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

Colorectal 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/C1FX7862

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 600 patients, 147 significant findings detected with P value < 0.05 and Q value < 0.25.

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

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, 147 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
7q gain	302 (50%)	298	0.0002 (0.161)	1e-05 (0.0094)	1e-05 (0.0094)	6e-05 (0.0497)	0.136 (1.00)	0.0258 (1.00)	2e-05 (0.017)	1e-05 (0.0094)	0.0129 (1.00)	0.238 (1.00)	4e-05 (0.0334)	1e-05 (0.0094)
13q gain	359 (60%)	241	1e-05 (0.0094)	1e-05 (0.0094)	1e-05 (0.0094)	1e-05 (0.0094)	0.243 (1.00)	0.346 (1.00)	1e-05 (0.0094)	1e-05 (0.0094)	0.00064 (0.499)	0.501 (1.00)	1e-05 (0.0094)	1e-05 (0.0094)
20q gain	454 (76%)	146	1e-05 (0.0094)	1e-05 (0.0094)	1e-05 (0.0094)	1e-05 (0.0094)	0.00506 (1.00)	0.00491 (1.00)	1e-05 (0.0094)	1e-05 (0.0094)	0.0201 (1.00)	0.00054 (0.423)	1e-05 (0.0094)	1e-05 (0.0094)
14q loss	199 (33%)	401	0.00021 (0.169)	8e-05 (0.0658)	1e-05 (0.0094)	1e-05 (0.0094)	0.00277 (1.00)	0.181 (1.00)	1e-05 (0.0094)	1e-05 (0.0094)	0.133 (1.00)	0.119 (1.00)	1e-05 (0.0094)	1e-05 (0.0094)
17p loss	330 (55%)	270	3e-05 (0.0252)	6e-05 (0.0497)	1e-05 (0.0094)	1e-05 (0.0094)	0.122 (1.00)	0.00842 (1.00)	1e-05 (0.0094)	1e-05 (0.0094)	0.0363 (1.00)	0.0245 (1.00)	1e-05 (0.0094)	1e-05 (0.0094)
18p loss	367 (61%)	233	1e-05 (0.0094)	1e-05 (0.0094)	1e-05 (0.0094)	1e-05 (0.0094)	0.0322 (1.00)	0.0482 (1.00)	1e-05 (0.0094)	1e-05 (0.0094)	0.0074 (1.00)	0.0096 (1.00)	1e-05 (0.0094)	1e-05 (0.0094)
18q loss	396 (66%)	204	1e-05 (0.0094)	1e-05 (0.0094)	1e-05 (0.0094)	1e-05 (0.0094)	0.0515 (1.00)	0.101 (1.00)	1e-05 (0.0094)	1e-05 (0.0094)	0.00109 (0.835)	0.00461 (1.00)	1e-05 (0.0094)	1e-05 (0.0094)
7p gain	339 (56%)	261	0.00047 (0.37)	1e-05 (0.0094)	1e-05 (0.0094)	1e-05 (0.0094)	0.00881 (1.00)	0.00843 (1.00)	2e-05 (0.017)	1e-05 (0.0094)	0.00625 (1.00)	0.177 (1.00)	3e-05 (0.0252)	1e-05 (0.0094)
20p gain	343 (57%)	257	0.00025 (0.199)	2e-05 (0.017)	1e-05 (0.0094)	0.00129 (0.979)	0.0188 (1.00)	0.104 (1.00)	9e-05 (0.0738)	1e-05 (0.0094)	0.349 (1.00)	0.064 (1.00)	0.00069 (0.537)	4e-05 (0.0334)
15q loss	222 (37%)	378	0.0001 (0.0816)	0.00174 (1.00)	1e-05 (0.0094)	0.00032 (0.254)	0.238 (1.00)	0.779 (1.00)	1e-05 (0.0094)	1e-05 (0.0094)	0.821 (1.00)	0.685 (1.00)	1e-05 (0.0094)	1e-05 (0.0094)
11q gain	74 (12%)	526	0.0162 (1.00)	0.00103 (0.792)	1e-05 (0.0094)	2e-05 (0.017)	0.194 (1.00)	0.374 (1.00)	1e-05 (0.0094)	3e-05 (0.0252)	0.301 (1.00)	0.0608 (1.00)	0.00019 (0.154)	0.00063 (0.492)
2p gain	117 (20%)	483	0.0409 (1.00)	0.0156 (1.00)	3e-05 (0.0252)	0.00353 (1.00)	0.623 (1.00)	0.564 (1.00)	1e-05 (0.0094)	1e-05 (0.0094)	0.0432 (1.00)	0.00221 (1.00)	0.242 (1.00)	0.00022 (0.177)
16p gain	141 (24%)	459	0.0061 (1.00)	0.00405 (1.00)	1e-05 (0.0094)	0.0154 (1.00)	0.142 (1.00)	0.667 (1.00)	0.00025 (0.199)	0.00024 (0.192)	0.491 (1.00)	0.439 (1.00)	0.0172 (1.00)	7e-05 (0.0578)
4q loss	184 (31%)	416	0.0423 (1.00)	0.0751 (1.00)	1e-05 (0.0094)	5e-05 (0.0415)	0.759 (1.00)	0.589 (1.00)	0.00078 (0.604)	0.00015 (0.122)	0.106 (1.00)	0.135 (1.00)	0.00101 (0.778)	0.00023 (0.184)
8p loss	212 (35%)	388	0.00912 (1.00)	0.00614 (1.00)	1e-05 (0.0094)	8e-05 (0.0658)	0.328 (1.00)	0.0398 (1.00)	0.00067 (0.522)	4e-05 (0.0334)	0.512 (1.00)	0.207 (1.00)	0.00069 (0.537)	2e-05 (0.017)
10q loss	106 (18%)	494	0.0225 (1.00)	0.254 (1.00)	1e-05 (0.0094)	0.0077 (1.00)	0.0132 (1.00)	0.4 (1.00)	3e-05 (0.0252)	2e-05 (0.017)	0.704 (1.00)	0.383 (1.00)	0.00036 (0.285)	0.00014 (0.114)
16q gain	139 (23%)	461	0.00835 (1.00)	0.00365 (1.00)	1e-05 (0.0094)	0.0291 (1.00)	0.232 (1.00)	0.472 (1.00)	0.00046 (0.363)	0.00019 (0.154)	0.786 (1.00)	0.477 (1.00)	0.00284 (1.00)	5e-05 (0.0415)
