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

Thyroid Adenocarcinoma (Primary solid tumor)

16 April 2014 | analyses__2014_04_16

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/C15X27MN

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 57 arm-level events and 10 molecular subtypes across 494 patients, 166 significant findings detected with P value < 0.05 and Q value < 0.25.

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

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 57 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, 166 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
7q gain	20 (4%)	474	6.92e-25 (3.69e-22)	9.82e-06 (0.00451)	0.571 (1.00)	0.000676 (0.249)	0.000166 (0.067)	7.82e-06 (0.00368)	0.000144 (0.0585)	1.15e-05 (0.00527)	4.38e-05 (0.0189)	9.06e-06 (0.00419)
5q gain	17 (3%)	477	1.76e-22 (9.35e-20)	3.39e-05 (0.0147)	0.85 (1.00)	0.00745 (1.00)	0.000345 (0.132)	1.56e-05 (0.00709)	0.000344 (0.132)	4.11e-05 (0.0178)	9.6e-05 (0.0395)	3.18e-05 (0.0139)
12p gain	14 (3%)	480	1.48e-16 (7.82e-14)	3.71e-06 (0.00178)	0.85 (1.00)	0.00745 (1.00)	1.56e-05 (0.00709)	6.26e-07 (0.000315)	6.05e-05 (0.0256)	8.86e-06 (0.0041)	9.65e-06 (0.00445)	8.52e-06 (0.00396)
12q gain	15 (3%)	479	2.14e-16 (1.12e-13)	1.32e-06 (0.000645)	0.85 (1.00)	0.00745 (1.00)	8.44e-06 (0.00395)	1.55e-07 (7.87e-05)	2.24e-05 (0.00988)	2.87e-06 (0.00139)	3.63e-06 (0.00175)	2.66e-06 (0.00129)
16p gain	15 (3%)	479	6.94e-18 (3.67e-15)	1.85e-05 (0.0083)	0.633 (1.00)	0.0106 (1.00)	0.000187 (0.0751)	8.24e-06 (0.00386)	0.000192 (0.0765)	4.25e-05 (0.0184)	3.07e-05 (0.0134)	3.96e-05 (0.0172)
17p gain	16 (3%)	478	4.23e-13 (2.2e-10)	5.64e-07 (0.000285)	0.538 (1.00)	0.00327 (1.00)	4.05e-06 (0.00194)	4.72e-08 (2.42e-05)	8.06e-06 (0.00379)	8.97e-07 (0.00045)	1.33e-06 (0.000649)	8.04e-07 (0.000404)
17q gain	18 (4%)	476	5.03e-14 (2.62e-11)	1.13e-06 (0.000563)	0.633 (1.00)	0.00271 (0.906)	1.47e-05 (0.0067)	3.38e-07 (0.000171)	1.17e-05 (0.00533)	1.46e-06 (0.00071)	3.69e-06 (0.00177)	1.09e-06 (0.000544)
19p gain	8 (2%)	486	2.19e-10 (1.13e-07)	0.000139 (0.0568)			0.000585 (0.217)	5.96e-05 (0.0253)	6.43e-05 (0.027)	1.99e-05 (0.0088)	0.000242 (0.0955)	1.75e-05 (0.00787)
19q gain	10 (2%)	484	1.92e-11 (9.93e-09)	8.44e-06 (0.00395)	0.636 (1.00)	0.0523 (1.00)	7.31e-05 (0.0305)	6.66e-06 (0.00315)	5.49e-06 (0.00262)	1.25e-06 (0.000613)	2.43e-05 (0.0107)	1.06e-06 (0.000533)
2p loss	10 (2%)	484	1.92e-11 (9.93e-09)	8.44e-06 (0.00395)	0.773 (1.00)	0.0122 (1.00)	7.31e-05 (0.0305)	6.66e-06 (0.00315)	5.49e-06 (0.00262)	1.25e-06 (0.000613)	2.43e-05 (0.0107)	1.06e-06 (0.000533)
2q loss	10 (2%)	484	6.03e-13 (3.13e-10)	8.44e-06 (0.00395)	0.773 (1.00)	0.0122 (1.00)	7.31e-05 (0.0305)	6.66e-06 (0.00315)	5.49e-06 (0.00262)	1.25e-06 (0.000613)	2.43e-05 (0.0107)	1.06e-06 (0.000533)
15q loss	8 (2%)	486	5.63e-05 (0.0241)	0.000139 (0.0568)	0.193 (1.00)	0.126 (1.00)	0.000585 (0.217)	5.96e-05 (0.0253)	6.43e-05 (0.027)	1.99e-05 (0.0088)	0.000242 (0.0955)	1.75e-05 (0.00787)
14q gain	11 (2%)	483	3.23e-10 (1.66e-07)	0.000161 (0.0652)	1 (1.00)	0.079 (1.00)	0.000557 (0.207)	6.26e-05 (0.0264)	0.000461 (0.174)	0.000151 (0.0611)	0.00123 (0.434)	0.000114 (0.0468)
22q loss	86 (17%)	408	7.48e-90 (4e-87)	1.1e-05 (0.00502)	0.123 (1.00)	0.15 (1.00)	3.38e-09 (1.74e-06)	8.03e-08 (4.09e-05)	0.000956 (0.35)	0.000342 (0.132)	3.12e-06 (0.00151)	0.000206 (0.0821)
7p gain	18 (4%)	476	6.29e-24 (3.35e-21)	7.19e-05 (0.03)	0.66 (1.00)	0.00219 (0.746)	0.00088 (0.324)	6.17e-05 (0.026)	0.00105 (0.379)	0.000121 (0.0498)	0.000259 (0.102)	7.61e-05 (0.0314)
16q gain	13 (3%)	481	6.49e-17 (3.43e-14)	0.000121 (0.0498)	0.795 (1.00)	0.0363 (1.00)	0.00105 (0.379)	7.59e-05 (0.0314)	0.00171 (0.602)	0.000387 (0.146)	0.000182 (0.073)	0.000336 (0.13)
5p gain	21 (4%)	473	4.18e-23 (2.22e-20)	0.00093 (0.341)	0.53 (1.00)	0.0969 (1.00)	0.00705 (1.00)	0.000485 (0.182)	0.00411 (1.00)	0.000523 (0.195)	0.0011 (0.396)	0.00031 (0.12)
20p gain	12 (2%)	482	1.42e-15 (7.47e-13)	0.000376 (0.143)	0.795 (1.00)	0.0193 (1.00)	0.003 (0.993)	0.00026 (0.102)	0.00466 (1.00)	0.00111 (0.397)	0.000508 (0.19)	0.000981 (0.358)
20q gain	12 (2%)	482	1.42e-15 (7.47e-13)	0.000376 (0.143)	0.795 (1.00)	0.0193 (1.00)	0.003 (0.993)	0.00026 (0.102)	0.00466 (1.00)	0.00111 (0.397)	0.000508 (0.19)	0.000981 (0.358)
1q gain	24 (5%)	470	9.81e-06 (0.00451)	0.0289 (1.00)	0.00112 (0.4)	0.0319 (1.00)	0.000993 (0.36)	5.04e-05 (0.0216)	0.146 (1.00)	0.0524 (1.00)	0.0941 (1.00)	0.0219 (1.00)
11q loss	9 (2%)	485	3.28e-06 (0.00158)	0.0106 (1.00)	0.321 (1.00)	0.794 (1.00)	0.0176 (1.00)	0.00994 (1.00)	0.000352 (0.134)	0.00336 (1.00)	0.00122 (0.432)	0.00275 (0.914)
3p gain	3 (1%)	491	0.0003 (0.117)	0.582 (1.00)			0.488 (1.00)	0.195 (1.00)	0.207 (1.00)	0.355 (1.00)	0.323 (1.00)	0.27 (1.00)
4p gain	5 (1%)	489	1.16e-06 (0.000575)	0.00581 (1.00)			0.0181 (1.00)	0.00529 (1.00)	0.0268 (1.00)	0.0215 (1.00)	0.0687 (1.00)	0.0216 (1.00)
4q gain	5 (1%)	489	1.16e-06 (0.000575)	0.00581 (1.00)			0.0181 (1.00)	0.00529 (1.00)	0.0268 (1.00)	0.0215 (1.00)	0.0687 (1.00)	0.0216 (1.00)
