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

Prostate Adenocarcinoma (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/C15Q4V0Q

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 78 arm-level events and 10 molecular subtypes across 492 patients, 91 significant findings detected with P value < 0.05 and Q value < 0.25.

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

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 78 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, 91 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	102 (21%)	390	1e-05 (0.00733)	1e-05 (0.00733)	0.412 (1.00)	0.587 (1.00)	1e-05 (0.00733)	0.00015 (0.0979)	0.0185 (1.00)	4e-05 (0.0269)	0.00029 (0.187)	0.00177 (1.00)
7q gain	95 (19%)	397	1e-05 (0.00733)	1e-05 (0.00733)	0.621 (1.00)	0.715 (1.00)	1e-05 (0.00733)	0.00111 (0.692)	0.0231 (1.00)	1e-05 (0.00733)	0.00028 (0.181)	0.00576 (1.00)
8q gain	124 (25%)	368	1e-05 (0.00733)	1e-05 (0.00733)	0.00412 (1.00)	0.00942 (1.00)	0.00042 (0.269)	0.0113 (1.00)	0.00056 (0.357)	1e-05 (0.00733)	1e-05 (0.00733)	1e-05 (0.00733)
8p loss	168 (34%)	324	1e-05 (0.00733)	1e-05 (0.00733)	0.545 (1.00)	0.933 (1.00)	1e-05 (0.00733)	7e-05 (0.0465)	0.00033 (0.212)	0.079 (1.00)	0.0574 (1.00)	0.0321 (1.00)
10p loss	41 (8%)	451	1e-05 (0.00733)	1e-05 (0.00733)	0.00711 (1.00)	0.0123 (1.00)	0.0004 (0.257)	0.00262 (1.00)	0.0849 (1.00)	8e-05 (0.053)	0.0109 (1.00)	5e-05 (0.0334)
4p loss	24 (5%)	468	1e-05 (0.00733)	0.193 (1.00)	0.117 (1.00)	0.151 (1.00)	0.0164 (1.00)	0.025 (1.00)	0.00136 (0.84)	0.00301 (1.00)	5e-05 (0.0334)	0.00011 (0.0723)
15q loss	36 (7%)	456	1e-05 (0.00733)	0.0295 (1.00)	0.0412 (1.00)	0.0922 (1.00)	0.00653 (1.00)	0.103 (1.00)	0.00011 (0.0723)	0.00705 (1.00)	0.00121 (0.751)	0.0001 (0.0659)
16q loss	107 (22%)	385	1e-05 (0.00733)	5e-05 (0.0334)	0.505 (1.00)	0.195 (1.00)	0.0605 (1.00)	0.00226 (1.00)	0.0809 (1.00)	0.0006 (0.382)	0.00419 (1.00)	0.0001 (0.0659)
17p loss	76 (15%)	416	1e-05 (0.00733)	0.00769 (1.00)	0.00297 (1.00)	0.01 (1.00)	0.00029 (0.187)	0.00053 (0.338)	0.0955 (1.00)	0.0321 (1.00)	0.0225 (1.00)	4e-05 (0.0269)
1q gain	26 (5%)	466	1e-05 (0.00733)	0.00685 (1.00)	0.0224 (1.00)	0.182 (1.00)	0.00013 (0.0851)	0.0038 (1.00)	0.0968 (1.00)	0.0337 (1.00)	0.503 (1.00)	0.196 (1.00)
3p gain	40 (8%)	452	1e-05 (0.00733)	0.0247 (1.00)	0.145 (1.00)	0.62 (1.00)	0.0293 (1.00)	0.371 (1.00)	0.0207 (1.00)	0.00519 (1.00)	0.00365 (1.00)	0.00027 (0.175)
3q gain	54 (11%)	438	1e-05 (0.00733)	0.0104 (1.00)	0.0743 (1.00)	0.288 (1.00)	0.0095 (1.00)	0.0349 (1.00)	0.00474 (1.00)	0.00441 (1.00)	0.015 (1.00)	2e-05 (0.0135)
8p gain	71 (14%)	421	1e-05 (0.00733)	1e-05 (0.00733)	0.00525 (1.00)	0.00807 (1.00)	0.00074 (0.469)	0.00204 (1.00)	0.123 (1.00)	0.00525 (1.00)	0.00233 (1.00)	0.00228 (1.00)
6q loss	40 (8%)	452	1e-05 (0.00733)	0.0639 (1.00)	0.0756 (1.00)	0.164 (1.00)	0.00808 (1.00)	0.0003 (0.193)	0.0128 (1.00)	0.0489 (1.00)	0.0043 (1.00)	0.00212 (1.00)
10q loss	43 (9%)	449	1e-05 (0.00733)	0.00194 (1.00)	0.0398 (1.00)	0.0389 (1.00)	0.00079 (0.499)	0.00731 (1.00)	0.039 (1.00)	0.00124 (0.769)	0.00161 (0.99)	6e-05 (0.0399)