17q gain	107 (18%)	493	0.0126 (1.00)	0.0051 (1.00)	1e-05 (0.0094)	0.00256 (1.00)	0.274 (1.00)	0.674 (1.00)	0.00016 (0.13)	2e-05 (0.017)	0.00212 (1.00)	0.0197 (1.00)	0.606 (1.00)	0.0388 (1.00)
4p loss	190 (32%)	410	0.0291 (1.00)	0.0154 (1.00)	1e-05 (0.0094)	0.00132 (1.00)	0.477 (1.00)	0.299 (1.00)	0.00046 (0.363)	0.00013 (0.106)	0.0813 (1.00)	0.465 (1.00)	7e-05 (0.0578)	0.00221 (1.00)
9q loss	72 (12%)	528	0.0485 (1.00)	0.0139 (1.00)	1e-05 (0.0094)	0.00274 (1.00)	0.93 (1.00)	0.251 (1.00)	9e-05 (0.0738)	0.00062 (0.485)	0.467 (1.00)	0.0162 (1.00)	0.00022 (0.177)	0.0268 (1.00)
22q loss	197 (33%)	403	0.00471 (1.00)	0.00031 (0.246)	1e-05 (0.0094)	0.0641 (1.00)	0.777 (1.00)	0.799 (1.00)	0.005 (1.00)	0.00024 (0.192)	0.977 (1.00)	0.07 (1.00)	0.00085 (0.656)	0.00434 (1.00)
2q gain	115 (19%)	485	0.026 (1.00)	0.00449 (1.00)	1e-05 (0.0094)	0.00135 (1.00)	0.648 (1.00)	0.854 (1.00)	0.00109 (0.835)	1e-05 (0.0094)	0.11 (1.00)	0.0131 (1.00)	0.414 (1.00)	0.00423 (1.00)
8q gain	306 (51%)	294	0.351 (1.00)	0.166 (1.00)	1e-05 (0.0094)	0.0172 (1.00)	0.0967 (1.00)	0.0745 (1.00)	0.00016 (0.13)	0.00605 (1.00)	0.372 (1.00)	0.0161 (1.00)	0.0519 (1.00)	0.0202 (1.00)
11p gain	82 (14%)	518	0.0126 (1.00)	0.00543 (1.00)	1e-05 (0.0094)	1e-05 (0.0094)	0.657 (1.00)	0.634 (1.00)	0.0017 (1.00)	0.00567 (1.00)	0.33 (1.00)	0.405 (1.00)	0.0179 (1.00)	0.0827 (1.00)
1p loss	135 (22%)	465	0.0657 (1.00)	0.0299 (1.00)	1e-05 (0.0094)	0.00238 (1.00)	0.99 (1.00)	0.868 (1.00)	0.00105 (0.806)	0.00027 (0.215)	0.298 (1.00)	0.0455 (1.00)	0.0447 (1.00)	0.00341 (1.00)
1q loss	76 (13%)	524	0.233 (1.00)	0.211 (1.00)	1e-05 (0.0094)	0.3 (1.00)	0.868 (1.00)	0.813 (1.00)	0.00021 (0.169)	0.0012 (0.913)	0.769 (1.00)	0.00986 (1.00)	0.126 (1.00)	0.0073 (1.00)
5q loss	115 (19%)	485	0.00866 (1.00)	0.0289 (1.00)	1e-05 (0.0094)	0.0325 (1.00)	0.111 (1.00)	0.101 (1.00)	0.0099 (1.00)	0.0391 (1.00)	0.624 (1.00)	0.636 (1.00)	0.00055 (0.431)	7e-05 (0.0578)
9p loss	73 (12%)	527	0.491 (1.00)	0.202 (1.00)	1e-05 (0.0094)	0.0115 (1.00)	0.844 (1.00)	0.472 (1.00)	9e-05 (0.0738)	0.00987 (1.00)	0.206 (1.00)	0.111 (1.00)	0.00137 (1.00)	0.0277 (1.00)
21q loss	187 (31%)	413	0.0258 (1.00)	0.0414 (1.00)	1e-05 (0.0094)	0.0285 (1.00)	0.702 (1.00)	0.536 (1.00)	7e-05 (0.0578)	0.045 (1.00)	0.123 (1.00)	0.13 (1.00)	0.00269 (1.00)	0.0178 (1.00)
3p gain	69 (12%)	531	0.013 (1.00)	0.0768 (1.00)	1e-05 (0.0094)	0.132 (1.00)	0.127 (1.00)	0.0425 (1.00)	0.361 (1.00)	0.2 (1.00)	0.151 (1.00)	0.507 (1.00)	0.0652 (1.00)	0.0735 (1.00)
3q gain	95 (16%)	505	0.0319 (1.00)	0.00194 (1.00)	1e-05 (0.0094)	0.0117 (1.00)	0.124 (1.00)	0.0196 (1.00)	0.0177 (1.00)	0.00643 (1.00)	0.0443 (1.00)	0.548 (1.00)	0.00479 (1.00)	0.0238 (1.00)
6p gain	121 (20%)	479	0.0146 (1.00)	0.00048 (0.378)	1e-05 (0.0094)	0.297 (1.00)	0.853 (1.00)	0.966 (1.00)	0.179 (1.00)	0.0342 (1.00)	0.457 (1.00)	0.71 (1.00)	0.0131 (1.00)	0.00218 (1.00)
6q gain	108 (18%)	492	0.159 (1.00)	0.001 (0.771)	1e-05 (0.0094)	0.35 (1.00)	0.828 (1.00)	0.742 (1.00)	0.187 (1.00)	0.0724 (1.00)	0.356 (1.00)	0.892 (1.00)	0.00273 (1.00)	0.0169 (1.00)
8p gain	164 (27%)	436	0.924 (1.00)	0.531 (1.00)	1e-05 (0.0094)	0.969 (1.00)	0.443 (1.00)	0.288 (1.00)	0.004 (1.00)	0.00469 (1.00)	0.289 (1.00)	0.375 (1.00)	0.8 (1.00)	0.383 (1.00)
18q gain	20 (3%)	580	0.0452 (1.00)	0.437 (1.00)	0.00777 (1.00)	0.00897 (1.00)	0.613 (1.00)	0.0141 (1.00)	0.00631 (1.00)	0.00022 (0.177)	0.129 (1.00)	0.0219 (1.00)	0.0396 (1.00)	0.0152 (1.00)
19p gain	100 (17%)	500	0.412 (1.00)	0.028 (1.00)	1e-05 (0.0094)	0.0631 (1.00)	0.158 (1.00)	0.771 (1.00)	0.223 (1.00)	0.00122 (0.927)	0.0795 (1.00)	0.733 (1.00)	0.0732 (1.00)	0.0129 (1.00)
19q gain	110 (18%)	490	0.0775 (1.00)	0.00891 (1.00)	3e-05 (0.0252)	0.0867 (1.00)	0.0309 (1.00)	0.461 (1.00)	0.611 (1.00)	0.00214 (1.00)	0.299 (1.00)	0.979 (1.00)	0.112 (1.00)	0.0209 (1.00)
