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

Thyroid 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/C1TD9W9V

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 501 patients, 134 significant findings detected with P value < 0.05 and Q value < 0.25.

1q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
4p gain cnv correlated to 'CN_CNMF'.
4q gain cnv correlated to 'CN_CNMF'.
5p gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
5q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
7p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
7q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
8p gain cnv correlated to 'CN_CNMF'.
8q 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', and 'MIRSEQ_CHIERARCHICAL'.
12q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
13q gain cnv correlated to 'CN_CNMF'.
14q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
16p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
16q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
17p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
17q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 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_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
19q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
20p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
20q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
21q gain cnv correlated to 'CN_CNMF'.
xq gain cnv correlated to 'CN_CNMF'.
1p loss cnv correlated to 'CN_CNMF'.
2p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
2q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
3q loss cnv correlated to 'CN_CNMF'.
6p loss cnv correlated to 'CN_CNMF'.
6q loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
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'.
13q loss cnv correlated to 'MIRSEQ_CHIERARCHICAL'.
15q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
22q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', '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, 134 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
22q loss	89 (18%)	412	1e-05 (0.00534)	1e-05 (0.00534)	0.116 (1.00)	0.503 (1.00)	1e-05 (0.00534)	1e-05 (0.00534)	0.00035 (0.144)	5e-05 (0.023)	0.00017 (0.0731)	0.00023 (0.0966)
7q gain	20 (4%)	481	1e-05 (0.00534)	1e-05 (0.00534)	0.572 (1.00)	0.0141 (1.00)	0.0001 (0.0445)	4e-05 (0.0187)	7e-05 (0.0316)	1e-05 (0.00534)	0.612 (1.00)	0.00062 (0.249)
17p gain	16 (3%)	485	1e-05 (0.00534)	1e-05 (0.00534)	0.538 (1.00)	0.0278 (1.00)	1e-05 (0.00534)	1e-05 (0.00534)	2e-05 (0.00962)	1e-05 (0.00534)	0.358 (1.00)	0.00024 (0.1)
17q gain	18 (4%)	483	1e-05 (0.00534)	1e-05 (0.00534)	0.635 (1.00)	0.0153 (1.00)	1e-05 (0.00534)	1e-05 (0.00534)	2e-05 (0.00962)	1e-05 (0.00534)	0.513 (1.00)	0.00027 (0.112)
2p loss	10 (2%)	491	1e-05 (0.00534)	3e-05 (0.0141)	0.775 (1.00)	0.092 (1.00)	8e-05 (0.0358)	2e-05 (0.00962)	1e-05 (0.00534)	2e-05 (0.00962)	0.235 (1.00)	0.00036 (0.148)
2q loss	10 (2%)	491	1e-05 (0.00534)	2e-05 (0.00962)	0.773 (1.00)	0.0893 (1.00)	0.00013 (0.0573)	5e-05 (0.023)	1e-05 (0.00534)	1e-05 (0.00534)	0.234 (1.00)	0.00056 (0.226)
5q gain	17 (3%)	484	1e-05 (0.00534)	5e-05 (0.023)	0.849 (1.00)	0.0795 (1.00)	0.00013 (0.0573)	3e-05 (0.0141)	0.0002 (0.0848)	1e-05 (0.00534)	0.84 (1.00)	0.00425 (1.00)
12p gain	14 (3%)	487	1e-05 (0.00534)	1e-05 (0.00534)	0.85 (1.00)	0.0811 (1.00)	2e-05 (0.00962)	1e-05 (0.00534)	6e-05 (0.0271)	1e-05 (0.00534)	0.552 (1.00)	0.00242 (0.888)
12q gain	15 (3%)	486	1e-05 (0.00534)	1e-05 (0.00534)	0.851 (1.00)	0.0789 (1.00)	1e-05 (0.00534)	1e-05 (0.00534)	3e-05 (0.0141)	1e-05 (0.00534)	0.383 (1.00)	0.00086 (0.337)