8p gain	6 (1%)	488	0.000364 (0.139)	0.551 (1.00)	0.457 (1.00)	0.655 (1.00)	0.625 (1.00)	0.301 (1.00)	0.526 (1.00)	0.294 (1.00)	0.334 (1.00)	0.341 (1.00)
8q gain	7 (1%)	487	4.62e-05 (0.0199)	0.378 (1.00)	0.457 (1.00)	0.655 (1.00)	0.866 (1.00)	0.561 (1.00)	0.799 (1.00)	0.561 (1.00)	0.318 (1.00)	0.629 (1.00)
11p gain	6 (1%)	488	0.000191 (0.0764)	0.0263 (1.00)	0.78 (1.00)	0.284 (1.00)	0.053 (1.00)	0.0106 (1.00)	0.0146 (1.00)	0.00351 (1.00)	0.00237 (0.801)	0.00392 (1.00)
11q gain	5 (1%)	489	1.6e-05 (0.00724)	0.0757 (1.00)	0.78 (1.00)	0.284 (1.00)	0.116 (1.00)	0.0275 (1.00)	0.0415 (1.00)	0.0115 (1.00)	0.00735 (1.00)	0.0127 (1.00)
13q gain	5 (1%)	489	1.16e-06 (0.000575)	0.0173 (1.00)	0.384 (1.00)	0.0523 (1.00)	0.046 (1.00)	0.0196 (1.00)	0.169 (1.00)	0.139 (1.00)	0.21 (1.00)	0.148 (1.00)
18p gain	6 (1%)	488	1.16e-06 (0.000575)	0.0973 (1.00)			0.108 (1.00)	0.0489 (1.00)	0.255 (1.00)	0.0841 (1.00)	0.0259 (1.00)	0.107 (1.00)
18q gain	6 (1%)	488	1.16e-06 (0.000575)	0.0973 (1.00)			0.108 (1.00)	0.0489 (1.00)	0.255 (1.00)	0.0841 (1.00)	0.0259 (1.00)	0.107 (1.00)
21q gain	5 (1%)	489	1.6e-05 (0.00724)	0.249 (1.00)			0.217 (1.00)	0.111 (1.00)	0.451 (1.00)	0.229 (1.00)	0.0687 (1.00)	0.318 (1.00)
xq gain	9 (2%)	485	2.7e-07 (0.000137)	0.0217 (1.00)	0.839 (1.00)	0.25 (1.00)	0.0976 (1.00)	0.0414 (1.00)	0.337 (1.00)	0.207 (1.00)	0.483 (1.00)	0.196 (1.00)
1p loss	4 (1%)	490	1.89e-05 (0.00846)	0.22 (1.00)			0.237 (1.00)	0.089 (1.00)	0.0755 (1.00)	0.0676 (1.00)	0.129 (1.00)	0.0942 (1.00)
1q loss	3 (1%)	491	0.0003 (0.117)	0.0585 (1.00)			0.0959 (1.00)	0.0721 (1.00)	0.0278 (1.00)	0.018 (1.00)	0.0701 (1.00)	0.0172 (1.00)
3p loss	3 (1%)	491	0.0003 (0.117)	0.0585 (1.00)			0.0959 (1.00)	0.0721 (1.00)	0.0278 (1.00)	0.018 (1.00)	0.0701 (1.00)	0.0172 (1.00)
3q loss	4 (1%)	490	1.89e-05 (0.00846)	0.0149 (1.00)	0.495 (1.00)	0.364 (1.00)	0.0429 (1.00)	0.0157 (1.00)	0.00833 (1.00)	0.00467 (1.00)	0.0227 (1.00)	0.00439 (1.00)
6q loss	7 (1%)	487	4.62e-05 (0.0199)	0.0038 (1.00)	0.0129 (1.00)	0.364 (1.00)	0.032 (1.00)	0.00901 (1.00)	0.00316 (1.00)	0.00196 (0.683)	0.00954 (1.00)	0.00199 (0.683)
8p loss	4 (1%)	490	1.89e-05 (0.00846)	0.0149 (1.00)			0.0429 (1.00)	0.0157 (1.00)	0.00833 (1.00)	0.00467 (1.00)	0.0227 (1.00)	0.00439 (1.00)
8q loss	4 (1%)	490	1.89e-05 (0.00846)	0.0149 (1.00)			0.0429 (1.00)	0.0157 (1.00)	0.00833 (1.00)	0.00467 (1.00)	0.0227 (1.00)	0.00439 (1.00)
9p loss	19 (4%)	475	2.94e-12 (1.53e-09)	0.0258 (1.00)	0.243 (1.00)	0.368 (1.00)	0.0313 (1.00)	0.0138 (1.00)	0.00659 (1.00)	0.00303 (0.996)	0.00966 (1.00)	0.00181 (0.635)
9q loss	24 (5%)	470	9.23e-15 (4.83e-12)	0.0481 (1.00)	0.173 (1.00)	0.0332 (1.00)	0.106 (1.00)	0.0204 (1.00)	0.00917 (1.00)	0.00675 (1.00)	0.0117 (1.00)	0.00437 (1.00)
10p loss	7 (1%)	487	3.94e-09 (2.02e-06)	0.00956 (1.00)	0.495 (1.00)	0.364 (1.00)	0.0211 (1.00)	0.00294 (0.976)	0.00316 (1.00)	0.00196 (0.683)	0.00954 (1.00)	0.00199 (0.683)
10q loss	6 (1%)	488	6.87e-08 (3.51e-05)	0.0263 (1.00)			0.053 (1.00)	0.0106 (1.00)	0.00929 (1.00)	0.00658 (1.00)	0.0259 (1.00)	0.00664 (1.00)
11p loss	7 (1%)	487	7.98e-08 (4.07e-05)	0.00956 (1.00)	0.495 (1.00)	1 (1.00)	0.00675 (1.00)	0.00901 (1.00)	0.00316 (1.00)	0.00196 (0.683)	0.00954 (1.00)	0.00199 (0.683)
18p loss	4 (1%)	490	0.000207 (0.0821)	0.22 (1.00)	1 (1.00)	0.284 (1.00)	0.237 (1.00)	0.089 (1.00)	0.115 (1.00)	0.037 (1.00)	0.0227 (1.00)	0.0402 (1.00)
18q loss	4 (1%)	490	0.000207 (0.0821)	0.22 (1.00)	1 (1.00)	0.284 (1.00)	0.237 (1.00)	0.089 (1.00)	0.115 (1.00)	0.037 (1.00)	0.0227 (1.00)	0.0402 (1.00)
21q loss	8 (2%)	486	5.63e-05 (0.0241)	0.221 (1.00)	0.384 (1.00)	0.0523 (1.00)	0.652 (1.00)	0.503 (1.00)	0.0744 (1.00)	0.307 (1.00)	0.0974 (1.00)	0.0642 (1.00)
1p gain	3 (1%)	491	0.253 (1.00)	0.745 (1.00)			0.559 (1.00)	1 (1.00)	0.413 (1.00)	0.621 (1.00)	0.216 (1.00)	0.485 (1.00)
9p gain	3 (1%)	491	0.00246 (0.83)	0.582 (1.00)			0.488 (1.00)	0.195 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)
9q gain	4 (1%)	490	0.0101 (1.00)	0.649 (1.00)			0.897 (1.00)	0.104 (1.00)	1 (1.00)	0.822 (1.00)	1 (1.00)	0.828 (1.00)
6p loss	4 (1%)	490	0.00236 (0.801)	0.0594 (1.00)			0.454 (1.00)	0.289 (1.00)	0.0755 (1.00)	0.0676 (1.00)	0.129 (1.00)	0.0942 (1.00)
13q loss	14 (3%)	480	0.00844 (1.00)	0.02 (1.00)	0.0614 (1.00)	0.893 (1.00)	0.00551 (1.00)	0.0043 (1.00)	0.00199 (0.683)	0.00197 (0.683)	0.00187 (0.651)	0.00261 (0.874)
17p loss	8 (2%)	486	0.00182 (0.636)	0.335 (1.00)	1 (1.00)	0.284 (1.00)	0.652 (1.00)	0.452 (1.00)	0.33 (1.00)	0.307 (1.00)	0.672 (1.00)	0.282 (1.00)
17q loss	4 (1%)	490	0.0538 (1.00)	0.649 (1.00)			0.897 (1.00)	0.626 (1.00)	0.399 (1.00)	0.689 (1.00)	0.847 (1.00)	0.573 (1.00)
19p loss	5 (1%)	489	0.0251 (1.00)	0.00581 (1.00)	0.321 (1.00)	0.118 (1.00)	0.0181 (1.00)	0.00529 (1.00)	0.00249 (0.836)	0.0012 (0.427)	0.00735 (1.00)	0.00111 (0.397)
xq loss	3 (1%)	491	0.0219 (1.00)	0.0585 (1.00)	0.278 (1.00)	0.364 (1.00)	0.0959 (1.00)	0.0721 (1.00)	0.0278 (1.00)	0.018 (1.00)	0.0701 (1.00)	0.0172 (1.00)