xq gain	101 (17%)	499	0.258 (1.00)	0.285 (1.00)	0.00014 (0.114)	0.124 (1.00)	0.108 (1.00)	0.0676 (1.00)	0.62 (1.00)	0.915 (1.00)	0.419 (1.00)	1 (1.00)	0.59 (1.00)	0.28 (1.00)
5p loss	81 (14%)	519	0.377 (1.00)	0.695 (1.00)	3e-05 (0.0252)	0.0308 (1.00)	0.687 (1.00)	0.76 (1.00)	0.78 (1.00)	0.293 (1.00)	1 (1.00)	0.207 (1.00)	0.109 (1.00)	0.00112 (0.856)
10p loss	98 (16%)	502	0.011 (1.00)	0.186 (1.00)	1e-05 (0.0094)	0.0136 (1.00)	0.0175 (1.00)	0.408 (1.00)	0.00081 (0.627)	0.00032 (0.254)	0.209 (1.00)	0.363 (1.00)	0.0215 (1.00)	0.00449 (1.00)
12p loss	70 (12%)	530	0.0668 (1.00)	0.0138 (1.00)	1e-05 (0.0094)	0.0476 (1.00)	0.877 (1.00)	0.582 (1.00)	0.0522 (1.00)	0.0366 (1.00)	0.823 (1.00)	0.82 (1.00)	0.0063 (1.00)	0.00221 (1.00)
12q loss	70 (12%)	530	0.124 (1.00)	0.0267 (1.00)	1e-05 (0.0094)	0.0598 (1.00)	0.643 (1.00)	0.975 (1.00)	0.00943 (1.00)	0.00478 (1.00)	0.262 (1.00)	0.884 (1.00)	0.00873 (1.00)	0.00187 (1.00)
19p loss	64 (11%)	536	0.377 (1.00)	0.476 (1.00)	9e-05 (0.0738)	0.257 (1.00)	0.696 (1.00)	0.247 (1.00)	0.0153 (1.00)	0.0576 (1.00)	0.157 (1.00)	0.00665 (1.00)	0.504 (1.00)	0.0669 (1.00)
19q loss	54 (9%)	546	0.668 (1.00)	0.147 (1.00)	0.00021 (0.169)	0.79 (1.00)	0.0889 (1.00)	0.407 (1.00)	0.108 (1.00)	0.325 (1.00)	0.272 (1.00)	0.0469 (1.00)	0.367 (1.00)	0.174 (1.00)
20p loss	64 (11%)	536	0.113 (1.00)	0.0194 (1.00)	4e-05 (0.0334)	0.00402 (1.00)	0.785 (1.00)	0.947 (1.00)	0.424 (1.00)	0.00857 (1.00)	0.745 (1.00)	0.511 (1.00)	0.11 (1.00)	0.0518 (1.00)
1p gain	48 (8%)	552	0.24 (1.00)	0.373 (1.00)	0.0285 (1.00)	0.685 (1.00)	0.00499 (1.00)	0.00352 (1.00)	0.996 (1.00)	0.565 (1.00)	0.315 (1.00)	0.192 (1.00)	0.0328 (1.00)	0.511 (1.00)
1q gain	116 (19%)	484	0.774 (1.00)	0.555 (1.00)	0.00307 (1.00)	0.486 (1.00)	0.125 (1.00)	0.0176 (1.00)	0.929 (1.00)	0.309 (1.00)	0.173 (1.00)	0.139 (1.00)	0.0155 (1.00)	0.235 (1.00)
4p gain	19 (3%)	581	0.813 (1.00)	0.569 (1.00)	0.0296 (1.00)	0.183 (1.00)	0.156 (1.00)	0.176 (1.00)	0.0933 (1.00)	0.355 (1.00)	0.582 (1.00)	0.505 (1.00)	0.254 (1.00)	0.113 (1.00)
4q gain	20 (3%)	580	0.228 (1.00)	0.214 (1.00)	0.00318 (1.00)	0.604 (1.00)	0.113 (1.00)	0.516 (1.00)	0.281 (1.00)	0.391 (1.00)	0.334 (1.00)	0.364 (1.00)	0.0568 (1.00)	0.961 (1.00)
5p gain	100 (17%)	500	0.499 (1.00)	0.129 (1.00)	0.00081 (0.627)	0.922 (1.00)	0.198 (1.00)	0.14 (1.00)	0.0251 (1.00)	0.0481 (1.00)	0.814 (1.00)	0.408 (1.00)	0.0151 (1.00)	0.0448 (1.00)
5q gain	63 (10%)	537	0.784 (1.00)	0.597 (1.00)	0.00711 (1.00)	0.975 (1.00)	0.724 (1.00)	0.589 (1.00)	0.199 (1.00)	0.305 (1.00)	0.742 (1.00)	0.00304 (1.00)	0.298 (1.00)	0.00729 (1.00)
9p gain	118 (20%)	482	0.538 (1.00)	0.59 (1.00)	0.174 (1.00)	0.568 (1.00)	0.127 (1.00)	0.256 (1.00)	0.81 (1.00)	0.576 (1.00)	0.979 (1.00)	0.921 (1.00)	0.0843 (1.00)	0.276 (1.00)
9q gain	99 (16%)	501	0.657 (1.00)	0.833 (1.00)	0.508 (1.00)	0.883 (1.00)	0.0928 (1.00)	0.274 (1.00)	0.935 (1.00)	0.794 (1.00)	0.577 (1.00)	0.4 (1.00)	0.717 (1.00)	0.755 (1.00)
10p gain	44 (7%)	556	0.109 (1.00)	0.11 (1.00)	0.00661 (1.00)	0.838 (1.00)	0.107 (1.00)	0.0493 (1.00)	0.477 (1.00)	0.857 (1.00)	0.506 (1.00)	0.301 (1.00)	0.0413 (1.00)	0.123 (1.00)
10q gain	24 (4%)	576	0.911 (1.00)	0.258 (1.00)	0.0523 (1.00)	0.144 (1.00)	0.167 (1.00)	0.705 (1.00)	0.973 (1.00)	0.636 (1.00)	0.517 (1.00)	0.661 (1.00)	0.131 (1.00)	0.837 (1.00)
12p gain	126 (21%)	474	0.359 (1.00)	0.361 (1.00)	0.114 (1.00)	0.00422 (1.00)	0.532 (1.00)	0.317 (1.00)	0.78 (1.00)	0.31 (1.00)	0.505 (1.00)	0.807 (1.00)	0.191 (1.00)	0.293 (1.00)
12q gain	110 (18%)	490	0.25 (1.00)	0.349 (1.00)	0.0438 (1.00)	0.00242 (1.00)	0.572 (1.00)	0.494 (1.00)	0.569 (1.00)	0.358 (1.00)	0.34 (1.00)	0.482 (1.00)	0.0749 (1.00)	0.131 (1.00)
