	1
1Q GAIN WILD-TYPE	62	45	102

Figure S4. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S5. Gene #2: '1q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	114	95
1Q GAIN MUTATED	4	0	13
1Q GAIN WILD-TYPE	74	114	82

Figure S5. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'1q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00025 (Fisher's exact test), Q value = 0.14

Table S6. Gene #2: '1q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	66	81	86
1Q GAIN MUTATED	8	0	1	8
1Q GAIN WILD-TYPE	47	66	80	78

Figure S6. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

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

'2q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

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

'3p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S9. 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 S9. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'

'3p gain' versus 'METHLYATION_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.19

Table S10. Gene #5: '3p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	58	103
3P GAIN MUTATED	18	5	37
3P GAIN WILD-TYPE	45	53	66

Figure S10. 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 = 0.064

Table S11. Gene #5: '3p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	17	22	29	22	27	39	25	25
3P GAIN MUTATED	11	9	5	4	1	7	10	4
3P GAIN WILD-TYPE	6	13	24	18	26	32	15	21

Figure S11. 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 = 0.0071

Table S12. Gene #5: '3p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	114	95
3P GAIN MUTATED	31	38	5
3P GAIN WILD-TYPE	47	76	90

Figure S12. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S13. Gene #5: '3p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	125	72	44	46
3P GAIN MUTATED	28	35	6	5
3P GAIN WILD-TYPE	97	37	38	41

Figure S13. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.041

Table S14. Gene #5: '3p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	66	81	86
3P GAIN MUTATED	10	18	35	11
3P GAIN WILD-TYPE	45	48	46	75

Figure S14. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S15. 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 S15. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

'3q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S16. Gene #6: '3q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	114	95
3Q GAIN MUTATED	38	46	10
3Q GAIN WILD-TYPE	40	68	85

Figure S16. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.08

Table S17. Gene #6: '3q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	125	72	44	46
3Q GAIN MUTATED	36	39	11	8
3Q GAIN WILD-TYPE	89	33	33	38

Figure S17. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.092

Table S18. Gene #6: '3q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	66	81	86
3Q GAIN MUTATED	18	19	41	16
3Q GAIN WILD-TYPE	37	47	40	70

Figure S18. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S19. 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 S19. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S20. 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 S20. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S21. 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 S21. 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 = 0.0071

Table S22. Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	58	103
7P GAIN MUTATED	34	17	84
7P GAIN WILD-TYPE	29	41	19

Figure S22. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p gain' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S23. Gene #13: '7p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	17	22	29	22	27	39	25	25
7P GAIN MUTATED	14	17	27	9	10	18	18	13
7P GAIN WILD-TYPE	3	5	2	13	17	21	7	12

Figure S23. 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 = 0.0071

Table S24. Gene #13: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	114	95
7P GAIN MUTATED	50	95	26
7P GAIN WILD-TYPE	28	19	69

Figure S24. 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 = 0.0071

Table S25. Gene #13: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	125	72	44	46
7P GAIN MUTATED	58	68	30	15
7P GAIN WILD-TYPE	67	4	14	31

Figure S25. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S26. Gene #13: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	66	81	86
7P GAIN MUTATED	21	39	67	45
7P GAIN WILD-TYPE	34	27	14	41

Figure S26. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.047

Table S27. Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	81	71
7P GAIN MUTATED	32	62	34
7P GAIN WILD-TYPE	37	19	37

Figure S27. 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 = 0.0071

Table S28. Gene #13: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	77	16	30
7P GAIN MUTATED	65	33	4	26
7P GAIN WILD-TYPE	33	44	12	4

Figure S28. 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 = 0.0071

Table S29. 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 S29. 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 = 0.0071

Table S30. Gene #14: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	58	103
7Q GAIN MUTATED	34	18	84
7Q GAIN WILD-TYPE	29	40	19

Figure S30. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q gain' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S31. Gene #14: '7q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	17	22	29	22	27	39	25	25
7Q GAIN MUTATED	14	17	27	9	11	18	18	13
7Q GAIN WILD-TYPE	3	5	2	13	16	21	7	12

Figure S31. 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 = 0.0071

Table S32. Gene #14: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	114	95
7Q GAIN MUTATED	50	95	27
7Q GAIN WILD-TYPE	28	19	68

Figure S32. 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 = 0.0071

Table S33. Gene #14: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	125	72	44	46
7Q GAIN MUTATED	59	68	30	15
7Q GAIN WILD-TYPE	66	4	14	31