'1q gain' versus 'CN_CNMF'

P value = 9.81e-06 (Fisher's exact test), Q value = 0.0045

Table S1. Gene #2: '1q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
1Q GAIN MUTATED	9	14	1
1Q GAIN WILD-TYPE	25	369	76

Figure S1. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #1: 'CN_CNMF'

'1q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.04e-05 (Fisher's exact test), Q value = 0.022

Table S2. Gene #2: '1q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	197	128	96	71
1Q GAIN MUTATED	21	2	1	0
1Q GAIN WILD-TYPE	176	126	95	71

Figure S2. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3p gain' versus 'CN_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.12

Table S3. Gene #3: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
3P GAIN MUTATED	3	0	0
3P GAIN WILD-TYPE	31	383	77

Figure S3. Get High-res Image Gene #3: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'

'4p gain' versus 'CN_CNMF'

P value = 1.16e-06 (Fisher's exact test), Q value = 0.00057

Table S4. Gene #4: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
4P GAIN MUTATED	5	0	0
4P GAIN WILD-TYPE	29	383	77

Figure S4. Get High-res Image Gene #4: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

'4q gain' versus 'CN_CNMF'

P value = 1.16e-06 (Fisher's exact test), Q value = 0.00057

Table S5. Gene #5: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
4Q GAIN MUTATED	5	0	0
4Q GAIN WILD-TYPE	29	383	77

Figure S5. Get High-res Image Gene #5: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'CN_CNMF'

P value = 4.18e-23 (Fisher's exact test), Q value = 2.2e-20

Table S6. Gene #6: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
5P GAIN MUTATED	19	2	0
5P GAIN WILD-TYPE	15	381	77

Figure S6. Get High-res Image Gene #6: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000485 (Fisher's exact test), Q value = 0.18

Table S7. Gene #6: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	197	128	96	71
5P GAIN MUTATED	6	14	1	0
5P GAIN WILD-TYPE	191	114	95	71

Figure S7. Get High-res Image Gene #6: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000523 (Fisher's exact test), Q value = 0.2

Table S8. Gene #6: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	130	208
5P GAIN MUTATED	1	13	7
5P GAIN WILD-TYPE	154	117	201

Figure S8. Get High-res Image Gene #6: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.12

Table S9. Gene #6: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	199	128	166
5P GAIN MUTATED	7	13	1
5P GAIN WILD-TYPE	192	115	165

Figure S9. Get High-res Image Gene #6: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q gain' versus 'CN_CNMF'

P value = 1.76e-22 (Fisher's exact test), Q value = 9.4e-20

Table S10. Gene #7: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
5Q GAIN MUTATED	17	0	0
5Q GAIN WILD-TYPE	17	383	77

Figure S10. Get High-res Image Gene #7: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

'5q gain' versus 'METHLYATION_CNMF'

P value = 3.39e-05 (Fisher's exact test), Q value = 0.015

Table S11. Gene #7: '5q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	83	260
5Q GAIN MUTATED	14	1	2
5Q GAIN WILD-TYPE	137	82	258

Figure S11. Get High-res Image Gene #7: '5q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q gain' versus 'MRNASEQ_CNMF'

P value = 0.000345 (Fisher's exact test), Q value = 0.13

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	154	55	116	167
5Q GAIN MUTATED	14	0	1	2
5Q GAIN WILD-TYPE	140	55	115	165

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

'5q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.56e-05 (Fisher's exact test), Q value = 0.0071

Table S13. Gene #7: '5q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	197	128	96	71
5Q GAIN MUTATED	2	14	1	0
5Q GAIN WILD-TYPE	195	114	95	71

Figure S13. Get High-res Image Gene #7: '5q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_CNMF'

P value = 0.000344 (Fisher's exact test), Q value = 0.13

Table S14. Gene #7: '5q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	173	170
5Q GAIN MUTATED	13	2	2
5Q GAIN WILD-TYPE	137	171	168

Figure S14. Get High-res Image Gene #7: '5q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'5q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.11e-05 (Fisher's exact test), Q value = 0.018

Table S15. Gene #7: '5q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	130	208
5Q GAIN MUTATED	1	13	3
5Q GAIN WILD-TYPE	154	117	205

Figure S15. Get High-res Image Gene #7: '5q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 9.6e-05 (Fisher's exact test), Q value = 0.04

Table S16. Gene #7: '5q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	169	161
5Q GAIN MUTATED	14	1	2
5Q GAIN WILD-TYPE	149	168	159

Figure S16. Get High-res Image Gene #7: '5q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'5q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.18e-05 (Fisher's exact test), Q value = 0.014

Table S17. Gene #7: '5q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	199	128	166
5Q GAIN MUTATED	3	13	1
5Q GAIN WILD-TYPE	196	115	165

Figure S17. Get High-res Image Gene #7: '5q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

P value = 6.29e-24 (Fisher's exact test), Q value = 3.3e-21

Table S18. Gene #8: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
7P GAIN MUTATED	18	0	0
7P GAIN WILD-TYPE	16	383	77

Figure S18. Get High-res Image Gene #8: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 7.19e-05 (Fisher's exact test), Q value = 0.03

Table S19. Gene #8: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	83	260
7P GAIN MUTATED	14	2	2
7P GAIN WILD-TYPE	137	81	258

Figure S19. Get High-res Image Gene #8: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.17e-05 (Fisher's exact test), Q value = 0.026

Table S20. Gene #8: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	197	128	96	71
7P GAIN MUTATED	2	14	1	1
7P GAIN WILD-TYPE	195	114	95	70

Figure S20. Get High-res Image Gene #8: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000121 (Fisher's exact test), Q value = 0.05

Table S21. Gene #8: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	130	208
7P GAIN MUTATED	1	13	4
7P GAIN WILD-TYPE	154	117	204

Figure S21. Get High-res Image Gene #8: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000259 (Fisher's exact test), Q value = 0.1

Table S22. Gene #8: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	169	161
7P GAIN MUTATED	14	1	3
7P GAIN WILD-TYPE	149	168	158

Figure S22. Get High-res Image Gene #8: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'7p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.61e-05 (Fisher's exact test), Q value = 0.031

Table S23. Gene #8: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	199	128	166
7P GAIN MUTATED	4	13	1
7P GAIN WILD-TYPE	195	115	165