14q gain	42 (7%)	558	0.736 (1.00)	0.397 (1.00)	0.0154 (1.00)	0.849 (1.00)	0.79 (1.00)	0.83 (1.00)	0.559 (1.00)	0.326 (1.00)	0.882 (1.00)	0.889 (1.00)	0.617 (1.00)	0.737 (1.00)
15q gain	15 (2%)	585	0.298 (1.00)	0.152 (1.00)	0.16 (1.00)	0.588 (1.00)	0.172 (1.00)	0.209 (1.00)	0.948 (1.00)	0.303 (1.00)	1 (1.00)	0.724 (1.00)	0.714 (1.00)	0.747 (1.00)
17p gain	37 (6%)	563	0.443 (1.00)	0.163 (1.00)	0.268 (1.00)	0.9 (1.00)	0.197 (1.00)	1 (1.00)	0.506 (1.00)	0.0676 (1.00)	0.167 (1.00)	0.72 (1.00)	0.617 (1.00)	0.514 (1.00)
18p gain	33 (6%)	567	0.309 (1.00)	0.371 (1.00)	0.00107 (0.821)	0.00074 (0.574)	0.608 (1.00)	0.0595 (1.00)	0.0339 (1.00)	0.00521 (1.00)	0.398 (1.00)	0.0784 (1.00)	0.112 (1.00)	0.035 (1.00)
21q gain	32 (5%)	568	0.313 (1.00)	0.263 (1.00)	0.00053 (0.416)	0.763 (1.00)	0.484 (1.00)	0.256 (1.00)	0.864 (1.00)	0.481 (1.00)	0.411 (1.00)	0.969 (1.00)	0.26 (1.00)	0.845 (1.00)
22q gain	23 (4%)	577	0.115 (1.00)	0.134 (1.00)	0.0201 (1.00)	0.311 (1.00)	0.86 (1.00)	0.693 (1.00)	0.148 (1.00)	0.658 (1.00)	0.691 (1.00)	0.917 (1.00)	0.13 (1.00)	0.446 (1.00)
2p loss	17 (3%)	583	1 (1.00)	0.616 (1.00)	0.00049 (0.385)	0.0333 (1.00)	0.346 (1.00)	0.811 (1.00)	0.165 (1.00)	0.0573 (1.00)	0.0939 (1.00)	0.228 (1.00)	0.74 (1.00)	0.616 (1.00)
2q loss	13 (2%)	587	0.805 (1.00)	0.215 (1.00)	0.0303 (1.00)	0.187 (1.00)	0.533 (1.00)	0.389 (1.00)	0.355 (1.00)	0.0904 (1.00)	0.162 (1.00)	0.0462 (1.00)	0.197 (1.00)	0.921 (1.00)
3p loss	68 (11%)	532	0.359 (1.00)	0.835 (1.00)	0.335 (1.00)	0.493 (1.00)	0.535 (1.00)	0.629 (1.00)	0.612 (1.00)	0.687 (1.00)	0.775 (1.00)	0.396 (1.00)	0.056 (1.00)	0.175 (1.00)
3q loss	44 (7%)	556	0.247 (1.00)	0.247 (1.00)	0.526 (1.00)	0.569 (1.00)	0.319 (1.00)	0.957 (1.00)	0.616 (1.00)	0.477 (1.00)	0.576 (1.00)	0.339 (1.00)	0.365 (1.00)	0.396 (1.00)
6p loss	45 (8%)	555	0.56 (1.00)	0.0218 (1.00)	0.0263 (1.00)	0.843 (1.00)	0.0682 (1.00)	0.0768 (1.00)	0.909 (1.00)	0.254 (1.00)	0.456 (1.00)	0.936 (1.00)	0.0681 (1.00)	0.444 (1.00)
6q loss	68 (11%)	532	0.445 (1.00)	0.313 (1.00)	0.0232 (1.00)	0.694 (1.00)	0.228 (1.00)	0.157 (1.00)	0.107 (1.00)	0.269 (1.00)	0.514 (1.00)	0.519 (1.00)	0.805 (1.00)	0.714 (1.00)
7q loss	4 (1%)	596			0.33 (1.00)	1 (1.00)	1 (1.00)	0.742 (1.00)	0.532 (1.00)	0.959 (1.00)	1 (1.00)	0.223 (1.00)
8q loss	33 (6%)	567	0.684 (1.00)	0.679 (1.00)	0.00116 (0.885)	0.805 (1.00)	0.966 (1.00)	0.27 (1.00)	0.6 (1.00)	0.565 (1.00)	0.433 (1.00)	0.449 (1.00)	0.522 (1.00)	0.139 (1.00)
11p loss	73 (12%)	527	0.953 (1.00)	1 (1.00)	0.0463 (1.00)	0.176 (1.00)	0.499 (1.00)	0.603 (1.00)	0.52 (1.00)	0.225 (1.00)	0.913 (1.00)	0.237 (1.00)	0.0448 (1.00)	0.229 (1.00)
11q loss	91 (15%)	509	0.846 (1.00)	0.683 (1.00)	0.0407 (1.00)	0.0395 (1.00)	0.956 (1.00)	0.7 (1.00)	0.994 (1.00)	0.764 (1.00)	0.806 (1.00)	0.416 (1.00)	0.149 (1.00)	0.392 (1.00)
13q loss	20 (3%)	580	0.296 (1.00)	0.0161 (1.00)	0.0981 (1.00)	0.326 (1.00)	0.294 (1.00)	0.00674 (1.00)	0.732 (1.00)	0.149 (1.00)	0.734 (1.00)	0.789 (1.00)	0.0192 (1.00)	0.625 (1.00)
16p loss	41 (7%)	559	0.0725 (1.00)	0.371 (1.00)	0.155 (1.00)	0.97 (1.00)	0.342 (1.00)	0.239 (1.00)	0.875 (1.00)	0.713 (1.00)	0.834 (1.00)	0.238 (1.00)	0.84 (1.00)	0.968 (1.00)
16q loss	43 (7%)	557	0.0259 (1.00)	0.585 (1.00)	0.0076 (1.00)	0.911 (1.00)	0.241 (1.00)	0.239 (1.00)	0.987 (1.00)	0.952 (1.00)	0.573 (1.00)	0.552 (1.00)	1 (1.00)	0.948 (1.00)
17q loss	89 (15%)	511	0.993 (1.00)	0.783 (1.00)	0.00119 (0.907)	0.673 (1.00)	0.883 (1.00)	0.0761 (1.00)	0.548 (1.00)	0.0363 (1.00)	0.946 (1.00)	0.417 (1.00)	0.0648 (1.00)	0.104 (1.00)
20q loss	5 (1%)	595			0.886 (1.00)	0.269 (1.00)	0.0949 (1.00)	0.7 (1.00)	0.401 (1.00)	0.651 (1.00)	0.828 (1.00)	0.689 (1.00)
xq loss	78 (13%)	522	0.987 (1.00)	0.689 (1.00)	0.0483 (1.00)	0.407 (1.00)	0.0526 (1.00)	0.436 (1.00)	0.5 (1.00)	0.153 (1.00)	0.0439 (1.00)	0.72 (1.00)	0.464 (1.00)	0.079 (1.00)