Figure S33. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S34. Gene #14: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	66	81	86
7Q GAIN MUTATED	22	39	67	45
7Q GAIN WILD-TYPE	33	27	14	41

Figure S34. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.069

Table S35. Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	81	71
7Q GAIN MUTATED	33	62	34
7Q GAIN WILD-TYPE	36	19	37

Figure S35. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'7q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S36. Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	77	16	30
7Q GAIN MUTATED	65	34	4	26
7Q GAIN WILD-TYPE	33	43	12	4

Figure S36. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q gain' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.018

Table S37. Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	58	103
8Q GAIN MUTATED	2	14	4
8Q GAIN WILD-TYPE	61	44	99

Figure S37. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11p gain' versus 'CN_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.18

Table S38. 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 S38. Get High-res Image Gene #20: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

'11q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S39. 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 S39. Get High-res Image Gene #21: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

'15q gain' versus 'CN_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.097

Table S40. 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 S40. Get High-res Image Gene #26: '15q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S41. 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 S41. Get High-res Image Gene #27: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S42. Gene #27: '16p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	114	95
16P GAIN MUTATED	59	64	29
16P GAIN WILD-TYPE	19	50	66

Figure S42. Get High-res Image Gene #27: '16p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S43. Gene #27: '16p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	125	72	44	46
16P GAIN MUTATED	74	55	13	10
16P GAIN WILD-TYPE	51	17	31	36

Figure S43. Get High-res Image Gene #27: '16p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S44. Gene #27: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	66	81	86
16P GAIN MUTATED	24	39	61	29
16P GAIN WILD-TYPE	31	27	20	57

Figure S44. Get High-res Image Gene #27: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.064

Table S45. Gene #27: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	77	16	30
16P GAIN MUTATED	67	30	5	12
16P GAIN WILD-TYPE	31	47	11	18

Figure S45. 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 = 0.0071

Table S46. 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 S46. Get High-res Image Gene #28: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S47. Gene #28: '16q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	114	95
16Q GAIN MUTATED	58	63	26
16Q GAIN WILD-TYPE	20	51	69

Figure S47. Get High-res Image Gene #28: '16q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S48. Gene #28: '16q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	125	72	44	46
16Q GAIN MUTATED	70	55	12	10
16Q GAIN WILD-TYPE	55	17	32	36

Figure S48. Get High-res Image Gene #28: '16q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S49. Gene #28: '16q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	103	96
16Q GAIN MUTATED	49	67	32
16Q GAIN WILD-TYPE	40	36	64

Figure S49. 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 = 0.0071

Table S50. Gene #28: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	66	81	86
16Q GAIN MUTATED	19	40	61	28
16Q GAIN WILD-TYPE	36	26	20	58

Figure S50. Get High-res Image Gene #28: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.03

Table S51. Gene #28: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	77	16	30
16Q GAIN MUTATED	67	26	5	11
16Q GAIN WILD-TYPE	31	51	11	19

Figure S51. 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 = 0.0071

Table S52. 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 S52. 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 = 0.0071

Table S53. Gene #29: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	58	103
17P GAIN MUTATED	32	19	88
17P GAIN WILD-TYPE	31	39	15

Figure S53. Get High-res Image Gene #29: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S54. Gene #29: '17p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	17	22	29	22	27	39	25	25
17P GAIN MUTATED	14	17	26	8	10	17	21	14
17P GAIN WILD-TYPE	3	5	3	14	17	22	4	11

Figure S54. 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 = 0.0071

Table S55. Gene #29: '17p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	114	95
17P GAIN MUTATED	49	100	24
17P GAIN WILD-TYPE	29	14	71

Figure S55. 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 = 0.0071

Table S56. Gene #29: '17p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	125	72	44	46
17P GAIN MUTATED	61	67	35	10
17P GAIN WILD-TYPE	64	5	9	36

Figure S56. Get High-res Image Gene #29: '17p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S57. Gene #29: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	66	81	86
17P GAIN MUTATED	20	40	67	47
17P GAIN WILD-TYPE	35	26	14	39

Figure S57. 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 = 0.0071

Table S58. Gene #29: '17p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	81	71
17P GAIN MUTATED	32	66	30
17P GAIN WILD-TYPE	37	15	41

Figure S58. 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 = 0.0071

Table S59. Gene #29: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	77	16	30
17P GAIN MUTATED	67	30	4	27
17P GAIN WILD-TYPE	31	47	12	3

