Correlation between copy number variations of arm-level result and molecular subtypes
Testicular Germ Cell Tumors (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C1XP747S
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1XP747S
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 74 arm-level events and 10 molecular subtypes across 150 patients, 371 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 1p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 1q gain cnv correlated to 'MIRSEQ_CNMF'.

  • 2p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 2q gain cnv correlated to 'METHLYATION_CNMF'.

  • 3p gain cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 3q gain cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 5p gain cnv correlated to 'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 5q gain cnv correlated to 'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 6p gain cnv correlated to 'CN_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 6q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 7p gain cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 7q gain cnv correlated to 'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 8p gain cnv correlated to 'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 8q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 11q gain cnv correlated to 'RPPA_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 12q gain cnv correlated to 'MIRSEQ_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 15q gain cnv correlated to 'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 16p gain cnv correlated to 'CN_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 16q gain cnv correlated to 'CN_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 17p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 17q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 19p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 19q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 20p gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • 20q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 22q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • xp gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • xq gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 1p loss cnv correlated to 'MIRSEQ_CNMF'.

  • 3p loss cnv correlated to 'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 3q loss cnv correlated to 'RPPA_CNMF' and 'MIRSEQ_MATURE_CNMF'.

  • 4p loss cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.

  • 4q loss cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 5p loss cnv correlated to 'RPPA_CNMF'.

  • 5q loss cnv correlated to 'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 6p loss cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 6q loss cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 8p loss cnv correlated to 'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 8q loss cnv correlated to 'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 9p loss cnv correlated to 'CN_CNMF'.

  • 9q loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 10p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 10q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 11p loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 11q loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 13q loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 14q loss cnv correlated to 'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 15q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 16p loss cnv correlated to 'METHLYATION_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 16q loss cnv correlated to 'MIRSEQ_CNMF'.

  • 17p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 17q loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 18p loss cnv correlated to 'MRNASEQ_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • 18q loss cnv correlated to 'MIRSEQ_CHIERARCHICAL' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 19p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 19q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 20p loss cnv correlated to 'MIRSEQ_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 22q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • xp loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • xq loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 74 arm-level events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 371 significant findings detected.

Clinical
Features 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
1p gain 37 (25%) 113 0.00282
(0.0115) 		0.0005
(0.00306) 		0.00317
(0.0125) 		0.011
(0.0312) 		0.00035
(0.00231) 		0.00221
(0.00997) 		0.00016
(0.00123) 		0.00012
(0.000955) 		1e-05
(0.000121) 		0.00052
(0.00313)
8q gain 111 (74%) 39 0.0205
(0.0498) 		0.00271
(0.0111) 		0.0121
(0.0335) 		0.00245
(0.0104) 		0.00017
(0.00128) 		0.00034
(0.00227) 		0.00011
(0.000894) 		0.00012
(0.000955) 		0.0004
(0.00257) 		0.00031
(0.0021)
17p gain 40 (27%) 110 1e-05
(0.000121) 		1e-05
(0.000121) 		3e-05
(0.000288) 		1e-05
(0.000121) 		1e-05
(0.000121) 		1e-05
(0.000121) 		1e-05
(0.000121) 		1e-05
(0.000121) 		1e-05
(0.000121) 		1e-05
(0.000121)
17q gain 51 (34%) 99 0.00025
(0.0018) 		6e-05
(0.000522) 		2e-05
(0.000203) 		1e-05
(0.000121) 		1e-05
(0.000121) 		1e-05
(0.000121) 		1e-05
(0.000121) 		1e-05
(0.000121) 		1e-05
(0.000121) 		1e-05
(0.000121)
19p gain 36 (24%) 114 0.0101
(0.0295) 		0.00011
(0.000894) 		0.00939
(0.0278) 		0.00318
(0.0125) 		0.0001
(0.000831) 		0.00091
(0.00503) 		0.0438
(0.0901) 		5e-05
(0.000457) 		0.00046
(0.00284) 		3e-05
(0.000288)
xp gain 22 (15%) 128 0.0006
(0.00352) 		0.0181
(0.0448) 		0.039
(0.0823) 		0.0088
(0.0264) 		0.00056
(0.00332) 		0.00331
(0.0128) 		0.00084
(0.00471) 		0.00017
(0.00128) 		0.00173
(0.00837) 		0.00452
(0.0162)
xq gain 22 (15%) 128 0.00196
(0.00912) 		0.018
(0.0448) 		0.0212
(0.0511) 		0.0143
(0.0373) 		0.00077
(0.00442) 		0.00397
(0.0148) 		0.00282
(0.0115) 		0.00041
(0.00257) 		0.00144
(0.0071) 		0.0041
(0.0151)
10p loss 77 (51%) 73 0.0207
(0.0499) 		0.00037
(0.00242) 		0.0083
(0.0258) 		0.00682
(0.0225) 		0.0003
(0.00206) 		0.0055
(0.019) 		0.0382
(0.0814) 		0.00085
(0.00473) 		0.00209
(0.00955) 		0.00127
(0.00648)
15q loss 29 (19%) 121 0.00548
(0.019) 		3e-05
(0.000288) 		1e-05
(0.000121) 		1e-05
(0.000121) 		1e-05
(0.000121) 		1e-05
(0.000121) 		1e-05
(0.000121) 		1e-05
(0.000121) 		1e-05
(0.000121) 		1e-05
(0.000121)
19p loss 50 (33%) 100 1e-05
(0.000121) 		1e-05
(0.000121) 		1e-05
(0.000121) 		1e-05
(0.000121) 		1e-05
(0.000121) 		1e-05
(0.000121) 		1e-05
(0.000121) 		1e-05
(0.000121) 		1e-05
(0.000121) 		1e-05
(0.000121)
19q loss 53 (35%) 97 1e-05
(0.000121) 		1e-05
(0.000121) 		1e-05
(0.000121) 		1e-05
(0.000121) 		1e-05
(0.000121) 		1e-05
(0.000121) 		1e-05
(0.000121) 		1e-05
(0.000121) 		1e-05
(0.000121) 		1e-05
(0.000121)
22q loss 45 (30%) 105 0.00234
(0.0101) 		1e-05
(0.000121) 		0.00022
(0.00161) 		2e-05
(0.000203) 		1e-05
(0.000121) 		1e-05
(0.000121) 		2e-05
(0.000203) 		1e-05
(0.000121) 		1e-05
(0.000121) 		1e-05
(0.000121)
7p gain 121 (81%) 29 0.00459
(0.0163) 		0.058
(0.11) 		0.0153
(0.0394) 		0.0206
(0.0498) 		0.0045
(0.0162) 		0.0088
(0.0264) 		0.00746
(0.0236) 		0.00733
(0.0235) 		0.00727
(0.0234) 		0.0229
(0.054)
8p gain 110 (73%) 40 0.0627
(0.117) 		0.0059
(0.02) 		0.00106
(0.00573) 		0.00014
(0.00109) 		1e-05
(0.000121) 		0.0003
(0.00206) 		4e-05
(0.000375) 		2e-05
(0.000203) 		2e-05
(0.000203) 		6e-05
(0.000522)
15q gain 51 (34%) 99 0.0513
(0.102) 		0.00227
(0.01) 		0.0019
(0.0089) 		0.0003
(0.00206) 		1e-05
(0.000121) 		2e-05
(0.000203) 		8e-05
(0.00068) 		1e-05
(0.000121) 		1e-05
(0.000121) 		1e-05
(0.000121)
19q gain 29 (19%) 121 0.0161
(0.0407) 		8e-05
(0.00068) 		0.00215
(0.00976) 		0.0026
(0.0108) 		4e-05
(0.000375) 		0.00062
(0.00358) 		0.146
(0.223) 		6e-05
(0.000522) 		0.00033
(0.00222) 		1e-05
(0.000121)
22q gain 38 (25%) 112 2e-05
(0.000203) 		0.00134
(0.00675) 		0.00924
(0.0275) 		0.00051
(0.00309) 		3e-05
(0.000288) 		1e-05
(0.000121) 		0.0558
(0.107) 		2e-05
(0.000203) 		6e-05
(0.000522) 		1e-05
(0.000121)
17p loss 37 (25%) 113 2e-05
(0.000203) 		0.0405
(0.0844) 		0.0443
(0.0906) 		0.00321
(0.0125) 		0.00462
(0.0164) 		0.00024
(0.00174) 		0.0568
(0.109) 		0.00314
(0.0125) 		0.00168
(0.00818) 		2e-05
(0.000203)
3p gain 27 (18%) 123 0.0221
(0.0524) 		0.398
(0.484) 		0.00179
(0.00849) 		0.0137
(0.0367) 		0.00691
(0.0226) 		0.00628
(0.0209) 		0.0811
(0.141) 		0.013
(0.0351) 		0.0153
(0.0394) 		0.0102
(0.0297)
5p gain 6 (4%) 144 0.668
(0.733) 		0.0262
(0.0603) 		0.00854
(0.0261) 		0.151
(0.227) 		0.0115
(0.0323) 		0.00815
(0.0256) 		0.00423
(0.0154) 		0.00637
(0.0211) 		0.00358
(0.0134) 		0.00568
(0.0195)
16p gain 16 (11%) 134 0.0116
(0.0324) 		0.0794
(0.139) 		0.0941
(0.158) 		0.00269
(0.0111) 		0.00411
(0.0151) 		0.0178
(0.0445) 		0.00228
(0.01) 		0.00609
(0.0205) 		0.00298
(0.012) 		0.0217
(0.0518)
20q gain 40 (27%) 110 0.00741
(0.0235) 		0.00569
(0.0195) 		0.0871
(0.148) 		0.0366
(0.0783) 		0.00715
(0.0232) 		0.0537
(0.104) 		0.0472
(0.0947) 		0.0126
(0.0344) 		0.0164
(0.0413) 		0.0144
(0.0376)
3p loss 30 (20%) 120 0.934
(0.955) 		0.0306
(0.0684) 		0.0162
(0.0409) 		0.318
(0.411) 		0.00121
(0.00635) 		0.00317
(0.0125) 		0.00122
(0.00636) 		0.00078
(0.00444) 		0.00241
(0.0103) 		0.00168
(0.00818)
8p loss 12 (8%) 138 0.355
(0.445) 		0.0508
(0.101) 		0.0274
(0.0622) 		0.00944
(0.0278) 		0.0103
(0.0297) 		0.047
(0.0947) 		0.00853
(0.0261) 		0.00207
(0.00951) 		0.0074
(0.0235) 		0.0226
(0.0535)
8q loss 5 (3%) 145 0.188
(0.268) 		0.0242
(0.0565) 		0.121
(0.191) 		0.0143
(0.0373) 		0.00237
(0.0102) 		0.0121
(0.0335) 		0.00132
(0.00669) 		0.00226
(0.01) 		0.0029
(0.0117) 		0.00335
(0.0128)
10q loss 72 (48%) 78 0.00878
(0.0264) 		1e-05
(0.000121) 		0.133
(0.206) 		0.0767
(0.136) 		0.00018
(0.00135) 		0.00229
(0.01) 		0.0322
(0.0706) 		0.00041
(0.00257) 		0.00123
(0.00636) 		0.00139
(0.00695)
14q loss 20 (13%) 130 0.119
(0.191) 		0.00079
(0.00446) 		0.0277
(0.0626) 		0.0937
(0.158) 		0.0043
(0.0156) 		5e-05
(0.000457) 		0.0308
(0.0684) 		0.00322
(0.0125) 		0.00247
(0.0104) 		0.0109
(0.0311)
3q gain 36 (24%) 114 0.00683
(0.0225) 		0.179
(0.257) 		0.00227
(0.01) 		0.00327
(0.0127) 		0.0321
(0.0706) 		0.0327
(0.0712) 		0.0804
(0.14) 		0.0216
(0.0518) 		0.0386
(0.082) 		0.0767
(0.136)
6p gain 28 (19%) 122 0.00042
(0.00261) 		0.753
(0.806) 		0.425
(0.511) 		0.0413
(0.0856) 		0.0124
(0.0342) 		0.00098
(0.00537) 		0.0168
(0.0419) 		0.00612
(0.0205) 		0.0541
(0.105) 		0.0197
(0.0484)
16q gain 14 (9%) 136 0.00719
(0.0232) 		0.14
(0.215) 		0.0859
(0.147) 		0.00858
(0.0261) 		0.00925
(0.0275) 		0.0486
(0.0969) 		0.0135
(0.0363) 		0.0125
(0.0343) 		0.00819
(0.0256) 		0.052
(0.102)
4q loss 108 (72%) 42 0.067
(0.123) 		0.0103
(0.0297) 		0.485
(0.57) 		0.55
(0.63) 		0.0108
(0.0308) 		0.0118
(0.033) 		0.0157
(0.0401) 		0.00502
(0.0176) 		0.0352
(0.0762) 		0.0257
(0.0594)
11p loss 98 (65%) 52 0.00854
(0.0261) 		0.184
(0.265) 		0.0772
(0.137) 		0.164
(0.241) 		0.00039
(0.00253) 		0.00055
(0.00328) 		0.00103
(0.0056) 		0.00041
(0.00257) 		0.00178
(0.00849) 		0.00125
(0.00642)
11q loss 115 (77%) 35 1e-05
(0.000121) 		0.123
(0.194) 		0.112
(0.182) 		0.0551
(0.106) 		9e-05
(0.000757) 		2e-05
(0.000203) 		0.00062
(0.00358) 		0.00014
(0.00109) 		0.00108
(0.00579) 		2e-05
(0.000203)
2p gain 46 (31%) 104 0.0138
(0.0367) 		0.00878
(0.0264) 		0.0689
(0.125) 		0.0385
(0.0818) 		0.0163
(0.0411) 		0.169
(0.247) 		0.0594
(0.112) 		0.0243
(0.0565) 		0.0301
(0.0674) 		0.0629
(0.117)
6q gain 23 (15%) 127 0.0231
(0.0541) 		0.88
(0.909) 		0.838
(0.876) 		0.215
(0.298) 		0.0138
(0.0367) 		0.00029
(0.00204) 		0.0125
(0.0343) 		0.00419
(0.0153) 		0.0508
(0.101) 		0.03
(0.0674)
7q gain 105 (70%) 45 0.549
(0.629) 		0.0683
(0.125) 		0.105
(0.172) 		0.438
(0.522) 		0.00437
(0.0158) 		0.0117
(0.0327) 		0.00255
(0.0107) 		0.00257
(0.0107) 		0.00202
(0.00934) 		0.00338
(0.0128)
5q loss 101 (67%) 49 0.0584
(0.11) 		0.0618
(0.116) 		0.0404
(0.0844) 		0.26
(0.35) 		0.0137
(0.0366) 		0.00338
(0.0128) 		0.306
(0.399) 		0.0103
(0.0297) 		0.02
(0.0489) 		0.00802
(0.0253)
13q loss 113 (75%) 37 0.0442
(0.0906) 		0.29
(0.382) 		0.094
(0.158) 		0.0524
(0.103) 		0.0327
(0.0712) 		0.00111
(0.00591) 		0.0451
(0.0918) 		0.0231
(0.0541) 		0.0996
(0.165) 		0.0014
(0.00695)
17q loss 16 (11%) 134 0.00581
(0.0198) 		0.131
(0.205) 		0.436
(0.522) 		0.0633
(0.117) 		0.0198
(0.0485) 		0.029
(0.0654) 		0.0684
(0.125) 		0.0146
(0.0379) 		0.0107
(0.0307) 		0.00489
(0.0172)
5q gain 3 (2%) 147 0.777
(0.827) 		0.0574
(0.109) 		0.0358
(0.0771) 		0.0411
(0.0855) 		0.111
(0.18) 		0.015
(0.0388) 		0.0134
(0.0361) 		0.0392
(0.0823)
6q loss 16 (11%) 134 0.12
(0.191) 		0.00963
(0.0283) 		0.158
(0.234) 		0.061
(0.114) 		0.0444
(0.0906) 		0.00117
(0.00618) 		0.107
(0.175) 		0.0273
(0.0622) 		0.0354
(0.0764) 		0.0993
(0.165)
xq loss 29 (19%) 121 0.00019
(0.00141) 		0.00187
(0.00881) 		0.155
(0.232) 		0.62
(0.693) 		0.162
(0.239) 		0.0984
(0.164) 		0.0254
(0.0589) 		0.0266
(0.0611) 		0.0527
(0.103) 		0.00393
(0.0147)
16p loss 44 (29%) 106 0.148
(0.224) 		0.00599
(0.0202) 		0.29
(0.382) 		0.252
(0.341) 		0.0804
(0.14) 		0.263
(0.354) 		0.00855
(0.0261) 		0.0112
(0.0316) 		0.0786
(0.138) 		0.21
(0.292)
xp loss 29 (19%) 121 0.00234
(0.0101) 		0.00175
(0.00841) 		0.761
(0.813) 		0.918
(0.939) 		0.162
(0.239) 		0.178
(0.257) 		0.074
(0.133) 		0.0926
(0.156) 		0.0536
(0.104) 		0.00352
(0.0133)
11q gain 4 (3%) 146 0.389
(0.475) 		0.149
(0.225) 		0.0399
(0.0837) 		0.148
(0.224) 		0.0784
(0.138) 		0.0142
(0.0373) 		0.38
(0.468) 		0.108
(0.177) 		0.106
(0.174) 		0.337
(0.427)
12q gain 100 (67%) 50 0.569
(0.648) 		0.842
(0.879) 		0.264
(0.354) 		0.548
(0.629) 		0.205
(0.287) 		0.339
(0.428) 		0.0479
(0.0959) 		0.176
(0.256) 		0.0757
(0.135) 		0.00716
(0.0232)
20p gain 34 (23%) 116 0.00525
(0.0183) 		0.115
(0.184) 		0.297
(0.388) 		0.171
(0.25) 		0.0415
(0.0859) 		0.285
(0.377) 		0.146
(0.223) 		0.148
(0.224) 		0.0604
(0.113) 		0.0637
(0.118)
3q loss 22 (15%) 128 0.738
(0.792) 		0.74
(0.793) 		0.047
(0.0947) 		0.152
(0.227) 		0.0867
(0.148) 		0.0573
(0.109) 		0.0717
(0.129) 		0.0725
(0.131) 		0.0472
(0.0947) 		0.126
(0.198)
4p loss 92 (61%) 58 0.629
(0.701) 		0.0454
(0.0921) 		0.365
(0.455) 		0.782
(0.831) 		0.0322
(0.0706) 		0.165
(0.242) 		0.102
(0.169) 		0.0789
(0.139) 		0.113
(0.183) 		0.333
(0.424)
6p loss 13 (9%) 137 0.268
(0.359) 		0.0361
(0.0774) 		0.311
(0.403) 		0.0828
(0.143) 		0.162
(0.239) 		0.0142
(0.0373) 		0.269
(0.36) 		0.114
(0.184) 		0.185
(0.265) 		0.321
(0.414)
9q loss 58 (39%) 92 0.00028
(0.00199) 		0.336
(0.427) 		0.145
(0.221) 		0.176
(0.256) 		0.308
(0.401) 		0.0185
(0.0456) 		0.657
(0.724) 		0.397
(0.484) 		0.364
(0.455) 		0.524
(0.607)
18p loss 116 (77%) 34 0.692
(0.748) 		0.075
(0.134) 		0.7
(0.754) 		0.854
(0.89) 		0.0432
(0.089) 		0.243
(0.33) 		0.0888
(0.151) 		0.016
(0.0407) 		0.278
(0.368) 		0.135
(0.209)
18q loss 122 (81%) 28 0.086
(0.147) 		0.315
(0.408) 		0.506
(0.589) 		0.874
(0.904) 		0.0689
(0.125) 		0.126
(0.198) 		0.0643
(0.119) 		0.032
(0.0706) 		0.201
(0.283) 		0.0205
(0.0498)
20p loss 30 (20%) 120 0.236
(0.322) 		0.188
(0.268) 		0.228
(0.314) 		0.426
(0.511) 		0.198
(0.28) 		0.172
(0.25) 		0.0157
(0.0401) 		0.15
(0.226) 		0.08
(0.14) 		0.0274
(0.0622)
1q gain 61 (41%) 89 0.439
(0.523) 		0.663
(0.729) 		0.2
(0.281) 		0.459
(0.544) 		0.826
(0.867) 		0.0595
(0.112) 		0.0391
(0.0823) 		0.635
(0.706) 		0.242
(0.329) 		0.0534
(0.104)
2q gain 42 (28%) 108 0.116
(0.186) 		0.0331
(0.0717) 		0.881
(0.909) 		0.346
(0.435) 		0.278
(0.368) 		0.749
(0.802) 		0.491
(0.575) 		0.4
(0.486) 		0.345
(0.435) 		0.415
(0.5)
1p loss 18 (12%) 132 0.121
(0.191) 		0.572
(0.649) 		0.488
(0.573) 		0.412
(0.498) 		0.649
(0.718) 		0.885
(0.912) 		0.0219
(0.052) 		0.357
(0.447) 		0.132
(0.205) 		0.369
(0.457)
5p loss 103 (69%) 47 0.115
(0.184) 		0.211
(0.294) 		0.0273
(0.0622) 		0.478
(0.566) 		0.116
(0.185) 		0.133
(0.206) 		0.49
(0.574) 		0.0835
(0.144) 		0.112
(0.182) 		0.105
(0.173)
9p loss 63 (42%) 87 0.0323
(0.0706) 		1
(1.00) 		0.627
(0.7) 		0.308
(0.401) 		0.868
(0.899) 		0.438
(0.522) 		0.783
(0.831) 		0.771
(0.822) 		0.911
(0.934) 		0.8
(0.847)
16q loss 51 (34%) 99 0.0795
(0.139) 		0.0665
(0.122) 		0.658
(0.724) 		0.591
(0.664) 		0.233
(0.32) 		0.483
(0.569) 		0.0307
(0.0684) 		0.121
(0.191) 		0.329
(0.421) 		0.691
(0.748)
4p gain 3 (2%) 147 0.636
(0.706) 		0.199
(0.281) 		0.862
(0.895) 		1
(1.00) 		1
(1.00) 		0.684
(0.745) 		0.493
(0.576) 		1
(1.00) 		1
(1.00) 		0.893
(0.919)
9p gain 16 (11%) 134 0.235
(0.322) 		0.333
(0.424) 		0.432
(0.518) 		0.696
(0.751) 		0.157
(0.234) 		0.293
(0.385) 		0.22
(0.304) 		0.139
(0.215) 		0.178
(0.257) 		0.329
(0.421)
9q gain 17 (11%) 133 0.152
(0.227) 		0.497
(0.579) 		0.803
(0.849) 		0.535
(0.619) 		1
(1.00) 		0.0776
(0.137) 		0.442
(0.526) 		0.895
(0.92) 		0.542
(0.625) 		0.382
(0.469)
10p gain 6 (4%) 144 0.585
(0.661) 		0.0952
(0.159) 		0.642
(0.711) 		0.827
(0.867) 		0.324
(0.416) 		0.343
(0.434) 		0.151
(0.227) 		0.324
(0.416) 		0.368
(0.457) 		0.0568
(0.109)
10q gain 8 (5%) 142 0.596
(0.669) 		0.388
(0.474) 		0.546
(0.628) 		0.179
(0.257) 		0.367
(0.456) 		0.227
(0.313) 		0.0545
(0.105) 		0.411
(0.497) 		0.515
(0.598) 		0.143
(0.22)
11p gain 10 (7%) 140 0.272
(0.363) 		0.187
(0.267) 		0.09
(0.152) 		0.13
(0.204) 		0.164
(0.241) 		0.0519
(0.102) 		0.197
(0.28) 		0.2
(0.282) 		0.203
(0.284) 		0.356
(0.446)
12p gain 146 (97%) 4 0.194
(0.276) 		0.384
(0.471) 		0.519
(0.602) 		0.537
(0.62) 		0.81
(0.855) 		0.37
(0.458) 		0.316
(0.409) 		0.583
(0.66) 		0.693
(0.748) 		0.087
(0.148)
14q gain 51 (34%) 99 0.253
(0.341) 		0.237
(0.324) 		0.588
(0.662) 		0.568
(0.648) 		0.584
(0.66) 		0.398
(0.484) 		0.822
(0.864) 		0.303
(0.396) 		0.202
(0.283) 		0.482
(0.568)
18p gain 4 (3%) 146 0.687
(0.746) 		0.0699
(0.127) 		0.69
(0.748) 		1
(1.00) 		0.379
(0.467) 		0.785
(0.833) 		0.675
(0.739) 		0.479
(0.566) 		0.572
(0.649) 		0.683
(0.745)
21q gain 125 (83%) 25 0.405
(0.491) 		0.274
(0.365) 		0.103
(0.17) 		0.333
(0.424) 		0.0824
(0.143) 		0.238
(0.324) 		0.217
(0.301) 		0.0894
(0.151) 		0.128
(0.2) 		0.131
(0.205)
1q loss 8 (5%) 142 0.346
(0.435) 		0.244
(0.331) 		0.817
(0.86) 		0.682
(0.745) 		0.293
(0.385) 		0.217
(0.301) 		0.382
(0.469) 		0.324
(0.416) 		0.157
(0.234) 		0.596
(0.669)
2p loss 5 (3%) 145 0.86
(0.895) 		0.378
(0.467) 		1
(1.00) 		1
(1.00) 		0.735
(0.791) 		1
(1.00) 		1
(1.00) 		0.813
(0.857)
2q loss 6 (4%) 144 0.445
(0.528) 		0.676
(0.739) 		0.862
(0.895) 		0.602
(0.674) 		0.557
(0.637) 		0.9
(0.924) 		0.666
(0.731) 		0.657
(0.724) 		0.564
(0.644) 		1
(1.00)
20q loss 15 (10%) 135 0.586
(0.661) 		0.489
(0.574) 		0.638
(0.708) 		0.832
(0.871) 		0.2
(0.281) 		0.273
(0.363) 		0.0697
(0.126) 		0.141
(0.217) 		0.101
(0.168) 		0.25
(0.338)
'1p gain' versus 'CN_CNMF'