'2p gain' versus 'CN_CNMF'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	235	217	113	35
2P GAIN MUTATED	27	57	19	14
2P GAIN WILD-TYPE	208	160	94	21

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

'2p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0094

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	127	130	139	188
2P GAIN MUTATED	26	11	46	30
2P GAIN WILD-TYPE	101	119	93	158

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

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0094

Table S3. Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	64	107	45	65	66	96	141
2P GAIN MUTATED	10	20	3	21	23	4	32
2P GAIN WILD-TYPE	54	87	42	44	43	92	109

Figure S3. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.18

Table S4. Gene #3: '2p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	82	52	67	33	60
2P GAIN MUTATED	12	14	18	16	6
2P GAIN WILD-TYPE	70	38	49	17	54

Figure S4. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0094

Table S5. Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	235	217	113	35
2Q GAIN MUTATED	23	57	20	15
2Q GAIN WILD-TYPE	212	160	93	20

Figure S5. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

'2q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0094

Table S6. Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	64	107	45	65	66	96	141
2Q GAIN MUTATED	10	19	3	18	23	5	33
2Q GAIN WILD-TYPE	54	88	42	47	43	91	108

Figure S6. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0094

Table S7. Gene #5: '3p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	235	217	113	35
3P GAIN MUTATED	12	47	8	2
3P GAIN WILD-TYPE	223	170	105	33

Figure S7. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #3: 'CN_CNMF'

'3q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0094

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	235	217	113	35
3Q GAIN MUTATED	13	63	15	4
3Q GAIN WILD-TYPE	222	154	98	31

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

'6p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0094

Table S9. Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	235	217	113	35
6P GAIN MUTATED	20	68	25	8
6P GAIN WILD-TYPE	215	149	88	27

Figure S9. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

'6q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0094

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	235	217	113	35
6Q GAIN MUTATED	17	62	23	6
6Q GAIN WILD-TYPE	218	155	90	29

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

'7p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0094

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	49	41	76	49
7P GAIN MUTATED	12	27	30	37
7P GAIN WILD-TYPE	37	14	46	12

Figure S11. 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 = 0.0094

Table S12. Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	235	217	113	35
7P GAIN MUTATED	80	161	72	26
7P GAIN WILD-TYPE	155	56	41	9

Figure S12. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0094

Table S13. Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	155	121
7P GAIN MUTATED	53	118	57
7P GAIN WILD-TYPE	45	37	64

Figure S13. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	127	130	139	188
7P GAIN MUTATED	76	54	104	98
7P GAIN WILD-TYPE	51	76	35	90

Figure S14. 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 = 0.0094

Table S15. Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	64	107	45	65	66	96	141
7P GAIN MUTATED	32	67	10	45	56	33	89
7P GAIN WILD-TYPE	32	40	35	20	10	63	52

Figure S15. 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 S16. Gene #13: '7p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	109	85
7P GAIN MUTATED	71	47	62
7P GAIN WILD-TYPE	29	62	23

Figure S16. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0094

Table S17. Gene #13: '7p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	82	52	67	33	60
7P GAIN MUTATED	58	38	51	20	13
7P GAIN WILD-TYPE	24	14	16	13	47

Figure S17. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q gain' versus 'MRNA_CNMF'

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

Table S18. Gene #14: '7q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	62	69	41
7Q GAIN MUTATED	9	36	36	12
7Q GAIN WILD-TYPE	34	26	33	29

Figure S18. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'7q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0094

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	49	41	76	49
7Q GAIN MUTATED	9	22	26	36
7Q GAIN WILD-TYPE	40	19	50	13

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 = 0.0094

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	235	217	113	35
7Q GAIN MUTATED	75	141	65	21
7Q GAIN WILD-TYPE	160	76	48	14

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

'7q gain' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.05

Table S21. Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	155	121
7Q GAIN MUTATED	46	104	52
7Q GAIN WILD-TYPE	52	51	69

Figure S21. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	127	130	139	188
7Q GAIN MUTATED	64	49	95	88
7Q GAIN WILD-TYPE	63	81	44	100

Figure S22. 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 = 0.0094

Table S23. Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	64	107	45	65	66	96	141
7Q GAIN MUTATED	29	62	9	40	48	29	79
7Q GAIN WILD-TYPE	35	45	36	25	18	67	62

Figure S23. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_MATURE_CNMF'

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

Table S24. Gene #14: '7q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	109	85
7Q GAIN MUTATED	62	42	58
7Q GAIN WILD-TYPE	38	67	27

Figure S24. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0094

Table S25. Gene #14: '7q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	82	52	67	33	60
7Q GAIN MUTATED	50	33	46	20	13
7Q GAIN WILD-TYPE	32	19	21	13	47

Figure S25. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0094

Table S26. Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	235	217	113	35
8P GAIN MUTATED	46	52	54	12
8P GAIN WILD-TYPE	189	165	59	23

Figure S26. 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 = 0.0094

Table S27. Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	235	217	113	35
8Q GAIN MUTATED	71	109	104	22
8Q GAIN WILD-TYPE	164	108	9	13

Figure S27. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'MRNASEQ_CNMF'

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

Table S28. Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	127	130	139	188
8Q GAIN MUTATED	73	47	86	92
8Q GAIN WILD-TYPE	54	83	53	96

Figure S28. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0094

Table S29. Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	235	217	113	35
11P GAIN MUTATED	10	48	14	10
11P GAIN WILD-TYPE	225	169	99	25

Figure S29. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

'11p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0094

Table S30. Gene #21: '11p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	155	121
11P GAIN MUTATED	12	37	6
11P GAIN WILD-TYPE	86	118	115

Figure S30. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0094

Table S31. Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	235	217	113	35
11Q GAIN MUTATED	5	45	13	11
11Q GAIN WILD-TYPE	230	172	100	24

Figure S31. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

'11q gain' versus 'METHLYATION_CNMF'

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

Table S32. Gene #22: '11q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	155	121
11Q GAIN MUTATED	8	34	5
11Q GAIN WILD-TYPE	90	121	116

Figure S32. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0094

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	127	130	139	188
11Q GAIN MUTATED	14	3	32	24
11Q GAIN WILD-TYPE	113	127	107	164

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

'11q gain' versus 'MRNASEQ_CHIERARCHICAL'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	64	107	45	65	66	96	141
11Q GAIN MUTATED	4	9	0	15	16	5	24
11Q GAIN WILD-TYPE	60	98	45	50	50	91	117

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

'11q gain' versus 'MIRSEQ_MATURE_CNMF'

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

Table S35. Gene #22: '11q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	109	85
11Q GAIN MUTATED	18	3	16
11Q GAIN WILD-TYPE	82	106	69

Figure S35. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'13q gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0094

Table S36. Gene #25: '13q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	62	69	41
13Q GAIN MUTATED	16	46	52	14
13Q GAIN WILD-TYPE	27	16	17	27

Figure S36. 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 = 0.0094

Table S37. Gene #25: '13q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	49	41	76	49
13Q GAIN MUTATED	12	29	48	39
13Q GAIN WILD-TYPE	37	12	28	10

Figure S37. 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 = 0.0094

Table S38. Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	235	217	113	35
13Q GAIN MUTATED	78	194	68	19
13Q GAIN WILD-TYPE	157	23	45	16

Figure S38. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

'13q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0094

Table S39. Gene #25: '13q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	155	121
13Q GAIN MUTATED	56	119	54
13Q GAIN WILD-TYPE	42	36	67

Figure S39. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0094

Table S40. Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	127	130	139	188
13Q GAIN MUTATED	70	56	105	120
13Q GAIN WILD-TYPE	57	74	34	68

Figure S40. 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 = 0.0094

Table S41. Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	64	107	45	65	66	96	141
13Q GAIN MUTATED	24	72	14	49	52	33	107
13Q GAIN WILD-TYPE	40	35	31	16	14	63	34

Figure S41. 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 = 0.0094

Table S42. Gene #25: '13q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	109	85
13Q GAIN MUTATED	78	48	62
13Q GAIN WILD-TYPE	22	61	23