Figure S23. Get High-res Image Gene #8: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 6.92e-25 (Fisher's exact test), Q value = 3.7e-22

Table S24. Gene #9: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
7Q GAIN MUTATED	19	0	1
7Q GAIN WILD-TYPE	15	383	76

Figure S24. Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 9.82e-06 (Fisher's exact test), Q value = 0.0045

Table S25. Gene #9: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	83	260
7Q GAIN MUTATED	16	2	2
7Q GAIN WILD-TYPE	135	81	258

Figure S25. Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.000676 (Fisher's exact test), Q value = 0.25

Table S26. Gene #9: '7q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	31	94	96
7Q GAIN MUTATED	5	0	7
7Q GAIN WILD-TYPE	26	94	89

Figure S26. Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 0.000166 (Fisher's exact test), Q value = 0.067

Table S27. Gene #9: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	154	55	116	167
7Q GAIN MUTATED	16	1	1	2
7Q GAIN WILD-TYPE	138	54	115	165

Figure S27. Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.82e-06 (Fisher's exact test), Q value = 0.0037

Table S28. Gene #9: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	197	128	96	71
7Q GAIN MUTATED	2	16	1	1
7Q GAIN WILD-TYPE	195	112	95	70

Figure S28. Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_CNMF'

P value = 0.000144 (Fisher's exact test), Q value = 0.058

Table S29. Gene #9: '7q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	173	170
7Q GAIN MUTATED	15	2	3
7Q GAIN WILD-TYPE	135	171	167

Figure S29. Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'7q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.15e-05 (Fisher's exact test), Q value = 0.0053

Table S30. Gene #9: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	130	208
7Q GAIN MUTATED	1	15	4
7Q GAIN WILD-TYPE	154	115	204

Figure S30. Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.38e-05 (Fisher's exact test), Q value = 0.019

Table S31. Gene #9: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	169	161
7Q GAIN MUTATED	16	1	3
7Q GAIN WILD-TYPE	147	168	158

Figure S31. Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'7q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9.06e-06 (Fisher's exact test), Q value = 0.0042

Table S32. Gene #9: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	199	128	166
7Q GAIN MUTATED	4	15	1
7Q GAIN WILD-TYPE	195	113	165

Figure S32. Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

P value = 0.000364 (Fisher's exact test), Q value = 0.14

Table S33. Gene #10: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
8P GAIN MUTATED	4	2	0
8P GAIN WILD-TYPE	30	381	77

Figure S33. Get High-res Image Gene #10: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

'8q gain' versus 'CN_CNMF'

P value = 4.62e-05 (Fisher's exact test), Q value = 0.02

Table S34. Gene #11: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
8Q GAIN MUTATED	5	2	0
8Q GAIN WILD-TYPE	29	381	77

Figure S34. Get High-res Image Gene #11: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

'11p gain' versus 'CN_CNMF'

P value = 0.000191 (Fisher's exact test), Q value = 0.076

Table S35. Gene #14: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
11P GAIN MUTATED	4	1	1
11P GAIN WILD-TYPE	30	382	76

Figure S35. Get High-res Image Gene #14: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

'11q gain' versus 'CN_CNMF'

P value = 1.6e-05 (Fisher's exact test), Q value = 0.0072

Table S36. Gene #15: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
11Q GAIN MUTATED	4	0	1
11Q GAIN WILD-TYPE	30	383	76

Figure S36. Get High-res Image Gene #15: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 1.48e-16 (Fisher's exact test), Q value = 7.8e-14

Table S37. Gene #16: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
12P GAIN MUTATED	13	0	1
12P GAIN WILD-TYPE	21	383	76

Figure S37. Get High-res Image Gene #16: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 3.71e-06 (Fisher's exact test), Q value = 0.0018

Table S38. Gene #16: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	83	260
12P GAIN MUTATED	13	0	1
12P GAIN WILD-TYPE	138	83	259

Figure S38. Get High-res Image Gene #16: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 1.56e-05 (Fisher's exact test), Q value = 0.0071

Table S39. Gene #16: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	154	55	116	167
12P GAIN MUTATED	13	0	1	0
12P GAIN WILD-TYPE	141	55	115	167

Figure S39. Get High-res Image Gene #16: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.26e-07 (Fisher's exact test), Q value = 0.00032

Table S40. Gene #16: '12p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	197	128	96	71
12P GAIN MUTATED	0	13	1	0
12P GAIN WILD-TYPE	197	115	95	71

Figure S40. Get High-res Image Gene #16: '12p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_CNMF'

P value = 6.05e-05 (Fisher's exact test), Q value = 0.026

Table S41. Gene #16: '12p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	173	170
12P GAIN MUTATED	12	1	1
12P GAIN WILD-TYPE	138	172	169

Figure S41. Get High-res Image Gene #16: '12p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'12p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.86e-06 (Fisher's exact test), Q value = 0.0041

Table S42. Gene #16: '12p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	130	208
12P GAIN MUTATED	1	12	1
12P GAIN WILD-TYPE	154	118	207

Figure S42. Get High-res Image Gene #16: '12p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 9.65e-06 (Fisher's exact test), Q value = 0.0044

Table S43. Gene #16: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	169	161
12P GAIN MUTATED	13	0	1
12P GAIN WILD-TYPE	150	169	160

Figure S43. Get High-res Image Gene #16: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'12p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8.52e-06 (Fisher's exact test), Q value = 0.004

Table S44. Gene #16: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	199	128	166
12P GAIN MUTATED	1	12	1
12P GAIN WILD-TYPE	198	116	165

Figure S44. Get High-res Image Gene #16: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q gain' versus 'CN_CNMF'

P value = 2.14e-16 (Fisher's exact test), Q value = 1.1e-13

Table S45. Gene #17: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
12Q GAIN MUTATED	13	0	2
12Q GAIN WILD-TYPE	21	383	75

Figure S45. Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

'12q gain' versus 'METHLYATION_CNMF'

P value = 1.32e-06 (Fisher's exact test), Q value = 0.00064

Table S46. Gene #17: '12q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	83	260
12Q GAIN MUTATED	14	0	1
12Q GAIN WILD-TYPE	137	83	259

Figure S46. Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12q gain' versus 'MRNASEQ_CNMF'

P value = 8.44e-06 (Fisher's exact test), Q value = 0.0039

Table S47. Gene #17: '12q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	154	55	116	167
12Q GAIN MUTATED	14	0	1	0
12Q GAIN WILD-TYPE	140	55	115	167

Figure S47. Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.55e-07 (Fisher's exact test), Q value = 7.9e-05

Table S48. Gene #17: '12q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	197	128	96	71
12Q GAIN MUTATED	0	14	1	0
12Q GAIN WILD-TYPE	197	114	95	71

Figure S48. Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_CNMF'

P value = 2.24e-05 (Fisher's exact test), Q value = 0.0099

Table S49. Gene #17: '12q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	173	170
12Q GAIN MUTATED	13	1	1
12Q GAIN WILD-TYPE	137	172	169

Figure S49. Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'12q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.87e-06 (Fisher's exact test), Q value = 0.0014

Table S50. Gene #17: '12q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	130	208
12Q GAIN MUTATED	1	13	1
12Q GAIN WILD-TYPE	154	117	207

Figure S50. Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.63e-06 (Fisher's exact test), Q value = 0.0017

Table S51. Gene #17: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	169	161
12Q GAIN MUTATED	14	0	1
12Q GAIN WILD-TYPE	149	169	160

Figure S51. Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'12q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.66e-06 (Fisher's exact test), Q value = 0.0013

Table S52. Gene #17: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	199	128	166
12Q GAIN MUTATED	1	13	1
12Q GAIN WILD-TYPE	198	115	165

Figure S52. Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q gain' versus 'CN_CNMF'

P value = 1.16e-06 (Fisher's exact test), Q value = 0.00057

Table S53. Gene #18: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
13Q GAIN MUTATED	5	0	0
13Q GAIN WILD-TYPE	29	383	77