Figure S59. 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 = 0.0071

Table S60. 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 S60. 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 = 0.0071

Table S61. Gene #30: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	58	103
17Q GAIN MUTATED	36	28	88
17Q GAIN WILD-TYPE	27	30	15

Figure S61. Get High-res Image Gene #30: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q gain' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S62. Gene #30: '17q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	17	22	29	22	27	39	25	25
17Q GAIN MUTATED	15	20	26	10	12	20	21	15
17Q GAIN WILD-TYPE	2	2	3	12	15	19	4	10

Figure S62. 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 = 0.0071

Table S63. Gene #30: '17q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	114	95
17Q GAIN MUTATED	54	100	36
17Q GAIN WILD-TYPE	24	14	59

Figure S63. 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 = 0.0071

Table S64. Gene #30: '17q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	125	72	44	46
17Q GAIN MUTATED	74	67	35	14
17Q GAIN WILD-TYPE	51	5	9	32

Figure S64. Get High-res Image Gene #30: '17q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.024

Table S65. Gene #30: '17q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	66	81	86
17Q GAIN MUTATED	26	45	69	51
17Q GAIN WILD-TYPE	29	21	12	35

Figure S65. Get High-res Image Gene #30: '17q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.12

Table S66. Gene #30: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	81	71
17Q GAIN MUTATED	38	66	38
17Q GAIN WILD-TYPE	31	15	33

Figure S66. Get High-res Image Gene #30: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.03

Table S67. Gene #30: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	77	16	30
17Q GAIN MUTATED	70	40	5	27
17Q GAIN WILD-TYPE	28	37	11	3

Figure S67. Get High-res Image Gene #30: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.018

Table S68. 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 S68. Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'CN_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.086

Table S69. 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 S69. Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'xq gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S70. Gene #39: '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 S70. Get High-res Image Gene #39: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

'xq gain' versus 'METHLYATION_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.14

Table S71. Gene #39: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	58	103
XQ GAIN MUTATED	14	10	46
XQ GAIN WILD-TYPE	49	48	57

Figure S71. Get High-res Image Gene #39: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S72. Gene #39: 'xq gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	114	95
XQ GAIN MUTATED	31	50	9
XQ GAIN WILD-TYPE	47	64	86

Figure S72. Get High-res Image Gene #39: 'xq gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xq gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S73. Gene #39: 'xq gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	125	72	44	46
XQ GAIN MUTATED	31	45	8	6
XQ GAIN WILD-TYPE	94	27	36	40

Figure S73. Get High-res Image Gene #39: 'xq gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xq gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S74. Gene #39: 'xq gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	66	81	86
XQ GAIN MUTATED	8	23	43	17
XQ GAIN WILD-TYPE	47	43	38	69

Figure S74. Get High-res Image Gene #39: 'xq gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S75. Gene #40: '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 S75. Get High-res Image Gene #40: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.15

Table S76. Gene #40: '1p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	114	95
1P LOSS MUTATED	5	5	20
1P LOSS WILD-TYPE	73	109	75

Figure S76. Get High-res Image Gene #40: '1p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'1q loss' versus 'CN_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.17

Table S77. Gene #41: '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 S77. Get High-res Image Gene #41: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

'3p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S78. Gene #44: '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 S78. Get High-res Image Gene #44: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.018

Table S79. Gene #44: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	58	103
3P LOSS MUTATED	3	12	1
3P LOSS WILD-TYPE	60	46	102

Figure S79. Get High-res Image Gene #44: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S80. Gene #44: '3p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	114	95
3P LOSS MUTATED	5	0	17
3P LOSS WILD-TYPE	73	114	78

Figure S80. Get High-res Image Gene #44: '3p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.059

Table S81. Gene #44: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	125	72	44	46
3P LOSS MUTATED	18	0	0	4
3P LOSS WILD-TYPE	107	72	44	42

Figure S81. Get High-res Image Gene #44: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S82. Gene #45: '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 S82. Get High-res Image Gene #45: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

'4p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S83. Gene #46: '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 S83. Get High-res Image Gene #46: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S84. Gene #46: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	58	103
4P LOSS MUTATED	3	17	1
4P LOSS WILD-TYPE	60	41	102

Figure S84. Get High-res Image Gene #46: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S85. Gene #46: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	114	95
4P LOSS MUTATED	1	1	23
4P LOSS WILD-TYPE	77	113	72