14q gain	11 (2%)	490	1e-05 (0.00534)	0.00022 (0.0931)	1 (1.00)	0.158 (1.00)	0.00049 (0.2)	9e-05 (0.0401)	0.0006 (0.242)	5e-05 (0.023)	0.852 (1.00)	0.00201 (0.748)
16p gain	15 (3%)	486	1e-05 (0.00534)	4e-05 (0.0187)	0.633 (1.00)	0.0796 (1.00)	0.00018 (0.077)	5e-05 (0.023)	0.00015 (0.0657)	1e-05 (0.00534)	0.435 (1.00)	0.00076 (0.3)
19q gain	10 (2%)	491	1e-05 (0.00534)	2e-05 (0.00962)	0.635 (1.00)	0.0642 (1.00)	0.0001 (0.0445)	4e-05 (0.0187)	2e-05 (0.00962)	1e-05 (0.00534)	0.637 (1.00)	0.0016 (0.603)
15q loss	8 (2%)	493	0.00023 (0.0966)	0.00022 (0.0931)	0.193 (1.00)	0.0879 (1.00)	0.00048 (0.196)	0.00026 (0.108)	7e-05 (0.0316)	5e-05 (0.023)	0.407 (1.00)	0.00154 (0.585)
7p gain	18 (4%)	483	1e-05 (0.00534)	5e-05 (0.023)	0.659 (1.00)	0.0524 (1.00)	0.00065 (0.259)	0.00013 (0.0573)	0.00034 (0.14)	4e-05 (0.0187)	0.578 (1.00)	0.00538 (1.00)
19p gain	8 (2%)	493	1e-05 (0.00534)	0.00019 (0.0809)			0.00063 (0.252)	0.00022 (0.0931)	7e-05 (0.0316)	2e-05 (0.00962)	0.449 (1.00)	0.0226 (1.00)
16q gain	13 (3%)	488	1e-05 (0.00534)	0.00016 (0.0696)	0.797 (1.00)	0.276 (1.00)	0.00094 (0.367)	0.00031 (0.129)	0.00181 (0.679)	0.00017 (0.0731)	0.617 (1.00)	0.00789 (1.00)
5p gain	21 (4%)	480	1e-05 (0.00534)	0.00198 (0.739)	0.529 (1.00)	0.233 (1.00)	0.00517 (1.00)	0.00011 (0.0486)	0.001 (0.389)	0.0001 (0.0445)	0.598 (1.00)	0.00366 (1.00)
20p gain	12 (2%)	489	1e-05 (0.00534)	0.00032 (0.132)	0.796 (1.00)	0.0929 (1.00)	0.00257 (0.935)	0.0009 (0.352)	0.00453 (1.00)	0.00049 (0.2)	0.913 (1.00)	0.095 (1.00)
1q gain	26 (5%)	475	1e-05 (0.00534)	0.0166 (1.00)	0.00281 (1.00)	0.0645 (1.00)	0.00112 (0.431)	7e-05 (0.0316)	0.0859 (1.00)	0.0506 (1.00)	0.0133 (1.00)	0.0156 (1.00)
20q gain	12 (2%)	489	1e-05 (0.00534)	0.00044 (0.18)	0.795 (1.00)	0.0927 (1.00)	0.00251 (0.916)	0.00067 (0.267)	0.00426 (1.00)	0.00077 (0.303)	0.915 (1.00)	0.0931 (1.00)
6q loss	7 (1%)	494	4e-05 (0.0187)	0.00219 (0.808)	0.0131 (1.00)	0.574 (1.00)	0.0272 (1.00)	0.0181 (1.00)	0.00489 (1.00)	0.0006 (0.242)	1 (1.00)	0.00995 (1.00)
11q loss	9 (2%)	492	1e-05 (0.00534)	0.0158 (1.00)	0.319 (1.00)	0.812 (1.00)	0.0152 (1.00)	0.0184 (1.00)	0.00051 (0.207)	0.00248 (0.908)	0.908 (1.00)	0.00201 (0.748)
4p gain	5 (1%)	496	1e-05 (0.00534)	0.00645 (1.00)			0.0164 (1.00)	0.0126 (1.00)	0.0416 (1.00)	0.0147 (1.00)	1 (1.00)	0.0767 (1.00)
4q gain	5 (1%)	496	5e-05 (0.023)	0.00676 (1.00)			0.0171 (1.00)	0.0123 (1.00)	0.0404 (1.00)	0.0142 (1.00)	1 (1.00)	0.0772 (1.00)
8p gain	6 (1%)	495	0.00015 (0.0657)	0.416 (1.00)	0.455 (1.00)	0.629 (1.00)	0.597 (1.00)	0.536 (1.00)	0.454 (1.00)	0.452 (1.00)	1 (1.00)	1 (1.00)
8q gain	7 (1%)	494	2e-05 (0.00962)	0.202 (1.00)	0.455 (1.00)	0.633 (1.00)	0.83 (1.00)	0.52 (1.00)	0.8 (1.00)	0.63 (1.00)	0.9 (1.00)	0.897 (1.00)
11q gain	5 (1%)	496	0.00016 (0.0696)	0.0604 (1.00)	0.779 (1.00)	0.3 (1.00)	0.11 (1.00)	0.124 (1.00)	0.0264 (1.00)	0.0225 (1.00)	0.311 (1.00)	0.273 (1.00)
13q gain	5 (1%)	496	4e-05 (0.0187)	0.0189 (1.00)	0.38 (1.00)	0.213 (1.00)	0.0492 (1.00)	0.102 (1.00)	0.239 (1.00)	0.0703 (1.00)	0.844 (1.00)	0.197 (1.00)
18p gain	6 (1%)	495	5e-05 (0.023)	0.0919 (1.00)			0.122 (1.00)	0.267 (1.00)	0.256 (1.00)	0.111 (1.00)	0.454 (1.00)	0.399 (1.00)
18q gain	6 (1%)	495	3e-05 (0.0141)	0.092 (1.00)			0.12 (1.00)	0.265 (1.00)	0.254 (1.00)	0.114 (1.00)	0.454 (1.00)	0.393 (1.00)
21q gain	5 (1%)	496	0.00015 (0.0657)	0.169 (1.00)			0.238 (1.00)	0.488 (1.00)	0.453 (1.00)	0.312 (1.00)	0.692 (1.00)	0.681 (1.00)
xq gain	9 (2%)	492	1e-05 (0.00534)	0.011 (1.00)	0.838 (1.00)	0.501 (1.00)	0.0974 (1.00)	0.141 (1.00)	0.277 (1.00)	0.133 (1.00)	0.908 (1.00)	0.398 (1.00)