13q loss	77 (16%)	415	1e-05 (0.00733)	0.124 (1.00)	0.554 (1.00)	0.461 (1.00)	0.118 (1.00)	0.0527 (1.00)	0.184 (1.00)	0.0409 (1.00)	0.226 (1.00)	0.00018 (0.117)
18q loss	101 (21%)	391	1e-05 (0.00733)	0.0023 (1.00)	0.0157 (1.00)	0.0194 (1.00)	0.0124 (1.00)	0.0981 (1.00)	0.00661 (1.00)	0.0034 (1.00)	0.0148 (1.00)	2e-05 (0.0135)
22q loss	47 (10%)	445	1e-05 (0.00733)	0.153 (1.00)	0.445 (1.00)	0.807 (1.00)	0.0614 (1.00)	0.0787 (1.00)	0.0675 (1.00)	0.0287 (1.00)	0.149 (1.00)	0.00019 (0.124)
xq loss	39 (8%)	453	1e-05 (0.00733)	0.00045 (0.288)	0.192 (1.00)	0.26 (1.00)	0.00258 (1.00)	0.00333 (1.00)	1e-05 (0.00733)	0.0352 (1.00)	0.00602 (1.00)	0.0965 (1.00)
1p gain	16 (3%)	476	1e-05 (0.00733)	0.0271 (1.00)	0.0406 (1.00)	0.337 (1.00)	0.00895 (1.00)	0.0564 (1.00)	0.313 (1.00)	0.0417 (1.00)	0.849 (1.00)	0.175 (1.00)
5p gain	23 (5%)	469	1e-05 (0.00733)	0.0154 (1.00)	0.298 (1.00)	0.31 (1.00)	0.0295 (1.00)	0.219 (1.00)	0.00139 (0.858)	0.0018 (1.00)	0.00171 (1.00)	0.00404 (1.00)
5q gain	12 (2%)	480	3e-05 (0.0202)	0.106 (1.00)			0.0369 (1.00)	0.157 (1.00)	0.377 (1.00)	0.157 (1.00)	0.124 (1.00)	0.325 (1.00)
9p gain	34 (7%)	458	1e-05 (0.00733)	0.00778 (1.00)	0.485 (1.00)	0.178 (1.00)	0.121 (1.00)	0.0978 (1.00)	0.485 (1.00)	0.113 (1.00)	0.0176 (1.00)	0.18 (1.00)
9q gain	50 (10%)	442	1e-05 (0.00733)	0.0388 (1.00)	0.0253 (1.00)	0.0126 (1.00)	0.0149 (1.00)	0.0173 (1.00)	0.36 (1.00)	0.0115 (1.00)	0.00726 (1.00)	0.013 (1.00)
10p gain	15 (3%)	477	7e-05 (0.0465)	0.158 (1.00)	0.787 (1.00)	0.781 (1.00)	0.381 (1.00)	0.206 (1.00)	0.575 (1.00)	0.013 (1.00)	0.172 (1.00)	0.00077 (0.487)
10q gain	14 (3%)	478	0.0002 (0.13)	0.204 (1.00)	0.0394 (1.00)	0.0392 (1.00)	0.15 (1.00)	0.195 (1.00)	0.589 (1.00)	0.0873 (1.00)	0.271 (1.00)	0.00164 (1.00)
11p gain	26 (5%)	466	1e-05 (0.00733)	0.0513 (1.00)	0.768 (1.00)	0.666 (1.00)	0.139 (1.00)	0.0297 (1.00)	0.598 (1.00)	0.0532 (1.00)	0.0349 (1.00)	0.177 (1.00)
11q gain	29 (6%)	463	1e-05 (0.00733)	0.105 (1.00)	0.766 (1.00)	0.668 (1.00)	0.0797 (1.00)	0.0517 (1.00)	0.69 (1.00)	0.0515 (1.00)	0.0861 (1.00)	0.125 (1.00)
12p gain	14 (3%)	478	4e-05 (0.0269)	0.116 (1.00)			0.333 (1.00)	0.381 (1.00)	0.365 (1.00)	0.00112 (0.697)	0.0238 (1.00)	0.208 (1.00)
14q gain	10 (2%)	482	4e-05 (0.0269)	0.583 (1.00)	0.784 (1.00)	0.779 (1.00)	0.242 (1.00)	0.404 (1.00)	0.114 (1.00)	0.257 (1.00)	0.492 (1.00)	0.467 (1.00)
16p gain	31 (6%)	461	1e-05 (0.00733)	0.199 (1.00)	0.52 (1.00)	0.523 (1.00)	0.0794 (1.00)	0.269 (1.00)	0.153 (1.00)	0.00408 (1.00)	0.0264 (1.00)	0.0124 (1.00)
18p gain	18 (4%)	474	1e-05 (0.00733)	0.607 (1.00)	1 (1.00)	0.719 (1.00)	0.199 (1.00)	0.455 (1.00)	0.69 (1.00)	0.614 (1.00)	0.723 (1.00)	0.448 (1.00)
19p gain	12 (2%)	480	1e-05 (0.00733)	0.466 (1.00)			0.0375 (1.00)	0.641 (1.00)	0.142 (1.00)	0.0849 (1.00)	0.515 (1.00)	0.12 (1.00)
19q gain	12 (2%)	480	1e-05 (0.00733)	0.298 (1.00)	0.787 (1.00)	0.779 (1.00)	0.0532 (1.00)	0.691 (1.00)	0.218 (1.00)	0.0604 (1.00)	0.508 (1.00)	0.153 (1.00)
20p gain	26 (5%)	466	1e-05 (0.00733)	0.0194 (1.00)	0.372 (1.00)	0.182 (1.00)	0.0262 (1.00)	0.297 (1.00)	0.00196 (1.00)	0.00407 (1.00)	0.0301 (1.00)	0.00493 (1.00)