Figure S85. Get High-res Image Gene #46: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S86. Gene #46: '4p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	125	72	44	46
4P LOSS MUTATED	12	0	1	12
4P LOSS WILD-TYPE	113	72	43	34

Figure S86. Get High-res Image Gene #46: '4p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S87. Gene #46: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	77	16	30
4P LOSS MUTATED	4	7	8	0
4P LOSS WILD-TYPE	94	70	8	30

Figure S87. Get High-res Image Gene #46: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S88. Gene #47: '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 S88. Get High-res Image Gene #47: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S89. Gene #47: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	58	103
4Q LOSS MUTATED	3	18	1
4Q LOSS WILD-TYPE	60	40	102

Figure S89. Get High-res Image Gene #47: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S90. Gene #47: '4q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	114	95
4Q LOSS MUTATED	2	1	23
4Q LOSS WILD-TYPE	76	113	72

Figure S90. Get High-res Image Gene #47: '4q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.018

Table S91. Gene #47: '4q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	125	72	44	46
4Q LOSS MUTATED	14	0	1	11
4Q LOSS WILD-TYPE	111	72	43	35

Figure S91. Get High-res Image Gene #47: '4q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.036

Table S92. Gene #47: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	77	16	30
4Q LOSS MUTATED	4	9	7	0
4Q LOSS WILD-TYPE	94	68	9	30

Figure S92. Get High-res Image Gene #47: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.13

Table S93. Gene #48: '5p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	125	72	44	46
5P LOSS MUTATED	1	0	1	6
5P LOSS WILD-TYPE	124	72	43	40

Figure S93. Get High-res Image Gene #48: '5p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.097

Table S94. Gene #48: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	77	16	30
5P LOSS MUTATED	2	1	5	0
5P LOSS WILD-TYPE	96	76	11	30

Figure S94. Get High-res Image Gene #48: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00037 (Fisher's exact test), Q value = 0.2

Table S95. Gene #49: '5q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	125	72	44	46
5Q LOSS MUTATED	1	0	1	6
5Q LOSS WILD-TYPE	124	72	43	40

Figure S95. Get High-res Image Gene #49: '5q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S96. Gene #49: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	77	16	30
5Q LOSS MUTATED	2	0	6	0
5Q LOSS WILD-TYPE	96	77	10	30

Figure S96. Get High-res Image Gene #49: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S97. Gene #50: '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 S97. Get High-res Image Gene #50: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.075

Table S98. Gene #50: '6p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	125	72	44	46
6P LOSS MUTATED	7	3	0	11
6P LOSS WILD-TYPE	118	69	44	35

Figure S98. Get High-res Image Gene #50: '6p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S99. Gene #51: '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 S99. Get High-res Image Gene #51: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

'6q loss' versus 'MRNASEQ_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.086

Table S100. Gene #51: '6q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	114	95
6Q LOSS MUTATED	5	3	18
6Q LOSS WILD-TYPE	73	111	77

Figure S100. Get High-res Image Gene #51: '6q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.064

Table S101. Gene #51: '6q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	125	72	44	46
6Q LOSS MUTATED	12	2	0	12
6Q LOSS WILD-TYPE	113	70	44	34

Figure S101. Get High-res Image Gene #51: '6q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S102. Gene #54: '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 S102. Get High-res Image Gene #54: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S103. Gene #54: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	58	103
9P LOSS MUTATED	8	16	1
9P LOSS WILD-TYPE	55	42	102

Figure S103. Get High-res Image Gene #54: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S104. Gene #54: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	114	95
9P LOSS MUTATED	5	0	28
9P LOSS WILD-TYPE	73	114	67

Figure S104. Get High-res Image Gene #54: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S105. Gene #54: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	125	72	44	46
9P LOSS MUTATED	19	0	0	14
9P LOSS WILD-TYPE	106	72	44	32

Figure S105. Get High-res Image Gene #54: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S106. Gene #55: '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 S106. Get High-res Image Gene #55: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S107. Gene #55: '9q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	58	103
9Q LOSS MUTATED	9	17	1
9Q LOSS WILD-TYPE	54	41	102

Figure S107. Get High-res Image Gene #55: '9q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S108. Gene #55: '9q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	114	95
9Q LOSS MUTATED	4	0	30
9Q LOSS WILD-TYPE	74	114	65

Figure S108. Get High-res Image Gene #55: '9q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S109. Gene #55: '9q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	125	72	44	46
9Q LOSS MUTATED	17	0	0	17
9Q LOSS WILD-TYPE	108	72	44	29