Figure S53. Get High-res Image Gene #18: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

'14q gain' versus 'CN_CNMF'

P value = 3.23e-10 (Fisher's exact test), Q value = 1.7e-07

Table S54. Gene #19: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
14Q GAIN MUTATED	9	1	1
14Q GAIN WILD-TYPE	25	382	76

Figure S54. Get High-res Image Gene #19: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

'14q gain' versus 'METHLYATION_CNMF'

P value = 0.000161 (Fisher's exact test), Q value = 0.065

Table S55. Gene #19: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	83	260
14Q GAIN MUTATED	10	0	1
14Q GAIN WILD-TYPE	141	83	259

Figure S55. Get High-res Image Gene #19: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'14q gain' versus 'MRNASEQ_CNMF'

P value = 0.000557 (Fisher's exact test), Q value = 0.21

Table S56. Gene #19: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	154	55	116	167
14Q GAIN MUTATED	10	0	0	1
14Q GAIN WILD-TYPE	144	55	116	166

Figure S56. Get High-res Image Gene #19: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.26e-05 (Fisher's exact test), Q value = 0.026

Table S57. Gene #19: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	197	128	96	71
14Q GAIN MUTATED	1	10	0	0
14Q GAIN WILD-TYPE	196	118	96	71

Figure S57. Get High-res Image Gene #19: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_CNMF'

P value = 0.000461 (Fisher's exact test), Q value = 0.17

Table S58. Gene #19: '14q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	173	170
14Q GAIN MUTATED	9	0	2
14Q GAIN WILD-TYPE	141	173	168

Figure S58. Get High-res Image Gene #19: '14q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'14q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000151 (Fisher's exact test), Q value = 0.061

Table S59. Gene #19: '14q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	130	208
14Q GAIN MUTATED	0	9	2
14Q GAIN WILD-TYPE	155	121	206

Figure S59. Get High-res Image Gene #19: '14q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000114 (Fisher's exact test), Q value = 0.047

Table S60. Gene #19: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	199	128	166
14Q GAIN MUTATED	2	9	0
14Q GAIN WILD-TYPE	197	119	166

Figure S60. Get High-res Image Gene #19: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p gain' versus 'CN_CNMF'

P value = 6.94e-18 (Fisher's exact test), Q value = 3.7e-15

Table S61. Gene #20: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
16P GAIN MUTATED	14	0	1
16P GAIN WILD-TYPE	20	383	76

Figure S61. Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

'16p gain' versus 'METHLYATION_CNMF'

P value = 1.85e-05 (Fisher's exact test), Q value = 0.0083

Table S62. Gene #20: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	83	260
16P GAIN MUTATED	13	1	1
16P GAIN WILD-TYPE	138	82	259

Figure S62. Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 0.000187 (Fisher's exact test), Q value = 0.075

Table S63. Gene #20: '16p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	154	55	116	167
16P GAIN MUTATED	13	0	1	1
16P GAIN WILD-TYPE	141	55	115	166

Figure S63. Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.24e-06 (Fisher's exact test), Q value = 0.0039

Table S64. Gene #20: '16p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	197	128	96	71
16P GAIN MUTATED	1	13	1	0
16P GAIN WILD-TYPE	196	115	95	71

Figure S64. Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_CNMF'

P value = 0.000192 (Fisher's exact test), Q value = 0.077

Table S65. Gene #20: '16p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	173	170
16P GAIN MUTATED	12	1	2
16P GAIN WILD-TYPE	138	172	168

Figure S65. Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.25e-05 (Fisher's exact test), Q value = 0.018

Table S66. Gene #20: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	130	208
16P GAIN MUTATED	1	12	2
16P GAIN WILD-TYPE	154	118	206

Figure S66. Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.07e-05 (Fisher's exact test), Q value = 0.013

Table S67. Gene #20: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	169	161
16P GAIN MUTATED	13	0	2
16P GAIN WILD-TYPE	150	169	159

Figure S67. Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.96e-05 (Fisher's exact test), Q value = 0.017

Table S68. Gene #20: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	199	128	166
16P GAIN MUTATED	2	12	1
16P GAIN WILD-TYPE	197	116	165

Figure S68. Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q gain' versus 'CN_CNMF'

P value = 6.49e-17 (Fisher's exact test), Q value = 3.4e-14

Table S69. Gene #21: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
16Q GAIN MUTATED	13	0	0
16Q GAIN WILD-TYPE	21	383	77

Figure S69. Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16q gain' versus 'METHLYATION_CNMF'

P value = 0.000121 (Fisher's exact test), Q value = 0.05

Table S70. Gene #21: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	83	260
16Q GAIN MUTATED	11	1	1
16Q GAIN WILD-TYPE	140	82	259

Figure S70. Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.59e-05 (Fisher's exact test), Q value = 0.031

Table S71. Gene #21: '16q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	197	128	96	71
16Q GAIN MUTATED	1	11	1	0
16Q GAIN WILD-TYPE	196	117	95	71

Figure S71. Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000387 (Fisher's exact test), Q value = 0.15

Table S72. Gene #21: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	130	208
16Q GAIN MUTATED	1	10	2
16Q GAIN WILD-TYPE	154	120	206

Figure S72. Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000182 (Fisher's exact test), Q value = 0.073

Table S73. Gene #21: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	169	161
16Q GAIN MUTATED	11	0	2
16Q GAIN WILD-TYPE	152	169	159

Figure S73. Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000336 (Fisher's exact test), Q value = 0.13

Table S74. Gene #21: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	199	128	166
16Q GAIN MUTATED	2	10	1
16Q GAIN WILD-TYPE	197	118	165

Figure S74. Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p gain' versus 'CN_CNMF'

P value = 4.23e-13 (Fisher's exact test), Q value = 2.2e-10

Table S75. Gene #22: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
17P GAIN MUTATED	12	2	2
17P GAIN WILD-TYPE	22	381	75

Figure S75. Get High-res Image Gene #22: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

'17p gain' versus 'METHLYATION_CNMF'

P value = 5.64e-07 (Fisher's exact test), Q value = 0.00028

Table S76. Gene #22: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	83	260
17P GAIN MUTATED	15	0	1
17P GAIN WILD-TYPE	136	83	259

Figure S76. Get High-res Image Gene #22: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p gain' versus 'MRNASEQ_CNMF'

P value = 4.05e-06 (Fisher's exact test), Q value = 0.0019

Table S77. Gene #22: '17p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	154	55	116	167
17P GAIN MUTATED	15	0	1	0
17P GAIN WILD-TYPE	139	55	115	167

Figure S77. Get High-res Image Gene #22: '17p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.72e-08 (Fisher's exact test), Q value = 2.4e-05

Table S78. Gene #22: '17p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	197	128	96	71
17P GAIN MUTATED	0	15	1	0
17P GAIN WILD-TYPE	197	113	95	71

Figure S78. Get High-res Image Gene #22: '17p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_CNMF'

P value = 8.06e-06 (Fisher's exact test), Q value = 0.0038

Table S79. Gene #22: '17p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	173	170
17P GAIN MUTATED	14	1	1
17P GAIN WILD-TYPE	136	172	169

Figure S79. Get High-res Image Gene #22: '17p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.97e-07 (Fisher's exact test), Q value = 0.00045

Table S80. Gene #22: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	130	208
17P GAIN MUTATED	1	14	1
17P GAIN WILD-TYPE	154	116	207

Figure S80. Get High-res Image Gene #22: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.33e-06 (Fisher's exact test), Q value = 0.00065

Table S81. Gene #22: '17p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	169	161
17P GAIN MUTATED	15	0	1
17P GAIN WILD-TYPE	148	169	160

Figure S81. Get High-res Image Gene #22: '17p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8.04e-07 (Fisher's exact test), Q value = 4e-04

Table S82. Gene #22: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	199	128	166
17P GAIN MUTATED	1	14	1
17P GAIN WILD-TYPE	198	114	165

