Correlation between copy number variations of arm-level result and molecular subtypes
Kidney Renal Clear Cell Carcinoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1Z89BDF
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/C1Z89BDF
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 82 arm-level events and 12 molecular subtypes across 528 patients, 444 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', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 2p gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 2q gain cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

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

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

  • 4p gain cnv correlated to 'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 4q gain cnv correlated to 'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 5p gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 5q gain cnv correlated to 'CN_CNMF'.

  • 6q gain cnv correlated to 'RPPA_CNMF'.

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

  • 7q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

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

  • 9p gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

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

  • 10p gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 10q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 11p gain cnv correlated to 'CN_CNMF'.

  • 11q gain cnv correlated to 'CN_CNMF'.

  • 12p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 12q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 13q gain cnv correlated to 'METHLYATION_CNMF'.

  • 14q gain cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 15q gain cnv correlated to 'CN_CNMF'.

  • 16p gain cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

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

  • 17p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 17q gain cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 18p gain cnv correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 18q gain cnv correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • 20p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

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

  • 21q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 22q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • xp gain cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • xq gain cnv correlated to 'RPPA_CNMF' and 'RPPA_CHIERARCHICAL'.

  • 1p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 1q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 2p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 2q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 3p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 3q loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 4p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 4q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 5p loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 5q loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 6p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 6q loss cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 7q loss cnv correlated to 'MRNASEQ_CNMF' and 'MIRSEQ_CNMF'.

  • 8p loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 8q loss cnv correlated to 'METHLYATION_CNMF'.

  • 9p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 9q loss cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 10p loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

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

  • 11p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

  • 13q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 14q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

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

  • 16p loss cnv correlated to 'RPPA_CHIERARCHICAL'.

  • 16q loss cnv correlated to 'CN_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 17p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 17q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 18p 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'.

  • 18q loss cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 19q loss cnv correlated to 'CN_CNMF'.

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

  • 20q loss cnv correlated to 'MIRSEQ_CHIERARCHICAL'.

  • 21q loss cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

  • xp loss cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • xq loss cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 82 arm-level events and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 444 significant findings detected.