20q gain	28 (6%)	464	1e-05 (0.00733)	0.0275 (1.00)	0.621 (1.00)	0.886 (1.00)	0.176 (1.00)	0.263 (1.00)	0.011 (1.00)	0.00817 (1.00)	0.102 (1.00)	0.00987 (1.00)
21q gain	21 (4%)	471	1e-05 (0.00733)	0.0292 (1.00)	0.445 (1.00)	0.451 (1.00)	0.0245 (1.00)	0.0929 (1.00)	0.0142 (1.00)	0.00323 (1.00)	0.0124 (1.00)	0.0295 (1.00)
1p loss	22 (4%)	470	1e-05 (0.00733)	0.00572 (1.00)	0.256 (1.00)	0.228 (1.00)	0.0135 (1.00)	0.00101 (0.633)	0.0259 (1.00)	0.00323 (1.00)	0.0201 (1.00)	0.0137 (1.00)
2p loss	16 (3%)	476	9e-05 (0.0594)	0.0734 (1.00)			0.318 (1.00)	0.793 (1.00)	0.134 (1.00)	0.0868 (1.00)	0.00367 (1.00)	0.0032 (1.00)
2q loss	18 (4%)	474	8e-05 (0.053)	0.17 (1.00)			0.536 (1.00)	0.533 (1.00)	0.126 (1.00)	0.0358 (1.00)	0.00853 (1.00)	0.0011 (0.687)
4q loss	17 (3%)	475	1e-05 (0.00733)	0.166 (1.00)	0.457 (1.00)	0.385 (1.00)	0.0537 (1.00)	0.0883 (1.00)	0.201 (1.00)	0.0472 (1.00)	0.0152 (1.00)	0.00531 (1.00)
5p loss	12 (2%)	480	1e-05 (0.00733)	0.239 (1.00)	0.785 (1.00)	1 (1.00)	0.0383 (1.00)	0.0334 (1.00)	0.863 (1.00)	0.00368 (1.00)	0.51 (1.00)	0.103 (1.00)
5q loss	22 (4%)	470	1e-05 (0.00733)	0.0283 (1.00)	0.256 (1.00)	0.227 (1.00)	0.0886 (1.00)	0.008 (1.00)	0.0578 (1.00)	0.0011 (0.687)	0.109 (1.00)	0.027 (1.00)
6p loss	25 (5%)	467	1e-05 (0.00733)	0.0393 (1.00)	0.255 (1.00)	0.228 (1.00)	0.0111 (1.00)	0.00337 (1.00)	0.0571 (1.00)	0.0313 (1.00)	0.0146 (1.00)	0.00385 (1.00)
9p loss	21 (4%)	471	1e-05 (0.00733)	0.556 (1.00)	0.0853 (1.00)	0.0729 (1.00)	0.00393 (1.00)	0.034 (1.00)	0.262 (1.00)	0.241 (1.00)	0.109 (1.00)	0.0625 (1.00)
12p loss	48 (10%)	444	2e-05 (0.0135)	0.157 (1.00)	0.192 (1.00)	0.438 (1.00)	0.00719 (1.00)	0.0766 (1.00)	0.455 (1.00)	0.017 (1.00)	0.00647 (1.00)	0.00262 (1.00)
12q loss	20 (4%)	472	1e-05 (0.00733)	0.393 (1.00)	0.174 (1.00)	0.122 (1.00)	0.243 (1.00)	0.229 (1.00)	1 (1.00)	0.052 (1.00)	0.0664 (1.00)	0.00849 (1.00)
14q loss	25 (5%)	467	1e-05 (0.00733)	0.00824 (1.00)	0.465 (1.00)	0.489 (1.00)	0.0785 (1.00)	0.507 (1.00)	0.403 (1.00)	0.0636 (1.00)	0.0972 (1.00)	0.067 (1.00)
17q loss	20 (4%)	472	1e-05 (0.00733)	0.0121 (1.00)	0.451 (1.00)	0.388 (1.00)	0.00675 (1.00)	0.0668 (1.00)	0.0124 (1.00)	0.0459 (1.00)	0.0304 (1.00)	0.145 (1.00)
18p loss	68 (14%)	424	1e-05 (0.00733)	0.00281 (1.00)	0.0631 (1.00)	0.0669 (1.00)	0.0266 (1.00)	0.215 (1.00)	0.0591 (1.00)	0.0308 (1.00)	0.0105 (1.00)	0.00509 (1.00)
19p loss	17 (3%)	475	0.00013 (0.0851)	0.3 (1.00)	0.626 (1.00)	0.491 (1.00)	0.133 (1.00)	0.507 (1.00)	0.133 (1.00)	0.161 (1.00)	0.00286 (1.00)	0.0106 (1.00)
19q loss	17 (3%)	475	0.00023 (0.149)	0.3 (1.00)	0.622 (1.00)	0.492 (1.00)	0.133 (1.00)	0.503 (1.00)	0.133 (1.00)	0.158 (1.00)	0.00276 (1.00)	0.00992 (1.00)
21q loss	24 (5%)	468	2e-05 (0.0135)	0.191 (1.00)	0.507 (1.00)	0.508 (1.00)	0.0151 (1.00)	0.0361 (1.00)	0.573 (1.00)	0.102 (1.00)	0.425 (1.00)	0.0402 (1.00)
2p gain	10 (2%)	482	0.00103 (0.645)	0.0176 (1.00)			0.01 (1.00)	0.203 (1.00)	0.115 (1.00)	0.0355 (1.00)	0.168 (1.00)	0.187 (1.00)
2q gain	7 (1%)	485	0.00095 (0.598)	0.107 (1.00)			0.17 (1.00)	0.877 (1.00)	0.507 (1.00)	0.0627 (1.00)	0.176 (1.00)	0.159 (1.00)