1p loss	4 (1%)	497	0.00019 (0.0809)	0.186 (1.00)			0.243 (1.00)	0.316 (1.00)	0.115 (1.00)	0.0663 (1.00)	0.845 (1.00)	0.195 (1.00)
3q loss	4 (1%)	497	0.00016 (0.0696)	0.0181 (1.00)	0.495 (1.00)	0.42 (1.00)	0.0372 (1.00)	0.0478 (1.00)	0.00878 (1.00)	0.00408 (1.00)	1 (1.00)	0.0669 (1.00)
6p loss	4 (1%)	497	0.00016 (0.0696)	0.0457 (1.00)			0.46 (1.00)	0.399 (1.00)	0.115 (1.00)	0.0675 (1.00)	0.401 (1.00)	0.195 (1.00)
8p loss	4 (1%)	497	0.00018 (0.077)	0.0181 (1.00)			0.0358 (1.00)	0.0471 (1.00)	0.00784 (1.00)	0.00398 (1.00)	0.11 (1.00)	0.0186 (1.00)
8q loss	4 (1%)	497	0.00016 (0.0696)	0.0182 (1.00)			0.0355 (1.00)	0.0464 (1.00)	0.00841 (1.00)	0.0039 (1.00)	0.11 (1.00)	0.0192 (1.00)
9p loss	19 (4%)	482	1e-05 (0.00534)	0.0377 (1.00)	0.243 (1.00)	0.648 (1.00)	0.0312 (1.00)	0.0624 (1.00)	0.00879 (1.00)	0.00706 (1.00)	0.303 (1.00)	0.00387 (1.00)
9q loss	25 (5%)	476	1e-05 (0.00534)	0.104 (1.00)	0.172 (1.00)	0.116 (1.00)	0.171 (1.00)	0.0628 (1.00)	0.00979 (1.00)	0.00637 (1.00)	0.279 (1.00)	0.00499 (1.00)
10p loss	7 (1%)	494	1e-05 (0.00534)	0.0111 (1.00)	0.493 (1.00)	0.42 (1.00)	0.0195 (1.00)	0.0153 (1.00)	0.00466 (1.00)	0.00069 (0.274)	1 (1.00)	0.0103 (1.00)
10q loss	6 (1%)	495	1e-05 (0.00534)	0.0291 (1.00)			0.0516 (1.00)	0.044 (1.00)	0.0144 (1.00)	0.00439 (1.00)	1 (1.00)	0.0287 (1.00)
11p loss	7 (1%)	494	1e-05 (0.00534)	0.0113 (1.00)	0.494 (1.00)	0.958 (1.00)	0.00722 (1.00)	0.0186 (1.00)	0.00477 (1.00)	0.00074 (0.293)	0.798 (1.00)	0.0109 (1.00)
13q loss	14 (3%)	487	0.00164 (0.617)	0.015 (1.00)	0.0611 (1.00)	0.139 (1.00)	0.00547 (1.00)	0.00864 (1.00)	0.00108 (0.418)	0.00055 (0.223)	0.104 (1.00)	0.013 (1.00)
1p gain	5 (1%)	496	0.00105 (0.407)	0.839 (1.00)			0.922 (1.00)	0.881 (1.00)	0.108 (1.00)	0.0516 (1.00)	0.276 (1.00)	0.142 (1.00)
3p gain	3 (1%)	498	0.00159 (0.601)	0.548 (1.00)			0.496 (1.00)	0.592 (1.00)	0.305 (1.00)	0.187 (1.00)	1 (1.00)	0.193 (1.00)
9p gain	3 (1%)	498	0.00143 (0.545)	0.55 (1.00)			0.495 (1.00)	0.588 (1.00)	1 (1.00)	1 (1.00)	0.421 (1.00)	0.632 (1.00)
9q gain	4 (1%)	497	0.011 (1.00)	0.793 (1.00)			0.9 (1.00)	0.361 (1.00)	0.839 (1.00)	1 (1.00)	0.167 (1.00)	0.568 (1.00)
11p gain	6 (1%)	495	0.00112 (0.431)	0.0284 (1.00)	0.779 (1.00)	0.301 (1.00)	0.0538 (1.00)	0.0442 (1.00)	0.00893 (1.00)	0.00685 (1.00)	0.468 (1.00)	0.0977 (1.00)
1q loss	3 (1%)	498	0.00137 (0.523)	0.0505 (1.00)			0.0972 (1.00)	0.154 (1.00)	0.028 (1.00)	0.0176 (1.00)	1 (1.00)	0.19 (1.00)
3p loss	3 (1%)	498	0.00123 (0.471)	0.0489 (1.00)			0.0995 (1.00)	0.152 (1.00)	0.0266 (1.00)	0.0162 (1.00)	1 (1.00)	0.192 (1.00)
17p loss	8 (2%)	493	0.0145 (1.00)	0.415 (1.00)	1 (1.00)	0.391 (1.00)	0.638 (1.00)	0.599 (1.00)	0.0919 (1.00)	0.162 (1.00)	0.129 (1.00)	0.205 (1.00)
17q loss	4 (1%)	497	0.113 (1.00)	0.79 (1.00)			0.901 (1.00)	0.666 (1.00)	0.466 (1.00)	0.568 (1.00)	0.331 (1.00)	0.684 (1.00)
18p loss	4 (1%)	497	0.00191 (0.714)	0.183 (1.00)	1 (1.00)	0.388 (1.00)	0.245 (1.00)	0.316 (1.00)	0.0758 (1.00)	0.0923 (1.00)	0.531 (1.00)	0.273 (1.00)
18q loss	4 (1%)	497	0.0021 (0.777)	0.185 (1.00)	1 (1.00)	0.387 (1.00)	0.246 (1.00)	0.318 (1.00)	0.0723 (1.00)	0.0906 (1.00)	0.534 (1.00)	0.277 (1.00)
19p loss	5 (1%)	496	0.00915 (1.00)	0.00743 (1.00)	0.321 (1.00)	0.237 (1.00)	0.017 (1.00)	0.0125 (1.00)	0.00239 (0.88)	0.00108 (0.418)	0.0876 (1.00)	0.00155 (0.587)
21q loss	8 (2%)	493	0.0008 (0.314)	0.163 (1.00)	0.384 (1.00)	0.215 (1.00)	0.711 (1.00)	0.42 (1.00)	0.0932 (1.00)	0.0291 (1.00)	0.46 (1.00)	0.0545 (1.00)
xq loss	3 (1%)	498	0.0507 (1.00)	0.049 (1.00)	0.28 (1.00)	0.199 (1.00)	0.0989 (1.00)	0.151 (1.00)	0.0276 (1.00)	0.0165 (1.00)	0.111 (1.00)	0.019 (1.00)

