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

Colon Adenocarcinoma (Primary solid tumor)

15 July 2014 | analyses__2014_07_15

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/C1W957WP

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 79 arm-level events and 12 molecular subtypes across 438 patients, 153 significant findings detected with P value < 0.05 and Q value < 0.25.

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

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 79 arm-level events and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 153 significant findings detected.


		Clinical Features	MRNA CNMF	MRNA CHIERARCHICAL	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	Fisher's exact test	Fisher's exact test
20q gain	312 (71%)	126	1e-05 (0.00927)	1e-05 (0.00927)	1e-05 (0.00927)	1e-05 (0.00927)	0.00046 (0.353)	0.00057 (0.435)	1e-05 (0.00927)	1e-05 (0.00927)	0.796 (1.00)	0.00109 (0.811)	1e-05 (0.00927)	1e-05 (0.00927)
18p loss	245 (56%)	193	1e-05 (0.00927)	1e-05 (0.00927)	1e-05 (0.00927)	1e-05 (0.00927)	0.00139 (1.00)	0.00404 (1.00)	1e-05 (0.00927)	1e-05 (0.00927)	0.991 (1.00)	0.019 (1.00)	1e-05 (0.00927)	4e-05 (0.0326)
18q loss	262 (60%)	176	1e-05 (0.00927)	1e-05 (0.00927)	1e-05 (0.00927)	1e-05 (0.00927)	0.00628 (1.00)	0.00342 (1.00)	1e-05 (0.00927)	1e-05 (0.00927)	0.746 (1.00)	0.0123 (1.00)	1e-05 (0.00927)	8e-05 (0.0641)
7p gain	238 (54%)	200	0.00571 (1.00)	1e-05 (0.00927)	1e-05 (0.00927)	0.00032 (0.248)	0.0002 (0.157)	0.00209 (1.00)	1e-05 (0.00927)	1e-05 (0.00927)	0.538 (1.00)	0.478 (1.00)	3e-05 (0.0247)	0.00973 (1.00)
14q loss	134 (31%)	304	1e-05 (0.00927)	3e-05 (0.0247)	1e-05 (0.00927)	2e-05 (0.0166)	0.00187 (1.00)	0.0237 (1.00)	1e-05 (0.00927)	1e-05 (0.00927)	0.251 (1.00)	0.0212 (1.00)	4e-05 (0.0326)	0.00175 (1.00)
17p loss	229 (52%)	209	1e-05 (0.00927)	1e-05 (0.00927)	1e-05 (0.00927)	1e-05 (0.00927)	0.0197 (1.00)	0.00409 (1.00)	1e-05 (0.00927)	1e-05 (0.00927)	0.798 (1.00)	0.039 (1.00)	1e-05 (0.00927)	0.00094 (0.705)
13q gain	250 (57%)	188	6e-05 (0.0486)	1e-05 (0.00927)	1e-05 (0.00927)	0.00059 (0.449)	0.0315 (1.00)	0.0932 (1.00)	1e-05 (0.00927)	1e-05 (0.00927)	0.433 (1.00)	0.739 (1.00)	1e-05 (0.00927)	0.00388 (1.00)
4p loss	132 (30%)	306	7e-05 (0.0563)	0.00139 (1.00)	1e-05 (0.00927)	0.00016 (0.127)	0.103 (1.00)	0.362 (1.00)	1e-05 (0.00927)	1e-05 (0.00927)	0.461 (1.00)	0.381 (1.00)	2e-05 (0.0166)	0.0327 (1.00)
4q loss	120 (27%)	318	0.00027 (0.21)	0.00919 (1.00)	1e-05 (0.00927)	1e-05 (0.00927)	0.106 (1.00)	0.252 (1.00)	1e-05 (0.00927)	1e-05 (0.00927)	0.257 (1.00)	0.251 (1.00)	4e-05 (0.0326)	0.00602 (1.00)
7q gain	215 (49%)	223	0.00371 (1.00)	1e-05 (0.00927)	1e-05 (0.00927)	0.0134 (1.00)	0.00582 (1.00)	0.00978 (1.00)	4e-05 (0.0326)	1e-05 (0.00927)	0.468 (1.00)	0.657 (1.00)	2e-05 (0.0166)	0.0141 (1.00)
11q gain	49 (11%)	389	0.00023 (0.18)	1e-05 (0.00927)	1e-05 (0.00927)	0.0023 (1.00)	0.0288 (1.00)	0.6 (1.00)	9e-05 (0.0719)	1e-05 (0.00927)	0.627 (1.00)	0.00631 (1.00)	0.00734 (1.00)	0.0241 (1.00)
16p gain	103 (24%)	335	0.0001 (0.0797)	1e-05 (0.00927)	1e-05 (0.00927)	0.165 (1.00)	0.158 (1.00)	0.104 (1.00)	1e-05 (0.00927)	1e-05 (0.00927)	0.571 (1.00)	0.186 (1.00)	0.0118 (1.00)	0.0149 (1.00)
16q gain	101 (23%)	337	3e-05 (0.0247)	1e-05 (0.00927)	1e-05 (0.00927)	0.254 (1.00)	0.183 (1.00)	0.155 (1.00)	1e-05 (0.00927)	1e-05 (0.00927)	0.805 (1.00)	0.182 (1.00)	0.00202 (1.00)	0.00182 (1.00)
8p loss	137 (31%)	301	0.0233 (1.00)	0.00094 (0.705)	1e-05 (0.00927)	0.0003 (0.233)	0.0175 (1.00)	0.0202 (1.00)	1e-05 (0.00927)	1e-05 (0.00927)	0.583 (1.00)	0.153 (1.00)	1e-05 (0.00927)	0.00404 (1.00)
22q loss	141 (32%)	297	0.0003 (0.233)	0.0004 (0.308)	1e-05 (0.00927)	0.00143 (1.00)	0.177 (1.00)	0.305 (1.00)	1e-05 (0.00927)	1e-05 (0.00927)	0.187 (1.00)	0.4 (1.00)	5e-05 (0.0405)	0.00238 (1.00)