P value = 0.00282 (Fisher's exact test), Q value = 0.011

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 44 58
1P GAIN MUTATED 9 5 23
1P GAIN WILD-TYPE 39 39 35

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

'1p gain' versus 'METHLYATION_CNMF'

P value = 5e-04 (Fisher's exact test), Q value = 0.0031

Table S2.  Gene #1: '1p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 49 45
1P GAIN MUTATED 8 22 7
1P GAIN WILD-TYPE 48 27 38

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

'1p gain' versus 'RPPA_CNMF'

P value = 0.00317 (Fisher's exact test), Q value = 0.013

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
1P GAIN MUTATED 6 2 4 9 11
1P GAIN WILD-TYPE 39 6 6 28 7

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

'1p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.011 (Fisher's exact test), Q value = 0.031

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
1P GAIN MUTATED 7 8 17
1P GAIN WILD-TYPE 44 17 25

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

'1p gain' versus 'MRNASEQ_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.0023

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 40
1P GAIN MUTATED 9 19 9
1P GAIN WILD-TYPE 61 21 31

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

'1p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00221 (Fisher's exact test), Q value = 0.01

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
1P GAIN MUTATED 6 3 3 8 4 12 1
1P GAIN WILD-TYPE 37 24 9 16 4 11 12

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

'1p gain' versus 'MIRSEQ_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.0012

Table S7.  Gene #1: '1p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 52 57 41
1P GAIN MUTATED 4 24 9
1P GAIN WILD-TYPE 48 33 32

Figure S7.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'1p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.00095

Table S8.  Gene #1: '1p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
1P GAIN MUTATED 9 19 9
1P GAIN WILD-TYPE 61 19 33

Figure S8.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'1p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S9.  Gene #1: '1p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
1P GAIN MUTATED 8 20 9
1P GAIN WILD-TYPE 61 16 36

Figure S9.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'1p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00052 (Fisher's exact test), Q value = 0.0031

Table S10.  Gene #1: '1p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 33 38 42
1P GAIN MUTATED 5 4 19 9
1P GAIN WILD-TYPE 32 29 19 33

Figure S10.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_CNMF'

P value = 0.0391 (Fisher's exact test), Q value = 0.082

Table S11.  Gene #2: '1q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 52 57 41
1Q GAIN MUTATED 15 30 16
1Q GAIN WILD-TYPE 37 27 25

Figure S11.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'2p gain' versus 'CN_CNMF'

P value = 0.0138 (Fisher's exact test), Q value = 0.037

Table S12.  Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 44 58
2P GAIN MUTATED 10 10 26
2P GAIN WILD-TYPE 38 34 32

Figure S12.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

'2p gain' versus 'METHLYATION_CNMF'

P value = 0.00878 (Fisher's exact test), Q value = 0.026

Table S13.  Gene #3: '2p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 49 45
2P GAIN MUTATED 9 18 19
2P GAIN WILD-TYPE 47 31 26

Figure S13.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0385 (Fisher's exact test), Q value = 0.082

Table S14.  Gene #3: '2p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
2P GAIN MUTATED 9 10 16
2P GAIN WILD-TYPE 42 15 26

Figure S14.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'2p gain' versus 'MRNASEQ_CNMF'

P value = 0.0163 (Fisher's exact test), Q value = 0.041

Table S15.  Gene #3: '2p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 40
2P GAIN MUTATED 14 14 18
2P GAIN WILD-TYPE 56 26 22

Figure S15.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0243 (Fisher's exact test), Q value = 0.057

Table S16.  Gene #3: '2p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
2P GAIN MUTATED 14 14 18
2P GAIN WILD-TYPE 56 24 24

Figure S16.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0301 (Fisher's exact test), Q value = 0.067

Table S17.  Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
2P GAIN MUTATED 14 13 19
2P GAIN WILD-TYPE 55 23 26

Figure S17.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'2q gain' versus 'METHLYATION_CNMF'

P value = 0.0331 (Fisher's exact test), Q value = 0.072

Table S18.  Gene #4: '2q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 49 45
2Q GAIN MUTATED 9 16 17
2Q GAIN WILD-TYPE 47 33 28

Figure S18.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p gain' versus 'CN_CNMF'

P value = 0.0221 (Fisher's exact test), Q value = 0.052

Table S19.  Gene #5: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 44 58
3P GAIN MUTATED 5 5 17
3P GAIN WILD-TYPE 43 39 41

Figure S19.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'

'3p gain' versus 'RPPA_CNMF'