Figure S82. Get High-res Image Gene #22: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q gain' versus 'CN_CNMF'

P value = 5.03e-14 (Fisher's exact test), Q value = 2.6e-11

Table S83. Gene #23: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
17Q GAIN MUTATED	13	2	3
17Q GAIN WILD-TYPE	21	381	74

Figure S83. Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 1.13e-06 (Fisher's exact test), Q value = 0.00056

Table S84. Gene #23: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	83	260
17Q GAIN MUTATED	16	0	2
17Q GAIN WILD-TYPE	135	83	258

Figure S84. Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 1.47e-05 (Fisher's exact test), Q value = 0.0067

Table S85. Gene #23: '17q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	154	55	116	167
17Q GAIN MUTATED	16	0	1	1
17Q GAIN WILD-TYPE	138	55	115	166

Figure S85. Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.38e-07 (Fisher's exact test), Q value = 0.00017

Table S86. Gene #23: '17q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	197	128	96	71
17Q GAIN MUTATED	1	16	1	0
17Q GAIN WILD-TYPE	196	112	95	71

Figure S86. Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_CNMF'

P value = 1.17e-05 (Fisher's exact test), Q value = 0.0053

Table S87. Gene #23: '17q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	173	170
17Q GAIN MUTATED	15	2	1
17Q GAIN WILD-TYPE	135	171	169

Figure S87. Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.46e-06 (Fisher's exact test), Q value = 0.00071

Table S88. Gene #23: '17q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	130	208
17Q GAIN MUTATED	1	15	2
17Q GAIN WILD-TYPE	154	115	206

Figure S88. Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.69e-06 (Fisher's exact test), Q value = 0.0018

Table S89. Gene #23: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	169	161
17Q GAIN MUTATED	16	1	1
17Q GAIN WILD-TYPE	147	168	160

Figure S89. Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.09e-06 (Fisher's exact test), Q value = 0.00054

Table S90. Gene #23: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	199	128	166
17Q GAIN MUTATED	2	15	1
17Q GAIN WILD-TYPE	197	113	165

Figure S90. Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p gain' versus 'CN_CNMF'

P value = 1.16e-06 (Fisher's exact test), Q value = 0.00057

Table S91. Gene #24: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
18P GAIN MUTATED	5	0	1
18P GAIN WILD-TYPE	29	383	76

Figure S91. Get High-res Image Gene #24: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

'18q gain' versus 'CN_CNMF'

P value = 1.16e-06 (Fisher's exact test), Q value = 0.00057

Table S92. Gene #25: '18q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
18Q GAIN MUTATED	5	0	1
18Q GAIN WILD-TYPE	29	383	76

Figure S92. Get High-res Image Gene #25: '18q gain' versus Molecular Subtype #1: 'CN_CNMF'

'19p gain' versus 'CN_CNMF'

P value = 2.19e-10 (Fisher's exact test), Q value = 1.1e-07

Table S93. Gene #26: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
19P GAIN MUTATED	8	0	0
19P GAIN WILD-TYPE	26	383	77

Figure S93. Get High-res Image Gene #26: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

'19p gain' versus 'METHLYATION_CNMF'

P value = 0.000139 (Fisher's exact test), Q value = 0.057

Table S94. Gene #26: '19p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	83	260
19P GAIN MUTATED	8	0	0
19P GAIN WILD-TYPE	143	83	260

Figure S94. Get High-res Image Gene #26: '19p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19p gain' versus 'MRNASEQ_CNMF'

P value = 0.000585 (Fisher's exact test), Q value = 0.22

Table S95. Gene #26: '19p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	154	55	116	167
19P GAIN MUTATED	8	0	0	0
19P GAIN WILD-TYPE	146	55	116	167

Figure S95. Get High-res Image Gene #26: '19p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.96e-05 (Fisher's exact test), Q value = 0.025

Table S96. Gene #26: '19p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	197	128	96	71
19P GAIN MUTATED	0	8	0	0
19P GAIN WILD-TYPE	197	120	96	71

Figure S96. Get High-res Image Gene #26: '19p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_CNMF'

P value = 6.43e-05 (Fisher's exact test), Q value = 0.027

Table S97. Gene #26: '19p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	173	170
19P GAIN MUTATED	8	0	0
19P GAIN WILD-TYPE	142	173	170

Figure S97. Get High-res Image Gene #26: '19p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'19p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.99e-05 (Fisher's exact test), Q value = 0.0088

Table S98. Gene #26: '19p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	130	208
19P GAIN MUTATED	0	8	0
19P GAIN WILD-TYPE	155	122	208

Figure S98. Get High-res Image Gene #26: '19p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000242 (Fisher's exact test), Q value = 0.095

Table S99. Gene #26: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	169	161
19P GAIN MUTATED	8	0	0
19P GAIN WILD-TYPE	155	169	161

Figure S99. Get High-res Image Gene #26: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'19p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.75e-05 (Fisher's exact test), Q value = 0.0079

Table S100. Gene #26: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	199	128	166
19P GAIN MUTATED	0	8	0
19P GAIN WILD-TYPE	199	120	166

Figure S100. Get High-res Image Gene #26: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q gain' versus 'CN_CNMF'

P value = 1.92e-11 (Fisher's exact test), Q value = 9.9e-09

Table S101. Gene #27: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
19Q GAIN MUTATED	9	0	1
19Q GAIN WILD-TYPE	25	383	76

Figure S101. Get High-res Image Gene #27: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

'19q gain' versus 'METHLYATION_CNMF'

P value = 8.44e-06 (Fisher's exact test), Q value = 0.0039

Table S102. Gene #27: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	83	260
19Q GAIN MUTATED	10	0	0
19Q GAIN WILD-TYPE	141	83	260

Figure S102. Get High-res Image Gene #27: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 7.31e-05 (Fisher's exact test), Q value = 0.03

Table S103. Gene #27: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	154	55	116	167
19Q GAIN MUTATED	10	0	0	0
19Q GAIN WILD-TYPE	144	55	116	167

Figure S103. Get High-res Image Gene #27: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.66e-06 (Fisher's exact test), Q value = 0.0032

Table S104. Gene #27: '19q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	197	128	96	71
19Q GAIN MUTATED	0	10	0	0
19Q GAIN WILD-TYPE	197	118	96	71

Figure S104. Get High-res Image Gene #27: '19q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_CNMF'

P value = 5.49e-06 (Fisher's exact test), Q value = 0.0026

Table S105. Gene #27: '19q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	173	170
19Q GAIN MUTATED	10	0	0
19Q GAIN WILD-TYPE	140	173	170

Figure S105. Get High-res Image Gene #27: '19q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'19q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.25e-06 (Fisher's exact test), Q value = 0.00061

Table S106. Gene #27: '19q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	130	208
19Q GAIN MUTATED	0	10	0
19Q GAIN WILD-TYPE	155	120	208

Figure S106. Get High-res Image Gene #27: '19q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.43e-05 (Fisher's exact test), Q value = 0.011

Table S107. Gene #27: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	169	161
19Q GAIN MUTATED	10	0	0
19Q GAIN WILD-TYPE	153	169	161

Figure S107. Get High-res Image Gene #27: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'19q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.06e-06 (Fisher's exact test), Q value = 0.00053

Table S108. Gene #27: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	199	128	166
19Q GAIN MUTATED	0	10	0
19Q GAIN WILD-TYPE	199	118	166

Figure S108. Get High-res Image Gene #27: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 1.42e-15 (Fisher's exact test), Q value = 7.5e-13

Table S109. Gene #28: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
20P GAIN MUTATED	12	0	0
20P GAIN WILD-TYPE	22	383	77

Figure S109. Get High-res Image Gene #28: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 0.000376 (Fisher's exact test), Q value = 0.14

Table S110. Gene #28: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	83	260
20P GAIN MUTATED	10	1	1
20P GAIN WILD-TYPE	141	82	259

Figure S110. Get High-res Image Gene #28: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.1