11p gain	52 (12%)	386	0.00061 (0.464)	0.00012 (0.0955)	1e-05 (0.00927)	0.00019 (0.15)	0.0919 (1.00)	0.432 (1.00)	0.00846 (1.00)	0.00013 (0.103)	0.82 (1.00)	0.00471 (1.00)	0.0314 (1.00)	0.047 (1.00)
20p gain	236 (54%)	202	0.00317 (1.00)	1e-05 (0.00927)	1e-05 (0.00927)	0.00055 (0.42)	0.0431 (1.00)	0.235 (1.00)	1e-05 (0.00927)	1e-05 (0.00927)	0.703 (1.00)	0.0708 (1.00)	0.00128 (0.951)	0.00476 (1.00)
15q loss	150 (34%)	288	0.00153 (1.00)	0.00154 (1.00)	1e-05 (0.00927)	0.00062 (0.471)	0.0117 (1.00)	0.0382 (1.00)	1e-05 (0.00927)	1e-05 (0.00927)	0.862 (1.00)	0.773 (1.00)	6e-05 (0.0486)	0.00088 (0.662)
6q gain	74 (17%)	364	0.185 (1.00)	1e-05 (0.00927)	1e-05 (0.00927)	0.33 (1.00)	0.957 (1.00)	0.52 (1.00)	0.0794 (1.00)	0.156 (1.00)	0.525 (1.00)	0.955 (1.00)	0.00017 (0.134)	0.127 (1.00)
1p loss	96 (22%)	342	0.0261 (1.00)	0.18 (1.00)	1e-05 (0.00927)	0.00198 (1.00)	0.583 (1.00)	0.772 (1.00)	6e-05 (0.0486)	1e-05 (0.00927)	0.779 (1.00)	0.0219 (1.00)	0.00464 (1.00)	0.00063 (0.478)
9q loss	51 (12%)	387	0.119 (1.00)	0.0601 (1.00)	1e-05 (0.00927)	7e-05 (0.0563)	0.976 (1.00)	0.662 (1.00)	0.00082 (0.617)	0.0027 (1.00)	0.446 (1.00)	0.165 (1.00)	3e-05 (0.0247)	0.0904 (1.00)
10q loss	70 (16%)	368	0.0237 (1.00)	0.0419 (1.00)	1e-05 (0.00927)	0.00039 (0.301)	0.0122 (1.00)	0.176 (1.00)	0.00133 (0.986)	1e-05 (0.00927)	0.612 (1.00)	0.391 (1.00)	0.00017 (0.134)	0.00561 (1.00)
2p gain	77 (18%)	361	0.0714 (1.00)	0.021 (1.00)	8e-05 (0.0641)	0.0071 (1.00)	0.111 (1.00)	0.131 (1.00)	3e-05 (0.0247)	0.01 (1.00)	0.405 (1.00)	0.0147 (1.00)	0.295 (1.00)	0.00154 (1.00)
3q gain	62 (14%)	376	0.0948 (1.00)	0.00013 (0.103)	1e-05 (0.00927)	0.0509 (1.00)	0.0916 (1.00)	0.284 (1.00)	0.116 (1.00)	0.0413 (1.00)	0.67 (1.00)	0.639 (1.00)	0.152 (1.00)	0.661 (1.00)
6p gain	82 (19%)	356	0.214 (1.00)	3e-05 (0.0247)	1e-05 (0.00927)	0.226 (1.00)	0.564 (1.00)	0.989 (1.00)	0.00548 (1.00)	0.0181 (1.00)	0.59 (1.00)	0.974 (1.00)	0.00193 (1.00)	0.115 (1.00)
17q gain	80 (18%)	358	0.121 (1.00)	0.056 (1.00)	1e-05 (0.00927)	0.00037 (0.286)	0.362 (1.00)	0.027 (1.00)	1e-05 (0.00927)	0.00037 (0.286)	0.0071 (1.00)	0.0966 (1.00)	0.0732 (1.00)	0.0375 (1.00)
18p gain	22 (5%)	416	0.0912 (1.00)	0.674 (1.00)	0.0002 (0.157)	0.00096 (0.718)	0.83 (1.00)	0.893 (1.00)	0.124 (1.00)	6e-05 (0.0486)	0.27 (1.00)	0.177 (1.00)	0.452 (1.00)	0.476 (1.00)
5q loss	74 (17%)	364	0.165 (1.00)	0.303 (1.00)	1e-05 (0.00927)	0.0126 (1.00)	0.0235 (1.00)	0.145 (1.00)	9e-05 (0.0719)	0.00624 (1.00)	0.903 (1.00)	0.697 (1.00)	0.00218 (1.00)	0.571 (1.00)
10p loss	66 (15%)	372	0.0208 (1.00)	0.0248 (1.00)	1e-05 (0.00927)	0.00142 (1.00)	0.0134 (1.00)	0.353 (1.00)	0.011 (1.00)	0.00027 (0.21)	0.497 (1.00)	0.233 (1.00)	0.00144 (1.00)	0.0153 (1.00)
11p loss	49 (11%)	389	0.224 (1.00)	0.193 (1.00)	0.00025 (0.195)	0.00716 (1.00)	0.808 (1.00)	0.871 (1.00)	0.0117 (1.00)	0.0302 (1.00)	0.91 (1.00)	0.24 (1.00)	2e-05 (0.0166)	0.208 (1.00)
11q loss	61 (14%)	377	0.0408 (1.00)	0.0151 (1.00)	0.00021 (0.165)	0.00099 (0.74)	0.604 (1.00)	0.931 (1.00)	0.0276 (1.00)	0.00302 (1.00)	0.84 (1.00)	0.682 (1.00)	0.00023 (0.18)	0.0582 (1.00)
12p loss	46 (11%)	392	0.0604 (1.00)	0.00756 (1.00)	1e-05 (0.00927)	0.00609 (1.00)	0.411 (1.00)	0.799 (1.00)	0.00354 (1.00)	7e-05 (0.0563)	0.88 (1.00)	0.408 (1.00)	0.00281 (1.00)	0.0848 (1.00)
12q loss	49 (11%)	389	0.11 (1.00)	0.00722 (1.00)	1e-05 (0.00927)	0.00733 (1.00)	0.524 (1.00)	0.687 (1.00)	0.00046 (0.353)	0.00017 (0.134)	0.954 (1.00)	0.683 (1.00)	0.00066 (0.5)	0.0155 (1.00)
17q loss	62 (14%)	376	0.111 (1.00)	0.516 (1.00)	0.00219 (1.00)	0.00799 (1.00)	0.566 (1.00)	0.62 (1.00)	0.00025 (0.195)	0.0455 (1.00)	0.361 (1.00)	0.302 (1.00)	0.00649 (1.00)	0.00015 (0.119)
2q gain	73 (17%)	365	0.071 (1.00)	0.0218 (1.00)	6e-05 (0.0486)	0.00399 (1.00)	0.288 (1.00)	0.145 (1.00)	0.0007 (0.528)	0.0077 (1.00)	0.492 (1.00)	0.0726 (1.00)	0.493 (1.00)	0.101 (1.00)