P value = 0.00179 (Fisher's exact test), Q value = 0.0085

Table S20.  Gene #5: '3p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
3P GAIN MUTATED 3 0 0 14 3
3P GAIN WILD-TYPE 42 8 10 23 15

Figure S20.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'3p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0137 (Fisher's exact test), Q value = 0.037

Table S21.  Gene #5: '3p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
3P GAIN MUTATED 3 7 10
3P GAIN WILD-TYPE 48 18 32

Figure S21.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'3p gain' versus 'MRNASEQ_CNMF'

P value = 0.00691 (Fisher's exact test), Q value = 0.023

Table S22.  Gene #5: '3p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 40
3P GAIN MUTATED 6 8 13
3P GAIN WILD-TYPE 64 32 27

Figure S22.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00628 (Fisher's exact test), Q value = 0.021

Table S23.  Gene #5: '3p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
3P GAIN MUTATED 4 2 3 5 3 3 7
3P GAIN WILD-TYPE 39 25 9 19 5 20 6

Figure S23.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.013 (Fisher's exact test), Q value = 0.035

Table S24.  Gene #5: '3p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
3P GAIN MUTATED 6 9 12
3P GAIN WILD-TYPE 64 29 30

Figure S24.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0153 (Fisher's exact test), Q value = 0.039

Table S25.  Gene #5: '3p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
3P GAIN MUTATED 6 8 13
3P GAIN WILD-TYPE 63 28 32

Figure S25.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'3p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0102 (Fisher's exact test), Q value = 0.03

Table S26.  Gene #5: '3p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 33 38 42
3P GAIN MUTATED 5 1 8 13
3P GAIN WILD-TYPE 32 32 30 29

Figure S26.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q gain' versus 'CN_CNMF'

P value = 0.00683 (Fisher's exact test), Q value = 0.022

Table S27.  Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 44 58
3Q GAIN MUTATED 5 10 21
3Q GAIN WILD-TYPE 43 34 37

Figure S27.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

'3q gain' versus 'RPPA_CNMF'

P value = 0.00227 (Fisher's exact test), Q value = 0.01

Table S28.  Gene #6: '3q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
3Q GAIN MUTATED 4 0 2 16 4
3Q GAIN WILD-TYPE 41 8 8 21 14

Figure S28.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'3q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00327 (Fisher's exact test), Q value = 0.013

Table S29.  Gene #6: '3q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
3Q GAIN MUTATED 4 9 13
3Q GAIN WILD-TYPE 47 16 29

Figure S29.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'3q gain' versus 'MRNASEQ_CNMF'

P value = 0.0321 (Fisher's exact test), Q value = 0.071

Table S30.  Gene #6: '3q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 40
3Q GAIN MUTATED 10 13 13
3Q GAIN WILD-TYPE 60 27 27

Figure S30.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0327 (Fisher's exact test), Q value = 0.071

Table S31.  Gene #6: '3q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
3Q GAIN MUTATED 5 5 5 5 3 6 7
3Q GAIN WILD-TYPE 38 22 7 19 5 17 6

Figure S31.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0216 (Fisher's exact test), Q value = 0.052

Table S32.  Gene #6: '3q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
3Q GAIN MUTATED 10 14 12
3Q GAIN WILD-TYPE 60 24 30

Figure S32.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0386 (Fisher's exact test), Q value = 0.082

Table S33.  Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
3Q GAIN MUTATED 10 12 14
3Q GAIN WILD-TYPE 59 24 31

Figure S33.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'5p gain' versus 'METHLYATION_CNMF'

P value = 0.0262 (Fisher's exact test), Q value = 0.06

Table S34.  Gene #8: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 49 45
5P GAIN MUTATED 1 5 0
5P GAIN WILD-TYPE 55 44 45

Figure S34.  Get High-res Image Gene #8: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p gain' versus 'RPPA_CNMF'

P value = 0.00854 (Fisher's exact test), Q value = 0.026

Table S35.  Gene #8: '5p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
5P GAIN MUTATED 1 0 0 0 4
5P GAIN WILD-TYPE 44 8 10 37 14

Figure S35.  Get High-res Image Gene #8: '5p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'5p gain' versus 'MRNASEQ_CNMF'

P value = 0.0115 (Fisher's exact test), Q value = 0.032

Table S36.  Gene #8: '5p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 40
5P GAIN MUTATED 1 5 0
5P GAIN WILD-TYPE 69 35 40

Figure S36.  Get High-res Image Gene #8: '5p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00815 (Fisher's exact test), Q value = 0.026

Table S37.  Gene #8: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
5P GAIN MUTATED 0 1 0 0 2 3 0
5P GAIN WILD-TYPE 43 26 12 24 6 20 13

Figure S37.  Get High-res Image Gene #8: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_CNMF'

P value = 0.00423 (Fisher's exact test), Q value = 0.015

Table S38.  Gene #8: '5p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 52 57 41
5P GAIN MUTATED 0 6 0
5P GAIN WILD-TYPE 52 51 41

Figure S38.  Get High-res Image Gene #8: '5p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'5p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00637 (Fisher's exact test), Q value = 0.021

Table S39.  Gene #8: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
5P GAIN MUTATED 1 5 0
5P GAIN WILD-TYPE 69 33 42

Figure S39.  Get High-res Image Gene #8: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00358 (Fisher's exact test), Q value = 0.013

Table S40.  Gene #8: '5p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
5P GAIN MUTATED 1 5 0
5P GAIN WILD-TYPE 68 31 45

Figure S40.  Get High-res Image Gene #8: '5p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'5p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00568 (Fisher's exact test), Q value = 0.019

Table S41.  Gene #8: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 33 38 42
5P GAIN MUTATED 0 1 5 0
5P GAIN WILD-TYPE 37 32 33 42

Figure S41.  Get High-res Image Gene #8: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q gain' versus 'MRNASEQ_CNMF'

P value = 0.0358 (Fisher's exact test), Q value = 0.077

Table S42.  Gene #9: '5q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 40
5Q GAIN MUTATED 0 3 0
5Q GAIN WILD-TYPE 70 37 40

Figure S42.  Get High-res Image Gene #9: '5q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0411 (Fisher's exact test), Q value = 0.085

Table S43.  Gene #9: '5q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
5Q GAIN MUTATED 0 0 0 0 1 2 0
5Q GAIN WILD-TYPE 43 27 12 24 7 21 13

Figure S43.  Get High-res Image Gene #9: '5q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.015 (Fisher's exact test), Q value = 0.039

Table S44.  Gene #9: '5q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
5Q GAIN MUTATED 0 3 0
5Q GAIN WILD-TYPE 70 35 42

Figure S44.  Get High-res Image Gene #9: '5q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0134 (Fisher's exact test), Q value = 0.036

Table S45.  Gene #9: '5q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
5Q GAIN MUTATED 0 3 0
5Q GAIN WILD-TYPE 69 33 45

Figure S45.  Get High-res Image Gene #9: '5q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'5q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0392 (Fisher's exact test), Q value = 0.082

Table S46.  Gene #9: '5q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 33 38 42
5Q GAIN MUTATED 0 0 3 0
5Q GAIN WILD-TYPE 37 33 35 42

Figure S46.  Get High-res Image Gene #9: '5q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p gain' versus 'CN_CNMF'

P value = 0.00042 (Fisher's exact test), Q value = 0.0026

Table S47.  Gene #10: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 44 58
6P GAIN MUTATED 9 1 18
6P GAIN WILD-TYPE 39 43 40

Figure S47.  Get High-res Image Gene #10: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

'6p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0413 (Fisher's exact test), Q value = 0.086

Table S48.  Gene #10: '6p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
6P GAIN MUTATED 6 9 6
6P GAIN WILD-TYPE 45 16 36

Figure S48.  Get High-res Image Gene #10: '6p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'6p gain' versus 'MRNASEQ_CNMF'

P value = 0.0124 (Fisher's exact test), Q value = 0.034

Table S49.  Gene #10: '6p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 40
6P GAIN MUTATED 9 5 14
6P GAIN WILD-TYPE 61 35 26

Figure S49.  Get High-res Image Gene #10: '6p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'6p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00098 (Fisher's exact test), Q value = 0.0054

Table S50.  Gene #10: '6p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
6P GAIN MUTATED 8 1 0 12 0 5 2
6P GAIN WILD-TYPE 35 26 12 12 8 18 11

Figure S50.  Get High-res Image Gene #10: '6p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_CNMF'

P value = 0.0168 (Fisher's exact test), Q value = 0.042

Table S51.  Gene #10: '6p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 52 57 41
6P GAIN MUTATED 7 7 14
6P GAIN WILD-TYPE 45 50 27

Figure S51.  Get High-res Image Gene #10: '6p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'6p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00612 (Fisher's exact test), Q value = 0.02

Table S52.  Gene #10: '6p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
6P GAIN MUTATED 9 4 15
6P GAIN WILD-TYPE 61 34 27

Figure S52.  Get High-res Image Gene #10: '6p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0197 (Fisher's exact test), Q value = 0.048

Table S53.  Gene #10: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 33 38 42
6P GAIN MUTATED 7 2 5 14
6P GAIN WILD-TYPE 30 31 33 28

Figure S53.  Get High-res Image Gene #10: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q gain' versus 'CN_CNMF'

P value = 0.0231 (Fisher's exact test), Q value = 0.054

Table S54.  Gene #11: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 44 58
6Q GAIN MUTATED 7 2 14
6Q GAIN WILD-TYPE 41 42 44

Figure S54.  Get High-res Image Gene #11: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

'6q gain' versus 'MRNASEQ_CNMF'

P value = 0.0138 (Fisher's exact test), Q value = 0.037

Table S55.  Gene #11: '6q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 40
6Q GAIN MUTATED 8 3 12
6Q GAIN WILD-TYPE 62 37 28

Figure S55.  Get High-res Image Gene #11: '6q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'6q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.002

Table S56.  Gene #11: '6q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
6Q GAIN MUTATED 8 0 0 11 0 3 1
6Q GAIN WILD-TYPE 35 27 12 13 8 20 12

Figure S56.  Get High-res Image Gene #11: '6q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6q gain' versus 'MIRSEQ_CNMF'

P value = 0.0125 (Fisher's exact test), Q value = 0.034

Table S57.  Gene #11: '6q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 52 57 41
6Q GAIN MUTATED 7 4 12
6Q GAIN WILD-TYPE 45 53 29

Figure S57.  Get High-res Image Gene #11: '6q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'6q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00419 (Fisher's exact test), Q value = 0.015

Table S58.  Gene #11: '6q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
6Q GAIN MUTATED 8 2 13
6Q GAIN WILD-TYPE 62 36 29

Figure S58.  Get High-res Image Gene #11: '6q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.03 (Fisher's exact test), Q value = 0.067

Table S59.  Gene #11: '6q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 33 38 42
6Q GAIN MUTATED 6 2 3 12
6Q GAIN WILD-TYPE 31 31 35 30

Figure S59.  Get High-res Image Gene #11: '6q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

P value = 0.00459 (Fisher's exact test), Q value = 0.016

Table S60.  Gene #12: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 44 58
7P GAIN MUTATED 34 42 45
7P GAIN WILD-TYPE 14 2 13

Figure S60.  Get High-res Image Gene #12: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'RPPA_CNMF'

P value = 0.0153 (Fisher's exact test), Q value = 0.039

Table S61.  Gene #12: '7p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
7P GAIN MUTATED 39 8 5 25 16
7P GAIN WILD-TYPE 6 0 5 12 2

Figure S61.  Get High-res Image Gene #12: '7p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'7p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0206 (Fisher's exact test), Q value = 0.05

Table S62.  Gene #12: '7p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
7P GAIN MUTATED 45 15 33
7P GAIN WILD-TYPE 6 10 9

Figure S62.  Get High-res Image Gene #12: '7p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 0.0045 (Fisher's exact test), Q value = 0.016

Table S63.  Gene #12: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 40
7P GAIN MUTATED 62 34 25
7P GAIN WILD-TYPE 8 6 15

Figure S63.  Get High-res Image Gene #12: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0088 (Fisher's exact test), Q value = 0.026

Table S64.  Gene #12: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
7P GAIN MUTATED 38 24 7 16 6 22 8
7P GAIN WILD-TYPE 5 3 5 8 2 1 5

Figure S64.  Get High-res Image Gene #12: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_CNMF'

P value = 0.00746 (Fisher's exact test), Q value = 0.024

Table S65.  Gene #12: '7p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 52 57 41
7P GAIN MUTATED 45 50 26
7P GAIN WILD-TYPE 7 7 15

Figure S65.  Get High-res Image Gene #12: '7p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'7p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00733 (Fisher's exact test), Q value = 0.023

Table S66.  Gene #12: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
7P GAIN MUTATED 62 32 27
7P GAIN WILD-TYPE 8 6 15

Figure S66.  Get High-res Image Gene #12: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00727 (Fisher's exact test), Q value = 0.023

Table S67.  Gene #12: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
7P GAIN MUTATED 61 31 29
7P GAIN WILD-TYPE 8 5 16

Figure S67.  Get High-res Image Gene #12: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'7p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0229 (Fisher's exact test), Q value = 0.054

Table S68.  Gene #12: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 33 38 42
7P GAIN MUTATED 32 30 32 27
7P GAIN WILD-TYPE 5 3 6 15

Figure S68.  Get High-res Image Gene #12: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 0.00437 (Fisher's exact test), Q value = 0.016

Table S69.  Gene #13: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 40
7Q GAIN MUTATED 52 33 20
7Q GAIN WILD-TYPE 18 7 20

Figure S69.  Get High-res Image Gene #13: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0117 (Fisher's exact test), Q value = 0.033

Table S70.  Gene #13: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
7Q GAIN MUTATED 36 16 8 11 6 20 8
7Q GAIN WILD-TYPE 7 11 4 13 2 3 5

Figure S70.  Get High-res Image Gene #13: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_CNMF'

P value = 0.00255 (Fisher's exact test), Q value = 0.011

Table S71.  Gene #13: '7q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 52 57 41
7Q GAIN MUTATED 39 46 20
7Q GAIN WILD-TYPE 13 11 21

Figure S71.  Get High-res Image Gene #13: '7q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'7q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00257 (Fisher's exact test), Q value = 0.011

Table S72.  Gene #13: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
7Q GAIN MUTATED 52 32 21
7Q GAIN WILD-TYPE 18 6 21

Figure S72.  Get High-res Image Gene #13: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00202 (Fisher's exact test), Q value = 0.0093

Table S73.  Gene #13: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
7Q GAIN MUTATED 51 31 23
7Q GAIN WILD-TYPE 18 5 22

Figure S73.  Get High-res Image Gene #13: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'7q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00338 (Fisher's exact test), Q value = 0.013

Table S74.  Gene #13: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 33 38 42
7Q GAIN MUTATED 30 22 32 21
7Q GAIN WILD-TYPE 7 11 6 21

Figure S74.  Get High-res Image Gene #13: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p gain' versus 'METHLYATION_CNMF'

P value = 0.0059 (Fisher's exact test), Q value = 0.02

Table S75.  Gene #14: '8p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 49 45
8P GAIN MUTATED 49 33 28
8P GAIN WILD-TYPE 7 16 17

Figure S75.  Get High-res Image Gene #14: '8p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8p gain' versus 'RPPA_CNMF'

P value = 0.00106 (Fisher's exact test), Q value = 0.0057

Table S76.  Gene #14: '8p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
8P GAIN MUTATED 41 6 4 22 12
8P GAIN WILD-TYPE 4 2 6 15 6