4p gain	9 (2%)	483	0.0285 (1.00)	0.449 (1.00)			0.483 (1.00)	0.699 (1.00)	0.917 (1.00)	0.416 (1.00)	0.603 (1.00)	0.575 (1.00)
4q gain	10 (2%)	482	0.0731 (1.00)	0.585 (1.00)			1 (1.00)	0.785 (1.00)	0.856 (1.00)	0.177 (1.00)	0.152 (1.00)	0.0699 (1.00)
6p gain	10 (2%)	482	0.00131 (0.811)	0.00617 (1.00)			0.124 (1.00)	0.17 (1.00)	0.67 (1.00)	0.106 (1.00)	0.0183 (1.00)	0.0731 (1.00)
6q gain	6 (1%)	486	0.021 (1.00)	0.0162 (1.00)			0.102 (1.00)	0.686 (1.00)	0.197 (1.00)	0.0387 (1.00)	0.271 (1.00)	0.567 (1.00)
12q gain	17 (3%)	475	0.00062 (0.394)	0.0708 (1.00)	0.47 (1.00)	0.633 (1.00)	0.33 (1.00)	0.366 (1.00)	0.784 (1.00)	0.0205 (1.00)	0.0157 (1.00)	0.0966 (1.00)
13q gain	8 (2%)	484	0.0147 (1.00)	0.132 (1.00)			0.637 (1.00)	0.896 (1.00)	0.823 (1.00)	0.562 (1.00)	0.739 (1.00)	0.865 (1.00)
15q gain	6 (1%)	486	0.0208 (1.00)	0.846 (1.00)			0.878 (1.00)	0.337 (1.00)	0.778 (1.00)	0.181 (1.00)	0.706 (1.00)	0.318 (1.00)
16q gain	8 (2%)	484	0.0839 (1.00)	0.218 (1.00)	0.677 (1.00)	0.561 (1.00)	0.606 (1.00)	0.603 (1.00)	0.102 (1.00)	0.0138 (1.00)	0.644 (1.00)	0.54 (1.00)
17p gain	8 (2%)	484	0.0148 (1.00)	0.523 (1.00)			0.058 (1.00)	0.0912 (1.00)	0.0197 (1.00)	0.0154 (1.00)	0.608 (1.00)	0.00396 (1.00)
17q gain	11 (2%)	481	0.00044 (0.282)	0.324 (1.00)			0.0188 (1.00)	0.0383 (1.00)	0.0907 (1.00)	0.11 (1.00)	0.473 (1.00)	0.0008 (0.505)
18q gain	9 (2%)	483	0.00418 (1.00)	0.854 (1.00)	1 (1.00)	0.488 (1.00)	0.105 (1.00)	0.0249 (1.00)	0.639 (1.00)	0.439 (1.00)	0.453 (1.00)	0.667 (1.00)
22q gain	4 (1%)	488	0.0959 (1.00)				0.777 (1.00)	0.0674 (1.00)	0.325 (1.00)	0.407 (1.00)	0.405 (1.00)	0.161 (1.00)
xq gain	7 (1%)	485	0.00097 (0.609)	0.185 (1.00)			0.185 (1.00)	0.128 (1.00)	0.509 (1.00)	0.0454 (1.00)	0.00644 (1.00)	0.0853 (1.00)
1q loss	6 (1%)	486	0.0212 (1.00)	0.0776 (1.00)			0.334 (1.00)	0.291 (1.00)	0.1 (1.00)	0.103 (1.00)	0.0517 (1.00)	0.393 (1.00)
3p loss	9 (2%)	483	0.0333 (1.00)	0.0602 (1.00)			0.129 (1.00)	0.145 (1.00)	0.103 (1.00)	0.412 (1.00)	0.0519 (1.00)	0.192 (1.00)
3q loss	5 (1%)	487	0.305 (1.00)	0.531 (1.00)			0.329 (1.00)	0.386 (1.00)	0.153 (1.00)	0.0317 (1.00)
8q loss	24 (5%)	468	0.029 (1.00)	0.0008 (0.505)	1 (1.00)	0.805 (1.00)	0.00965 (1.00)	0.0146 (1.00)	0.102 (1.00)	0.992 (1.00)	0.217 (1.00)	0.245 (1.00)
9q loss	10 (2%)	482	0.00144 (0.887)	0.614 (1.00)	0.445 (1.00)	0.452 (1.00)	0.265 (1.00)	0.219 (1.00)	0.615 (1.00)	0.548 (1.00)	0.521 (1.00)	0.0368 (1.00)
11p loss	8 (2%)	484	0.00225 (1.00)	0.497 (1.00)			0.231 (1.00)	0.101 (1.00)	0.326 (1.00)	0.261 (1.00)	0.113 (1.00)	0.101 (1.00)
11q loss	5 (1%)	487	0.0142 (1.00)	0.654 (1.00)			0.06 (1.00)	0.0843 (1.00)	0.633 (1.00)	0.188 (1.00)	0.0214 (1.00)	0.289 (1.00)
16p loss	32 (7%)	460	0.00173 (1.00)	0.251 (1.00)	0.752 (1.00)	0.477 (1.00)	0.55 (1.00)	0.256 (1.00)	0.647 (1.00)	0.322 (1.00)	0.224 (1.00)	0.0322 (1.00)
20p loss	19 (4%)	473	0.038 (1.00)	0.0291 (1.00)	0.895 (1.00)	1 (1.00)	0.293 (1.00)	0.494 (1.00)	0.49 (1.00)	0.187 (1.00)	1 (1.00)	0.581 (1.00)
20q loss	9 (2%)	483	0.0283 (1.00)	0.0487 (1.00)	1 (1.00)	1 (1.00)	0.0952 (1.00)	0.106 (1.00)	0.0722 (1.00)	0.0606 (1.00)	1 (1.00)	0.501 (1.00)