Figure S109. Get High-res Image Gene #55: '9q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.064

Table S110. Gene #55: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	77	16	30
9Q LOSS MUTATED	8	15	7	0
9Q LOSS WILD-TYPE	90	62	9	30

Figure S110. Get High-res Image Gene #55: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S111. Gene #56: '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 S111. Get High-res Image Gene #56: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.069

Table S112. Gene #56: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	58	103
10P LOSS MUTATED	0	9	2
10P LOSS WILD-TYPE	63	49	101

Figure S112. Get High-res Image Gene #56: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.097

Table S113. Gene #56: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	114	95
10P LOSS MUTATED	2	1	13
10P LOSS WILD-TYPE	76	113	82

Figure S113. Get High-res Image Gene #56: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S114. Gene #57: '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 S114. Get High-res Image Gene #57: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.018

Table S115. Gene #57: '10q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	114	95
10Q LOSS MUTATED	2	1	14
10Q LOSS WILD-TYPE	76	113	81

Figure S115. Get High-res Image Gene #57: '10q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'11p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S116. Gene #58: '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 S116. Get High-res Image Gene #58: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 0.00043 (Fisher's exact test), Q value = 0.24

Table S117. Gene #58: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	58	103
11P LOSS MUTATED	2	10	2
11P LOSS WILD-TYPE	61	48	101

Figure S117. Get High-res Image Gene #58: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11p loss' versus 'MRNASEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.12

Table S118. Gene #58: '11p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	114	95
11P LOSS MUTATED	2	2	14
11P LOSS WILD-TYPE	76	112	81

Figure S118. Get High-res Image Gene #58: '11p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'11q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S119. Gene #59: '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 S119. Get High-res Image Gene #59: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'MRNASEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.069

Table S120. Gene #59: '11q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	114	95
11Q LOSS MUTATED	3	2	16
11Q LOSS WILD-TYPE	75	112	79

Figure S120. Get High-res Image Gene #59: '11q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'13q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S121. Gene #60: '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 S121. Get High-res Image Gene #60: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S122. Gene #60: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	58	103
13Q LOSS MUTATED	2	16	3
13Q LOSS WILD-TYPE	61	42	100

Figure S122. Get High-res Image Gene #60: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q loss' versus 'RPPA_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.03

Table S123. Gene #60: '13q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	17	22	29	22	27	39	25	25
13Q LOSS MUTATED	2	2	0	0	11	1	2	3
13Q LOSS WILD-TYPE	15	20	29	22	16	38	23	22

Figure S123. Get High-res Image Gene #60: '13q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S124. Gene #60: '13q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	114	95
13Q LOSS MUTATED	0	2	22
13Q LOSS WILD-TYPE	78	112	73

Figure S124. Get High-res Image Gene #60: '13q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S125. Gene #60: '13q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	125	72	44	46
13Q LOSS MUTATED	9	1	0	14
13Q LOSS WILD-TYPE	116	71	44	32

Figure S125. Get High-res Image Gene #60: '13q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.036

Table S126. Gene #60: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	77	16	30
13Q LOSS MUTATED	4	8	7	0
13Q LOSS WILD-TYPE	94	69	9	30

Figure S126. Get High-res Image Gene #60: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S127. Gene #61: '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 S127. Get High-res Image Gene #61: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

'14q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 0.16

Table S128. Gene #61: '14q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	17	22	29	22	27	39	25	25
14Q LOSS MUTATED	3	4	0	3	9	1	4	9
14Q LOSS WILD-TYPE	14	18	29	19	18	38	21	16

Figure S128. Get High-res Image Gene #61: '14q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S129. Gene #61: '14q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	114	95
14Q LOSS MUTATED	9	5	33
14Q LOSS WILD-TYPE	69	109	62

Figure S129. Get High-res Image Gene #61: '14q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S130. Gene #61: '14q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	125	72	44	46
14Q LOSS MUTATED	24	2	2	19
14Q LOSS WILD-TYPE	101	70	42	27

Figure S130. Get High-res Image Gene #61: '14q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S131. Gene #62: '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 S131. Get High-res Image Gene #62: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.018

Table S132. Gene #62: '15q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	114	95
15Q LOSS MUTATED	6	3	22
15Q LOSS WILD-TYPE	72	111	73

Figure S132. Get High-res Image Gene #62: '15q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S133. Gene #62: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	125	72	44	46
15Q LOSS MUTATED	13	2	1	15
15Q LOSS WILD-TYPE	112	70	43	31