Figure S42. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'13q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0094

Table S43. Gene #25: '13q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	82	52	67	33	60
13Q GAIN MUTATED	54	42	55	21	16
13Q GAIN WILD-TYPE	28	10	12	12	44

Figure S43. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0094

Table S44. Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	235	217	113	35
16P GAIN MUTATED	15	97	21	8
16P GAIN WILD-TYPE	220	120	92	27

Figure S44. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

'16p gain' versus 'MRNASEQ_CNMF'

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

Table S45. Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	127	130	139	188
16P GAIN MUTATED	25	16	45	53
16P GAIN WILD-TYPE	102	114	94	135

Figure S45. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.19

Table S46. Gene #28: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	64	107	45	65	66	96	141
16P GAIN MUTATED	15	20	3	15	22	15	49
16P GAIN WILD-TYPE	49	87	42	50	44	81	92

Figure S46. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.058

Table S47. Gene #28: '16p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	82	52	67	33	60
16P GAIN MUTATED	22	14	23	9	2
16P GAIN WILD-TYPE	60	38	44	24	58

Figure S47. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0094

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	235	217	113	35
16Q GAIN MUTATED	14	97	20	8
16Q GAIN WILD-TYPE	221	120	93	27

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

'16q gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S49. Gene #29: '16q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	64	107	45	65	66	96	141
16Q GAIN MUTATED	15	19	3	16	24	14	46
16Q GAIN WILD-TYPE	49	88	42	49	42	82	95

Figure S49. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S50. Gene #29: '16q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	82	52	67	33	60
16Q GAIN MUTATED	21	15	25	9	2
16Q GAIN WILD-TYPE	61	37	42	24	58

Figure S50. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0094

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	235	217	113	35
17Q GAIN MUTATED	19	57	26	5
17Q GAIN WILD-TYPE	216	160	87	30

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

'17q gain' versus 'MRNASEQ_CNMF'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	127	130	139	188
17Q GAIN MUTATED	16	15	43	31
17Q GAIN WILD-TYPE	111	115	96	157

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

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S53. Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	64	107	45	65	66	96	141
17Q GAIN MUTATED	6	19	2	21	16	7	34
17Q GAIN WILD-TYPE	58	88	43	44	50	89	107

Figure S53. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.18

Table S54. Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	64	107	45	65	66	96	141
18Q GAIN MUTATED	7	2	4	1	1	5	0
18Q GAIN WILD-TYPE	57	105	41	64	65	91	141

Figure S54. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0094

Table S55. Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	235	217	113	35
19P GAIN MUTATED	16	58	20	6
19P GAIN WILD-TYPE	219	159	93	29

Figure S55. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

'19q gain' versus 'CN_CNMF'

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

Table S56. Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	235	217	113	35
19Q GAIN MUTATED	22	61	20	7
19Q GAIN WILD-TYPE	213	156	93	28

Figure S56. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'MRNA_CNMF'

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

Table S57. Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	62	69	41
20P GAIN MUTATED	16	40	51	18
20P GAIN WILD-TYPE	27	22	18	23

Figure S57. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20p gain' versus 'MRNA_CHIERARCHICAL'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	49	41	76	49
20P GAIN MUTATED	13	27	50	35
20P GAIN WILD-TYPE	36	14	26	14

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 = 0.0094

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	235	217	113	35
20P GAIN MUTATED	92	151	65	35
20P GAIN WILD-TYPE	143	66	48	0

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

'20p gain' versus 'MRNASEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.074

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	127	130	139	188
20P GAIN MUTATED	70	54	93	117
20P GAIN WILD-TYPE	57	76	46	71

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 = 0.0094

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	64	107	45	65	66	96	141
20P GAIN MUTATED	30	68	12	48	41	35	100
20P GAIN WILD-TYPE	34	39	33	17	25	61	41

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

'20p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S62. Gene #36: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	82	52	67	33	60
20P GAIN MUTATED	54	34	45	21	17
20P GAIN WILD-TYPE	28	18	22	12	43

Figure S62. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0094

Table S63. Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	62	69	41
20Q GAIN MUTATED	18	60	63	22
20Q GAIN WILD-TYPE	25	2	6	19

Figure S63. 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 = 0.0094

Table S64. Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	49	41	76	49
20Q GAIN MUTATED	15	39	61	48
20Q GAIN WILD-TYPE	34	2	15	1

Figure S64. 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 = 0.0094

Table S65. Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	235	217	113	35
20Q GAIN MUTATED	111	213	95	35
20Q GAIN WILD-TYPE	124	4	18	0

Figure S65. 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 = 0.0094

Table S66. Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	155	121
20Q GAIN MUTATED	68	150	67
20Q GAIN WILD-TYPE	30	5	54

Figure S66. 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 = 0.0094

Table S67. Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	127	130	139	188
20Q GAIN MUTATED	93	67	135	147
20Q GAIN WILD-TYPE	34	63	4	41

Figure S67. 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 = 0.0094

Table S68. Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	64	107	45	65	66	96	141
20Q GAIN MUTATED	39	86	13	62	64	43	135
20Q GAIN WILD-TYPE	25	21	32	3	2	53	6

Figure S68. 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 = 0.0094

Table S69. Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	109	85
20Q GAIN MUTATED	93	59	75
20Q GAIN WILD-TYPE	7	50	10

Figure S69. 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 = 0.0094

Table S70. Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	82	52	67	33	60
20Q GAIN MUTATED	68	47	62	31	19
20Q GAIN WILD-TYPE	14	5	5	2	41

Figure S70. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq gain' versus 'CN_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.11

Table S71. Gene #40: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	235	217	113	35
XQ GAIN MUTATED	22	49	27	3
XQ GAIN WILD-TYPE	213	168	86	32

Figure S71. Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0094

Table S72. Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	235	217	113	35
1P LOSS MUTATED	24	75	17	19
1P LOSS WILD-TYPE	211	142	96	16

Figure S72. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S73. Gene #41: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	64	107	45	65	66	96	141
1P LOSS MUTATED	9	19	4	23	21	13	40
1P LOSS WILD-TYPE	55	88	41	42	45	83	101

Figure S73. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0094

Table S74. Gene #42: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	235	217	113	35
1Q LOSS MUTATED	14	39	10	13
1Q LOSS WILD-TYPE	221	178	103	22

Figure S74. Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

'1q loss' versus 'MRNASEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.17

Table S75. Gene #42: '1q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	127	130	139	188
1Q LOSS MUTATED	17	4	27	24
1Q LOSS WILD-TYPE	110	126	112	164

Figure S75. Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0094

Table S76. Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	235	217	113	35
4P LOSS MUTATED	34	100	30	26
4P LOSS WILD-TYPE	201	117	83	9

Figure S76. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.11

Table S77. Gene #47: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	64	107	45	65	66	96	141
4P LOSS MUTATED	14	27	6	30	28	25	54
4P LOSS WILD-TYPE	50	80	39	35	38	71	87

Figure S77. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.058

Table S78. Gene #47: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	109	85
4P LOSS MUTATED	43	18	31
4P LOSS WILD-TYPE	57	91	54