'1p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
1P GAIN MUTATED	2	14	0
1P GAIN WILD-TYPE	271	120	85

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

'1q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S2. Gene #2: '1q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
1Q GAIN MUTATED	5	21	0
1Q GAIN WILD-TYPE	268	113	85

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

'1q gain' versus 'MRNASEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.085

Table S3. Gene #2: '1q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	162	175
1Q GAIN MUTATED	0	10	16
1Q GAIN WILD-TYPE	145	152	159

Figure S3. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S4. Gene #5: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
3P GAIN MUTATED	3	32	5
3P GAIN WILD-TYPE	270	102	80

Figure S4. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'

'3p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 0.17

Table S5. Gene #5: '3p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
3P GAIN MUTATED	2	2	11	7	0	2
3P GAIN WILD-TYPE	68	39	29	75	25	58

Figure S5. 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 = 0.0073

Table S6. Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
3Q GAIN MUTATED	9	37	8
3Q GAIN WILD-TYPE	264	97	77

Figure S6. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

'3q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S7. Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
3Q GAIN MUTATED	2	3	14	9	1	2
3Q GAIN WILD-TYPE	68	38	26	73	24	58

Figure S7. 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 = 0.0073

Table S8. Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
5P GAIN MUTATED	2	21	0
5P GAIN WILD-TYPE	271	113	85

Figure S8. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5q gain' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S9. Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
5Q GAIN MUTATED	1	11	0
5Q GAIN WILD-TYPE	272	123	85

Figure S9. 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 = 0.0073

Table S10. Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
7P GAIN MUTATED	13	67	22
7P GAIN WILD-TYPE	260	67	63

Figure S10. 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 = 0.0073

Table S11. Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	134	126	121	39
7P GAIN MUTATED	10	45	16	12
7P GAIN WILD-TYPE	124	81	105	27

Figure S11. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S12. Gene #13: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	162	175
7P GAIN MUTATED	12	58	29
7P GAIN WILD-TYPE	133	104	146