3p gain	43 (10%)	395	0.139 (1.00)	0.00718 (1.00)	2e-05 (0.0166)	0.251 (1.00)	0.144 (1.00)	0.125 (1.00)	0.382 (1.00)	0.366 (1.00)	0.689 (1.00)	0.849 (1.00)	0.631 (1.00)	0.255 (1.00)
8p gain	126 (29%)	312	0.975 (1.00)	0.965 (1.00)	3e-05 (0.0247)	0.961 (1.00)	0.438 (1.00)	0.164 (1.00)	0.00606 (1.00)	0.0633 (1.00)	0.512 (1.00)	0.117 (1.00)	0.966 (1.00)	0.059 (1.00)
8q gain	217 (50%)	221	0.883 (1.00)	0.0167 (1.00)	1e-05 (0.00927)	0.0299 (1.00)	0.128 (1.00)	0.0406 (1.00)	0.00354 (1.00)	0.00038 (0.293)	0.715 (1.00)	0.02 (1.00)	0.0246 (1.00)	0.0662 (1.00)
18q gain	13 (3%)	425	0.144 (1.00)	1 (1.00)	0.00729 (1.00)	0.00845 (1.00)	0.677 (1.00)	0.473 (1.00)	0.0112 (1.00)	1e-05 (0.00927)	0.558 (1.00)	0.188 (1.00)	0.243 (1.00)	0.44 (1.00)
19p gain	68 (16%)	370	0.148 (1.00)	0.075 (1.00)	3e-05 (0.0247)	0.0453 (1.00)	0.258 (1.00)	0.267 (1.00)	0.438 (1.00)	0.00105 (0.783)	0.0745 (1.00)	0.24 (1.00)	0.00577 (1.00)	0.12 (1.00)
19q gain	77 (18%)	361	0.114 (1.00)	0.055 (1.00)	0.00312 (1.00)	0.219 (1.00)	0.0423 (1.00)	0.0409 (1.00)	0.353 (1.00)	0.00023 (0.18)	0.148 (1.00)	0.643 (1.00)	0.0239 (1.00)	0.0574 (1.00)
1q loss	54 (12%)	384	0.409 (1.00)	0.58 (1.00)	2e-05 (0.0166)	0.0807 (1.00)	0.646 (1.00)	0.783 (1.00)	0.00518 (1.00)	0.0147 (1.00)	0.644 (1.00)	0.00179 (1.00)	0.00694 (1.00)	0.00666 (1.00)
5p loss	54 (12%)	384	0.781 (1.00)	0.946 (1.00)	6e-05 (0.0486)	0.00447 (1.00)	0.362 (1.00)	0.731 (1.00)	0.0111 (1.00)	0.0185 (1.00)	0.837 (1.00)	0.731 (1.00)	0.0987 (1.00)	0.78 (1.00)
9p loss	51 (12%)	387	0.568 (1.00)	0.0644 (1.00)	1e-05 (0.00927)	0.00106 (0.79)	0.909 (1.00)	0.36 (1.00)	0.00088 (0.662)	0.00068 (0.514)	0.372 (1.00)	0.278 (1.00)	0.00071 (0.535)	0.277 (1.00)
20p loss	43 (10%)	395	0.089 (1.00)	0.00227 (1.00)	1e-05 (0.00927)	0.0922 (1.00)	0.909 (1.00)	0.26 (1.00)	0.0807 (1.00)	0.0235 (1.00)	0.827 (1.00)	0.0459 (1.00)	0.0602 (1.00)	0.237 (1.00)
21q loss	120 (27%)	318	0.00954 (1.00)	0.0853 (1.00)	1e-05 (0.00927)	0.0523 (1.00)	0.225 (1.00)	0.597 (1.00)	0.00131 (0.972)	0.0181 (1.00)	0.455 (1.00)	0.0516 (1.00)	0.00174 (1.00)	0.0694 (1.00)
1p gain	32 (7%)	406	0.811 (1.00)	0.636 (1.00)	0.0793 (1.00)	0.765 (1.00)	0.0112 (1.00)	0.074 (1.00)	0.84 (1.00)	0.259 (1.00)	0.677 (1.00)	0.102 (1.00)	0.795 (1.00)	0.742 (1.00)
1q gain	79 (18%)	359	0.873 (1.00)	0.666 (1.00)	0.00985 (1.00)	0.157 (1.00)	0.239 (1.00)	0.013 (1.00)	0.359 (1.00)	0.395 (1.00)	0.884 (1.00)	0.0868 (1.00)	0.0328 (1.00)	0.802 (1.00)
4p gain	11 (3%)	427			0.00747 (1.00)	0.126 (1.00)	0.315 (1.00)	0.923 (1.00)	0.325 (1.00)	0.862 (1.00)	0.61 (1.00)	0.577 (1.00)	0.506 (1.00)	0.714 (1.00)
4q gain	16 (4%)	422	0.127 (1.00)	0.119 (1.00)	0.00175 (1.00)	0.793 (1.00)	0.00689 (1.00)	0.12 (1.00)	0.11 (1.00)	0.416 (1.00)	0.148 (1.00)	0.133 (1.00)	0.393 (1.00)	0.782 (1.00)
5p gain	66 (15%)	372	0.415 (1.00)	0.18 (1.00)	0.00045 (0.346)	0.414 (1.00)	0.467 (1.00)	0.998 (1.00)	0.105 (1.00)	0.123 (1.00)	0.819 (1.00)	0.361 (1.00)	0.227 (1.00)	0.786 (1.00)
5q gain	41 (9%)	397	0.874 (1.00)	0.775 (1.00)	0.00255 (1.00)	0.5 (1.00)	0.474 (1.00)	0.64 (1.00)	0.0989 (1.00)	0.0749 (1.00)	0.509 (1.00)	0.0952 (1.00)	0.774 (1.00)	0.947 (1.00)
9p gain	76 (17%)	362	0.194 (1.00)	0.137 (1.00)	0.0865 (1.00)	0.821 (1.00)	0.00198 (1.00)	0.384 (1.00)	0.768 (1.00)	0.258 (1.00)	0.876 (1.00)	0.924 (1.00)	0.0781 (1.00)	0.779 (1.00)
9q gain	66 (15%)	372	0.166 (1.00)	0.202 (1.00)	0.359 (1.00)	0.494 (1.00)	0.00039 (0.301)	0.57 (1.00)	0.937 (1.00)	0.653 (1.00)	0.423 (1.00)	0.263 (1.00)	0.311 (1.00)	0.764 (1.00)
10p gain	32 (7%)	406	0.598 (1.00)	1 (1.00)	0.006 (1.00)	0.865 (1.00)	0.0211 (1.00)	0.0704 (1.00)	0.0603 (1.00)	0.508 (1.00)	0.426 (1.00)	0.721 (1.00)	0.00843 (1.00)	0.376 (1.00)
10q gain	18 (4%)	420	0.17 (1.00)	0.441 (1.00)	0.00826 (1.00)	0.107 (1.00)	0.364 (1.00)	0.596 (1.00)	0.783 (1.00)	0.889 (1.00)	0.755 (1.00)	0.864 (1.00)	0.0373 (1.00)	0.456 (1.00)