'1q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
1Q GAIN MUTATED	18	7	1
1Q GAIN WILD-TYPE	38	349	88

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

'1q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.032

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	105	134	86	96	78
1Q GAIN MUTATED	16	2	1	3	4
1Q GAIN WILD-TYPE	89	132	85	93	74

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

'4p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
4P GAIN MUTATED	5	0	0
4P GAIN WILD-TYPE	51	356	89

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

'4q gain' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.023

Table S4. Gene #5: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
4Q GAIN MUTATED	5	0	0
4Q GAIN WILD-TYPE	51	356	89

Figure S4. Get High-res Image Gene #5: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S5. Gene #6: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
5P GAIN MUTATED	21	0	0
5P GAIN WILD-TYPE	35	356	89

Figure S5. Get High-res Image Gene #6: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.049

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	105	134	86	96	78
5P GAIN MUTATED	6	14	0	1	0
5P GAIN WILD-TYPE	99	120	86	95	78

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

'5p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.044

Table S7. Gene #6: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	128	193
5P GAIN MUTATED	7	13	1
5P GAIN WILD-TYPE	172	115	192

Figure S7. Get High-res Image Gene #6: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S8. Gene #7: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
5Q GAIN MUTATED	17	0	0
5Q GAIN WILD-TYPE	39	356	89

Figure S8. Get High-res Image Gene #7: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

'5q gain' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.023

Table S9. Gene #7: '5q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	277	154	70
5Q GAIN MUTATED	2	14	1
5Q GAIN WILD-TYPE	275	140	69

Figure S9. Get High-res Image Gene #7: '5q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q gain' versus 'MRNASEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.057

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	168	155	59	117
5Q GAIN MUTATED	2	14	0	1
5Q GAIN WILD-TYPE	166	141	59	116

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

'5q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.014

Table S11. Gene #7: '5q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	105	134	86	96	78
5Q GAIN MUTATED	2	14	0	1	0
5Q GAIN WILD-TYPE	103	120	86	95	78

Figure S11. Get High-res Image Gene #7: '5q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.085

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	151	167
5Q GAIN MUTATED	3	13	1
5Q GAIN WILD-TYPE	179	138	166

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

'5q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S13. Gene #7: '5q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	128	193
5Q GAIN MUTATED	3	13	1
5Q GAIN WILD-TYPE	176	115	192

Figure S13. Get High-res Image Gene #7: '5q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S14. Gene #8: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
7P GAIN MUTATED	18	0	0
7P GAIN WILD-TYPE	38	356	89

Figure S14. Get High-res Image Gene #8: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.023

Table S15. Gene #8: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	277	154	70
7P GAIN MUTATED	2	14	2
7P GAIN WILD-TYPE	275	140	68

Figure S15. Get High-res Image Gene #8: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.057

Table S16. Gene #8: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	105	134	86	96	78
7P GAIN MUTATED	2	14	1	1	0
7P GAIN WILD-TYPE	103	120	85	95	78

Figure S16. Get High-res Image Gene #8: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.14

Table S17. Gene #8: '7p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	151	167
7P GAIN MUTATED	4	13	1
7P GAIN WILD-TYPE	178	138	166

Figure S17. Get High-res Image Gene #8: '7p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'7p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.019

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	128	193
7P GAIN MUTATED	4	13	1
7P GAIN WILD-TYPE	175	115	192

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

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S19. Gene #9: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
7Q GAIN MUTATED	19	0	1
7Q GAIN WILD-TYPE	37	356	88

Figure S19. Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S20. Gene #9: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	277	154	70
7Q GAIN MUTATED	2	16	2
7Q GAIN WILD-TYPE	275	138	68

Figure S20. Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.044

Table S21. Gene #9: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	168	155	59	117
7Q GAIN MUTATED	2	16	1	1
7Q GAIN WILD-TYPE	166	139	58	116

Figure S21. Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.019

Table S22. Gene #9: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	105	134	86	96	78
7Q GAIN MUTATED	2	16	1	1	0
7Q GAIN WILD-TYPE	103	118	85	95	78

Figure S22. Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.032

Table S23. Gene #9: '7q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	151	167
7Q GAIN MUTATED	4	15	1
7Q GAIN WILD-TYPE	178	136	166

Figure S23. Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'7q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S24. Gene #9: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	128	193
7Q GAIN MUTATED	4	15	1
7Q GAIN WILD-TYPE	175	113	192

Figure S24. Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00062 (Fisher's exact test), Q value = 0.25

Table S25. Gene #9: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	126	179
7Q GAIN MUTATED	5	11	1
7Q GAIN WILD-TYPE	160	115	178

Figure S25. Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.066

Table S26. Gene #10: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
8P GAIN MUTATED	5	1	0
8P GAIN WILD-TYPE	51	355	89

Figure S26. Get High-res Image Gene #10: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

'8q gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0096

Table S27. Gene #11: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
8Q GAIN MUTATED	6	1	0
8Q GAIN WILD-TYPE	50	355	89

Figure S27. Get High-res Image Gene #11: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