Figure S12. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.098

Table S13. Gene #13: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	173	166
7P GAIN MUTATED	17	52	30
7P GAIN WILD-TYPE	126	121	136

Figure S13. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.027

Table S14. Gene #13: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
7P GAIN MUTATED	16	28	15	38	4
7P GAIN WILD-TYPE	131	70	44	90	52

Figure S14. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.19

Table S15. Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	106	60	90
7P GAIN MUTATED	4	36	11	18
7P GAIN WILD-TYPE	58	70	49	72

Figure S15. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S16. Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
7Q GAIN MUTATED	13	61	21
7Q GAIN WILD-TYPE	260	73	64

Figure S16. 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 = 0.0073

Table S17. Gene #14: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	134	126	121	39
7Q GAIN MUTATED	9	43	14	12
7Q GAIN WILD-TYPE	125	83	107	27

Figure S17. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S18. Gene #14: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	162	175
7Q GAIN MUTATED	12	53	27
7Q GAIN WILD-TYPE	133	109	148

Figure S18. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S19. Gene #14: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
7Q GAIN MUTATED	14	27	14	35	4
7Q GAIN WILD-TYPE	133	71	45	93	52

Figure S19. 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 = 0.18

Table S20. Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	106	60	90
7Q GAIN MUTATED	4	35	11	16
7Q GAIN WILD-TYPE	58	71	49	74

Figure S20. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'8p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S21. Gene #15: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
8P GAIN MUTATED	13	49	9
8P GAIN WILD-TYPE	260	85	76

Figure S21. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

'8p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S22. Gene #15: '8p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	134	126	121	39
8P GAIN MUTATED	6	34	7	7
8P GAIN WILD-TYPE	128	92	114	32

Figure S22. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S23. Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
8Q GAIN MUTATED	36	77	11
8Q GAIN WILD-TYPE	237	57	74

Figure S23. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S24. Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	134	126	121	39
8Q GAIN MUTATED	12	51	19	13
8Q GAIN WILD-TYPE	122	75	102	26

Figure S24. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S25. Gene #16: '8q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
8Q GAIN MUTATED	17	24	18	54	9
8Q GAIN WILD-TYPE	130	74	41	74	47

Figure S25. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S26. Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	106	60	90
8Q GAIN MUTATED	6	46	11	18
8Q GAIN WILD-TYPE	56	60	49	72

Figure S26. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'8q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S27. Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
8Q GAIN MUTATED	8	9	13	37	3	11
8Q GAIN WILD-TYPE	62	32	27	45	22	49

Figure S27. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S28. Gene #17: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
9P GAIN MUTATED	4	30	0
9P GAIN WILD-TYPE	269	104	85

Figure S28. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

'9q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S29. Gene #18: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
9Q GAIN MUTATED	8	42	0
9Q GAIN WILD-TYPE	265	92	85

Figure S29. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

'10p gain' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.046

Table S30. Gene #19: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
10P GAIN MUTATED	3	12	0
10P GAIN WILD-TYPE	270	122	85

Figure S30. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

'10q gain' versus 'CN_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.13

Table S31. Gene #20: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
10Q GAIN MUTATED	3	11	0
10Q GAIN WILD-TYPE	270	123	85

Figure S31. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

'11p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S32. Gene #21: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
11P GAIN MUTATED	3	21	2
11P GAIN WILD-TYPE	270	113	83

Figure S32. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

'11q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S33. Gene #22: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
11Q GAIN MUTATED	3	24	2
11Q GAIN WILD-TYPE	270	110	83

Figure S33. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.027

Table S34. Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
12P GAIN MUTATED	2	12	0
12P GAIN WILD-TYPE	271	122	85

Figure S34. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

'14q gain' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.027

Table S35. Gene #26: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
14Q GAIN MUTATED	0	9	1
14Q GAIN WILD-TYPE	273	125	84

Figure S35. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S36. Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
16P GAIN MUTATED	8	23	0
16P GAIN WILD-TYPE	265	111	85

Figure S36. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

'18p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S37. Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
18P GAIN MUTATED	3	15	0
18P GAIN WILD-TYPE	270	119	85

Figure S37. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

'19p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S38. Gene #34: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
19P GAIN MUTATED	0	12	0
19P GAIN WILD-TYPE	273	122	85

Figure S38. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

'19q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S39. Gene #35: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
19Q GAIN MUTATED	0	12	0
19Q GAIN WILD-TYPE	273	122	85

Figure S39. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S40. Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
20P GAIN MUTATED	3	22	1
20P GAIN WILD-TYPE	270	112	84

Figure S40. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S41. Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
20Q GAIN MUTATED	3	24	1
20Q GAIN WILD-TYPE	270	110	84

Figure S41. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'21q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S42. Gene #38: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
21Q GAIN MUTATED	0	21	0
21Q GAIN WILD-TYPE	273	113	85