12p gain	90 (21%)	348	0.177 (1.00)	1 (1.00)	0.0194 (1.00)	0.00688 (1.00)	0.727 (1.00)	0.767 (1.00)	0.974 (1.00)	0.144 (1.00)	0.281 (1.00)	0.418 (1.00)	0.461 (1.00)	0.734 (1.00)
12q gain	83 (19%)	355	0.197 (1.00)	0.898 (1.00)	0.0116 (1.00)	0.00534 (1.00)	0.546 (1.00)	0.793 (1.00)	0.91 (1.00)	0.221 (1.00)	0.111 (1.00)	0.102 (1.00)	0.27 (1.00)	0.631 (1.00)
14q gain	34 (8%)	404	0.338 (1.00)	0.635 (1.00)	0.00225 (1.00)	0.924 (1.00)	0.406 (1.00)	0.759 (1.00)	0.27 (1.00)	0.197 (1.00)	0.673 (1.00)	0.181 (1.00)	0.323 (1.00)	0.892 (1.00)
15q gain	12 (3%)	426	1 (1.00)	0.809 (1.00)	0.0253 (1.00)	0.81 (1.00)	0.081 (1.00)	0.0804 (1.00)	1 (1.00)	0.941 (1.00)	0.922 (1.00)	0.765 (1.00)	0.675 (1.00)	0.761 (1.00)
17p gain	27 (6%)	411	0.839 (1.00)	0.564 (1.00)	0.289 (1.00)	0.447 (1.00)	0.209 (1.00)	0.43 (1.00)	0.862 (1.00)	0.179 (1.00)	0.52 (1.00)	0.828 (1.00)	0.939 (1.00)	0.188 (1.00)
21q gain	22 (5%)	416	0.0359 (1.00)	0.298 (1.00)	0.0451 (1.00)	0.814 (1.00)	0.73 (1.00)	0.973 (1.00)	0.955 (1.00)	0.466 (1.00)	0.221 (1.00)	0.266 (1.00)	0.371 (1.00)	1 (1.00)
22q gain	12 (3%)	426	1 (1.00)	0.791 (1.00)	0.162 (1.00)	0.128 (1.00)	0.605 (1.00)	0.321 (1.00)	0.369 (1.00)	0.379 (1.00)	1 (1.00)	0.686 (1.00)	0.517 (1.00)	0.407 (1.00)
xq gain	71 (16%)	367	0.0133 (1.00)	0.264 (1.00)	0.0066 (1.00)	0.117 (1.00)	0.199 (1.00)	0.439 (1.00)	0.149 (1.00)	0.592 (1.00)	0.375 (1.00)	0.952 (1.00)	0.157 (1.00)	0.71 (1.00)
2p loss	6 (1%)	432	0.898 (1.00)	0.813 (1.00)	0.0134 (1.00)		0.701 (1.00)	0.788 (1.00)	0.144 (1.00)	0.444 (1.00)	0.64 (1.00)	0.481 (1.00)
2q loss	7 (2%)	431	1 (1.00)	0.506 (1.00)	0.0932 (1.00)		0.309 (1.00)	0.439 (1.00)	0.0462 (1.00)	0.286 (1.00)	0.387 (1.00)	0.244 (1.00)
3p loss	53 (12%)	385	0.779 (1.00)	0.488 (1.00)	0.00191 (1.00)	0.348 (1.00)	0.596 (1.00)	0.626 (1.00)	0.031 (1.00)	0.152 (1.00)	0.612 (1.00)	0.605 (1.00)	0.00058 (0.442)	0.214 (1.00)
3q loss	33 (8%)	405	0.822 (1.00)	1 (1.00)	0.0199 (1.00)	0.762 (1.00)	0.407 (1.00)	0.872 (1.00)	0.199 (1.00)	0.461 (1.00)	0.261 (1.00)	0.933 (1.00)	0.0149 (1.00)	0.609 (1.00)
6p loss	33 (8%)	405	1 (1.00)	0.456 (1.00)	0.00178 (1.00)	0.367 (1.00)	0.174 (1.00)	0.138 (1.00)	0.505 (1.00)	0.959 (1.00)	0.617 (1.00)	0.785 (1.00)	0.0321 (1.00)	0.659 (1.00)
6q loss	45 (10%)	393	0.823 (1.00)	1 (1.00)	0.00327 (1.00)	0.424 (1.00)	0.199 (1.00)	0.0978 (1.00)	0.324 (1.00)	0.519 (1.00)	0.61 (1.00)	0.964 (1.00)	0.325 (1.00)	0.678 (1.00)
7q loss	3 (1%)	435			0.142 (1.00)	0.481 (1.00)			0.714 (1.00)	0.914 (1.00)	0.562 (1.00)	0.628 (1.00)
8q loss	24 (5%)	414	0.81 (1.00)	0.401 (1.00)	0.0145 (1.00)	0.366 (1.00)	0.271 (1.00)	0.467 (1.00)	0.0172 (1.00)	0.0553 (1.00)	0.526 (1.00)	0.549 (1.00)	0.139 (1.00)	0.145 (1.00)
13q loss	12 (3%)	426	0.874 (1.00)	0.438 (1.00)	0.0544 (1.00)	0.0408 (1.00)	0.00155 (1.00)	0.0913 (1.00)	0.172 (1.00)	0.971 (1.00)	0.599 (1.00)	0.104 (1.00)	0.0784 (1.00)	0.159 (1.00)
16p loss	31 (7%)	407	0.406 (1.00)	0.688 (1.00)	0.245 (1.00)	0.386 (1.00)	0.388 (1.00)	0.013 (1.00)	0.504 (1.00)	0.436 (1.00)	0.501 (1.00)	0.481 (1.00)	0.25 (1.00)	0.98 (1.00)
16q loss	28 (6%)	410	0.404 (1.00)	0.688 (1.00)	0.0663 (1.00)	0.577 (1.00)	0.217 (1.00)	0.0331 (1.00)	0.572 (1.00)	0.779 (1.00)	0.523 (1.00)	0.754 (1.00)	0.229 (1.00)	1 (1.00)
19p loss	41 (9%)	397	1 (1.00)	0.343 (1.00)	0.0133 (1.00)	0.252 (1.00)	0.611 (1.00)	0.387 (1.00)	0.0162 (1.00)	0.00728 (1.00)	0.0403 (1.00)	0.00256 (1.00)	0.486 (1.00)	0.0476 (1.00)
19q loss	36 (8%)	402	0.734 (1.00)	0.707 (1.00)	0.0112 (1.00)	0.372 (1.00)	0.231 (1.00)	0.13 (1.00)	0.015 (1.00)	0.0111 (1.00)	0.289 (1.00)	0.0675 (1.00)	0.266 (1.00)	0.136 (1.00)
20q loss	4 (1%)	434			0.735 (1.00)				0.208 (1.00)	0.585 (1.00)	0.388 (1.00)	0.304 (1.00)
xq loss	51 (12%)	387	0.016 (1.00)	0.247 (1.00)	0.00049 (0.375)	0.135 (1.00)	0.112 (1.00)	0.386 (1.00)	0.0885 (1.00)	0.222 (1.00)	0.0797 (1.00)	0.597 (1.00)	0.0474 (1.00)	0.195 (1.00)