Table S111. Gene #28: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	197	128	96	71
20P GAIN MUTATED	1	10	1	0
20P GAIN WILD-TYPE	196	118	95	71

Figure S111. Get High-res Image Gene #28: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000508 (Fisher's exact test), Q value = 0.19

Table S112. Gene #28: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	169	161
20P GAIN MUTATED	10	0	2
20P GAIN WILD-TYPE	153	169	159

Figure S112. Get High-res Image Gene #28: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'CN_CNMF'

P value = 1.42e-15 (Fisher's exact test), Q value = 7.5e-13

Table S113. Gene #29: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
20Q GAIN MUTATED	12	0	0
20Q GAIN WILD-TYPE	22	383	77

Figure S113. Get High-res Image Gene #29: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 0.000376 (Fisher's exact test), Q value = 0.14

Table S114. Gene #29: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	83	260
20Q GAIN MUTATED	10	1	1
20Q GAIN WILD-TYPE	141	82	259

Figure S114. Get High-res Image Gene #29: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.1

Table S115. Gene #29: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	197	128	96	71
20Q GAIN MUTATED	1	10	1	0
20Q GAIN WILD-TYPE	196	118	95	71

Figure S115. Get High-res Image Gene #29: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000508 (Fisher's exact test), Q value = 0.19

Table S116. Gene #29: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	169	161
20Q GAIN MUTATED	10	0	2
20Q GAIN WILD-TYPE	153	169	159

Figure S116. Get High-res Image Gene #29: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'21q gain' versus 'CN_CNMF'

P value = 1.6e-05 (Fisher's exact test), Q value = 0.0072

Table S117. Gene #30: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
21Q GAIN MUTATED	4	0	1
21Q GAIN WILD-TYPE	30	383	76

Figure S117. Get High-res Image Gene #30: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

'xq gain' versus 'CN_CNMF'

P value = 2.7e-07 (Fisher's exact test), Q value = 0.00014

Table S118. Gene #31: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
XQ GAIN MUTATED	7	2	0
XQ GAIN WILD-TYPE	27	381	77

Figure S118. Get High-res Image Gene #31: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

'1p loss' versus 'CN_CNMF'

P value = 1.89e-05 (Fisher's exact test), Q value = 0.0085

Table S119. Gene #32: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
1P LOSS MUTATED	4	0	0
1P LOSS WILD-TYPE	30	383	77

Figure S119. Get High-res Image Gene #32: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

'1q loss' versus 'CN_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.12

Table S120. Gene #33: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
1Q LOSS MUTATED	3	0	0
1Q LOSS WILD-TYPE	31	383	77

Figure S120. Get High-res Image Gene #33: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

'2p loss' versus 'CN_CNMF'

P value = 1.92e-11 (Fisher's exact test), Q value = 9.9e-09

Table S121. Gene #34: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
2P LOSS MUTATED	9	0	1
2P LOSS WILD-TYPE	25	383	76

Figure S121. Get High-res Image Gene #34: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

'2p loss' versus 'METHLYATION_CNMF'

P value = 8.44e-06 (Fisher's exact test), Q value = 0.0039

Table S122. Gene #34: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	83	260
2P LOSS MUTATED	10	0	0
2P LOSS WILD-TYPE	141	83	260

Figure S122. Get High-res Image Gene #34: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2p loss' versus 'MRNASEQ_CNMF'

P value = 7.31e-05 (Fisher's exact test), Q value = 0.03

Table S123. Gene #34: '2p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	154	55	116	167
2P LOSS MUTATED	10	0	0	0
2P LOSS WILD-TYPE	144	55	116	167

Figure S123. Get High-res Image Gene #34: '2p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.66e-06 (Fisher's exact test), Q value = 0.0032

Table S124. Gene #34: '2p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	197	128	96	71
2P LOSS MUTATED	0	10	0	0
2P LOSS WILD-TYPE	197	118	96	71

Figure S124. Get High-res Image Gene #34: '2p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_CNMF'

P value = 5.49e-06 (Fisher's exact test), Q value = 0.0026

Table S125. Gene #34: '2p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	173	170
2P LOSS MUTATED	10	0	0
2P LOSS WILD-TYPE	140	173	170

Figure S125. Get High-res Image Gene #34: '2p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'2p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.25e-06 (Fisher's exact test), Q value = 0.00061

Table S126. Gene #34: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	130	208
2P LOSS MUTATED	0	10	0
2P LOSS WILD-TYPE	155	120	208

Figure S126. Get High-res Image Gene #34: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.43e-05 (Fisher's exact test), Q value = 0.011

Table S127. Gene #34: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	169	161
2P LOSS MUTATED	10	0	0
2P LOSS WILD-TYPE	153	169	161

Figure S127. Get High-res Image Gene #34: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'2p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.06e-06 (Fisher's exact test), Q value = 0.00053

Table S128. Gene #34: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	199	128	166
2P LOSS MUTATED	0	10	0
2P LOSS WILD-TYPE	199	118	166

Figure S128. Get High-res Image Gene #34: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q loss' versus 'CN_CNMF'

P value = 6.03e-13 (Fisher's exact test), Q value = 3.1e-10

Table S129. Gene #35: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
2Q LOSS MUTATED	10	0	0
2Q LOSS WILD-TYPE	24	383	77

Figure S129. Get High-res Image Gene #35: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

'2q loss' versus 'METHLYATION_CNMF'

P value = 8.44e-06 (Fisher's exact test), Q value = 0.0039

Table S130. Gene #35: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	83	260
2Q LOSS MUTATED	10	0	0
2Q LOSS WILD-TYPE	141	83	260

Figure S130. Get High-res Image Gene #35: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2q loss' versus 'MRNASEQ_CNMF'

P value = 7.31e-05 (Fisher's exact test), Q value = 0.03

Table S131. Gene #35: '2q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	154	55	116	167
2Q LOSS MUTATED	10	0	0	0
2Q LOSS WILD-TYPE	144	55	116	167

Figure S131. Get High-res Image Gene #35: '2q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.66e-06 (Fisher's exact test), Q value = 0.0032

Table S132. Gene #35: '2q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	197	128	96	71
2Q LOSS MUTATED	0	10	0	0
2Q LOSS WILD-TYPE	197	118	96	71

Figure S132. Get High-res Image Gene #35: '2q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_CNMF'

P value = 5.49e-06 (Fisher's exact test), Q value = 0.0026

Table S133. Gene #35: '2q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	173	170
2Q LOSS MUTATED	10	0	0
2Q LOSS WILD-TYPE	140	173	170

Figure S133. Get High-res Image Gene #35: '2q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'2q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.25e-06 (Fisher's exact test), Q value = 0.00061

Table S134. Gene #35: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	130	208
2Q LOSS MUTATED	0	10	0
2Q LOSS WILD-TYPE	155	120	208

Figure S134. Get High-res Image Gene #35: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.43e-05 (Fisher's exact test), Q value = 0.011

Table S135. Gene #35: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	169	161
2Q LOSS MUTATED	10	0	0
2Q LOSS WILD-TYPE	153	169	161

Figure S135. Get High-res Image Gene #35: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'2q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.06e-06 (Fisher's exact test), Q value = 0.00053

Table S136. Gene #35: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	199	128	166
2Q LOSS MUTATED	0	10	0
2Q LOSS WILD-TYPE	199	118	166

Figure S136. Get High-res Image Gene #35: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3p loss' versus 'CN_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.12

Table S137. Gene #36: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
3P LOSS MUTATED	3	0	0
3P LOSS WILD-TYPE	31	383	77

Figure S137. Get High-res Image Gene #36: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

'3q loss' versus 'CN_CNMF'

P value = 1.89e-05 (Fisher's exact test), Q value = 0.0085

Table S138. Gene #37: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
3Q LOSS MUTATED	4	0	0
3Q LOSS WILD-TYPE	30	383	77

Figure S138. Get High-res Image Gene #37: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