Clinical
Features 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
3q gain 61 (12%) 467 0.012
(0.0349) 		0.0315
(0.0765) 		1e-05
(7.08e-05) 		0.00382
(0.0131) 		0.00073
(0.0031) 		1e-05
(7.08e-05) 		4e-05
(0.000236) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		0.00046
(0.00203) 		0.00158
(0.00598) 		0.0798
(0.159)
12p gain 121 (23%) 407 0.0133
(0.0381) 		0.0322
(0.0778) 		1e-05
(7.08e-05) 		2e-05
(0.00013) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		0.00164
(0.00618) 		0.102
(0.19)
12q gain 122 (23%) 406 0.0132
(0.0379) 		0.0333
(0.0798) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		0.00312
(0.0111) 		0.126
(0.222)
20q gain 115 (22%) 413 0.0409
(0.0942) 		0.0726
(0.148) 		1e-05
(7.08e-05) 		3e-05
(0.000186) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		0.0323
(0.0778)
6p loss 100 (19%) 428 0.0109
(0.0321) 		0.0142
(0.0401) 		1e-05
(7.08e-05) 		5e-05
(0.000286) 		8e-05
(0.000445) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		0.0815
(0.161) 		0.0246
(0.0634)
9p loss 149 (28%) 379 0.00388
(0.0133) 		0.0362
(0.086) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		0.0001
(0.000544) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		0.0161
(0.0445) 		0.0968
(0.182)
9q loss 150 (28%) 378 0.0104
(0.031) 		0.0589
(0.127) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		0.00012
(0.000638) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		0.00372
(0.013) 		0.0365
(0.0865)
14q loss 216 (41%) 312 2e-05
(0.00013) 		6e-05
(0.000337) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		0.0499
(0.111) 		0.879
(1.00)
18q loss 95 (18%) 433 0.0452
(0.101) 		0.222
(0.342) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		2e-05
(0.00013) 		0.0001
(0.000544) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		0.00299
(0.0107) 		0.0312
(0.0759)
3p loss 380 (72%) 148 0.00381
(0.0131) 		0.0104
(0.031) 		1e-05
(7.08e-05) 		0.00053
(0.00232) 		0.0338
(0.0809) 		0.0445
(0.1) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		0.0226
(0.0591) 		0.00856
(0.0264) 		0.0928
(0.176) 		0.733
(0.876)
6q loss 128 (24%) 400 0.0495
(0.11) 		0.0517
(0.114) 		1e-05
(7.08e-05) 		0.00576
(0.0187) 		7e-05
(0.000391) 		3e-05
(0.000186) 		0.00022
(0.0011) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		2e-05
(0.00013) 		0.169
(0.277) 		0.0259
(0.0656)
13q loss 71 (13%) 457 0.00339
(0.012) 		0.0466
(0.104) 		1e-05
(7.08e-05) 		0.00027
(0.00132) 		4e-05
(0.000236) 		2e-05
(0.00013) 		2e-05
(0.00013) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		0.108
(0.196) 		0.106
(0.195)
18p loss 93 (18%) 435 0.0574
(0.124) 		0.457
(0.591) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		0.00025
(0.00122) 		0.00403
(0.0137)
22q loss 39 (7%) 489 0.0103
(0.0309) 		0.00146
(0.00559) 		1e-05
(7.08e-05) 		0.00378
(0.0131) 		0.0012
(0.00474) 		0.0681
(0.143) 		1e-05
(7.08e-05) 		3e-05
(0.000186) 		1e-05
(7.08e-05) 		0.00343
(0.0121) 		0.025
(0.0643) 		0.26
(0.383)
1p gain 24 (5%) 504 0.819
(0.954) 		0.925
(1.00) 		1e-05
(7.08e-05) 		0.00074
(0.00313) 		0.00105
(0.00422) 		0.0255
(0.0647) 		0.00086
(0.00351) 		0.00146
(0.00559) 		0.00211
(0.00775) 		0.00608
(0.0194) 		0.75
(0.893) 		0.0391
(0.0908)
8q gain 62 (12%) 466 0.226
(0.346) 		0.105
(0.195) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		0.00037
(0.00168) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		0.00011