'11q gain' versus 'CN_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.07

Table S28. Gene #15: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
11Q GAIN MUTATED	4	0	1
11Q GAIN WILD-TYPE	52	356	88

Figure S28. Get High-res Image Gene #15: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S29. Gene #16: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
12P GAIN MUTATED	13	0	1
12P GAIN WILD-TYPE	43	356	88

Figure S29. Get High-res Image Gene #16: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S30. Gene #16: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	277	154	70
12P GAIN MUTATED	1	13	0
12P GAIN WILD-TYPE	276	141	70

Figure S30. Get High-res Image Gene #16: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0096

Table S31. Gene #16: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	168	155	59	117
12P GAIN MUTATED	0	13	0	1
12P GAIN WILD-TYPE	168	142	59	116

Figure S31. Get High-res Image Gene #16: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S32. Gene #16: '12p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	105	134	86	96	78
12P GAIN MUTATED	0	13	0	1	0
12P GAIN WILD-TYPE	105	121	86	95	78

Figure S32. Get High-res Image Gene #16: '12p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.027

Table S33. Gene #16: '12p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	151	167
12P GAIN MUTATED	1	12	1
12P GAIN WILD-TYPE	181	139	166

Figure S33. Get High-res Image Gene #16: '12p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'12p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S34. Gene #16: '12p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	128	193
12P GAIN MUTATED	1	12	1
12P GAIN WILD-TYPE	178	116	192

Figure S34. Get High-res Image Gene #16: '12p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S35. Gene #17: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
12Q GAIN MUTATED	14	0	1
12Q GAIN WILD-TYPE	42	356	88

Figure S35. Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

'12q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S36. Gene #17: '12q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	277	154	70
12Q GAIN MUTATED	1	14	0
12Q GAIN WILD-TYPE	276	140	70

Figure S36. Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S37. Gene #17: '12q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	168	155	59	117
12Q GAIN MUTATED	0	14	0	1
12Q GAIN WILD-TYPE	168	141	59	116

Figure S37. Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S38. Gene #17: '12q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	105	134	86	96	78
12Q GAIN MUTATED	0	14	0	1	0
12Q GAIN WILD-TYPE	105	120	86	95	78

Figure S38. Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.014

Table S39. Gene #17: '12q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	151	167
12Q GAIN MUTATED	1	13	1
12Q GAIN WILD-TYPE	181	138	166

Figure S39. Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'12q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S40. Gene #17: '12q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	128	193
12Q GAIN MUTATED	1	13	1
12Q GAIN WILD-TYPE	178	115	192

Figure S40. Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'13q gain' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.019

Table S41. Gene #18: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
13Q GAIN MUTATED	5	0	0
13Q GAIN WILD-TYPE	51	356	89

Figure S41. Get High-res Image Gene #18: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

'14q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S42. Gene #19: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
14Q GAIN MUTATED	10	0	1
14Q GAIN WILD-TYPE	46	356	88

Figure S42. Get High-res Image Gene #19: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

'14q gain' versus 'METHLYATION_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.093

Table S43. Gene #19: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	277	154	70
14Q GAIN MUTATED	1	10	0
14Q GAIN WILD-TYPE	276	144	70

Figure S43. Get High-res Image Gene #19: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'14q gain' versus 'MRNASEQ_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.2

Table S44. Gene #19: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	168	155	59	117
14Q GAIN MUTATED	1	10	0	0
14Q GAIN WILD-TYPE	167	145	59	117

Figure S44. Get High-res Image Gene #19: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.04

Table S45. Gene #19: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	105	134	86	96	78
14Q GAIN MUTATED	0	10	0	0	1
14Q GAIN WILD-TYPE	105	124	86	96	77

Figure S45. Get High-res Image Gene #19: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_CNMF'

P value = 6e-04 (Fisher's exact test), Q value = 0.24

Table S46. Gene #19: '14q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	151	167
14Q GAIN MUTATED	2	9	0
14Q GAIN WILD-TYPE	180	142	167

Figure S46. Get High-res Image Gene #19: '14q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'14q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.023

Table S47. Gene #19: '14q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	128	193
14Q GAIN MUTATED	2	9	0
14Q GAIN WILD-TYPE	177	119	193

Figure S47. Get High-res Image Gene #19: '14q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S48. Gene #20: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
16P GAIN MUTATED	14	0	1
16P GAIN WILD-TYPE	42	356	88

Figure S48. Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

'16p gain' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.019

Table S49. Gene #20: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	277	154	70
16P GAIN MUTATED	1	13	1
16P GAIN WILD-TYPE	276	141	69

Figure S49. Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.077

Table S50. Gene #20: '16p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	168	155	59	117
16P GAIN MUTATED	1	13	0	1
16P GAIN WILD-TYPE	167	142	59	116

Figure S50. Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.023

Table S51. Gene #20: '16p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	105	134	86	96	78
16P GAIN MUTATED	1	13	0	1	0
16P GAIN WILD-TYPE	104	121	86	95	78

Figure S51. Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.066

Table S52. Gene #20: '16p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	151	167
16P GAIN MUTATED	2	12	1
16P GAIN WILD-TYPE	180	139	166

Figure S52. Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S53. Gene #20: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	128	193
16P GAIN MUTATED	2	12	1
16P GAIN WILD-TYPE	177	116	192

Figure S53. Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S54. Gene #21: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
16Q GAIN MUTATED	13	0	0
16Q GAIN WILD-TYPE	43	356	89

Figure S54. Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16q gain' versus 'METHLYATION_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.07

Table S55. Gene #21: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	277	154	70
16Q GAIN MUTATED	1	11	1
16Q GAIN WILD-TYPE	276	143	69