'6q loss' versus 'CN_CNMF'

P value = 4.62e-05 (Fisher's exact test), Q value = 0.02

Table S139. Gene #39: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
6Q LOSS MUTATED	5	2	0
6Q LOSS WILD-TYPE	29	381	77

Figure S139. Get High-res Image Gene #39: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

'8p loss' versus 'CN_CNMF'

P value = 1.89e-05 (Fisher's exact test), Q value = 0.0085

Table S140. Gene #40: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
8P LOSS MUTATED	4	0	0
8P LOSS WILD-TYPE	30	383	77

Figure S140. Get High-res Image Gene #40: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'8q loss' versus 'CN_CNMF'

P value = 1.89e-05 (Fisher's exact test), Q value = 0.0085

Table S141. Gene #41: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
8Q LOSS MUTATED	4	0	0
8Q LOSS WILD-TYPE	30	383	77

Figure S141. Get High-res Image Gene #41: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 2.94e-12 (Fisher's exact test), Q value = 1.5e-09

Table S142. Gene #42: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
9P LOSS MUTATED	13	5	1
9P LOSS WILD-TYPE	21	378	76

Figure S142. Get High-res Image Gene #42: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9q loss' versus 'CN_CNMF'

P value = 9.23e-15 (Fisher's exact test), Q value = 4.8e-12

Table S143. Gene #43: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
9Q LOSS MUTATED	16	7	1
9Q LOSS WILD-TYPE	18	376	76

Figure S143. Get High-res Image Gene #43: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

'10p loss' versus 'CN_CNMF'

P value = 3.94e-09 (Fisher's exact test), Q value = 2e-06

Table S144. Gene #44: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
10P LOSS MUTATED	7	0	0
10P LOSS WILD-TYPE	27	383	77

Figure S144. Get High-res Image Gene #44: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'CN_CNMF'

P value = 6.87e-08 (Fisher's exact test), Q value = 3.5e-05

Table S145. Gene #45: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
10Q LOSS MUTATED	6	0	0
10Q LOSS WILD-TYPE	28	383	77

Figure S145. Get High-res Image Gene #45: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11p loss' versus 'CN_CNMF'

P value = 7.98e-08 (Fisher's exact test), Q value = 4.1e-05

Table S146. Gene #46: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
11P LOSS MUTATED	6	0	1
11P LOSS WILD-TYPE	28	383	76

Figure S146. Get High-res Image Gene #46: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'CN_CNMF'

P value = 3.28e-06 (Fisher's exact test), Q value = 0.0016

Table S147. Gene #47: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
11Q LOSS MUTATED	6	2	1
11Q LOSS WILD-TYPE	28	381	76

Figure S147. Get High-res Image Gene #47: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'MIRSEQ_CNMF'

P value = 0.000352 (Fisher's exact test), Q value = 0.13

Table S148. Gene #47: '11q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	173	170
11Q LOSS MUTATED	8	0	1
11Q LOSS WILD-TYPE	142	173	169

Figure S148. Get High-res Image Gene #47: '11q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'15q loss' versus 'CN_CNMF'

P value = 5.63e-05 (Fisher's exact test), Q value = 0.024

Table S149. Gene #49: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
15Q LOSS MUTATED	5	2	1
15Q LOSS WILD-TYPE	29	381	76

Figure S149. Get High-res Image Gene #49: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 0.000139 (Fisher's exact test), Q value = 0.057

Table S150. Gene #49: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	83	260
15Q LOSS MUTATED	8	0	0
15Q LOSS WILD-TYPE	143	83	260

Figure S150. Get High-res Image Gene #49: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 0.000585 (Fisher's exact test), Q value = 0.22

Table S151. Gene #49: '15q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	154	55	116	167
15Q LOSS MUTATED	8	0	0	0
15Q LOSS WILD-TYPE	146	55	116	167

Figure S151. Get High-res Image Gene #49: '15q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.96e-05 (Fisher's exact test), Q value = 0.025

Table S152. Gene #49: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	197	128	96	71
15Q LOSS MUTATED	0	8	0	0
15Q LOSS WILD-TYPE	197	120	96	71

Figure S152. Get High-res Image Gene #49: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_CNMF'

P value = 6.43e-05 (Fisher's exact test), Q value = 0.027

Table S153. Gene #49: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	173	170
15Q LOSS MUTATED	8	0	0
15Q LOSS WILD-TYPE	142	173	170

Figure S153. Get High-res Image Gene #49: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.99e-05 (Fisher's exact test), Q value = 0.0088

Table S154. Gene #49: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	130	208
15Q LOSS MUTATED	0	8	0
15Q LOSS WILD-TYPE	155	122	208

Figure S154. Get High-res Image Gene #49: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000242 (Fisher's exact test), Q value = 0.095

Table S155. Gene #49: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	169	161
15Q LOSS MUTATED	8	0	0
15Q LOSS WILD-TYPE	155	169	161

Figure S155. Get High-res Image Gene #49: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.75e-05 (Fisher's exact test), Q value = 0.0079

Table S156. Gene #49: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	199	128	166
15Q LOSS MUTATED	0	8	0
15Q LOSS WILD-TYPE	199	120	166

Figure S156. Get High-res Image Gene #49: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 0.000207 (Fisher's exact test), Q value = 0.082

Table S157. Gene #52: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
18P LOSS MUTATED	3	0	1
18P LOSS WILD-TYPE	31	383	76

Figure S157. Get High-res Image Gene #52: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 0.000207 (Fisher's exact test), Q value = 0.082

Table S158. Gene #53: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
18Q LOSS MUTATED	3	0	1
18Q LOSS WILD-TYPE	31	383	76

Figure S158. Get High-res Image Gene #53: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 5.63e-05 (Fisher's exact test), Q value = 0.024

Table S159. Gene #55: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
21Q LOSS MUTATED	5	2	1
21Q LOSS WILD-TYPE	29	381	76

Figure S159. Get High-res Image Gene #55: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 7.48e-90 (Fisher's exact test), Q value = 4e-87

Table S160. Gene #56: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
22Q LOSS MUTATED	9	0	77
22Q LOSS WILD-TYPE	25	383	0

Figure S160. Get High-res Image Gene #56: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 1.1e-05 (Fisher's exact test), Q value = 0.005

Table S161. Gene #56: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	83	260
22Q LOSS MUTATED	45	7	34
22Q LOSS WILD-TYPE	106	76	226

Figure S161. Get High-res Image Gene #56: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 3.38e-09 (Fisher's exact test), Q value = 1.7e-06

Table S162. Gene #56: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	154	55	116	167
22Q LOSS MUTATED	45	8	26	7
22Q LOSS WILD-TYPE	109	47	90	160

Figure S162. Get High-res Image Gene #56: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.03e-08 (Fisher's exact test), Q value = 4.1e-05

Table S163. Gene #56: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	197	128	96	71
22Q LOSS MUTATED	13	39	23	11
22Q LOSS WILD-TYPE	184	89	73	60

Figure S163. Get High-res Image Gene #56: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000342 (Fisher's exact test), Q value = 0.13

Table S164. Gene #56: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	130	208
22Q LOSS MUTATED	22	38	26
22Q LOSS WILD-TYPE	133	92	182

Figure S164. Get High-res Image Gene #56: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.12e-06 (Fisher's exact test), Q value = 0.0015

Table S165. Gene #56: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	169	161
22Q LOSS MUTATED	49	18	19
22Q LOSS WILD-TYPE	114	151	142

Figure S165. Get High-res Image Gene #56: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'22q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000206 (Fisher's exact test), Q value = 0.082

Table S166. Gene #56: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	199	128	166
22Q LOSS MUTATED	24	38	24
22Q LOSS WILD-TYPE	175	90	142

Figure S166. Get High-res Image Gene #56: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtypes file = THCA-TP.transferedmergedcluster.txt
Number of patients = 494
Number of significantly arm-level cnvs = 57
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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