'2p gain' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.064

Table S1. Gene #3: '2p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
2P GAIN MUTATED	12	39	18	8
2P GAIN WILD-TYPE	25	116	174	46

Figure S1. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #3: 'CN_CNMF'

'2p gain' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.025

Table S2. Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
2P GAIN MUTATED	8	34	10	4	18
2P GAIN WILD-TYPE	25	79	61	86	98

Figure S2. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2q gain' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.049

Table S3. Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
2Q GAIN MUTATED	13	35	16	9
2Q GAIN WILD-TYPE	24	120	176	45

Figure S3. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

'3p gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.017

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
3P GAIN MUTATED	5	29	8	1
3P GAIN WILD-TYPE	32	126	184	53

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

'3q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.1

Table S5. Gene #6: '3q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
3Q GAIN MUTATED	2	6	12
3Q GAIN WILD-TYPE	40	66	20

Figure S5. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'3q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
3Q GAIN MUTATED	6	40	9	7
3Q GAIN WILD-TYPE	31	115	183	47

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

'6p gain' versus 'MRNA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.025

Table S7. Gene #11: '6p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
6P GAIN MUTATED	5	7	16
6P GAIN WILD-TYPE	37	65	16

Figure S7. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S8. Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
6P GAIN MUTATED	10	49	14	9
6P GAIN WILD-TYPE	27	106	178	45

Figure S8. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

'6q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S9. Gene #12: '6q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
6Q GAIN MUTATED	5	4	14
6Q GAIN WILD-TYPE	37	68	18

Figure S9. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S10. Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
6Q GAIN MUTATED	6	44	14	10
6Q GAIN WILD-TYPE	31	111	178	44

Figure S10. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

'6q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.13

Table S11. Gene #12: '6q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
6Q GAIN MUTATED	25	6	7
6Q GAIN WILD-TYPE	54	72	56

Figure S11. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S12. Gene #13: '7p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
7P GAIN MUTATED	10	33	26
7P GAIN WILD-TYPE	32	39	6

Figure S12. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S13. Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
7P GAIN MUTATED	29	112	63	34
7P GAIN WILD-TYPE	8	43	129	20

Figure S13. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.25

Table S14. Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	92	71
7P GAIN MUTATED	85	43	36
7P GAIN WILD-TYPE	33	49	35

Figure S14. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p gain' versus 'RPPA_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.16

Table S15. Gene #13: '7p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	78	127	26	94
7P GAIN MUTATED	53	63	19	37
7P GAIN WILD-TYPE	25	64	7	57

Figure S15. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S16. Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
7P GAIN MUTATED	23	80	38	29	62
7P GAIN WILD-TYPE	10	33	33	61	54

Figure S16. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S17. Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	96	88	128	36
7P GAIN MUTATED	55	65	29	75	8
7P GAIN WILD-TYPE	20	31	59	53	28

Figure S17. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.025

Table S18. Gene #13: '7p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
7P GAIN MUTATED	57	28	41
7P GAIN WILD-TYPE	22	50	22

Figure S18. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S19. Gene #14: '7q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
7Q GAIN MUTATED	8	27	24
7Q GAIN WILD-TYPE	34	45	8

Figure S19. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S20. Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
7Q GAIN MUTATED	27	98	59	31
7Q GAIN WILD-TYPE	10	57	133	23

Figure S20. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.033

Table S21. Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
7Q GAIN MUTATED	22	69	37	27	55
7Q GAIN WILD-TYPE	11	44	34	63	61

Figure S21. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S22. Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	96	88	128	36
7Q GAIN MUTATED	51	59	28	67	5
7Q GAIN WILD-TYPE	24	37	60	61	31

Figure S22. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.017

Table S23. Gene #14: '7q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
7Q GAIN MUTATED	50	25	41
7Q GAIN WILD-TYPE	29	53	22

Figure S23. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8p gain' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.025

Table S24. Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
8P GAIN MUTATED	21	34	46	25
8P GAIN WILD-TYPE	16	121	146	29

Figure S24. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S25. Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
8Q GAIN MUTATED	25	79	62	51
8Q GAIN WILD-TYPE	12	76	130	3

Figure S25. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

'11p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.096

Table S26. Gene #21: '11p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
11P GAIN MUTATED	1	5	11
11P GAIN WILD-TYPE	41	67	21

Figure S26. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'11p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S27. Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
11P GAIN MUTATED	8	35	3	6
11P GAIN WILD-TYPE	29	120	189	48

Figure S27. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

'11p gain' versus 'METHLYATION_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.15

Table S28. Gene #21: '11p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	92	71
11P GAIN MUTATED	25	3	7
11P GAIN WILD-TYPE	93	89	64

Figure S28. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.1

Table S29. Gene #21: '11p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	96	88	128	36
11P GAIN MUTATED	14	13	2	22	0
11P GAIN WILD-TYPE	61	83	86	106	36

Figure S29. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q gain' versus 'MRNA_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.18

Table S30. Gene #22: '11q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
11Q GAIN MUTATED	1	9	0	8
11Q GAIN WILD-TYPE	34	52	29	13

Figure S30. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'11q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S31. Gene #22: '11q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
11Q GAIN MUTATED	1	4	13
11Q GAIN WILD-TYPE	41	68	19

Figure S31. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'11q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S32. Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
11Q GAIN MUTATED	9	32	1	7
11Q GAIN WILD-TYPE	28	123	191	47

Figure S32. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

'11q gain' versus 'MRNASEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.072

Table S33. Gene #22: '11q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
11Q GAIN MUTATED	5	21	4	1	17
11Q GAIN WILD-TYPE	28	92	67	89	99

Figure S33. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S34. Gene #22: '11q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	96	88	128	36
11Q GAIN MUTATED	14	14	0	20	0
11Q GAIN WILD-TYPE	61	82	88	108	36

Figure S34. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q gain' versus 'MRNA_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.049

Table S35. Gene #25: '13q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
13Q GAIN MUTATED	14	47	10	15
13Q GAIN WILD-TYPE	21	14	19	6

Figure S35. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'13q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S36. Gene #25: '13q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
13Q GAIN MUTATED	12	46	28
13Q GAIN WILD-TYPE	30	26	4