Figure S55. Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.13

Table S56. Gene #21: '16q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	105	134	86	96	78
16Q GAIN MUTATED	1	11	0	1	0
16Q GAIN WILD-TYPE	104	123	86	95	78

Figure S56. Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.073

Table S57. Gene #21: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	128	193
16Q GAIN MUTATED	2	10	1
16Q GAIN WILD-TYPE	177	118	192

Figure S57. Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S58. Gene #22: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
17P GAIN MUTATED	12	2	2
17P GAIN WILD-TYPE	44	354	87

Figure S58. Get High-res Image Gene #22: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

'17p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S59. Gene #22: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	277	154	70
17P GAIN MUTATED	1	15	0
17P GAIN WILD-TYPE	276	139	70

Figure S59. Get High-res Image Gene #22: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S60. Gene #22: '17p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	168	155	59	117
17P GAIN MUTATED	0	15	0	1
17P GAIN WILD-TYPE	168	140	59	116

Figure S60. Get High-res Image Gene #22: '17p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S61. Gene #22: '17p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	105	134	86	96	78
17P GAIN MUTATED	0	15	0	1	0
17P GAIN WILD-TYPE	105	119	86	95	78

Figure S61. Get High-res Image Gene #22: '17p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0096

Table S62. Gene #22: '17p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	151	167
17P GAIN MUTATED	1	14	1
17P GAIN WILD-TYPE	181	137	166

Figure S62. Get High-res Image Gene #22: '17p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S63. Gene #22: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	128	193
17P GAIN MUTATED	1	14	1
17P GAIN WILD-TYPE	178	114	192

Figure S63. Get High-res Image Gene #22: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.1

Table S64. Gene #22: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	126	179
17P GAIN MUTATED	2	10	1
17P GAIN WILD-TYPE	163	116	178

Figure S64. Get High-res Image Gene #22: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S65. Gene #23: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
17Q GAIN MUTATED	13	2	3
17Q GAIN WILD-TYPE	43	354	86

Figure S65. Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S66. Gene #23: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	277	154	70
17Q GAIN MUTATED	2	16	0
17Q GAIN WILD-TYPE	275	138	70

Figure S66. Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S67. Gene #23: '17q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	168	155	59	117
17Q GAIN MUTATED	1	16	0	1
17Q GAIN WILD-TYPE	167	139	59	116

Figure S67. Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S68. Gene #23: '17q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	105	134	86	96	78
17Q GAIN MUTATED	1	16	0	1	0
17Q GAIN WILD-TYPE	104	118	86	95	78

Figure S68. Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0096

Table S69. Gene #23: '17q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	151	167
17Q GAIN MUTATED	2	15	1
17Q GAIN WILD-TYPE	180	136	166

Figure S69. Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S70. Gene #23: '17q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	128	193
17Q GAIN MUTATED	2	15	1
17Q GAIN WILD-TYPE	177	113	192

Figure S70. Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 0.11

Table S71. Gene #23: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	126	179
17Q GAIN MUTATED	3	11	1
17Q GAIN WILD-TYPE	162	115	178

Figure S71. Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p gain' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.023

Table S72. Gene #24: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
18P GAIN MUTATED	5	0	1
18P GAIN WILD-TYPE	51	356	88

Figure S72. Get High-res Image Gene #24: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

'18q gain' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.014

Table S73. Gene #25: '18q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
18Q GAIN MUTATED	5	0	1
18Q GAIN WILD-TYPE	51	356	88

Figure S73. Get High-res Image Gene #25: '18q gain' versus Molecular Subtype #1: 'CN_CNMF'

'19p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S74. Gene #26: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
19P GAIN MUTATED	8	0	0
19P GAIN WILD-TYPE	48	356	89

Figure S74. Get High-res Image Gene #26: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

'19p gain' versus 'METHLYATION_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.081

Table S75. Gene #26: '19p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	277	154	70
19P GAIN MUTATED	0	8	0
19P GAIN WILD-TYPE	277	146	70

Figure S75. Get High-res Image Gene #26: '19p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.093

Table S76. Gene #26: '19p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	105	134	86	96	78
19P GAIN MUTATED	0	8	0	0	0
19P GAIN WILD-TYPE	105	126	86	96	78

Figure S76. Get High-res Image Gene #26: '19p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.032

Table S77. Gene #26: '19p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	151	167
19P GAIN MUTATED	0	8	0
19P GAIN WILD-TYPE	182	143	167

Figure S77. Get High-res Image Gene #26: '19p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'19p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0096

Table S78. Gene #26: '19p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	128	193
19P GAIN MUTATED	0	8	0
19P GAIN WILD-TYPE	179	120	193

Figure S78. Get High-res Image Gene #26: '19p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S79. Gene #27: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
19Q GAIN MUTATED	10	0	0
19Q GAIN WILD-TYPE	46	356	89

Figure S79. Get High-res Image Gene #27: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

'19q gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0096

Table S80. Gene #27: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	277	154	70
19Q GAIN MUTATED	0	10	0
19Q GAIN WILD-TYPE	277	144	70

Figure S80. Get High-res Image Gene #27: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.044

Table S81. Gene #27: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	168	155	59	117
19Q GAIN MUTATED	0	10	0	0
19Q GAIN WILD-TYPE	168	145	59	117

Figure S81. Get High-res Image Gene #27: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.019

Table S82. Gene #27: '19q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	105	134	86	96	78
19Q GAIN MUTATED	0	10	0	0	0
19Q GAIN WILD-TYPE	105	124	86	96	78

Figure S82. Get High-res Image Gene #27: '19q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0096