Figure S76.  Get High-res Image Gene #14: '8p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'8p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.0011

Table S77.  Gene #14: '8p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
8P GAIN MUTATED 46 12 27
8P GAIN WILD-TYPE 5 13 15

Figure S77.  Get High-res Image Gene #14: '8p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'8p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S78.  Gene #14: '8p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 40
8P GAIN MUTATED 63 26 21
8P GAIN WILD-TYPE 7 14 19

Figure S78.  Get High-res Image Gene #14: '8p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.0021

Table S79.  Gene #14: '8p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
8P GAIN MUTATED 37 26 8 14 5 15 5
8P GAIN WILD-TYPE 6 1 4 10 3 8 8

Figure S79.  Get High-res Image Gene #14: '8p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8p gain' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00037

Table S80.  Gene #14: '8p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 52 57 41
8P GAIN MUTATED 46 44 20
8P GAIN WILD-TYPE 6 13 21

Figure S80.  Get High-res Image Gene #14: '8p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'8p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 2e-04

Table S81.  Gene #14: '8p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
8P GAIN MUTATED 63 26 21
8P GAIN WILD-TYPE 7 12 21

Figure S81.  Get High-res Image Gene #14: '8p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'8p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 2e-04

Table S82.  Gene #14: '8p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
8P GAIN MUTATED 62 24 24
8P GAIN WILD-TYPE 7 12 21

Figure S82.  Get High-res Image Gene #14: '8p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'8p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00052

Table S83.  Gene #14: '8p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 33 38 42
8P GAIN MUTATED 32 31 26 21
8P GAIN WILD-TYPE 5 2 12 21

Figure S83.  Get High-res Image Gene #14: '8p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q gain' versus 'CN_CNMF'

P value = 0.0205 (Fisher's exact test), Q value = 0.05

Table S84.  Gene #15: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 44 58
8Q GAIN MUTATED 34 39 38
8Q GAIN WILD-TYPE 14 5 20

Figure S84.  Get High-res Image Gene #15: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 0.00271 (Fisher's exact test), Q value = 0.011

Table S85.  Gene #15: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 49 45
8Q GAIN MUTATED 49 36 26
8Q GAIN WILD-TYPE 7 13 19

Figure S85.  Get High-res Image Gene #15: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8q gain' versus 'RPPA_CNMF'

P value = 0.0121 (Fisher's exact test), Q value = 0.033

Table S86.  Gene #15: '8q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
8Q GAIN MUTATED 40 6 6 21 13
8Q GAIN WILD-TYPE 5 2 4 16 5

Figure S86.  Get High-res Image Gene #15: '8q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'8q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00245 (Fisher's exact test), Q value = 0.01

Table S87.  Gene #15: '8q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
8Q GAIN MUTATED 45 14 27
8Q GAIN WILD-TYPE 6 11 15

Figure S87.  Get High-res Image Gene #15: '8q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.0013

Table S88.  Gene #15: '8q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 40
8Q GAIN MUTATED 62 28 21
8Q GAIN WILD-TYPE 8 12 19

Figure S88.  Get High-res Image Gene #15: '8q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00034 (Fisher's exact test), Q value = 0.0023

Table S89.  Gene #15: '8q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
8Q GAIN MUTATED 40 22 8 15 5 17 4
8Q GAIN WILD-TYPE 3 5 4 9 3 6 9

Figure S89.  Get High-res Image Gene #15: '8q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00089

Table S90.  Gene #15: '8q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 52 57 41
8Q GAIN MUTATED 47 43 21
8Q GAIN WILD-TYPE 5 14 20

Figure S90.  Get High-res Image Gene #15: '8q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'8q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.00095

Table S91.  Gene #15: '8q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
8Q GAIN MUTATED 62 27 22
8Q GAIN WILD-TYPE 8 11 20

Figure S91.  Get High-res Image Gene #15: '8q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.0026

Table S92.  Gene #15: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
8Q GAIN MUTATED 61 25 25
8Q GAIN WILD-TYPE 8 11 20

Figure S92.  Get High-res Image Gene #15: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'8q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.0021

Table S93.  Gene #15: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 33 38 42
8Q GAIN MUTATED 34 28 27 22
8Q GAIN WILD-TYPE 3 5 11 20

Figure S93.  Get High-res Image Gene #15: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q gain' versus 'RPPA_CNMF'

P value = 0.0399 (Fisher's exact test), Q value = 0.084

Table S94.  Gene #21: '11q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
11Q GAIN MUTATED 0 0 0 1 3
11Q GAIN WILD-TYPE 45 8 10 36 15

Figure S94.  Get High-res Image Gene #21: '11q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'11q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0142 (Fisher's exact test), Q value = 0.037

Table S95.  Gene #21: '11q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
11Q GAIN MUTATED 0 0 0 0 1 1 2
11Q GAIN WILD-TYPE 43 27 12 24 7 22 11

Figure S95.  Get High-res Image Gene #21: '11q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_CNMF'

P value = 0.0479 (Fisher's exact test), Q value = 0.096

Table S96.  Gene #23: '12q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 52 57 41
12Q GAIN MUTATED 34 44 22
12Q GAIN WILD-TYPE 18 13 19

Figure S96.  Get High-res Image Gene #23: '12q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'12q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00716 (Fisher's exact test), Q value = 0.023

Table S97.  Gene #23: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 33 38 42
12Q GAIN MUTATED 21 29 27 23
12Q GAIN WILD-TYPE 16 4 11 19

Figure S97.  Get High-res Image Gene #23: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q gain' versus 'METHLYATION_CNMF'

P value = 0.00227 (Fisher's exact test), Q value = 0.01

Table S98.  Gene #25: '15q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 49 45
15Q GAIN MUTATED 29 11 11
15Q GAIN WILD-TYPE 27 38 34

Figure S98.  Get High-res Image Gene #25: '15q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'15q gain' versus 'RPPA_CNMF'

P value = 0.0019 (Fisher's exact test), Q value = 0.0089

Table S99.  Gene #25: '15q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
15Q GAIN MUTATED 24 2 2 5 4
15Q GAIN WILD-TYPE 21 6 8 32 14

Figure S99.  Get High-res Image Gene #25: '15q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'15q gain' versus 'RPPA_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.0021

Table S100.  Gene #25: '15q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
15Q GAIN MUTATED 26 3 8
15Q GAIN WILD-TYPE 25 22 34

Figure S100.  Get High-res Image Gene #25: '15q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'15q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S101.  Gene #25: '15q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 40
15Q GAIN MUTATED 38 8 5
15Q GAIN WILD-TYPE 32 32 35

Figure S101.  Get High-res Image Gene #25: '15q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'15q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 2e-04

Table S102.  Gene #25: '15q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
15Q GAIN MUTATED 26 12 1 4 0 7 1
15Q GAIN WILD-TYPE 17 15 11 20 8 16 12

Figure S102.  Get High-res Image Gene #25: '15q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'15q gain' versus 'MIRSEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00068

Table S103.  Gene #25: '15q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 52 57 41
15Q GAIN MUTATED 28 18 5
15Q GAIN WILD-TYPE 24 39 36

Figure S103.  Get High-res Image Gene #25: '15q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'15q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S104.  Gene #25: '15q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
15Q GAIN MUTATED 38 8 5
15Q GAIN WILD-TYPE 32 30 37

Figure S104.  Get High-res Image Gene #25: '15q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'15q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S105.  Gene #25: '15q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
15Q GAIN MUTATED 37 8 6
15Q GAIN WILD-TYPE 32 28 39

Figure S105.  Get High-res Image Gene #25: '15q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'15q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S106.  Gene #25: '15q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 33 38 42
15Q GAIN MUTATED 22 16 8 5
15Q GAIN WILD-TYPE 15 17 30 37

Figure S106.  Get High-res Image Gene #25: '15q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p gain' versus 'CN_CNMF'

P value = 0.0116 (Fisher's exact test), Q value = 0.032

Table S107.  Gene #26: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 44 58
16P GAIN MUTATED 2 2 12
16P GAIN WILD-TYPE 46 42 46

Figure S107.  Get High-res Image Gene #26: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

'16p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00269 (Fisher's exact test), Q value = 0.011

Table S108.  Gene #26: '16p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
16P GAIN MUTATED 2 8 4
16P GAIN WILD-TYPE 49 17 38

Figure S108.  Get High-res Image Gene #26: '16p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 0.00411 (Fisher's exact test), Q value = 0.015

Table S109.  Gene #26: '16p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 40
16P GAIN MUTATED 3 3 10
16P GAIN WILD-TYPE 67 37 30

Figure S109.  Get High-res Image Gene #26: '16p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0178 (Fisher's exact test), Q value = 0.044

Table S110.  Gene #26: '16p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
16P GAIN MUTATED 2 1 1 8 0 2 2
16P GAIN WILD-TYPE 41 26 11 16 8 21 11

Figure S110.  Get High-res Image Gene #26: '16p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_CNMF'

P value = 0.00228 (Fisher's exact test), Q value = 0.01

Table S111.  Gene #26: '16p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 52 57 41
16P GAIN MUTATED 1 5 10
16P GAIN WILD-TYPE 51 52 31

Figure S111.  Get High-res Image Gene #26: '16p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00609 (Fisher's exact test), Q value = 0.02

Table S112.  Gene #26: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
16P GAIN MUTATED 3 3 10
16P GAIN WILD-TYPE 67 35 32

Figure S112.  Get High-res Image Gene #26: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00298 (Fisher's exact test), Q value = 0.012

Table S113.  Gene #26: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
16P GAIN MUTATED 3 2 11
16P GAIN WILD-TYPE 66 34 34

Figure S113.  Get High-res Image Gene #26: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0217 (Fisher's exact test), Q value = 0.052

Table S114.  Gene #26: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 33 38 42
16P GAIN MUTATED 2 1 3 10
16P GAIN WILD-TYPE 35 32 35 32

Figure S114.  Get High-res Image Gene #26: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q gain' versus 'CN_CNMF'

P value = 0.00719 (Fisher's exact test), Q value = 0.023

Table S115.  Gene #27: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 44 58
16Q GAIN MUTATED 2 1 11
16Q GAIN WILD-TYPE 46 43 47

Figure S115.  Get High-res Image Gene #27: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00858 (Fisher's exact test), Q value = 0.026

Table S116.  Gene #27: '16q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
16Q GAIN MUTATED 1 6 4
16Q GAIN WILD-TYPE 50 19 38

Figure S116.  Get High-res Image Gene #27: '16q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'16q gain' versus 'MRNASEQ_CNMF'

P value = 0.00925 (Fisher's exact test), Q value = 0.027

Table S117.  Gene #27: '16q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 40
16Q GAIN MUTATED 2 4 8
16Q GAIN WILD-TYPE 68 36 32

Figure S117.  Get High-res Image Gene #27: '16q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0486 (Fisher's exact test), Q value = 0.097

Table S118.  Gene #27: '16q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
16Q GAIN MUTATED 1 1 1 6 0 3 2
16Q GAIN WILD-TYPE 42 26 11 18 8 20 11

Figure S118.  Get High-res Image Gene #27: '16q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_CNMF'

P value = 0.0135 (Fisher's exact test), Q value = 0.036

Table S119.  Gene #27: '16q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 52 57 41
16Q GAIN MUTATED 1 5 8
16Q GAIN WILD-TYPE 51 52 33

Figure S119.  Get High-res Image Gene #27: '16q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0125 (Fisher's exact test), Q value = 0.034

Table S120.  Gene #27: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
16Q GAIN MUTATED 2 4 8
16Q GAIN WILD-TYPE 68 34 34

Figure S120.  Get High-res Image Gene #27: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00819 (Fisher's exact test), Q value = 0.026

Table S121.  Gene #27: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
16Q GAIN MUTATED 2 3 9
16Q GAIN WILD-TYPE 67 33 36

Figure S121.  Get High-res Image Gene #27: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S122.  Gene #28: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 44 58
17P GAIN MUTATED 9 2 29
17P GAIN WILD-TYPE 39 42 29

Figure S122.  Get High-res Image Gene #28: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

'17p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S123.  Gene #28: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 49 45
17P GAIN MUTATED 3 23 14
17P GAIN WILD-TYPE 53 26 31

Figure S123.  Get High-res Image Gene #28: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p gain' versus 'RPPA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00029

Table S124.  Gene #28: '17p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
17P GAIN MUTATED 2 0 5 15 8
17P GAIN WILD-TYPE 43 8 5 22 10

Figure S124.  Get High-res Image Gene #28: '17p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'17p gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S125.  Gene #28: '17p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
17P GAIN MUTATED 2 11 17
17P GAIN WILD-TYPE 49 14 25

Figure S125.  Get High-res Image Gene #28: '17p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'17p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S126.  Gene #28: '17p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 40
17P GAIN MUTATED 3 19 18
17P GAIN WILD-TYPE 67 21 22

Figure S126.  Get High-res Image Gene #28: '17p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S127.  Gene #28: '17p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
17P GAIN MUTATED 2 1 5 11 4 12 5
17P GAIN WILD-TYPE 41 26 7 13 4 11 8

Figure S127.  Get High-res Image Gene #28: '17p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S128.  Gene #28: '17p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 52 57 41
17P GAIN MUTATED 2 21 17
17P GAIN WILD-TYPE 50 36 24

Figure S128.  Get High-res Image Gene #28: '17p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S129.  Gene #28: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
17P GAIN MUTATED 3 19 18
17P GAIN WILD-TYPE 67 19 24

Figure S129.  Get High-res Image Gene #28: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S130.  Gene #28: '17p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
17P GAIN MUTATED 3 17 20
17P GAIN WILD-TYPE 66 19 25

Figure S130.  Get High-res Image Gene #28: '17p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S131.  Gene #28: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 33 38 42
17P GAIN MUTATED 1 2 20 17
17P GAIN WILD-TYPE 36 31 18 25

Figure S131.  Get High-res Image Gene #28: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q gain' versus 'CN_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.0018

Table S132.  Gene #29: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 44 58
17Q GAIN MUTATED 13 7 31
17Q GAIN WILD-TYPE 35 37 27

Figure S132.  Get High-res Image Gene #29: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00052

Table S133.  Gene #29: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 49 45
17Q GAIN MUTATED 8 27 16
17Q GAIN WILD-TYPE 48 22 29

Figure S133.  Get High-res Image Gene #29: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q gain' versus 'RPPA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 2e-04

Table S134.  Gene #29: '17q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
17Q GAIN MUTATED 5 0 6 19 10
17Q GAIN WILD-TYPE 40 8 4 18 8

Figure S134.  Get High-res Image Gene #29: '17q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'17q gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S135.  Gene #29: '17q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
17Q GAIN MUTATED 5 13 22
17Q GAIN WILD-TYPE 46 12 20

Figure S135.  Get High-res Image Gene #29: '17q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S136.  Gene #29: '17q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 40
17Q GAIN MUTATED 7 23 21
17Q GAIN WILD-TYPE 63 17 19

Figure S136.  Get High-res Image Gene #29: '17q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S137.  Gene #29: '17q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
17Q GAIN MUTATED 4 3 6 13 4 15 6
17Q GAIN WILD-TYPE 39 24 6 11 4 8 7