Figure S36. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'13q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S37. Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
13Q GAIN MUTATED	23	141	56	30
13Q GAIN WILD-TYPE	14	14	136	24

Figure S37. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

'13q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S38. Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
13Q GAIN MUTATED	22	81	39	24	77
13Q GAIN WILD-TYPE	11	32	32	66	39

Figure S38. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S39. Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	96	88	128	36
13Q GAIN MUTATED	59	63	25	87	9
13Q GAIN WILD-TYPE	16	33	63	41	27

Figure S39. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S40. Gene #25: '13q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
13Q GAIN MUTATED	59	29	41
13Q GAIN WILD-TYPE	20	49	22

Figure S40. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16p gain' versus 'MRNA_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.08

Table S41. Gene #28: '16p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
16P GAIN MUTATED	5	21	2	13
16P GAIN WILD-TYPE	30	40	27	8

Figure S41. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'16p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S42. Gene #28: '16p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
16P GAIN MUTATED	4	16	21
16P GAIN WILD-TYPE	38	56	11

Figure S42. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'16p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S43. Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
16P GAIN MUTATED	12	72	12	7
16P GAIN WILD-TYPE	25	83	180	47

Figure S43. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S44. Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
16P GAIN MUTATED	7	34	14	6	41
16P GAIN WILD-TYPE	26	79	57	84	75

Figure S44. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S45. Gene #28: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	96	88	128	36
16P GAIN MUTATED	25	19	8	50	0
16P GAIN WILD-TYPE	50	77	80	78	36

Figure S45. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16q gain' versus 'MRNA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.025

Table S46. Gene #29: '16q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
16Q GAIN MUTATED	4	19	2	13
16Q GAIN WILD-TYPE	31	42	27	8

Figure S46. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'16q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S47. Gene #29: '16q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
16Q GAIN MUTATED	3	16	19
16Q GAIN WILD-TYPE	39	56	13

Figure S47. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'16q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S48. Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
16Q GAIN MUTATED	11	71	11	8
16Q GAIN WILD-TYPE	26	84	181	46

Figure S48. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

'16q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S49. Gene #29: '16q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
16Q GAIN MUTATED	7	35	13	6	39
16Q GAIN WILD-TYPE	26	78	58	84	77

Figure S49. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S50. Gene #29: '16q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	96	88	128	36
16Q GAIN MUTATED	25	20	8	47	0
16Q GAIN WILD-TYPE	50	76	80	81	36

Figure S50. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S51. Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
17Q GAIN MUTATED	8	45	15	12
17Q GAIN WILD-TYPE	29	110	177	42

Figure S51. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S52. Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
17Q GAIN MUTATED	6	40	6	7	19
17Q GAIN WILD-TYPE	27	73	65	83	97

Figure S52. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p gain' versus 'CN_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.16

Table S53. Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
18P GAIN MUTATED	1	0	16	5
18P GAIN WILD-TYPE	36	155	176	49

Figure S53. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

'18p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.049

Table S54. Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	96	88	128	36
18P GAIN MUTATED	1	3	12	1	4
18P GAIN WILD-TYPE	74	93	76	127	32

Figure S54. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S55. Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	96	88	128	36
18Q GAIN MUTATED	1	0	8	0	4
18Q GAIN WILD-TYPE	74	96	80	128	32

Figure S55. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.025

Table S56. Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
19P GAIN MUTATED	12	32	13	11
19P GAIN WILD-TYPE	25	123	179	43

Figure S56. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

'19q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.18

Table S57. Gene #35: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	96	88	128	36
19Q GAIN MUTATED	24	16	12	23	0
19Q GAIN WILD-TYPE	51	80	76	105	36

Figure S57. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S58. Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
20P GAIN MUTATED	10	52	21
20P GAIN WILD-TYPE	32	20	11

Figure S58. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S59. Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
20P GAIN MUTATED	37	103	63	33
20P GAIN WILD-TYPE	0	52	129	21

Figure S59. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S60. Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
20P GAIN MUTATED	25	74	35	22	72
20P GAIN WILD-TYPE	8	39	36	68	44

Figure S60. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S61. Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	96	88	128	36
20P GAIN MUTATED	43	63	29	89	4
20P GAIN WILD-TYPE	32	33	59	39	32

Figure S61. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S62. Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
20Q GAIN MUTATED	13	58	15	18
20Q GAIN WILD-TYPE	22	3	14	3

Figure S62. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S63. Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
20Q GAIN MUTATED	12	61	31
20Q GAIN WILD-TYPE	30	11	1

Figure S63. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S64. Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
20Q GAIN MUTATED	37	150	77	48
20Q GAIN WILD-TYPE	0	5	115	6

Figure S64. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S65. Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	92	71
20Q GAIN MUTATED	112	46	44
20Q GAIN WILD-TYPE	6	46	27

Figure S65. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S66. Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
20Q GAIN MUTATED	26	110	50	27	88
20Q GAIN WILD-TYPE	7	3	21	63	28

Figure S66. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S67. Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	96	88	128	36
20Q GAIN MUTATED	69	82	33	112	5
20Q GAIN WILD-TYPE	6	14	55	16	31

Figure S67. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S68. Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
20Q GAIN MUTATED	74	34	51
20Q GAIN WILD-TYPE	5	44	12

Figure S68. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S69. Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	66	51	83	20
20Q GAIN MUTATED	58	24	58	19
20Q GAIN WILD-TYPE	8	27	25	1

Figure S69. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S70. Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
1P LOSS MUTATED	14	61	15	6
1P LOSS WILD-TYPE	23	94	177	48

Figure S70. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.049

Table S71. Gene #41: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
1P LOSS MUTATED	6	33	17	4	30
1P LOSS WILD-TYPE	27	80	54	86	86

Figure S71. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S72. Gene #41: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	96	88	128	36
1P LOSS MUTATED	29	18	7	33	3
1P LOSS WILD-TYPE	46	78	81	95	33

Figure S72. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1q loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.017

Table S73. Gene #42: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
1Q LOSS MUTATED	7	33	9	5
1Q LOSS WILD-TYPE	30	122	183	49

Figure S73. Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'MRNA_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.056

Table S74. Gene #47: '4p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
4P LOSS MUTATED	8	28	1	9
4P LOSS WILD-TYPE	27	33	28	12

Figure S74. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'4p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S75. Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
4P LOSS MUTATED	23	74	22	13
4P LOSS WILD-TYPE	14	81	170	41

Figure S75. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.13

Table S76. Gene #47: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	92	71
4P LOSS MUTATED	49	14	20
4P LOSS WILD-TYPE	69	78	51

Figure S76. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S77. Gene #47: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
4P LOSS MUTATED	8	47	23	6	42
4P LOSS WILD-TYPE	25	66	48	84	74

Figure S77. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S78. Gene #47: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	96	88	128	36
4P LOSS MUTATED	33	31	9	49	4
4P LOSS WILD-TYPE	42	65	79	79	32