Table S83. Gene #27: '19q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	151	167
19Q GAIN MUTATED	0	10	0
19Q GAIN WILD-TYPE	182	141	167

Figure S83. Get High-res Image Gene #27: '19q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'19q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S84. Gene #27: '19q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	128	193
19Q GAIN MUTATED	0	10	0
19Q GAIN WILD-TYPE	179	118	193

Figure S84. Get High-res Image Gene #27: '19q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S85. Gene #28: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
20P GAIN MUTATED	12	0	0
20P GAIN WILD-TYPE	44	356	89

Figure S85. Get High-res Image Gene #28: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.13

Table S86. Gene #28: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	277	154	70
20P GAIN MUTATED	1	10	1
20P GAIN WILD-TYPE	276	144	69

Figure S86. Get High-res Image Gene #28: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00049 (Fisher's exact test), Q value = 0.2

Table S87. Gene #28: '20p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	128	193
20P GAIN MUTATED	2	9	1
20P GAIN WILD-TYPE	177	119	192

Figure S87. Get High-res Image Gene #28: '20p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S88. Gene #29: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
20Q GAIN MUTATED	12	0	0
20Q GAIN WILD-TYPE	44	356	89

Figure S88. Get High-res Image Gene #29: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.18

Table S89. Gene #29: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	277	154	70
20Q GAIN MUTATED	1	10	1
20Q GAIN WILD-TYPE	276	144	69

Figure S89. Get High-res Image Gene #29: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'21q gain' versus 'CN_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.066

Table S90. Gene #30: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
21Q GAIN MUTATED	4	0	1
21Q GAIN WILD-TYPE	52	356	88

Figure S90. Get High-res Image Gene #30: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

'xq gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S91. Gene #31: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
XQ GAIN MUTATED	8	1	0
XQ GAIN WILD-TYPE	48	355	89

Figure S91. Get High-res Image Gene #31: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

'1p loss' versus 'CN_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.081

Table S92. Gene #32: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
1P LOSS MUTATED	4	0	0
1P LOSS WILD-TYPE	52	356	89

Figure S92. Get High-res Image Gene #32: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

'2p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S93. Gene #34: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
2P LOSS MUTATED	9	0	1
2P LOSS WILD-TYPE	47	356	88

Figure S93. Get High-res Image Gene #34: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

'2p loss' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.014

Table S94. Gene #34: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	277	154	70
2P LOSS MUTATED	0	10	0
2P LOSS WILD-TYPE	277	144	70

Figure S94. Get High-res Image Gene #34: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2p loss' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.036

Table S95. Gene #34: '2p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	168	155	59	117
2P LOSS MUTATED	0	10	0	0
2P LOSS WILD-TYPE	168	145	59	117

Figure S95. Get High-res Image Gene #34: '2p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0096

Table S96. Gene #34: '2p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	105	134	86	96	78
2P LOSS MUTATED	0	10	0	0	0
2P LOSS WILD-TYPE	105	124	86	96	78

Figure S96. Get High-res Image Gene #34: '2p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S97. Gene #34: '2p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	151	167
2P LOSS MUTATED	0	10	0
2P LOSS WILD-TYPE	182	141	167

Figure S97. Get High-res Image Gene #34: '2p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'2p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0096

Table S98. Gene #34: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	128	193
2P LOSS MUTATED	0	10	0
2P LOSS WILD-TYPE	179	118	193

Figure S98. Get High-res Image Gene #34: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00036 (Fisher's exact test), Q value = 0.15

Table S99. Gene #34: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	126	179
2P LOSS MUTATED	1	7	0
2P LOSS WILD-TYPE	164	119	179

Figure S99. Get High-res Image Gene #34: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S100. Gene #35: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
2Q LOSS MUTATED	10	0	0
2Q LOSS WILD-TYPE	46	356	89

Figure S100. Get High-res Image Gene #35: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

'2q loss' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0096

Table S101. Gene #35: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	277	154	70
2Q LOSS MUTATED	0	10	0
2Q LOSS WILD-TYPE	277	144	70

Figure S101. Get High-res Image Gene #35: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2q loss' versus 'MRNASEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.057

Table S102. Gene #35: '2q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	168	155	59	117
2Q LOSS MUTATED	0	10	0	0
2Q LOSS WILD-TYPE	168	145	59	117

Figure S102. Get High-res Image Gene #35: '2q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.023

Table S103. Gene #35: '2q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	105	134	86	96	78
2Q LOSS MUTATED	0	10	0	0	0
2Q LOSS WILD-TYPE	105	124	86	96	78

Figure S103. Get High-res Image Gene #35: '2q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S104. Gene #35: '2q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	151	167
2Q LOSS MUTATED	0	10	0
2Q LOSS WILD-TYPE	182	141	167

Figure S104. Get High-res Image Gene #35: '2q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'2q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S105. Gene #35: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	128	193
2Q LOSS MUTATED	0	10	0
2Q LOSS WILD-TYPE	179	118	193

Figure S105. Get High-res Image Gene #35: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00056 (Fisher's exact test), Q value = 0.23

Table S106. Gene #35: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	126	179
2Q LOSS MUTATED	1	7	0
2Q LOSS WILD-TYPE	164	119	179

Figure S106. Get High-res Image Gene #35: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.07

Table S107. Gene #37: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
3Q LOSS MUTATED	4	0	0
3Q LOSS WILD-TYPE	52	356	89

Figure S107. Get High-res Image Gene #37: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

'6p loss' versus 'CN_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.07

Table S108. Gene #38: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
6P LOSS MUTATED	4	0	0
6P LOSS WILD-TYPE	52	356	89