Figure S137.  Get High-res Image Gene #29: '17q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S138.  Gene #29: '17q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 52 57 41
17Q GAIN MUTATED 4 26 21
17Q GAIN WILD-TYPE 48 31 20

Figure S138.  Get High-res Image Gene #29: '17q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S139.  Gene #29: '17q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
17Q GAIN MUTATED 7 22 22
17Q GAIN WILD-TYPE 63 16 20

Figure S139.  Get High-res Image Gene #29: '17q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S140.  Gene #29: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
17Q GAIN MUTATED 6 21 24
17Q GAIN WILD-TYPE 63 15 21

Figure S140.  Get High-res Image Gene #29: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S141.  Gene #29: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 33 38 42
17Q GAIN MUTATED 2 5 22 22
17Q GAIN WILD-TYPE 35 28 16 20

Figure S141.  Get High-res Image Gene #29: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p gain' versus 'CN_CNMF'

P value = 0.0101 (Fisher's exact test), Q value = 0.03

Table S142.  Gene #31: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 44 58
19P GAIN MUTATED 8 18 10
19P GAIN WILD-TYPE 40 26 48

Figure S142.  Get High-res Image Gene #31: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

'19p gain' versus 'METHLYATION_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00089

Table S143.  Gene #31: '19p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 49 45
19P GAIN MUTATED 23 3 10
19P GAIN WILD-TYPE 33 46 35

Figure S143.  Get High-res Image Gene #31: '19p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19p gain' versus 'RPPA_CNMF'

P value = 0.00939 (Fisher's exact test), Q value = 0.028

Table S144.  Gene #31: '19p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
19P GAIN MUTATED 20 1 1 5 3
19P GAIN WILD-TYPE 25 7 9 32 15

Figure S144.  Get High-res Image Gene #31: '19p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'19p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00318 (Fisher's exact test), Q value = 0.013

Table S145.  Gene #31: '19p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
19P GAIN MUTATED 21 3 6
19P GAIN WILD-TYPE 30 22 36

Figure S145.  Get High-res Image Gene #31: '19p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'19p gain' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00083

Table S146.  Gene #31: '19p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 40
19P GAIN MUTATED 28 3 5
19P GAIN WILD-TYPE 42 37 35

Figure S146.  Get High-res Image Gene #31: '19p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00091 (Fisher's exact test), Q value = 0.005

Table S147.  Gene #31: '19p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
19P GAIN MUTATED 14 14 0 4 0 3 1
19P GAIN WILD-TYPE 29 13 12 20 8 20 12

Figure S147.  Get High-res Image Gene #31: '19p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_CNMF'

P value = 0.0438 (Fisher's exact test), Q value = 0.09

Table S148.  Gene #31: '19p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 52 57 41
19P GAIN MUTATED 18 13 5
19P GAIN WILD-TYPE 34 44 36

Figure S148.  Get High-res Image Gene #31: '19p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'19p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00046

Table S149.  Gene #31: '19p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
19P GAIN MUTATED 28 2 6
19P GAIN WILD-TYPE 42 36 36

Figure S149.  Get High-res Image Gene #31: '19p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.0028

Table S150.  Gene #31: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
19P GAIN MUTATED 27 4 5
19P GAIN WILD-TYPE 42 32 40

Figure S150.  Get High-res Image Gene #31: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'19p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00029

Table S151.  Gene #31: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 33 38 42
19P GAIN MUTATED 10 18 3 5
19P GAIN WILD-TYPE 27 15 35 37

Figure S151.  Get High-res Image Gene #31: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q gain' versus 'CN_CNMF'

P value = 0.0161 (Fisher's exact test), Q value = 0.041

Table S152.  Gene #32: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 44 58
19Q GAIN MUTATED 7 15 7
19Q GAIN WILD-TYPE 41 29 51

Figure S152.  Get High-res Image Gene #32: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

'19q gain' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00068

Table S153.  Gene #32: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 49 45
19Q GAIN MUTATED 20 2 7
19Q GAIN WILD-TYPE 36 47 38

Figure S153.  Get High-res Image Gene #32: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19q gain' versus 'RPPA_CNMF'

P value = 0.00215 (Fisher's exact test), Q value = 0.0098

Table S154.  Gene #32: '19q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
19Q GAIN MUTATED 18 0 1 4 1
19Q GAIN WILD-TYPE 27 8 9 33 17

Figure S154.  Get High-res Image Gene #32: '19q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'19q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0026 (Fisher's exact test), Q value = 0.011

Table S155.  Gene #32: '19q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
19Q GAIN MUTATED 18 2 4
19Q GAIN WILD-TYPE 33 23 38

Figure S155.  Get High-res Image Gene #32: '19q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00037

Table S156.  Gene #32: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 40
19Q GAIN MUTATED 24 1 4
19Q GAIN WILD-TYPE 46 39 36

Figure S156.  Get High-res Image Gene #32: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00062 (Fisher's exact test), Q value = 0.0036

Table S157.  Gene #32: '19q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
19Q GAIN MUTATED 11 13 0 3 0 1 1
19Q GAIN WILD-TYPE 32 14 12 21 8 22 12

Figure S157.  Get High-res Image Gene #32: '19q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00052

Table S158.  Gene #32: '19q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
19Q GAIN MUTATED 24 1 4
19Q GAIN WILD-TYPE 46 37 38

Figure S158.  Get High-res Image Gene #32: '19q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.0022

Table S159.  Gene #32: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
19Q GAIN MUTATED 23 2 4
19Q GAIN WILD-TYPE 46 34 41

Figure S159.  Get High-res Image Gene #32: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'19q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S160.  Gene #32: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 33 38 42
19Q GAIN MUTATED 8 16 1 4
19Q GAIN WILD-TYPE 29 17 37 38

Figure S160.  Get High-res Image Gene #32: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 0.00525 (Fisher's exact test), Q value = 0.018

Table S161.  Gene #33: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 44 58
20P GAIN MUTATED 5 8 21
20P GAIN WILD-TYPE 43 36 37

Figure S161.  Get High-res Image Gene #33: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 0.0415 (Fisher's exact test), Q value = 0.086

Table S162.  Gene #33: '20p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 40
20P GAIN MUTATED 12 7 15
20P GAIN WILD-TYPE 58 33 25

Figure S162.  Get High-res Image Gene #33: '20p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20q gain' versus 'CN_CNMF'

P value = 0.00741 (Fisher's exact test), Q value = 0.024

Table S163.  Gene #34: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 44 58
20Q GAIN MUTATED 8 8 24
20Q GAIN WILD-TYPE 40 36 34

Figure S163.  Get High-res Image Gene #34: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 0.00569 (Fisher's exact test), Q value = 0.019

Table S164.  Gene #34: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 49 45
20Q GAIN MUTATED 7 16 17
20Q GAIN WILD-TYPE 49 33 28

Figure S164.  Get High-res Image Gene #34: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0366 (Fisher's exact test), Q value = 0.078

Table S165.  Gene #34: '20q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
20Q GAIN MUTATED 8 10 14
20Q GAIN WILD-TYPE 43 15 28

Figure S165.  Get High-res Image Gene #34: '20q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 0.00715 (Fisher's exact test), Q value = 0.023

Table S166.  Gene #34: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 40
20Q GAIN MUTATED 12 10 18
20Q GAIN WILD-TYPE 58 30 22

Figure S166.  Get High-res Image Gene #34: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 0.0472 (Fisher's exact test), Q value = 0.095

Table S167.  Gene #34: '20q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 52 57 41
20Q GAIN MUTATED 10 13 17
20Q GAIN WILD-TYPE 42 44 24

Figure S167.  Get High-res Image Gene #34: '20q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0126 (Fisher's exact test), Q value = 0.034

Table S168.  Gene #34: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
20Q GAIN MUTATED 12 10 18
20Q GAIN WILD-TYPE 58 28 24

Figure S168.  Get High-res Image Gene #34: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0164 (Fisher's exact test), Q value = 0.041

Table S169.  Gene #34: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
20Q GAIN MUTATED 12 9 19
20Q GAIN WILD-TYPE 57 27 26

Figure S169.  Get High-res Image Gene #34: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0144 (Fisher's exact test), Q value = 0.038

Table S170.  Gene #34: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 33 38 42
20Q GAIN MUTATED 4 8 10 18
20Q GAIN WILD-TYPE 33 25 28 24

Figure S170.  Get High-res Image Gene #34: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 2e-04

Table S171.  Gene #36: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 44 58
22Q GAIN MUTATED 9 23 6
22Q GAIN WILD-TYPE 39 21 52

Figure S171.  Get High-res Image Gene #36: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

'22q gain' versus 'METHLYATION_CNMF'

P value = 0.00134 (Fisher's exact test), Q value = 0.0067

Table S172.  Gene #36: '22q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 49 45
22Q GAIN MUTATED 21 4 13
22Q GAIN WILD-TYPE 35 45 32

Figure S172.  Get High-res Image Gene #36: '22q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q gain' versus 'RPPA_CNMF'

P value = 0.00924 (Fisher's exact test), Q value = 0.027

Table S173.  Gene #36: '22q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
22Q GAIN MUTATED 19 2 2 4 2
22Q GAIN WILD-TYPE 26 6 8 33 16

Figure S173.  Get High-res Image Gene #36: '22q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'22q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00051 (Fisher's exact test), Q value = 0.0031

Table S174.  Gene #36: '22q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
22Q GAIN MUTATED 21 1 7
22Q GAIN WILD-TYPE 30 24 35

Figure S174.  Get High-res Image Gene #36: '22q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'22q gain' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00029

Table S175.  Gene #36: '22q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 40
22Q GAIN MUTATED 30 3 5
22Q GAIN WILD-TYPE 40 37 35

Figure S175.  Get High-res Image Gene #36: '22q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'22q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S176.  Gene #36: '22q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
22Q GAIN MUTATED 11 19 1 4 1 1 1
22Q GAIN WILD-TYPE 32 8 11 20 7 22 12

Figure S176.  Get High-res Image Gene #36: '22q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 2e-04

Table S177.  Gene #36: '22q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
22Q GAIN MUTATED 30 3 5
22Q GAIN WILD-TYPE 40 35 37

Figure S177.  Get High-res Image Gene #36: '22q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00052

Table S178.  Gene #36: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
22Q GAIN MUTATED 29 4 5
22Q GAIN WILD-TYPE 40 32 40

Figure S178.  Get High-res Image Gene #36: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'22q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S179.  Gene #36: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 33 38 42
22Q GAIN MUTATED 10 20 3 5
22Q GAIN WILD-TYPE 27 13 35 37

Figure S179.  Get High-res Image Gene #36: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xp gain' versus 'CN_CNMF'

P value = 6e-04 (Fisher's exact test), Q value = 0.0035

Table S180.  Gene #37: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 44 58
XP GAIN MUTATED 3 2 17
XP GAIN WILD-TYPE 45 42 41

Figure S180.  Get High-res Image Gene #37: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'

'xp gain' versus 'METHLYATION_CNMF'

P value = 0.0181 (Fisher's exact test), Q value = 0.045

Table S181.  Gene #37: 'xp gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 49 45
XP GAIN MUTATED 3 8 11
XP GAIN WILD-TYPE 53 41 34

Figure S181.  Get High-res Image Gene #37: 'xp gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xp gain' versus 'RPPA_CNMF'

P value = 0.039 (Fisher's exact test), Q value = 0.082

Table S182.  Gene #37: 'xp gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
XP GAIN MUTATED 3 0 2 10 5
XP GAIN WILD-TYPE 42 8 8 27 13

Figure S182.  Get High-res Image Gene #37: 'xp gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'xp gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0088 (Fisher's exact test), Q value = 0.026

Table S183.  Gene #37: 'xp gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
XP GAIN MUTATED 3 5 12
XP GAIN WILD-TYPE 48 20 30

Figure S183.  Get High-res Image Gene #37: 'xp gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'xp gain' versus 'MRNASEQ_CNMF'

P value = 0.00056 (Fisher's exact test), Q value = 0.0033

Table S184.  Gene #37: 'xp gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 40
XP GAIN MUTATED 3 7 12
XP GAIN WILD-TYPE 67 33 28

Figure S184.  Get High-res Image Gene #37: 'xp gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xp gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00331 (Fisher's exact test), Q value = 0.013

Table S185.  Gene #37: 'xp gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
XP GAIN MUTATED 2 1 3 7 0 4 5
XP GAIN WILD-TYPE 41 26 9 17 8 19 8

Figure S185.  Get High-res Image Gene #37: 'xp gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xp gain' versus 'MIRSEQ_CNMF'

P value = 0.00084 (Fisher's exact test), Q value = 0.0047

Table S186.  Gene #37: 'xp gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 52 57 41
XP GAIN MUTATED 2 7 13
XP GAIN WILD-TYPE 50 50 28

Figure S186.  Get High-res Image Gene #37: 'xp gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'xp gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.0013

Table S187.  Gene #37: 'xp gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
XP GAIN MUTATED 3 5 14
XP GAIN WILD-TYPE 67 33 28

Figure S187.  Get High-res Image Gene #37: 'xp gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'xp gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00173 (Fisher's exact test), Q value = 0.0084

Table S188.  Gene #37: 'xp gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
XP GAIN MUTATED 3 7 12
XP GAIN WILD-TYPE 66 29 33

Figure S188.  Get High-res Image Gene #37: 'xp gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xp gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00452 (Fisher's exact test), Q value = 0.016

Table S189.  Gene #37: 'xp gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 33 38 42
XP GAIN MUTATED 2 1 7 12
XP GAIN WILD-TYPE 35 32 31 30

Figure S189.  Get High-res Image Gene #37: 'xp gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq gain' versus 'CN_CNMF'

P value = 0.00196 (Fisher's exact test), Q value = 0.0091

Table S190.  Gene #38: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 44 58
XQ GAIN MUTATED 4 2 16
XQ GAIN WILD-TYPE 44 42 42

Figure S190.  Get High-res Image Gene #38: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

'xq gain' versus 'METHLYATION_CNMF'

P value = 0.018 (Fisher's exact test), Q value = 0.045

Table S191.  Gene #38: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 49 45
XQ GAIN MUTATED 3 8 11
XQ GAIN WILD-TYPE 53 41 34

Figure S191.  Get High-res Image Gene #38: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq gain' versus 'RPPA_CNMF'

P value = 0.0212 (Fisher's exact test), Q value = 0.051

Table S192.  Gene #38: 'xq gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
XQ GAIN MUTATED 3 0 4 8 5
XQ GAIN WILD-TYPE 42 8 6 29 13

Figure S192.  Get High-res Image Gene #38: 'xq gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'xq gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0143 (Fisher's exact test), Q value = 0.037

Table S193.  Gene #38: 'xq gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
XQ GAIN MUTATED 3 6 11
XQ GAIN WILD-TYPE 48 19 31

Figure S193.  Get High-res Image Gene #38: 'xq gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'xq gain' versus 'MRNASEQ_CNMF'

P value = 0.00077 (Fisher's exact test), Q value = 0.0044

Table S194.  Gene #38: 'xq gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 40
XQ GAIN MUTATED 3 7 12
XQ GAIN WILD-TYPE 67 33 28

Figure S194.  Get High-res Image Gene #38: 'xq gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xq gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00397 (Fisher's exact test), Q value = 0.015

Table S195.  Gene #38: 'xq gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
XQ GAIN MUTATED 2 1 2 7 0 5 5
XQ GAIN WILD-TYPE 41 26 10 17 8 18 8