Figure S42. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

'1p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S43. Gene #41: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
1P LOSS MUTATED	1	20	1
1P LOSS WILD-TYPE	272	114	84

Figure S43. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

'2p loss' versus 'CN_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.059

Table S44. Gene #43: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
2P LOSS MUTATED	2	12	2
2P LOSS WILD-TYPE	271	122	83

Figure S44. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

'2q loss' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.053

Table S45. Gene #44: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
2Q LOSS MUTATED	3	13	2
2Q LOSS WILD-TYPE	270	121	83

Figure S45. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

'4p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S46. Gene #47: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
4P LOSS MUTATED	2	21	1
4P LOSS WILD-TYPE	271	113	84

Figure S46. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

'4p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.033

Table S47. Gene #47: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	106	60	90
4P LOSS MUTATED	0	14	3	0
4P LOSS WILD-TYPE	62	92	57	90

Figure S47. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.072

Table S48. Gene #47: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
4P LOSS MUTATED	1	0	7	9	0	0
4P LOSS WILD-TYPE	69	41	33	73	25	60

Figure S48. 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 = 0.0073

Table S49. Gene #48: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
4Q LOSS MUTATED	2	15	0
4Q LOSS WILD-TYPE	271	119	85

Figure S49. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

'5p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S50. Gene #49: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
5P LOSS MUTATED	1	11	0
5P LOSS WILD-TYPE	272	123	85

Figure S50. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'

'5q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S51. Gene #50: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
5Q LOSS MUTATED	0	22	0
5Q LOSS WILD-TYPE	273	112	85

Figure S51. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

'6p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S52. Gene #51: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
6P LOSS MUTATED	4	21	0
6P LOSS WILD-TYPE	269	113	85

Figure S52. Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

'6q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S53. Gene #52: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
6Q LOSS MUTATED	5	32	3
6Q LOSS WILD-TYPE	268	102	82

Figure S53. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.19

Table S54. Gene #52: '6q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	173	166
6Q LOSS MUTATED	2	17	20
6Q LOSS WILD-TYPE	141	156	146

Figure S54. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S55. Gene #53: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
8P LOSS MUTATED	104	55	9
8P LOSS WILD-TYPE	169	79	76

Figure S55. Get High-res Image Gene #53: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S56. Gene #53: '8p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	134	126	121	39
8P LOSS MUTATED	17	41	58	23
8P LOSS WILD-TYPE	117	85	63	16

Figure S56. Get High-res Image Gene #53: '8p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S57. Gene #53: '8p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	162	175
8P LOSS MUTATED	31	45	90
8P LOSS WILD-TYPE	114	117	85

Figure S57. Get High-res Image Gene #53: '8p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.046

Table S58. Gene #53: '8p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	173	166
8P LOSS MUTATED	33	56	77
8P LOSS WILD-TYPE	110	117	89

Figure S58. Get High-res Image Gene #53: '8p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.21

Table S59. Gene #53: '8p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	147	183
8P LOSS MUTATED	43	41	83
8P LOSS WILD-TYPE	115	106	100

Figure S59. Get High-res Image Gene #53: '8p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S60. Gene #55: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
9P LOSS MUTATED	5	16	0
9P LOSS WILD-TYPE	268	118	85

Figure S60. Get High-res Image Gene #55: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S61. Gene #57: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
10P LOSS MUTATED	9	30	2
10P LOSS WILD-TYPE	264	104	83

Figure S61. Get High-res Image Gene #57: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S62. Gene #57: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	134	126	121	39
10P LOSS MUTATED	0	10	18	3
10P LOSS WILD-TYPE	134	116	103	36

Figure S62. Get High-res Image Gene #57: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.053

Table S63. Gene #57: '10p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	147	98	59	128	56
10P LOSS MUTATED	3	5	7	22	2
10P LOSS WILD-TYPE	144	93	52	106	54

Figure S63. Get High-res Image Gene #57: '10p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.033

Table S64. Gene #57: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
10P LOSS MUTATED	0	0	6	13	0	6
10P LOSS WILD-TYPE	70	41	34	69	25	54

Figure S64. 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 = 0.0073

Table S65. Gene #58: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
10Q LOSS MUTATED	9	31	3
10Q LOSS WILD-TYPE	264	103	82

Figure S65. Get High-res Image Gene #58: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.04

Table S66. Gene #58: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
10Q LOSS MUTATED	1	0	9	12	0	8
10Q LOSS WILD-TYPE	69	41	31	70	25	52

Figure S66. Get High-res Image Gene #58: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12p loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S67. Gene #61: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
12P LOSS MUTATED	22	26	0
12P LOSS WILD-TYPE	251	108	85

Figure S67. Get High-res Image Gene #61: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

'12q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S68. Gene #62: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
12Q LOSS MUTATED	5	15	0
12Q LOSS WILD-TYPE	268	119	85