Figure S78. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0094

Table S79. Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	235	217	113	35
4Q LOSS MUTATED	32	97	32	23
4Q LOSS WILD-TYPE	203	120	81	12

Figure S79. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	155	121
4Q LOSS MUTATED	29	65	20
4Q LOSS WILD-TYPE	69	90	101

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

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S81. Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	64	107	45	65	66	96	141
4Q LOSS MUTATED	14	28	4	29	26	24	52
4Q LOSS WILD-TYPE	50	79	41	36	40	72	89

Figure S81. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S82. Gene #48: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	82	52	67	33	60
4Q LOSS MUTATED	24	21	25	13	5
4Q LOSS WILD-TYPE	58	31	42	20	55

Figure S82. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p loss' versus 'CN_CNMF'

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

Table S83. Gene #49: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	235	217	113	35
5P LOSS MUTATED	15	35	19	12
5P LOSS WILD-TYPE	220	182	94	23

Figure S83. 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 = 0.0094

Table S84. Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	235	217	113	35
5Q LOSS MUTATED	18	52	31	14
5Q LOSS WILD-TYPE	217	165	82	21

Figure S84. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

'5q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.058

Table S85. Gene #50: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	82	52	67	33	60
5Q LOSS MUTATED	17	19	15	8	1
5Q LOSS WILD-TYPE	65	33	52	25	59

Figure S85. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0094

Table S86. Gene #54: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	235	217	113	35
8P LOSS MUTATED	32	112	56	12
8P LOSS WILD-TYPE	203	105	57	23

Figure S86. Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.066

Table S87. Gene #54: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	155	121
8P LOSS MUTATED	29	73	27
8P LOSS WILD-TYPE	69	82	94

Figure S87. Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S88. Gene #54: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	64	107	45	65	66	96	141
8P LOSS MUTATED	21	36	4	22	30	26	67
8P LOSS WILD-TYPE	43	71	41	43	36	70	74

Figure S88. Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S89. Gene #54: '8p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	82	52	67	33	60
8P LOSS MUTATED	36	24	28	10	6
8P LOSS WILD-TYPE	46	28	39	23	54

Figure S89. Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0094

Table S90. Gene #56: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	235	217	113	35
9P LOSS MUTATED	11	42	13	7
9P LOSS WILD-TYPE	224	175	100	28

Figure S90. Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.074

Table S91. Gene #56: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	127	130	139	188
9P LOSS MUTATED	17	6	31	17
9P LOSS WILD-TYPE	110	124	108	171

Figure S91. Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0094

Table S92. Gene #57: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	235	217	113	35
9Q LOSS MUTATED	10	44	12	6
9Q LOSS WILD-TYPE	225	173	101	29

Figure S92. Get High-res Image Gene #57: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.074

Table S93. Gene #57: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	127	130	139	188
9Q LOSS MUTATED	19	5	29	17
9Q LOSS WILD-TYPE	108	125	110	171

Figure S93. Get High-res Image Gene #57: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.18

Table S94. Gene #57: '9q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	109	85
9Q LOSS MUTATED	20	4	16
9Q LOSS WILD-TYPE	80	105	69

Figure S94. 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 = 0.0094

Table S95. Gene #58: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	235	217	113	35
10P LOSS MUTATED	16	43	25	14
10P LOSS WILD-TYPE	219	174	88	21

Figure S95. Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

'10q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0094

Table S96. Gene #59: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	235	217	113	35
10Q LOSS MUTATED	13	46	30	17
10Q LOSS WILD-TYPE	222	171	83	18

Figure S96. Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

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

Table S97. Gene #59: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	127	130	139	188
10Q LOSS MUTATED	20	9	40	34
10Q LOSS WILD-TYPE	107	121	99	154

Figure S97. Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S98. Gene #59: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	64	107	45	65	66	96	141
10Q LOSS MUTATED	7	15	1	13	27	14	26
10Q LOSS WILD-TYPE	57	92	44	52	39	82	115

Figure S98. Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.11

Table S99. Gene #59: '10q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	82	52	67	33	60
10Q LOSS MUTATED	11	16	19	6	2
10Q LOSS WILD-TYPE	71	36	48	27	58

Figure S99. Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0094

Table S100. Gene #62: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	235	217	113	35
12P LOSS MUTATED	5	42	15	8
12P LOSS WILD-TYPE	230	175	98	27

Figure S100. Get High-res Image Gene #62: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

'12q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0094

Table S101. Gene #63: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	235	217	113	35
12Q LOSS MUTATED	8	40	13	9
12Q LOSS WILD-TYPE	227	177	100	26

Figure S101. Get High-res Image Gene #63: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

'14q loss' versus 'MRNA_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.17

Table S102. Gene #65: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	62	69	41
14Q LOSS MUTATED	10	29	33	6
14Q LOSS WILD-TYPE	33	33	36	35

Figure S102. Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'14q loss' versus 'MRNA_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.066

Table S103. Gene #65: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	49	41	76	49
14Q LOSS MUTATED	6	20	27	25
14Q LOSS WILD-TYPE	43	21	49	24

Figure S103. 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 = 0.0094

Table S104. Gene #65: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	235	217	113	35
14Q LOSS MUTATED	25	141	19	14
14Q LOSS WILD-TYPE	210	76	94	21

Figure S104. Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0094

Table S105. Gene #65: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	155	121
14Q LOSS MUTATED	28	72	20
14Q LOSS WILD-TYPE	70	83	101

Figure S105. 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 = 0.0094

Table S106. Gene #65: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	127	130	139	188
14Q LOSS MUTATED	28	19	71	74
14Q LOSS WILD-TYPE	99	111	68	114

Figure S106. 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 = 0.0094

Table S107. Gene #65: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	64	107	45	65	66	96	141
14Q LOSS MUTATED	11	35	3	27	32	15	69
14Q LOSS WILD-TYPE	53	72	42	38	34	81	72

Figure S107. Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0094

Table S108. Gene #65: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	109	85
14Q LOSS MUTATED	49	15	30
14Q LOSS WILD-TYPE	51	94	55

Figure S108. Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'14q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0094

Table S109. Gene #65: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	82	52	67	33	60
14Q LOSS MUTATED	30	20	27	15	2
14Q LOSS WILD-TYPE	52	32	40	18	58

Figure S109. Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q loss' versus 'MRNA_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.082

Table S110. Gene #66: '15q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	62	69	41
15Q LOSS MUTATED	11	32	36	7
15Q LOSS WILD-TYPE	32	30	33	34

Figure S110. Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'15q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0094

Table S111. Gene #66: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	235	217	113	35
15Q LOSS MUTATED	31	119	46	26
15Q LOSS WILD-TYPE	204	98	67	9

Figure S111. 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 = 0.0094

Table S112. Gene #66: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	127	130	139	188
15Q LOSS MUTATED	47	26	66	77
15Q LOSS WILD-TYPE	80	104	73	111

Figure S112. 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 = 0.0094

Table S113. Gene #66: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	64	107	45	65	66	96	141
15Q LOSS MUTATED	16	35	0	28	40	31	66
15Q LOSS WILD-TYPE	48	72	45	37	26	65	75

Figure S113. Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0094

Table S114. Gene #66: '15q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	109	85
15Q LOSS MUTATED	48	21	39
15Q LOSS WILD-TYPE	52	88	46