Figure S195.  Get High-res Image Gene #38: 'xq gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xq gain' versus 'MIRSEQ_CNMF'

P value = 0.00282 (Fisher's exact test), Q value = 0.011

Table S196.  Gene #38: 'xq gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 52 57 41
XQ GAIN MUTATED 2 8 12
XQ GAIN WILD-TYPE 50 49 29

Figure S196.  Get High-res Image Gene #38: 'xq gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'xq gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00041 (Fisher's exact test), Q value = 0.0026

Table S197.  Gene #38: 'xq gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
XQ GAIN MUTATED 3 6 13
XQ GAIN WILD-TYPE 67 32 29

Figure S197.  Get High-res Image Gene #38: 'xq gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'xq gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00144 (Fisher's exact test), Q value = 0.0071

Table S198.  Gene #38: 'xq gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
XQ GAIN MUTATED 3 7 12
XQ GAIN WILD-TYPE 66 29 33

Figure S198.  Get High-res Image Gene #38: 'xq gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xq gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0041 (Fisher's exact test), Q value = 0.015

Table S199.  Gene #38: 'xq gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 33 38 42
XQ GAIN MUTATED 2 1 7 12
XQ GAIN WILD-TYPE 35 32 31 30

Figure S199.  Get High-res Image Gene #38: 'xq gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_CNMF'

P value = 0.0219 (Fisher's exact test), Q value = 0.052

Table S200.  Gene #39: '1p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 52 57 41
1P LOSS MUTATED 10 2 6
1P LOSS WILD-TYPE 42 55 35

Figure S200.  Get High-res Image Gene #39: '1p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 0.0306 (Fisher's exact test), Q value = 0.068

Table S201.  Gene #43: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 49 45
3P LOSS MUTATED 11 15 4
3P LOSS WILD-TYPE 45 34 41

Figure S201.  Get High-res Image Gene #43: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p loss' versus 'RPPA_CNMF'

P value = 0.0162 (Fisher's exact test), Q value = 0.041

Table S202.  Gene #43: '3p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
3P LOSS MUTATED 8 3 2 1 5
3P LOSS WILD-TYPE 37 5 8 36 13

Figure S202.  Get High-res Image Gene #43: '3p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 0.00121 (Fisher's exact test), Q value = 0.0064

Table S203.  Gene #43: '3p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 40
3P LOSS MUTATED 17 12 1
3P LOSS WILD-TYPE 53 28 39

Figure S203.  Get High-res Image Gene #43: '3p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00317 (Fisher's exact test), Q value = 0.013

Table S204.  Gene #43: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
3P LOSS MUTATED 13 4 1 1 1 10 0
3P LOSS WILD-TYPE 30 23 11 23 7 13 13

Figure S204.  Get High-res Image Gene #43: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CNMF'

P value = 0.00122 (Fisher's exact test), Q value = 0.0064

Table S205.  Gene #43: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 52 57 41
3P LOSS MUTATED 13 16 1
3P LOSS WILD-TYPE 39 41 40

Figure S205.  Get High-res Image Gene #43: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00078 (Fisher's exact test), Q value = 0.0044

Table S206.  Gene #43: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
3P LOSS MUTATED 17 12 1
3P LOSS WILD-TYPE 53 26 41

Figure S206.  Get High-res Image Gene #43: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00241 (Fisher's exact test), Q value = 0.01

Table S207.  Gene #43: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
3P LOSS MUTATED 17 11 2
3P LOSS WILD-TYPE 52 25 43

Figure S207.  Get High-res Image Gene #43: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'3p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00168 (Fisher's exact test), Q value = 0.0082

Table S208.  Gene #43: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 33 38 42
3P LOSS MUTATED 10 7 12 1
3P LOSS WILD-TYPE 27 26 26 41

Figure S208.  Get High-res Image Gene #43: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q loss' versus 'RPPA_CNMF'

P value = 0.047 (Fisher's exact test), Q value = 0.095

Table S209.  Gene #44: '3q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
3Q LOSS MUTATED 7 3 1 1 3
3Q LOSS WILD-TYPE 38 5 9 36 15

Figure S209.  Get High-res Image Gene #44: '3q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'3q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0472 (Fisher's exact test), Q value = 0.095

Table S210.  Gene #44: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
3Q LOSS MUTATED 14 6 2
3Q LOSS WILD-TYPE 55 30 43

Figure S210.  Get High-res Image Gene #44: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 0.0454 (Fisher's exact test), Q value = 0.092

Table S211.  Gene #45: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 49 45
4P LOSS MUTATED 36 35 21
4P LOSS WILD-TYPE 20 14 24

Figure S211.  Get High-res Image Gene #45: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 0.0322 (Fisher's exact test), Q value = 0.071

Table S212.  Gene #45: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 40
4P LOSS MUTATED 45 29 18
4P LOSS WILD-TYPE 25 11 22

Figure S212.  Get High-res Image Gene #45: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 0.0103 (Fisher's exact test), Q value = 0.03

Table S213.  Gene #46: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 49 45
4Q LOSS MUTATED 40 42 26
4Q LOSS WILD-TYPE 16 7 19

Figure S213.  Get High-res Image Gene #46: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 0.0108 (Fisher's exact test), Q value = 0.031

Table S214.  Gene #46: '4q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 40
4Q LOSS MUTATED 50 35 23
4Q LOSS WILD-TYPE 20 5 17

Figure S214.  Get High-res Image Gene #46: '4q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0118 (Fisher's exact test), Q value = 0.033

Table S215.  Gene #46: '4q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
4Q LOSS MUTATED 27 23 10 13 7 21 7
4Q LOSS WILD-TYPE 16 4 2 11 1 2 6

Figure S215.  Get High-res Image Gene #46: '4q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_CNMF'

P value = 0.0157 (Fisher's exact test), Q value = 0.04

Table S216.  Gene #46: '4q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 52 57 41
4Q LOSS MUTATED 36 48 24
4Q LOSS WILD-TYPE 16 9 17

Figure S216.  Get High-res Image Gene #46: '4q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'4q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00502 (Fisher's exact test), Q value = 0.018

Table S217.  Gene #46: '4q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
4Q LOSS MUTATED 50 34 24
4Q LOSS WILD-TYPE 20 4 18

Figure S217.  Get High-res Image Gene #46: '4q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0352 (Fisher's exact test), Q value = 0.076

Table S218.  Gene #46: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
4Q LOSS MUTATED 50 31 27
4Q LOSS WILD-TYPE 19 5 18

Figure S218.  Get High-res Image Gene #46: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'4q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0257 (Fisher's exact test), Q value = 0.059

Table S219.  Gene #46: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 33 38 42
4Q LOSS MUTATED 24 26 33 25
4Q LOSS WILD-TYPE 13 7 5 17

Figure S219.  Get High-res Image Gene #46: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p loss' versus 'RPPA_CNMF'

P value = 0.0273 (Fisher's exact test), Q value = 0.062

Table S220.  Gene #47: '5p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
5P LOSS MUTATED 31 7 4 27 7
5P LOSS WILD-TYPE 14 1 6 10 11

Figure S220.  Get High-res Image Gene #47: '5p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'5q loss' versus 'RPPA_CNMF'

P value = 0.0404 (Fisher's exact test), Q value = 0.084

Table S221.  Gene #48: '5q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
5Q LOSS MUTATED 33 6 4 26 7
5Q LOSS WILD-TYPE 12 2 6 11 11

Figure S221.  Get High-res Image Gene #48: '5q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 0.0137 (Fisher's exact test), Q value = 0.037

Table S222.  Gene #48: '5q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 40
5Q LOSS MUTATED 55 21 25
5Q LOSS WILD-TYPE 15 19 15

Figure S222.  Get High-res Image Gene #48: '5q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00338 (Fisher's exact test), Q value = 0.013

Table S223.  Gene #48: '5q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
5Q LOSS MUTATED 29 26 8 15 3 12 8
5Q LOSS WILD-TYPE 14 1 4 9 5 11 5

Figure S223.  Get High-res Image Gene #48: '5q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0103 (Fisher's exact test), Q value = 0.03

Table S224.  Gene #48: '5q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
5Q LOSS MUTATED 55 19 27
5Q LOSS WILD-TYPE 15 19 15

Figure S224.  Get High-res Image Gene #48: '5q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.02 (Fisher's exact test), Q value = 0.049

Table S225.  Gene #48: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
5Q LOSS MUTATED 54 19 28
5Q LOSS WILD-TYPE 15 17 17

Figure S225.  Get High-res Image Gene #48: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'5q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00802 (Fisher's exact test), Q value = 0.025

Table S226.  Gene #48: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 33 38 42
5Q LOSS MUTATED 27 28 18 28
5Q LOSS WILD-TYPE 10 5 20 14

Figure S226.  Get High-res Image Gene #48: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p loss' versus 'METHLYATION_CNMF'

P value = 0.0361 (Fisher's exact test), Q value = 0.077

Table S227.  Gene #49: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 49 45
6P LOSS MUTATED 1 7 5
6P LOSS WILD-TYPE 55 42 40

Figure S227.  Get High-res Image Gene #49: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0142 (Fisher's exact test), Q value = 0.037

Table S228.  Gene #49: '6p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
6P LOSS MUTATED 1 2 2 0 1 3 4
6P LOSS WILD-TYPE 42 25 10 24 7 20 9

Figure S228.  Get High-res Image Gene #49: '6p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'METHLYATION_CNMF'

P value = 0.00963 (Fisher's exact test), Q value = 0.028

Table S229.  Gene #50: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 49 45
6Q LOSS MUTATED 1 9 6
6Q LOSS WILD-TYPE 55 40 39

Figure S229.  Get High-res Image Gene #50: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q loss' versus 'MRNASEQ_CNMF'

P value = 0.0444 (Fisher's exact test), Q value = 0.091

Table S230.  Gene #50: '6q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 40
6Q LOSS MUTATED 3 7 6
6Q LOSS WILD-TYPE 67 33 34

Figure S230.  Get High-res Image Gene #50: '6q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00117 (Fisher's exact test), Q value = 0.0062

Table S231.  Gene #50: '6q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
6Q LOSS MUTATED 1 2 2 0 2 4 5
6Q LOSS WILD-TYPE 42 25 10 24 6 19 8

Figure S231.  Get High-res Image Gene #50: '6q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0273 (Fisher's exact test), Q value = 0.062

Table S232.  Gene #50: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
6Q LOSS MUTATED 3 8 5
6Q LOSS WILD-TYPE 67 30 37

Figure S232.  Get High-res Image Gene #50: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0354 (Fisher's exact test), Q value = 0.076

Table S233.  Gene #50: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
6Q LOSS MUTATED 3 7 6
6Q LOSS WILD-TYPE 66 29 39

Figure S233.  Get High-res Image Gene #50: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'8p loss' versus 'RPPA_CNMF'

P value = 0.0274 (Fisher's exact test), Q value = 0.062

Table S234.  Gene #51: '8p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
8P LOSS MUTATED 0 0 0 5 3
8P LOSS WILD-TYPE 45 8 10 32 15

Figure S234.  Get High-res Image Gene #51: '8p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'8p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00944 (Fisher's exact test), Q value = 0.028

Table S235.  Gene #51: '8p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
8P LOSS MUTATED 0 4 4
8P LOSS WILD-TYPE 51 21 38

Figure S235.  Get High-res Image Gene #51: '8p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 0.0103 (Fisher's exact test), Q value = 0.03

Table S236.  Gene #51: '8p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 40
8P LOSS MUTATED 1 5 6
8P LOSS WILD-TYPE 69 35 34

Figure S236.  Get High-res Image Gene #51: '8p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.047 (Fisher's exact test), Q value = 0.095

Table S237.  Gene #51: '8p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
8P LOSS MUTATED 1 0 1 3 1 3 3
8P LOSS WILD-TYPE 42 27 11 21 7 20 10

Figure S237.  Get High-res Image Gene #51: '8p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_CNMF'

P value = 0.00853 (Fisher's exact test), Q value = 0.026

Table S238.  Gene #51: '8p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 52 57 41
8P LOSS MUTATED 1 3 8
8P LOSS WILD-TYPE 51 54 33

Figure S238.  Get High-res Image Gene #51: '8p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'8p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00207 (Fisher's exact test), Q value = 0.0095

Table S239.  Gene #51: '8p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
8P LOSS MUTATED 1 3 8
8P LOSS WILD-TYPE 69 35 34

Figure S239.  Get High-res Image Gene #51: '8p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0074 (Fisher's exact test), Q value = 0.024

Table S240.  Gene #51: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
8P LOSS MUTATED 1 4 7
8P LOSS WILD-TYPE 68 32 38

Figure S240.  Get High-res Image Gene #51: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'8p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0226 (Fisher's exact test), Q value = 0.053

Table S241.  Gene #51: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 33 38 42
8P LOSS MUTATED 1 0 4 7
8P LOSS WILD-TYPE 36 33 34 35

Figure S241.  Get High-res Image Gene #51: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q loss' versus 'METHLYATION_CNMF'

P value = 0.0242 (Fisher's exact test), Q value = 0.057

Table S242.  Gene #52: '8q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 49 45
8Q LOSS MUTATED 0 1 4
8Q LOSS WILD-TYPE 56 48 41

Figure S242.  Get High-res Image Gene #52: '8q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0143 (Fisher's exact test), Q value = 0.037

Table S243.  Gene #52: '8q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
8Q LOSS MUTATED 0 3 1
8Q LOSS WILD-TYPE 51 22 41

Figure S243.  Get High-res Image Gene #52: '8q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'8q loss' versus 'MRNASEQ_CNMF'

P value = 0.00237 (Fisher's exact test), Q value = 0.01

Table S244.  Gene #52: '8q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 40
8Q LOSS MUTATED 0 0 5
8Q LOSS WILD-TYPE 70 40 35

Figure S244.  Get High-res Image Gene #52: '8q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0121 (Fisher's exact test), Q value = 0.033

Table S245.  Gene #52: '8q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
8Q LOSS MUTATED 0 0 0 3 0 0 2
8Q LOSS WILD-TYPE 43 27 12 21 8 23 11

Figure S245.  Get High-res Image Gene #52: '8q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8q loss' versus 'MIRSEQ_CNMF'

P value = 0.00132 (Fisher's exact test), Q value = 0.0067

Table S246.  Gene #52: '8q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 52 57 41
8Q LOSS MUTATED 0 0 5
8Q LOSS WILD-TYPE 52 57 36

Figure S246.  Get High-res Image Gene #52: '8q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'8q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00226 (Fisher's exact test), Q value = 0.01

Table S247.  Gene #52: '8q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
8Q LOSS MUTATED 0 0 5
8Q LOSS WILD-TYPE 70 38 37

Figure S247.  Get High-res Image Gene #52: '8q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'8q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0029 (Fisher's exact test), Q value = 0.012

Table S248.  Gene #52: '8q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
8Q LOSS MUTATED 0 0 5
8Q LOSS WILD-TYPE 69 36 40

Figure S248.  Get High-res Image Gene #52: '8q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'8q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00335 (Fisher's exact test), Q value = 0.013

Table S249.  Gene #52: '8q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 33 38 42
8Q LOSS MUTATED 0 0 0 5
8Q LOSS WILD-TYPE 37 33 38 37

Figure S249.  Get High-res Image Gene #52: '8q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