Figure S133. Get High-res Image Gene #62: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'CN_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.23

Table S134. Gene #64: '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 S134. Get High-res Image Gene #64: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.14

Table S135. Gene #64: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	58	103
16Q LOSS MUTATED	0	6	0
16Q LOSS WILD-TYPE	63	52	103

Figure S135. Get High-res Image Gene #64: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.2

Table S136. Gene #64: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	114	95
16Q LOSS MUTATED	0	0	7
16Q LOSS WILD-TYPE	78	114	88

Figure S136. Get High-res Image Gene #64: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.03

Table S137. Gene #65: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	58	103
17P LOSS MUTATED	0	7	0
17P LOSS WILD-TYPE	63	51	103

Figure S137. Get High-res Image Gene #65: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.12

Table S138. Gene #65: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	114	95
17P LOSS MUTATED	2	0	10
17P LOSS WILD-TYPE	76	114	85

Figure S138. Get High-res Image Gene #65: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'18p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S139. Gene #66: '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 S139. Get High-res Image Gene #66: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S140. Gene #66: '18p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	58	103
18P LOSS MUTATED	7	21	4
18P LOSS WILD-TYPE	56	37	99

Figure S140. Get High-res Image Gene #66: '18p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S141. Gene #66: '18p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	114	95
18P LOSS MUTATED	10	4	28
18P LOSS WILD-TYPE	68	110	67

Figure S141. Get High-res Image Gene #66: '18p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'18p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S142. Gene #66: '18p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	125	72	44	46
18P LOSS MUTATED	24	1	2	15
18P LOSS WILD-TYPE	101	71	42	31

Figure S142. Get High-res Image Gene #66: '18p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S143. Gene #67: '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 S143. Get High-res Image Gene #67: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S144. Gene #67: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	58	103
18Q LOSS MUTATED	8	23	4
18Q LOSS WILD-TYPE	55	35	99

Figure S144. Get High-res Image Gene #67: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18q loss' versus 'RPPA_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.047

Table S145. Gene #67: '18q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	17	22	29	22	27	39	25	25
18Q LOSS MUTATED	1	4	0	2	12	7	1	7
18Q LOSS WILD-TYPE	16	18	29	20	15	32	24	18

Figure S145. Get High-res Image Gene #67: '18q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S146. Gene #67: '18q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	114	95
18Q LOSS MUTATED	10	3	32
18Q LOSS WILD-TYPE	68	111	63

Figure S146. Get High-res Image Gene #67: '18q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S147. Gene #67: '18q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	125	72	44	46
18Q LOSS MUTATED	28	1	2	14
18Q LOSS WILD-TYPE	97	71	42	32

Figure S147. Get High-res Image Gene #67: '18q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00032 (Fisher's exact test), Q value = 0.18

Table S148. Gene #67: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	77	16	30
18Q LOSS MUTATED	12	19	8	1
18Q LOSS WILD-TYPE	86	58	8	29

Figure S148. Get High-res Image Gene #67: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.059

Table S149. Gene #68: '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 S149. Get High-res Image Gene #68: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

'19q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S150. Gene #69: '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 S150. Get High-res Image Gene #69: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S151. Gene #71: '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 S151. Get High-res Image Gene #71: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S152. Gene #71: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	58	103
22Q LOSS MUTATED	9	30	10
22Q LOSS WILD-TYPE	54	28	93

Figure S152. Get High-res Image Gene #71: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S153. Gene #71: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	114	95
22Q LOSS MUTATED	14	7	39
22Q LOSS WILD-TYPE	64	107	56

Figure S153. Get High-res Image Gene #71: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S154. Gene #71: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	125	72	44	46
22Q LOSS MUTATED	36	5	2	17
22Q LOSS WILD-TYPE	89	67	42	29

Figure S154. Get High-res Image Gene #71: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xq loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S155. Gene #72: '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 S155. Get High-res Image Gene #72: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.053

Table S156. Gene #72: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	58	103
XQ LOSS MUTATED	4	14	3
XQ LOSS WILD-TYPE	59	44	100

Figure S156. Get High-res Image Gene #72: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S157. Gene #72: 'xq loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	114	95
XQ LOSS MUTATED	4	3	23
XQ LOSS WILD-TYPE	74	111	72

Figure S157. Get High-res Image Gene #72: 'xq loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtypes file = KIRP-TP.transferedmergedcluster.txt
Number of patients = 288
Number of significantly arm-level cnvs = 72
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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