Figure S114. Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0094

Table S115. Gene #66: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	82	52	67	33	60
15Q LOSS MUTATED	33	19	36	14	6
15Q LOSS WILD-TYPE	49	33	31	19	54

Figure S115. Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'MRNA_CNMF'

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

Table S116. Gene #69: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	62	69	41
17P LOSS MUTATED	15	44	47	15
17P LOSS WILD-TYPE	28	18	22	26

Figure S116. Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17p loss' versus 'MRNA_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.05

Table S117. Gene #69: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	49	41	76	49
17P LOSS MUTATED	13	27	47	34
17P LOSS WILD-TYPE	36	14	29	15

Figure S117. 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 = 0.0094

Table S118. Gene #69: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	235	217	113	35
17P LOSS MUTATED	61	165	78	26
17P LOSS WILD-TYPE	174	52	35	9

Figure S118. 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 = 0.0094

Table S119. Gene #69: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	155	121
17P LOSS MUTATED	43	113	50
17P LOSS WILD-TYPE	55	42	71

Figure S119. 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 = 0.0094

Table S120. Gene #69: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	127	130	139	188
17P LOSS MUTATED	69	45	97	110
17P LOSS WILD-TYPE	58	85	42	78

Figure S120. 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 = 0.0094

Table S121. Gene #69: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	64	107	45	65	66	96	141
17P LOSS MUTATED	32	58	6	43	47	40	95
17P LOSS WILD-TYPE	32	49	39	22	19	56	46

Figure S121. 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 = 0.0094

Table S122. Gene #69: '17p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	109	85
17P LOSS MUTATED	72	40	51
17P LOSS WILD-TYPE	28	69	34

Figure S122. Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'17p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0094

Table S123. Gene #69: '17p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	82	52	67	33	60
17P LOSS MUTATED	51	37	46	20	9
17P LOSS WILD-TYPE	31	15	21	13	51

Figure S123. Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0094

Table S124. Gene #71: '18p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	62	69	41
18P LOSS MUTATED	13	52	54	12
18P LOSS WILD-TYPE	30	10	15	29

Figure S124. 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 = 0.0094

Table S125. Gene #71: '18p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	49	41	76	49
18P LOSS MUTATED	10	35	44	42
18P LOSS WILD-TYPE	39	6	32	7

Figure S125. 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 = 0.0094

Table S126. Gene #71: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	235	217	113	35
18P LOSS MUTATED	62	197	78	30
18P LOSS WILD-TYPE	173	20	35	5

Figure S126. 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 = 0.0094

Table S127. Gene #71: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	155	121
18P LOSS MUTATED	50	141	43
18P LOSS WILD-TYPE	48	14	78

Figure S127. 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 = 0.0094

Table S128. Gene #71: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	127	130	139	188
18P LOSS MUTATED	73	41	125	119
18P LOSS WILD-TYPE	54	89	14	69

Figure S128. 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 = 0.0094

Table S129. Gene #71: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	64	107	45	65	66	96	141
18P LOSS MUTATED	25	65	7	56	59	35	111
18P LOSS WILD-TYPE	39	42	38	9	7	61	30

Figure S129. 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 = 0.0094

Table S130. Gene #71: '18p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	109	85
18P LOSS MUTATED	87	36	60
18P LOSS WILD-TYPE	13	73	25

Figure S130. Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0094

Table S131. Gene #71: '18p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	82	52	67	33	60
18P LOSS MUTATED	53	40	52	28	10
18P LOSS WILD-TYPE	29	12	15	5	50

Figure S131. 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 = 0.0094

Table S132. Gene #72: '18q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	62	69	41
18Q LOSS MUTATED	16	54	56	14
18Q LOSS WILD-TYPE	27	8	13	27

Figure S132. 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 = 0.0094

Table S133. Gene #72: '18q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	49	41	76	49
18Q LOSS MUTATED	13	36	49	42
18Q LOSS WILD-TYPE	36	5	27	7

Figure S133. 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 = 0.0094

Table S134. Gene #72: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	235	217	113	35
18Q LOSS MUTATED	73	200	90	33
18Q LOSS WILD-TYPE	162	17	23	2

Figure S134. 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 = 0.0094

Table S135. Gene #72: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	155	121
18Q LOSS MUTATED	57	142	54
18Q LOSS WILD-TYPE	41	13	67

Figure S135. 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 = 0.0094

Table S136. Gene #72: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	127	130	139	188
18Q LOSS MUTATED	82	50	126	128
18Q LOSS WILD-TYPE	45	80	13	60

Figure S136. 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 = 0.0094

Table S137. Gene #72: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	64	107	45	65	66	96	141
18Q LOSS MUTATED	31	71	9	56	63	41	115
18Q LOSS WILD-TYPE	33	36	36	9	3	55	26

Figure S137. 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 = 0.0094

Table S138. Gene #72: '18q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	109	85
18Q LOSS MUTATED	89	44	64
18Q LOSS WILD-TYPE	11	65	21

Figure S138. Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0094

Table S139. Gene #72: '18q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	82	52	67	33	60
18Q LOSS MUTATED	60	44	54	28	11
18Q LOSS WILD-TYPE	22	8	13	5	49

Figure S139. Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.074

Table S140. Gene #73: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	235	217	113	35
19P LOSS MUTATED	10	29	17	8
19P LOSS WILD-TYPE	225	188	96	27

Figure S140. Get High-res Image Gene #73: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

'19q loss' versus 'CN_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.17

Table S141. Gene #74: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	235	217	113	35
19Q LOSS MUTATED	9	21	17	7
19Q LOSS WILD-TYPE	226	196	96	28

Figure S141. Get High-res Image Gene #74: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

'20p loss' versus 'CN_CNMF'

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

Table S142. Gene #75: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	235	217	113	35
20P LOSS MUTATED	12	35	17	0
20P LOSS WILD-TYPE	223	182	96	35

Figure S142. 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 = 0.0094

Table S143. Gene #77: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	235	217	113	35
21Q LOSS MUTATED	46	96	26	19
21Q LOSS WILD-TYPE	189	121	87	16

Figure S143. Get High-res Image Gene #77: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

'21q loss' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.058

Table S144. Gene #77: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	127	130	139	188
21Q LOSS MUTATED	35	25	64	58
21Q LOSS WILD-TYPE	92	105	75	130

Figure S144. Get High-res Image Gene #77: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.25

Table S145. Gene #78: '22q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	49	41	76	49
22Q LOSS MUTATED	5	16	31	22
22Q LOSS WILD-TYPE	44	25	45	27

Figure S145. Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0094

Table S146. Gene #78: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	235	217	113	35
22Q LOSS MUTATED	38	111	29	19
22Q LOSS WILD-TYPE	197	106	84	16

Figure S146. Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.19

Table S147. Gene #78: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	64	107	45	65	66	96	141
22Q LOSS MUTATED	17	36	4	26	26	23	60
22Q LOSS WILD-TYPE	47	71	41	39	40	73	81

Figure S147. Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtypes file = COADREAD-TP.transferedmergedcluster.txt
Number of patients = 600
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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