P value = 0.0323 (Fisher's exact test), Q value = 0.071

Table S250.  Gene #53: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 44 58
9P LOSS MUTATED 15 16 32
9P LOSS WILD-TYPE 33 28 26

Figure S250.  Get High-res Image Gene #53: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9q loss' versus 'CN_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.002

Table S251.  Gene #54: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 44 58
9Q LOSS MUTATED 11 13 34
9Q LOSS WILD-TYPE 37 31 24

Figure S251.  Get High-res Image Gene #54: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0185 (Fisher's exact test), Q value = 0.046

Table S252.  Gene #54: '9q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
9Q LOSS MUTATED 13 10 8 13 0 11 3
9Q LOSS WILD-TYPE 30 17 4 11 8 12 10

Figure S252.  Get High-res Image Gene #54: '9q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 0.0207 (Fisher's exact test), Q value = 0.05

Table S253.  Gene #55: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 44 58
10P LOSS MUTATED 20 19 38
10P LOSS WILD-TYPE 28 25 20

Figure S253.  Get High-res Image Gene #55: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.0024

Table S254.  Gene #55: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 49 45
10P LOSS MUTATED 20 36 21
10P LOSS WILD-TYPE 36 13 24

Figure S254.  Get High-res Image Gene #55: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10p loss' versus 'RPPA_CNMF'

P value = 0.0083 (Fisher's exact test), Q value = 0.026

Table S255.  Gene #55: '10p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
10P LOSS MUTATED 16 3 4 24 14
10P LOSS WILD-TYPE 29 5 6 13 4

Figure S255.  Get High-res Image Gene #55: '10p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'10p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00682 (Fisher's exact test), Q value = 0.022

Table S256.  Gene #55: '10p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
10P LOSS MUTATED 18 15 28
10P LOSS WILD-TYPE 33 10 14

Figure S256.  Get High-res Image Gene #55: '10p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.0021

Table S257.  Gene #55: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 40
10P LOSS MUTATED 27 31 19
10P LOSS WILD-TYPE 43 9 21

Figure S257.  Get High-res Image Gene #55: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0055 (Fisher's exact test), Q value = 0.019

Table S258.  Gene #55: '10p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
10P LOSS MUTATED 16 11 9 13 6 18 4
10P LOSS WILD-TYPE 27 16 3 11 2 5 9

Figure S258.  Get High-res Image Gene #55: '10p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_CNMF'

P value = 0.0382 (Fisher's exact test), Q value = 0.081

Table S259.  Gene #55: '10p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 52 57 41
10P LOSS MUTATED 20 36 21
10P LOSS WILD-TYPE 32 21 20

Figure S259.  Get High-res Image Gene #55: '10p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'10p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00085 (Fisher's exact test), Q value = 0.0047

Table S260.  Gene #55: '10p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
10P LOSS MUTATED 27 29 21
10P LOSS WILD-TYPE 43 9 21

Figure S260.  Get High-res Image Gene #55: '10p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00209 (Fisher's exact test), Q value = 0.0095

Table S261.  Gene #55: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
10P LOSS MUTATED 27 27 23
10P LOSS WILD-TYPE 42 9 22

Figure S261.  Get High-res Image Gene #55: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'10p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00127 (Fisher's exact test), Q value = 0.0065

Table S262.  Gene #55: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 33 38 42
10P LOSS MUTATED 12 15 29 21
10P LOSS WILD-TYPE 25 18 9 21

Figure S262.  Get High-res Image Gene #55: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 0.00878 (Fisher's exact test), Q value = 0.026

Table S263.  Gene #56: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 44 58
10Q LOSS MUTATED 19 16 37
10Q LOSS WILD-TYPE 29 28 21

Figure S263.  Get High-res Image Gene #56: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S264.  Gene #56: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 49 45
10Q LOSS MUTATED 16 36 20
10Q LOSS WILD-TYPE 40 13 25

Figure S264.  Get High-res Image Gene #56: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.0013

Table S265.  Gene #56: '10q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 40
10Q LOSS MUTATED 24 30 18
10Q LOSS WILD-TYPE 46 10 22

Figure S265.  Get High-res Image Gene #56: '10q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00229 (Fisher's exact test), Q value = 0.01

Table S266.  Gene #56: '10q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
10Q LOSS MUTATED 16 8 9 12 5 18 4
10Q LOSS WILD-TYPE 27 19 3 12 3 5 9

Figure S266.  Get High-res Image Gene #56: '10q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_CNMF'

P value = 0.0322 (Fisher's exact test), Q value = 0.071

Table S267.  Gene #56: '10q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 52 57 41
10Q LOSS MUTATED 18 34 20
10Q LOSS WILD-TYPE 34 23 21

Figure S267.  Get High-res Image Gene #56: '10q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00041 (Fisher's exact test), Q value = 0.0026

Table S268.  Gene #56: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
10Q LOSS MUTATED 24 28 20
10Q LOSS WILD-TYPE 46 10 22

Figure S268.  Get High-res Image Gene #56: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00123 (Fisher's exact test), Q value = 0.0064

Table S269.  Gene #56: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
10Q LOSS MUTATED 24 26 22
10Q LOSS WILD-TYPE 45 10 23

Figure S269.  Get High-res Image Gene #56: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'10q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00139 (Fisher's exact test), Q value = 0.0069

Table S270.  Gene #56: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 33 38 42
10Q LOSS MUTATED 12 12 28 20
10Q LOSS WILD-TYPE 25 21 10 22

Figure S270.  Get High-res Image Gene #56: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 0.00854 (Fisher's exact test), Q value = 0.026

Table S271.  Gene #57: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 44 58
11P LOSS MUTATED 25 36 37
11P LOSS WILD-TYPE 23 8 21

Figure S271.  Get High-res Image Gene #57: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

'11p loss' versus 'MRNASEQ_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.0025

Table S272.  Gene #57: '11p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 40
11P LOSS MUTATED 54 28 16
11P LOSS WILD-TYPE 16 12 24

Figure S272.  Get High-res Image Gene #57: '11p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'11p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00055 (Fisher's exact test), Q value = 0.0033

Table S273.  Gene #57: '11p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
11P LOSS MUTATED 32 22 8 12 4 18 2
11P LOSS WILD-TYPE 11 5 4 12 4 5 11

Figure S273.  Get High-res Image Gene #57: '11p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_CNMF'

P value = 0.00103 (Fisher's exact test), Q value = 0.0056

Table S274.  Gene #57: '11p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 52 57 41
11P LOSS MUTATED 38 43 17
11P LOSS WILD-TYPE 14 14 24

Figure S274.  Get High-res Image Gene #57: '11p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'11p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00041 (Fisher's exact test), Q value = 0.0026

Table S275.  Gene #57: '11p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
11P LOSS MUTATED 54 27 17
11P LOSS WILD-TYPE 16 11 25

Figure S275.  Get High-res Image Gene #57: '11p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00178 (Fisher's exact test), Q value = 0.0085

Table S276.  Gene #57: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
11P LOSS MUTATED 53 25 20
11P LOSS WILD-TYPE 16 11 25

Figure S276.  Get High-res Image Gene #57: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'11p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00125 (Fisher's exact test), Q value = 0.0064

Table S277.  Gene #57: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 33 38 42
11P LOSS MUTATED 28 26 27 17
11P LOSS WILD-TYPE 9 7 11 25

Figure S277.  Get High-res Image Gene #57: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S278.  Gene #58: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 44 58
11Q LOSS MUTATED 30 44 41
11Q LOSS WILD-TYPE 18 0 17

Figure S278.  Get High-res Image Gene #58: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'MRNASEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00076

Table S279.  Gene #58: '11q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 40
11Q LOSS MUTATED 62 32 21
11Q LOSS WILD-TYPE 8 8 19

Figure S279.  Get High-res Image Gene #58: '11q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'11q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 2e-04

Table S280.  Gene #58: '11q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
11Q LOSS MUTATED 35 27 11 15 6 18 3
11Q LOSS WILD-TYPE 8 0 1 9 2 5 10

Figure S280.  Get High-res Image Gene #58: '11q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_CNMF'

P value = 0.00062 (Fisher's exact test), Q value = 0.0036

Table S281.  Gene #58: '11q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 52 57 41
11Q LOSS MUTATED 44 49 22
11Q LOSS WILD-TYPE 8 8 19

Figure S281.  Get High-res Image Gene #58: '11q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'11q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.0011

Table S282.  Gene #58: '11q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
11Q LOSS MUTATED 62 31 22
11Q LOSS WILD-TYPE 8 7 20

Figure S282.  Get High-res Image Gene #58: '11q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00108 (Fisher's exact test), Q value = 0.0058

Table S283.  Gene #58: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
11Q LOSS MUTATED 61 28 26
11Q LOSS WILD-TYPE 8 8 19

Figure S283.  Get High-res Image Gene #58: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'11q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 2e-04

Table S284.  Gene #58: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 33 38 42
11Q LOSS MUTATED 29 33 30 23
11Q LOSS WILD-TYPE 8 0 8 19

Figure S284.  Get High-res Image Gene #58: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 0.0442 (Fisher's exact test), Q value = 0.091

Table S285.  Gene #59: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 44 58
13Q LOSS MUTATED 34 39 40
13Q LOSS WILD-TYPE 14 5 18

Figure S285.  Get High-res Image Gene #59: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 0.0327 (Fisher's exact test), Q value = 0.071

Table S286.  Gene #59: '13q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 40
13Q LOSS MUTATED 58 31 24
13Q LOSS WILD-TYPE 12 9 16

Figure S286.  Get High-res Image Gene #59: '13q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00111 (Fisher's exact test), Q value = 0.0059

Table S287.  Gene #59: '13q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
13Q LOSS MUTATED 31 27 11 14 6 17 7
13Q LOSS WILD-TYPE 12 0 1 10 2 6 6

Figure S287.  Get High-res Image Gene #59: '13q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_CNMF'

P value = 0.0451 (Fisher's exact test), Q value = 0.092

Table S288.  Gene #59: '13q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 52 57 41
13Q LOSS MUTATED 43 45 25
13Q LOSS WILD-TYPE 9 12 16

Figure S288.  Get High-res Image Gene #59: '13q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'13q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0231 (Fisher's exact test), Q value = 0.054

Table S289.  Gene #59: '13q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
13Q LOSS MUTATED 58 30 25
13Q LOSS WILD-TYPE 12 8 17

Figure S289.  Get High-res Image Gene #59: '13q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0014 (Fisher's exact test), Q value = 0.007

Table S290.  Gene #59: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 33 38 42
13Q LOSS MUTATED 26 32 29 26
13Q LOSS WILD-TYPE 11 1 9 16

Figure S290.  Get High-res Image Gene #59: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q loss' versus 'METHLYATION_CNMF'

P value = 0.00079 (Fisher's exact test), Q value = 0.0045

Table S291.  Gene #60: '14q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 49 45
14Q LOSS MUTATED 2 14 4
14Q LOSS WILD-TYPE 54 35 41

Figure S291.  Get High-res Image Gene #60: '14q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'14q loss' versus 'RPPA_CNMF'

P value = 0.0277 (Fisher's exact test), Q value = 0.063

Table S292.  Gene #60: '14q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
14Q LOSS MUTATED 3 1 1 4 7
14Q LOSS WILD-TYPE 42 7 9 33 11

Figure S292.  Get High-res Image Gene #60: '14q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 0.0043 (Fisher's exact test), Q value = 0.016

Table S293.  Gene #60: '14q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 40
14Q LOSS MUTATED 3 10 7
14Q LOSS WILD-TYPE 67 30 33

Figure S293.  Get High-res Image Gene #60: '14q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00046

Table S294.  Gene #60: '14q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
14Q LOSS MUTATED 0 3 0 5 0 10 2
14Q LOSS WILD-TYPE 43 24 12 19 8 13 11

Figure S294.  Get High-res Image Gene #60: '14q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_CNMF'

P value = 0.0308 (Fisher's exact test), Q value = 0.068

Table S295.  Gene #60: '14q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 52 57 41
14Q LOSS MUTATED 2 11 7
14Q LOSS WILD-TYPE 50 46 34

Figure S295.  Get High-res Image Gene #60: '14q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'14q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00322 (Fisher's exact test), Q value = 0.013

Table S296.  Gene #60: '14q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
14Q LOSS MUTATED 3 10 7
14Q LOSS WILD-TYPE 67 28 35

Figure S296.  Get High-res Image Gene #60: '14q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00247 (Fisher's exact test), Q value = 0.01

Table S297.  Gene #60: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
14Q LOSS MUTATED 3 10 7
14Q LOSS WILD-TYPE 66 26 38

Figure S297.  Get High-res Image Gene #60: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'14q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0109 (Fisher's exact test), Q value = 0.031

Table S298.  Gene #60: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 33 38 42
14Q LOSS MUTATED 1 2 10 7
14Q LOSS WILD-TYPE 36 31 28 35

Figure S298.  Get High-res Image Gene #60: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 0.00548 (Fisher's exact test), Q value = 0.019

Table S299.  Gene #61: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 44 58
15Q LOSS MUTATED 11 2 16
15Q LOSS WILD-TYPE 37 42 42

Figure S299.  Get High-res Image Gene #61: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00029

Table S300.  Gene #61: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 49 45
15Q LOSS MUTATED 1 17 11
15Q LOSS WILD-TYPE 55 32 34

Figure S300.  Get High-res Image Gene #61: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'15q loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S301.  Gene #61: '15q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
15Q LOSS MUTATED 0 0 4 14 7
15Q LOSS WILD-TYPE 45 8 6 23 11

Figure S301.  Get High-res Image Gene #61: '15q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'15q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S302.  Gene #61: '15q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
15Q LOSS MUTATED 0 10 15
15Q LOSS WILD-TYPE 51 15 27

Figure S302.  Get High-res Image Gene #61: '15q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S303.  Gene #61: '15q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 40
15Q LOSS MUTATED 1 13 15
15Q LOSS WILD-TYPE 69 27 25

Figure S303.  Get High-res Image Gene #61: '15q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S304.  Gene #61: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
15Q LOSS MUTATED 0 1 3 7 4 8 6
15Q LOSS WILD-TYPE 43 26 9 17 4 15 7

Figure S304.  Get High-res Image Gene #61: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S305.  Gene #61: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 52 57 41
15Q LOSS MUTATED 0 14 15
15Q LOSS WILD-TYPE 52 43 26

Figure S305.  Get High-res Image Gene #61: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S306.  Gene #61: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
15Q LOSS MUTATED 1 13 15
15Q LOSS WILD-TYPE 69 25 27

Figure S306.  Get High-res Image Gene #61: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S307.  Gene #61: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
15Q LOSS MUTATED 1 12 16
15Q LOSS WILD-TYPE 68 24 29

Figure S307.  Get High-res Image Gene #61: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S308.  Gene #61: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 33 38 42
15Q LOSS MUTATED 0 1 13 15
15Q LOSS WILD-TYPE 37 32 25 27

Figure S308.  Get High-res Image Gene #61: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p loss' versus 'METHLYATION_CNMF'

P value = 0.00599 (Fisher's exact test), Q value = 0.02

Table S309.  Gene #62: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 49 45
16P LOSS MUTATED 17 21 6
16P LOSS WILD-TYPE 39 28 39

Figure S309.  Get High-res Image Gene #62: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p loss' versus 'MIRSEQ_CNMF'