Figure S108. Get High-res Image Gene #38: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

'6q loss' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.019

Table S109. Gene #39: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
6Q LOSS MUTATED	6	1	0
6Q LOSS WILD-TYPE	50	355	89

Figure S109. Get High-res Image Gene #39: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

'6q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-04 (Fisher's exact test), Q value = 0.24

Table S110. Gene #39: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	128	193
6Q LOSS MUTATED	1	6	0
6Q LOSS WILD-TYPE	178	122	193

Figure S110. Get High-res Image Gene #39: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.077

Table S111. Gene #40: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
8P LOSS MUTATED	4	0	0
8P LOSS WILD-TYPE	52	356	89

Figure S111. Get High-res Image Gene #40: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'8q loss' versus 'CN_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.07

Table S112. Gene #41: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
8Q LOSS MUTATED	4	0	0
8Q LOSS WILD-TYPE	52	356	89

Figure S112. Get High-res Image Gene #41: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S113. Gene #42: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
9P LOSS MUTATED	15	2	2
9P LOSS WILD-TYPE	41	354	87

Figure S113. Get High-res Image Gene #42: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S114. Gene #43: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
9Q LOSS MUTATED	20	2	3
9Q LOSS WILD-TYPE	36	354	86

Figure S114. Get High-res Image Gene #43: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

'10p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S115. Gene #44: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
10P LOSS MUTATED	7	0	0
10P LOSS WILD-TYPE	49	356	89

Figure S115. Get High-res Image Gene #44: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S116. Gene #45: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
10Q LOSS MUTATED	6	0	0
10Q LOSS WILD-TYPE	50	356	89

Figure S116. Get High-res Image Gene #45: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S117. Gene #46: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
11P LOSS MUTATED	6	0	1
11P LOSS WILD-TYPE	50	356	88

Figure S117. Get High-res Image Gene #46: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S118. Gene #47: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
11Q LOSS MUTATED	7	1	1
11Q LOSS WILD-TYPE	49	355	88

Figure S118. Get High-res Image Gene #47: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'MIRSEQ_CNMF'

P value = 0.00051 (Fisher's exact test), Q value = 0.21

Table S119. Gene #47: '11q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	151	167
11Q LOSS MUTATED	1	8	0
11Q LOSS WILD-TYPE	181	143	167

Figure S119. Get High-res Image Gene #47: '11q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'13q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00055 (Fisher's exact test), Q value = 0.22

Table S120. Gene #48: '13q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	128	193
13Q LOSS MUTATED	0	9	5
13Q LOSS WILD-TYPE	179	119	188

Figure S120. Get High-res Image Gene #48: '13q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.097

Table S121. Gene #49: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
15Q LOSS MUTATED	5	1	2
15Q LOSS WILD-TYPE	51	355	87

Figure S121. Get High-res Image Gene #49: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.093

Table S122. Gene #49: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	277	154	70
15Q LOSS MUTATED	0	8	0
15Q LOSS WILD-TYPE	277	146	70

Figure S122. Get High-res Image Gene #49: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 0.00048 (Fisher's exact test), Q value = 0.2

Table S123. Gene #49: '15q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	168	155	59	117
15Q LOSS MUTATED	0	8	0	0
15Q LOSS WILD-TYPE	168	147	59	117

Figure S123. Get High-res Image Gene #49: '15q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.11

Table S124. Gene #49: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	105	134	86	96	78
15Q LOSS MUTATED	0	8	0	0	0
15Q LOSS WILD-TYPE	105	126	86	96	78

Figure S124. Get High-res Image Gene #49: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.032

Table S125. Gene #49: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	151	167
15Q LOSS MUTATED	0	8	0
15Q LOSS WILD-TYPE	182	143	167

Figure S125. Get High-res Image Gene #49: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.023

Table S126. Gene #49: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	128	193
15Q LOSS MUTATED	0	8	0
15Q LOSS WILD-TYPE	179	120	193

Figure S126. Get High-res Image Gene #49: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S127. Gene #56: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
22Q LOSS MUTATED	13	0	76
22Q LOSS WILD-TYPE	43	356	13

Figure S127. Get High-res Image Gene #56: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S128. Gene #56: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	277	154	70
22Q LOSS MUTATED	36	47	6
22Q LOSS WILD-TYPE	241	107	64

Figure S128. Get High-res Image Gene #56: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S129. Gene #56: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	168	155	59	117
22Q LOSS MUTATED	8	47	8	26
22Q LOSS WILD-TYPE	160	108	51	91

Figure S129. Get High-res Image Gene #56: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S130. Gene #56: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	105	134	86	96	78
22Q LOSS MUTATED	9	42	13	23	2
22Q LOSS WILD-TYPE	96	92	73	73	76

Figure S130. Get High-res Image Gene #56: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.14

Table S131. Gene #56: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	151	167
22Q LOSS MUTATED	23	43	23
22Q LOSS WILD-TYPE	159	108	144

Figure S131. Get High-res Image Gene #56: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.023

Table S132. Gene #56: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	128	193
22Q LOSS MUTATED	21	40	28
22Q LOSS WILD-TYPE	158	88	165

Figure S132. Get High-res Image Gene #56: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.073

Table S133. Gene #56: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	164	146
22Q LOSS MUTATED	17	23	41
22Q LOSS WILD-TYPE	143	141	105

Figure S133. Get High-res Image Gene #56: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'22q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.097

Table S134. Gene #56: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	126	179
22Q LOSS MUTATED	22	37	22
22Q LOSS WILD-TYPE	143	89	157

Figure S134. 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 = 501
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)

Made with Nozzle