Figure S68. Get High-res Image Gene #62: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'

'13q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S69. Gene #63: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
13Q LOSS MUTATED	19	49	9
13Q LOSS WILD-TYPE	254	85	76

Figure S69. Get High-res Image Gene #63: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

'13q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S70. Gene #63: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
13Q LOSS MUTATED	4	5	14	21	2	6
13Q LOSS WILD-TYPE	66	36	26	61	23	54

Figure S70. Get High-res Image Gene #63: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S71. Gene #64: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
14Q LOSS MUTATED	6	18	1
14Q LOSS WILD-TYPE	267	116	84

Figure S71. Get High-res Image Gene #64: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

'15q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S72. Gene #65: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
15Q LOSS MUTATED	4	30	2
15Q LOSS WILD-TYPE	269	104	83

Figure S72. Get High-res Image Gene #65: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'15q loss' versus 'MIRSEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.072

Table S73. Gene #65: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	147	183
15Q LOSS MUTATED	2	10	23
15Q LOSS WILD-TYPE	156	137	160

Figure S73. Get High-res Image Gene #65: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.066

Table S74. Gene #65: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
15Q LOSS MUTATED	0	1	8	12	0	6
15Q LOSS WILD-TYPE	70	40	32	70	25	54

Figure S74. Get High-res Image Gene #65: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S75. Gene #67: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
16Q LOSS MUTATED	40	62	5
16Q LOSS WILD-TYPE	233	72	80

Figure S75. Get High-res Image Gene #67: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.033

Table S76. Gene #67: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	134	126	121	39
16Q LOSS MUTATED	12	31	28	16
16Q LOSS WILD-TYPE	122	95	93	23

Figure S76. Get High-res Image Gene #67: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.066

Table S77. Gene #67: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
16Q LOSS MUTATED	7	4	15	30	3	12
16Q LOSS WILD-TYPE	63	37	25	52	22	48

Figure S77. Get High-res Image Gene #67: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S78. Gene #68: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
17P LOSS MUTATED	21	52	3
17P LOSS WILD-TYPE	252	82	82

Figure S78. Get High-res Image Gene #68: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.19

Table S79. Gene #68: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	162	175
17P LOSS MUTATED	12	20	42
17P LOSS WILD-TYPE	133	142	133

Figure S79. Get High-res Image Gene #68: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.027

Table S80. Gene #68: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
17P LOSS MUTATED	5	1	15	19	2	10
17P LOSS WILD-TYPE	65	40	25	63	23	50

Figure S80. Get High-res Image Gene #68: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S81. Gene #69: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
17Q LOSS MUTATED	2	16	2
17Q LOSS WILD-TYPE	271	118	83

Figure S81. Get High-res Image Gene #69: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

'18p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S82. Gene #70: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
18P LOSS MUTATED	21	43	4
18P LOSS WILD-TYPE	252	91	81

Figure S82. Get High-res Image Gene #70: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S83. Gene #71: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
18Q LOSS MUTATED	30	64	7
18Q LOSS WILD-TYPE	243	70	78

Figure S83. Get High-res Image Gene #71: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S84. Gene #71: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
18Q LOSS MUTATED	6	3	18	26	3	12
18Q LOSS WILD-TYPE	64	38	22	56	22	48

Figure S84. Get High-res Image Gene #71: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.085

Table S85. Gene #72: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
19P LOSS MUTATED	2	11	4
19P LOSS WILD-TYPE	271	123	81

Figure S85. Get High-res Image Gene #72: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

'19q loss' versus 'CN_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.15

Table S86. Gene #73: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
19Q LOSS MUTATED	2	11	4
19Q LOSS WILD-TYPE	271	123	81

Figure S86. Get High-res Image Gene #73: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S87. Gene #76: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
21Q LOSS MUTATED	7	17	0
21Q LOSS WILD-TYPE	266	117	85

Figure S87. Get High-res Image Gene #76: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S88. Gene #77: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
22Q LOSS MUTATED	12	32	3
22Q LOSS WILD-TYPE	261	102	82

Figure S88. Get High-res Image Gene #77: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.12

Table S89. Gene #77: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	41	40	82	25	60
22Q LOSS MUTATED	1	2	12	8	2	4
22Q LOSS WILD-TYPE	69	39	28	74	23	56

Figure S89. Get High-res Image Gene #77: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S90. Gene #78: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	134	85
XQ LOSS MUTATED	7	29	3
XQ LOSS WILD-TYPE	266	105	82

Figure S90. Get High-res Image Gene #78: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

'xq loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S91. Gene #78: 'xq loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	147	183
XQ LOSS MUTATED	4	4	30
XQ LOSS WILD-TYPE	154	143	153

Figure S91. Get High-res Image Gene #78: 'xq loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtypes file = PRAD-TP.transferedmergedcluster.txt
Number of patients = 492
Number of significantly arm-level cnvs = 78
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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