P value = 0.00855 (Fisher's exact test), Q value = 0.026

Table S310.  Gene #62: '16p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 52 57 41
16P LOSS MUTATED 12 25 7
16P LOSS WILD-TYPE 40 32 34

Figure S310.  Get High-res Image Gene #62: '16p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0112 (Fisher's exact test), Q value = 0.032

Table S311.  Gene #62: '16p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
16P LOSS MUTATED 19 18 7
16P LOSS WILD-TYPE 51 20 35

Figure S311.  Get High-res Image Gene #62: '16p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_CNMF'

P value = 0.0307 (Fisher's exact test), Q value = 0.068

Table S312.  Gene #63: '16q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 52 57 41
16Q LOSS MUTATED 13 27 11
16Q LOSS WILD-TYPE 39 30 30

Figure S312.  Get High-res Image Gene #63: '16q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17p loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 2e-04

Table S313.  Gene #64: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 44 58
17P LOSS MUTATED 5 23 9
17P LOSS WILD-TYPE 43 21 49

Figure S313.  Get High-res Image Gene #64: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 0.0405 (Fisher's exact test), Q value = 0.084

Table S314.  Gene #64: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 49 45
17P LOSS MUTATED 18 6 13
17P LOSS WILD-TYPE 38 43 32

Figure S314.  Get High-res Image Gene #64: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p loss' versus 'RPPA_CNMF'

P value = 0.0443 (Fisher's exact test), Q value = 0.091

Table S315.  Gene #64: '17p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
17P LOSS MUTATED 17 2 1 7 1
17P LOSS WILD-TYPE 28 6 9 30 17

Figure S315.  Get High-res Image Gene #64: '17p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'17p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00321 (Fisher's exact test), Q value = 0.013

Table S316.  Gene #64: '17p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
17P LOSS MUTATED 19 1 8
17P LOSS WILD-TYPE 32 24 34

Figure S316.  Get High-res Image Gene #64: '17p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 0.00462 (Fisher's exact test), Q value = 0.016

Table S317.  Gene #64: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 40
17P LOSS MUTATED 26 5 6
17P LOSS WILD-TYPE 44 35 34

Figure S317.  Get High-res Image Gene #64: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.0017

Table S318.  Gene #64: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
17P LOSS MUTATED 10 16 2 1 0 4 4
17P LOSS WILD-TYPE 33 11 10 23 8 19 9

Figure S318.  Get High-res Image Gene #64: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00314 (Fisher's exact test), Q value = 0.013

Table S319.  Gene #64: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
17P LOSS MUTATED 26 4 7
17P LOSS WILD-TYPE 44 34 35

Figure S319.  Get High-res Image Gene #64: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00168 (Fisher's exact test), Q value = 0.0082

Table S320.  Gene #64: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
17P LOSS MUTATED 26 3 8
17P LOSS WILD-TYPE 43 33 37

Figure S320.  Get High-res Image Gene #64: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 2e-04

Table S321.  Gene #64: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 33 38 42
17P LOSS MUTATED 7 19 3 8
17P LOSS WILD-TYPE 30 14 35 34

Figure S321.  Get High-res Image Gene #64: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

P value = 0.00581 (Fisher's exact test), Q value = 0.02

Table S322.  Gene #65: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 44 58
17Q LOSS MUTATED 1 10 5
17Q LOSS WILD-TYPE 47 34 53

Figure S322.  Get High-res Image Gene #65: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

'17q loss' versus 'MRNASEQ_CNMF'

P value = 0.0198 (Fisher's exact test), Q value = 0.049

Table S323.  Gene #65: '17q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 40
17Q LOSS MUTATED 13 2 1
17Q LOSS WILD-TYPE 57 38 39

Figure S323.  Get High-res Image Gene #65: '17q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.029 (Fisher's exact test), Q value = 0.065

Table S324.  Gene #65: '17q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
17Q LOSS MUTATED 5 8 0 0 0 2 1
17Q LOSS WILD-TYPE 38 19 12 24 8 21 12

Figure S324.  Get High-res Image Gene #65: '17q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0146 (Fisher's exact test), Q value = 0.038

Table S325.  Gene #65: '17q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
17Q LOSS MUTATED 13 2 1
17Q LOSS WILD-TYPE 57 36 41

Figure S325.  Get High-res Image Gene #65: '17q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0107 (Fisher's exact test), Q value = 0.031

Table S326.  Gene #65: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
17Q LOSS MUTATED 13 2 1
17Q LOSS WILD-TYPE 56 34 44

Figure S326.  Get High-res Image Gene #65: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00489 (Fisher's exact test), Q value = 0.017

Table S327.  Gene #65: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 33 38 42
17Q LOSS MUTATED 4 9 2 1
17Q LOSS WILD-TYPE 33 24 36 41

Figure S327.  Get High-res Image Gene #65: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p loss' versus 'MRNASEQ_CNMF'

P value = 0.0432 (Fisher's exact test), Q value = 0.089

Table S328.  Gene #66: '18p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 40
18P LOSS MUTATED 53 36 27
18P LOSS WILD-TYPE 17 4 13

Figure S328.  Get High-res Image Gene #66: '18p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'18p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.016 (Fisher's exact test), Q value = 0.041

Table S329.  Gene #66: '18p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
18P LOSS MUTATED 53 35 28
18P LOSS WILD-TYPE 17 3 14

Figure S329.  Get High-res Image Gene #66: '18p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.032 (Fisher's exact test), Q value = 0.071

Table S330.  Gene #67: '18q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
18Q LOSS MUTATED 58 35 29
18Q LOSS WILD-TYPE 12 3 13

Figure S330.  Get High-res Image Gene #67: '18q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0205 (Fisher's exact test), Q value = 0.05

Table S331.  Gene #67: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 33 38 42
18Q LOSS MUTATED 27 31 34 30
18Q LOSS WILD-TYPE 10 2 4 12

Figure S331.  Get High-res Image Gene #67: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S332.  Gene #68: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 44 58
19P LOSS MUTATED 12 5 33
19P LOSS WILD-TYPE 36 39 25

Figure S332.  Get High-res Image Gene #68: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S333.  Gene #68: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 49 45
19P LOSS MUTATED 2 31 17
19P LOSS WILD-TYPE 54 18 28

Figure S333.  Get High-res Image Gene #68: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19p loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S334.  Gene #68: '19p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
19P LOSS MUTATED 2 2 4 21 12
19P LOSS WILD-TYPE 43 6 6 16 6

Figure S334.  Get High-res Image Gene #68: '19p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'19p loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S335.  Gene #68: '19p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
19P LOSS MUTATED 2 14 25
19P LOSS WILD-TYPE 49 11 17

Figure S335.  Get High-res Image Gene #68: '19p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'19p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S336.  Gene #68: '19p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 40
19P LOSS MUTATED 2 27 21
19P LOSS WILD-TYPE 68 13 19

Figure S336.  Get High-res Image Gene #68: '19p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S337.  Gene #68: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
19P LOSS MUTATED 0 2 9 12 5 16 6
19P LOSS WILD-TYPE 43 25 3 12 3 7 7

Figure S337.  Get High-res Image Gene #68: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S338.  Gene #68: '19p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 52 57 41
19P LOSS MUTATED 1 28 21
19P LOSS WILD-TYPE 51 29 20

Figure S338.  Get High-res Image Gene #68: '19p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'19p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S339.  Gene #68: '19p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
19P LOSS MUTATED 2 27 21
19P LOSS WILD-TYPE 68 11 21

Figure S339.  Get High-res Image Gene #68: '19p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S340.  Gene #68: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
19P LOSS MUTATED 2 24 24
19P LOSS WILD-TYPE 67 12 21

Figure S340.  Get High-res Image Gene #68: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'19p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S341.  Gene #68: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 33 38 42
19P LOSS MUTATED 0 2 26 22
19P LOSS WILD-TYPE 37 31 12 20

Figure S341.  Get High-res Image Gene #68: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S342.  Gene #69: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 44 58
19Q LOSS MUTATED 11 7 35
19Q LOSS WILD-TYPE 37 37 23

Figure S342.  Get High-res Image Gene #69: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S343.  Gene #69: '19q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 49 45
19Q LOSS MUTATED 1 34 18
19Q LOSS WILD-TYPE 55 15 27

Figure S343.  Get High-res Image Gene #69: '19q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19q loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S344.  Gene #69: '19q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
19Q LOSS MUTATED 1 2 4 22 14
19Q LOSS WILD-TYPE 44 6 6 15 4

Figure S344.  Get High-res Image Gene #69: '19q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'19q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S345.  Gene #69: '19q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
19Q LOSS MUTATED 1 14 28
19Q LOSS WILD-TYPE 50 11 14

Figure S345.  Get High-res Image Gene #69: '19q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'19q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S346.  Gene #69: '19q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 40
19Q LOSS MUTATED 1 30 22
19Q LOSS WILD-TYPE 69 10 18

Figure S346.  Get High-res Image Gene #69: '19q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S347.  Gene #69: '19q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
19Q LOSS MUTATED 0 1 9 13 5 19 6
19Q LOSS WILD-TYPE 43 26 3 11 3 4 7

Figure S347.  Get High-res Image Gene #69: '19q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S348.  Gene #69: '19q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 52 57 41
19Q LOSS MUTATED 1 30 22
19Q LOSS WILD-TYPE 51 27 19

Figure S348.  Get High-res Image Gene #69: '19q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'19q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S349.  Gene #69: '19q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
19Q LOSS MUTATED 1 30 22
19Q LOSS WILD-TYPE 69 8 20

Figure S349.  Get High-res Image Gene #69: '19q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S350.  Gene #69: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
19Q LOSS MUTATED 1 27 25
19Q LOSS WILD-TYPE 68 9 20

Figure S350.  Get High-res Image Gene #69: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'19q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S351.  Gene #69: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 33 38 42
19Q LOSS MUTATED 0 1 29 23
19Q LOSS WILD-TYPE 37 32 9 19

Figure S351.  Get High-res Image Gene #69: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p loss' versus 'MIRSEQ_CNMF'

P value = 0.0157 (Fisher's exact test), Q value = 0.04

Table S352.  Gene #70: '20p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 52 57 41
20P LOSS MUTATED 5 18 7
20P LOSS WILD-TYPE 47 39 34

Figure S352.  Get High-res Image Gene #70: '20p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'20p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0274 (Fisher's exact test), Q value = 0.062

Table S353.  Gene #70: '20p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 33 38 42
20P LOSS MUTATED 3 8 13 6
20P LOSS WILD-TYPE 34 25 25 36

Figure S353.  Get High-res Image Gene #70: '20p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 0.00234 (Fisher's exact test), Q value = 0.01

Table S354.  Gene #72: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 44 58
22Q LOSS MUTATED 9 9 27
22Q LOSS WILD-TYPE 39 35 31

Figure S354.  Get High-res Image Gene #72: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S355.  Gene #72: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 49 45
22Q LOSS MUTATED 4 28 13
22Q LOSS WILD-TYPE 52 21 32

Figure S355.  Get High-res Image Gene #72: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q loss' versus 'RPPA_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.0016

Table S356.  Gene #72: '22q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
22Q LOSS MUTATED 4 1 5 16 9
22Q LOSS WILD-TYPE 41 7 5 21 9

Figure S356.  Get High-res Image Gene #72: '22q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'22q loss' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 2e-04

Table S357.  Gene #72: '22q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
22Q LOSS MUTATED 4 15 16
22Q LOSS WILD-TYPE 47 10 26

Figure S357.  Get High-res Image Gene #72: '22q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S358.  Gene #72: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 40
22Q LOSS MUTATED 6 23 16
22Q LOSS WILD-TYPE 64 17 24

Figure S358.  Get High-res Image Gene #72: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S359.  Gene #72: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
22Q LOSS MUTATED 5 1 7 10 4 13 5
22Q LOSS WILD-TYPE 38 26 5 14 4 10 8

Figure S359.  Get High-res Image Gene #72: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 2e-04

Table S360.  Gene #72: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 52 57 41
22Q LOSS MUTATED 4 24 17
22Q LOSS WILD-TYPE 48 33 24

Figure S360.  Get High-res Image Gene #72: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S361.  Gene #72: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
22Q LOSS MUTATED 6 21 18
22Q LOSS WILD-TYPE 64 17 24

Figure S361.  Get High-res Image Gene #72: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S362.  Gene #72: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
22Q LOSS MUTATED 6 19 20
22Q LOSS WILD-TYPE 63 17 25

Figure S362.  Get High-res Image Gene #72: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'22q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S363.  Gene #72: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 33 38 42
22Q LOSS MUTATED 4 2 21 18
22Q LOSS WILD-TYPE 33 31 17 24

Figure S363.  Get High-res Image Gene #72: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xp loss' versus 'CN_CNMF'

P value = 0.00234 (Fisher's exact test), Q value = 0.01

Table S364.  Gene #73: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 44 58
XP LOSS MUTATED 2 11 16
XP LOSS WILD-TYPE 46 33 42

Figure S364.  Get High-res Image Gene #73: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'

'xp loss' versus 'METHLYATION_CNMF'

P value = 0.00175 (Fisher's exact test), Q value = 0.0084

Table S365.  Gene #73: 'xp loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 49 45
XP LOSS MUTATED 6 6 17
XP LOSS WILD-TYPE 50 43 28

Figure S365.  Get High-res Image Gene #73: 'xp loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xp loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00352 (Fisher's exact test), Q value = 0.013

Table S366.  Gene #73: 'xp loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 33 38 42
XP LOSS MUTATED 2 9 4 14
XP LOSS WILD-TYPE 35 24 34 28

Figure S366.  Get High-res Image Gene #73: 'xp loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq loss' versus 'CN_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.0014

Table S367.  Gene #74: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 44 58
XQ LOSS MUTATED 1 11 17
XQ LOSS WILD-TYPE 47 33 41

Figure S367.  Get High-res Image Gene #74: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 0.00187 (Fisher's exact test), Q value = 0.0088

Table S368.  Gene #74: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 49 45
XQ LOSS MUTATED 6 6 17
XQ LOSS WILD-TYPE 50 43 28

Figure S368.  Get High-res Image Gene #74: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq loss' versus 'MIRSEQ_CNMF'

P value = 0.0254 (Fisher's exact test), Q value = 0.059

Table S369.  Gene #74: 'xq loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 52 57 41
XQ LOSS MUTATED 7 8 14
XQ LOSS WILD-TYPE 45 49 27

Figure S369.  Get High-res Image Gene #74: 'xq loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'xq loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0266 (Fisher's exact test), Q value = 0.061

Table S370.  Gene #74: 'xq loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
XQ LOSS MUTATED 11 4 14
XQ LOSS WILD-TYPE 59 34 28

Figure S370.  Get High-res Image Gene #74: 'xq loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00393 (Fisher's exact test), Q value = 0.015

Table S371.  Gene #74: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 33 38 42
XQ LOSS MUTATED 2 9 4 14
XQ LOSS WILD-TYPE 35 24 34 28

Figure S371.  Get High-res Image Gene #74: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data
Input

  • Copy number data file = broad_values_by_arm.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/TGCT-TP/19781848/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/TGCT-TP/20140863/TGCT-TP.transferedmergedcluster.txt

  • Number of patients = 150

  • Number of significantly arm-level cnvs = 74

  • Number of molecular subtypes = 10

  • Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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