Figure S78. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.017

Table S79. Gene #47: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
4P LOSS MUTATED	32	8	21
4P LOSS WILD-TYPE	47	70	42

Figure S79. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4q loss' versus 'MRNA_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.21

Table S80. Gene #48: '4q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
4Q LOSS MUTATED	7	25	1	9
4Q LOSS WILD-TYPE	28	36	28	12

Figure S80. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'4q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S81. Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
4Q LOSS MUTATED	19	68	20	13
4Q LOSS WILD-TYPE	18	87	172	41

Figure S81. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S82. Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	92	71
4Q LOSS MUTATED	47	10	18
4Q LOSS WILD-TYPE	71	82	53

Figure S82. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S83. Gene #48: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
4Q LOSS MUTATED	9	40	20	5	39
4Q LOSS WILD-TYPE	24	73	51	85	77

Figure S83. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S84. Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	96	88	128	36
4Q LOSS MUTATED	32	27	6	44	4
4Q LOSS WILD-TYPE	43	69	82	84	32

Figure S84. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.033

Table S85. Gene #48: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
4Q LOSS MUTATED	27	6	20
4Q LOSS WILD-TYPE	52	72	43

Figure S85. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5p loss' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.049

Table S86. Gene #49: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
5P LOSS MUTATED	8	26	9	11
5P LOSS WILD-TYPE	29	129	183	43

Figure S86. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

'5q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S87. Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
5Q LOSS MUTATED	10	38	12	14
5Q LOSS WILD-TYPE	27	117	180	40

Figure S87. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.072

Table S88. Gene #50: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
5Q LOSS MUTATED	7	26	15	2	22
5Q LOSS WILD-TYPE	26	87	56	88	94

Figure S88. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S89. Gene #54: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
8P LOSS MUTATED	6	84	19	28
8P LOSS WILD-TYPE	31	71	173	26

Figure S89. Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.23

Table S90. Gene #54: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	92	71
8P LOSS MUTATED	52	17	19
8P LOSS WILD-TYPE	66	75	52

Figure S90. Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S91. Gene #54: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
8P LOSS MUTATED	12	40	22	9	49
8P LOSS WILD-TYPE	21	73	49	81	67

Figure S91. Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S92. Gene #54: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	96	88	128	36
8P LOSS MUTATED	35	30	11	53	3
8P LOSS WILD-TYPE	40	66	77	75	33

Figure S92. Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S93. Gene #54: '8p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
8P LOSS MUTATED	35	9	25
8P LOSS WILD-TYPE	44	69	38

Figure S93. Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S94. Gene #56: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
9P LOSS MUTATED	7	32	7	5
9P LOSS WILD-TYPE	30	123	185	49

Figure S94. Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S95. Gene #57: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
9Q LOSS MUTATED	5	34	7	5
9Q LOSS WILD-TYPE	32	121	185	49

Figure S95. Get High-res Image Gene #57: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.056

Table S96. Gene #57: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	92	71
9Q LOSS MUTATED	24	2	10
9Q LOSS WILD-TYPE	94	90	61

Figure S96. Get High-res Image Gene #57: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.025

Table S97. Gene #57: '9q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
9Q LOSS MUTATED	20	1	9
9Q LOSS WILD-TYPE	59	77	54

Figure S97. Get High-res Image Gene #57: '9q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S98. Gene #58: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
10P LOSS MUTATED	13	35	7	11
10P LOSS WILD-TYPE	24	120	185	43

Figure S98. Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 0.21

Table S99. Gene #58: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	96	88	128	36
10P LOSS MUTATED	20	16	6	21	0
10P LOSS WILD-TYPE	55	80	82	107	36

Figure S99. Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S100. Gene #59: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
10Q LOSS MUTATED	13	40	6	11
10Q LOSS WILD-TYPE	24	115	186	43

Figure S100. Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S101. Gene #59: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	96	88	128	36
10Q LOSS MUTATED	22	17	4	24	0
10Q LOSS WILD-TYPE	53	79	84	104	36

Figure S101. Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.13

Table S102. Gene #59: '10q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
10Q LOSS MUTATED	21	3	13
10Q LOSS WILD-TYPE	58	75	50

Figure S102. Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11p loss' versus 'CN_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.2

Table S103. Gene #60: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
11P LOSS MUTATED	11	23	12	3
11P LOSS WILD-TYPE	26	132	180	51

Figure S103. Get High-res Image Gene #60: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

'11p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.017

Table S104. Gene #60: '11p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
11P LOSS MUTATED	16	0	8
11P LOSS WILD-TYPE	63	78	55

Figure S104. Get High-res Image Gene #60: '11p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11q loss' versus 'CN_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.16

Table S105. Gene #61: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
11Q LOSS MUTATED	11	30	14	6
11Q LOSS WILD-TYPE	26	125	178	48

Figure S105. Get High-res Image Gene #61: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

'11q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.18

Table S106. Gene #61: '11q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
11Q LOSS MUTATED	17	2	13
11Q LOSS WILD-TYPE	62	76	50

Figure S106. Get High-res Image Gene #61: '11q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S107. Gene #62: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
12P LOSS MUTATED	7	31	2	6
12P LOSS WILD-TYPE	30	124	190	48

Figure S107. Get High-res Image Gene #62: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

'12p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.056

Table S108. Gene #62: '12p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	96	88	128	36
12P LOSS MUTATED	15	10	1	18	0
12P LOSS WILD-TYPE	60	86	87	110	36

Figure S108. Get High-res Image Gene #62: '12p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S109. Gene #63: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
12Q LOSS MUTATED	7	32	4	6
12Q LOSS WILD-TYPE	30	123	188	48

Figure S109. Get High-res Image Gene #63: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

'12q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.13

Table S110. Gene #63: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	96	88	128	36
12Q LOSS MUTATED	15	12	2	18	0
12Q LOSS WILD-TYPE	60	84	86	110	36

Figure S110. Get High-res Image Gene #63: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S111. Gene #65: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
14Q LOSS MUTATED	5	33	2	11
14Q LOSS WILD-TYPE	30	28	27	10

Figure S111. Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'14q loss' versus 'MRNA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.025

Table S112. Gene #65: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
14Q LOSS MUTATED	4	29	18
14Q LOSS WILD-TYPE	38	43	14

Figure S112. Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S113. Gene #65: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
14Q LOSS MUTATED	14	97	14	9
14Q LOSS WILD-TYPE	23	58	178	45

Figure S113. Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.017

Table S114. Gene #65: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	92	71
14Q LOSS MUTATED	54	12	15
14Q LOSS WILD-TYPE	64	80	56

Figure S114. Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S115. Gene #65: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
14Q LOSS MUTATED	8	49	18	5	48
14Q LOSS WILD-TYPE	25	64	53	85	68