(0.000595) 		0.00032
(0.00149) 		0.406
(0.545)
20p gain 112 (21%) 416 0.115
(0.207) 		0.116
(0.208) 		1e-05
(7.08e-05) 		6e-05
(0.000337) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		0.0517
(0.114)
2p loss 14 (3%) 514 4e-05
(0.000236) 		0.00046
(0.00203) 		1e-05
(7.08e-05) 		0.663
(0.811) 		0.00019
(0.000964) 		4e-05
(0.000236) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		2e-05
(0.00013) 		5e-05
(0.000286) 		0.133
(0.228) 		0.0967
(0.182)
2q loss 14 (3%) 514 0.00032
(0.00149) 		0.00078
(0.00324) 		3e-05
(0.000186) 		1
(1.00) 		0.00035
(0.00159) 		2e-05
(0.00013) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		0.132
(0.228) 		0.0985
(0.184)
17p loss 46 (9%) 482 0.00018
(0.000927) 		0.00024
(0.00118) 		1e-05
(7.08e-05) 		0.0873
(0.169) 		0.0094
(0.0285) 		0.00039
(0.00175) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		0.00015
(0.000789) 		0.203
(0.321) 		0.0871
(0.169)
1q gain 51 (10%) 477 0.409
(0.547) 		0.901
(1.00) 		1e-05
(7.08e-05) 		0.0142
(0.0401) 		0.0279
(0.0692) 		0.016
(0.0441) 		1e-05
(7.08e-05) 		0.00173
(0.00647) 		1e-05
(7.08e-05) 		0.00545
(0.0178) 		0.421
(0.558) 		0.756
(0.899)
7p gain 171 (32%) 357 0.453
(0.587) 		0.859
(0.991) 		1e-05
(7.08e-05) 		0.00154
(0.00585) 		0.00032
(0.00149) 		0.00541
(0.0177) 		0.00012
(0.000638) 		0.00913
(0.0278) 		0.0041
(0.0139) 		0.0295
(0.0729) 		0.103
(0.191) 		0.768
(0.911)
7q gain 172 (33%) 356 0.45
(0.586) 		0.859
(0.991) 		1e-05
(7.08e-05) 		0.00381
(0.0131) 		0.00023
(0.00114) 		0.00243
(0.00886) 		9e-05
(0.000495) 		0.00629
(0.02) 		0.00532
(0.0175) 		0.0183
(0.0493) 		0.172
(0.28) 		0.586
(0.728)
8p gain 31 (6%) 497 1e-05
(7.08e-05) 		0.00035
(0.00159) 		0.0102
(0.0305) 		0.0637
(0.136) 		3e-05
(0.000186) 		5e-05
(0.000286) 		1e-05
(7.08e-05) 		0.00511
(0.017) 		0.0117
(0.0342) 		0.107
(0.196)
1p loss 57 (11%) 471 0.00092
(0.00374) 		0.00276
(0.00998) 		1e-05
(7.08e-05) 		0.677
(0.823) 		0.00131
(0.00509) 		0.155
(0.26) 		0.115
(0.207) 		3e-05
(0.000186) 		0.00784
(0.0244) 		0.0218
(0.0576) 		0.0367
(0.0866) 		0.822
(0.957)
1q loss 36 (7%) 492 0.0107
(0.0315) 		0.0114
(0.0334) 		1e-05
(7.08e-05) 		0.37
(0.506) 		0.0283
(0.07) 		0.106
(0.195) 		0.00416
(0.0141) 		1e-05
(7.08e-05) 		0.00585
(0.0189) 		0.0418
(0.0959) 		0.223
(0.343) 		0.71
(0.852)
17q loss 28 (5%) 500 0.00073
(0.0031) 		0.00042
(0.00187) 		1e-05
(7.08e-05) 		0.582
(0.725) 		0.278
(0.403) 		0.00775
(0.0242) 		4e-05
(0.000236) 		1e-05
(7.08e-05) 		2e-05
(0.00013) 		0.00512
(0.017) 		0.458
(0.591) 		0.151
(0.255)
19p loss 11 (2%) 517 1e-05
(7.08e-05) 		0.0317
(0.0769) 		0.00517
(0.0171) 		0.00041
(0.00183) 		0.17
(0.277) 		0.0106
(0.0315) 		0.244
(0.363) 		0.0096
(0.029) 		0.034
(0.081) 		0.039
(0.0908)
21q loss 55 (10%) 473 0.0265
(0.0668) 		0.0892
(0.171) 		1e-05
(7.08e-05) 		0.0133
(0.038) 		0.0741
(0.149) 		0.00109
(0.00436) 		0.00294
(0.0105) 		0.00012
(0.000638) 		0.00678
(0.0215) 		0.00906
(0.0277) 		0.885
(1.00) 		1
(1.00)
19q gain 57 (11%) 471 0.102
(0.19) 		0.224
(0.344) 		1e-05
(7.08e-05) 		1e-05
(7.08e-05) 		0.00022
(0.0011) 		0.0132
(0.038) 		0.00066
(0.00285) 		9e-05
(0.000495) 		4e-05
(0.000236) 		0.169
(0.277) 		0.579
(0.723) 		0.288
(0.416)
21q gain 50 (9%) 478 0.267
(0.391) 		0.209
(0.326) 		1e-05
(7.08e-05) 		0.00121
(0.00476) 		0.00184
(0.00683) 		0.519
(0.659) 		0.0003