Figure S115. Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S116. Gene #65: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	96	88	128	36
14Q LOSS MUTATED	31	35	4	57	1
14Q LOSS WILD-TYPE	44	61	84	71	35

Figure S116. Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.033

Table S117. Gene #65: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
14Q LOSS MUTATED	33	8	19
14Q LOSS WILD-TYPE	46	70	44

Figure S117. Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'15q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S118. Gene #66: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
15Q LOSS MUTATED	21	94	22	13
15Q LOSS WILD-TYPE	16	61	170	41

Figure S118. Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S119. Gene #66: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
15Q LOSS MUTATED	10	47	28	7	52
15Q LOSS WILD-TYPE	23	66	43	83	64

Figure S119. Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S120. Gene #66: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	96	88	128	36
15Q LOSS MUTATED	38	36	9	59	2
15Q LOSS WILD-TYPE	37	60	79	69	34

Figure S120. Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.049

Table S121. Gene #66: '15q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
15Q LOSS MUTATED	35	12	28
15Q LOSS WILD-TYPE	44	66	35

Figure S121. Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'17p loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S122. Gene #69: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
17P LOSS MUTATED	9	46	8	15
17P LOSS WILD-TYPE	26	15	21	6

Figure S122. Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17p loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S123. Gene #69: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
17P LOSS MUTATED	8	46	24
17P LOSS WILD-TYPE	34	26	8

Figure S123. Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S124. Gene #69: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
17P LOSS MUTATED	22	127	41	39
17P LOSS WILD-TYPE	15	28	151	15

Figure S124. Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S125. Gene #69: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	92	71
17P LOSS MUTATED	87	28	32
17P LOSS WILD-TYPE	31	64	39

Figure S125. Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S126. Gene #69: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
17P LOSS MUTATED	21	83	37	11	69
17P LOSS WILD-TYPE	12	30	34	79	47

Figure S126. Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S127. Gene #69: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	96	88	128	36
17P LOSS MUTATED	52	62	17	86	4
17P LOSS WILD-TYPE	23	34	71	42	32

Figure S127. Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S128. Gene #69: '17p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
17P LOSS MUTATED	60	20	35
17P LOSS WILD-TYPE	19	58	28

Figure S128. Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'17q loss' versus 'MRNASEQ_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.2

Table S129. Gene #70: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
17Q LOSS MUTATED	6	20	10	1	22
17Q LOSS WILD-TYPE	27	93	61	89	94

Figure S129. Get High-res Image Gene #70: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.12

Table S130. Gene #70: '17q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	66	51	83	20
17Q LOSS MUTATED	11	0	10	7
17Q LOSS WILD-TYPE	55	51	73	13

Figure S130. Get High-res Image Gene #70: '17q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S131. Gene #71: '18p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
18P LOSS MUTATED	7	51	6	16
18P LOSS WILD-TYPE	28	10	23	5

Figure S131. Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'18p loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S132. Gene #71: '18p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
18P LOSS MUTATED	6	46	28
18P LOSS WILD-TYPE	36	26	4

Figure S132. Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S133. Gene #71: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
18P LOSS MUTATED	31	140	38	36
18P LOSS WILD-TYPE	6	15	154	18

Figure S133. Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S134. Gene #71: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	92	71
18P LOSS MUTATED	103	26	33
18P LOSS WILD-TYPE	15	66	38

Figure S134. Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S135. Gene #71: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
18P LOSS MUTATED	17	99	37	13	71
18P LOSS WILD-TYPE	16	14	34	77	45

Figure S135. Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S136. Gene #71: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	96	88	128	36
18P LOSS MUTATED	58	70	16	92	1
18P LOSS WILD-TYPE	17	26	72	36	35

Figure S136. Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S137. Gene #71: '18p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
18P LOSS MUTATED	66	18	38
18P LOSS WILD-TYPE	13	60	25

Figure S137. Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.033

Table S138. Gene #71: '18p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	66	51	83	20
18P LOSS MUTATED	43	18	43	18
18P LOSS WILD-TYPE	23	33	40	2

Figure S138. Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S139. Gene #72: '18q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
18Q LOSS MUTATED	8	52	7	16
18Q LOSS WILD-TYPE	27	9	22	5

Figure S139. Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'18q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S140. Gene #72: '18q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
18Q LOSS MUTATED	7	48	28
18Q LOSS WILD-TYPE	35	24	4

Figure S140. Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S141. Gene #72: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
18Q LOSS MUTATED	31	141	47	43
18Q LOSS WILD-TYPE	6	14	145	11

Figure S141. Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S142. Gene #72: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	92	71
18Q LOSS MUTATED	104	34	37
18Q LOSS WILD-TYPE	14	58	34

Figure S142. Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S143. Gene #72: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
18Q LOSS MUTATED	20	99	42	16	76
18Q LOSS WILD-TYPE	13	14	29	74	40

Figure S143. Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S144. Gene #72: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	96	88	128	36
18Q LOSS MUTATED	62	74	21	95	1
18Q LOSS WILD-TYPE	13	22	67	33	35

Figure S144. Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S145. Gene #72: '18q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
18Q LOSS MUTATED	68	23	42
18Q LOSS WILD-TYPE	11	55	21

Figure S145. Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.064

Table S146. Gene #72: '18q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	66	51	83	20
18Q LOSS MUTATED	49	20	46	18
18Q LOSS WILD-TYPE	17	31	37	2

Figure S146. Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S147. Gene #75: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
20P LOSS MUTATED	0	27	7	9
20P LOSS WILD-TYPE	37	128	185	45

Figure S147. Get High-res Image Gene #75: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S148. Gene #77: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
21Q LOSS MUTATED	19	64	30	7
21Q LOSS WILD-TYPE	18	91	162	47

Figure S148. Get High-res Image Gene #77: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'MRNA_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.23

Table S149. Gene #78: '22q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
22Q LOSS MUTATED	7	32	4	9
22Q LOSS WILD-TYPE	28	29	25	12

Figure S149. Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S150. Gene #78: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	155	192	54
22Q LOSS MUTATED	20	86	25	10
22Q LOSS WILD-TYPE	17	69	167	44

Figure S150. Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S151. Gene #78: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	113	71	90	116
22Q LOSS MUTATED	8	47	25	9	47
22Q LOSS WILD-TYPE	25	66	46	81	69

Figure S151. Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S152. Gene #78: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	96	88	128	36
22Q LOSS MUTATED	33	34	10	56	3
22Q LOSS WILD-TYPE	42	62	78	72	33

Figure S152. Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.041

Table S153. Gene #78: '22q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
22Q LOSS MUTATED	31	8	24
22Q LOSS WILD-TYPE	48	70	39

Figure S153. Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtypes file = COAD-TP.transferedmergedcluster.txt
Number of patients = 438
Number of significantly arm-level cnvs = 79
Number of molecular subtypes = 12
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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