(0.00144) 		0.00262
(0.00951) 		0.00294
(0.0105) 		0.0324
(0.078) 		0.355
(0.489) 		0.478
(0.612)
15q loss 36 (7%) 492 0.119
(0.212) 		0.333
(0.464) 		1e-05
(7.08e-05) 		0.00075
(0.00315) 		0.0299
(0.0735) 		0.107
(0.196) 		1e-05
(7.08e-05) 		2e-05
(0.00013) 		0.00083
(0.0034) 		0.0164
(0.0451) 		0.0711
(0.146) 		0.133
(0.228)
xq loss 46 (9%) 482 0.0235
(0.0608) 		0.0641
(0.136) 		1e-05
(7.08e-05) 		0.00904
(0.0277) 		0.33
(0.461) 		0.00169
(0.00635) 		0.0916
(0.174) 		0.0276
(0.0691) 		0.0186
(0.0499) 		0.00328
(0.0116) 		0.229
(0.348) 		0.177
(0.285)
3p gain 19 (4%) 509 0.0538
(0.118) 		0.434
(0.57) 		0.00034
(0.00156) 		0.58
(0.724) 		0.0239
(0.0617) 		0.00205
(0.00758) 		0.00914
(0.0278) 		0.00017
(0.000885) 		0.00015
(0.000789) 		0.128
(0.223) 		0.39
(0.527) 		0.737
(0.879)
14q gain 16 (3%) 512 0.77
(0.913) 		0.571
(0.715) 		0.00123
(0.00482) 		0.35
(0.482) 		0.00593
(0.019) 		0.0407
(0.0941) 		0.00689
(0.0217) 		0.0003
(0.00144) 		0.00378
(0.0131) 		0.113
(0.204)
19p gain 51 (10%) 477 0.228
(0.348) 		0.485
(0.62) 		1e-05
(7.08e-05) 		5e-05
(0.000286) 		0.00383
(0.0131) 		0.132
(0.227) 		0.00145
(0.00559) 		0.00078
(0.00324) 		5e-05
(0.000286) 		0.357
(0.49) 		0.922
(1.00) 		0.626
(0.771)
10q loss 89 (17%) 439 0.328
(0.459) 		0.398
(0.536) 		1e-05
(7.08e-05) 		0.00425
(0.0143) 		0.985
(1.00) 		0.0209
(0.0554) 		0.122
(0.215) 		0.00214
(0.00783) 		0.0387
(0.0905) 		0.00055
(0.00239) 		0.802
(0.94) 		0.435
(0.57)
11q loss 23 (4%) 505 0.188
(0.3) 		0.373
(0.509) 		1e-05
(7.08e-05) 		0.00594
(0.019) 		0.183
(0.293) 		0.0698
(0.145) 		0.0141
(0.0401) 		0.00032
(0.00149) 		0.023
(0.0597) 		0.037
(0.087) 		0.299
(0.426) 		0.31
(0.438)
xp loss 46 (9%) 482 0.0407
(0.0941) 		0.0656
(0.138) 		0.00019
(0.000964) 		0.0714
(0.146) 		0.237
(0.356) 		0.00277
(0.00998) 		0.21
(0.328) 		0.0127
(0.0366) 		0.0389
(0.0906) 		0.00082
(0.00338) 		0.11
(0.2) 		0.159
(0.266)
4p gain 13 (2%) 515 0.0741
(0.149) 		0.373
(0.509) 		0.0706
(0.146) 		0.0101
(0.0305) 		0.00029
(0.00141) 		0.00056
(0.00243) 		0.00034
(0.00156) 		0.0435
(0.0986)
16p gain 107 (20%) 421 0.271
(0.395) 		0.38
(0.516) 		6e-05
(0.000337) 		0.167
(0.276) 		0.0377
(0.0884) 		0.412
(0.548) 		0.00735
(0.023) 		0.00419
(0.0141) 		0.0616
(0.132) 		0.0251
(0.0644) 		0.131
(0.226) 		0.392
(0.529)
17p gain 26 (5%) 502 0.0176
(0.0479) 		0.00554
(0.0181) 		1e-05
(7.08e-05) 		0.818
(0.954) 		0.096
(0.181) 		0.145
(0.248) 		0.15
(0.254) 		0.00484
(0.0161) 		0.146
(0.25) 		0.263
(0.386) 		0.0365
(0.0865) 		0.737
(0.879)
xp gain 32 (6%) 496 1
(1.00) 		0.525
(0.665) 		0.00582
(0.0188) 		0.225
(0.344) 		0.00032
(0.00149) 		0.00068
(0.00292) 		0.0154
(0.0431) 		0.00096
(0.00389) 		0.126
(0.221) 		0.141
(0.241) 		0.559
(0.703) 		0.901
(1.00)
4p loss 72 (14%) 456 0.533
(0.672) 		0.818
(0.954) 		1e-05
(7.08e-05) 		0.00016
(0.000837) 		0.204
(0.321) 		0.289
(0.417) 		0.00082
(0.00338) 		0.00116
(0.0046) 		0.57
(0.714) 		0.0723
(0.147) 		0.0804
(0.16) 		0.00723
(0.0227)
2q gain 79 (15%) 449 0.561
(0.704) 		0.267
(0.391) 		1e-05
(7.08e-05) 		0.169
(0.277) 		0.0432
(0.0983) 		1
(1.00) 		0.231
(0.35) 		0.0179
(0.0485) 		0.709
(0.852) 		0.0254
(0.0647) 		0.318
(0.447) 		0.657
(0.804)
4q gain 13 (2%) 515 0.212
(0.33) 		0.454
(0.588) 		0.0715
(0.146) 		0.0521
(0.114) 		0.00039
(0.00175) 		0.00434
(0.0145) 		0.00032
(0.00149) 		0.043
(0.0982)
10p gain 17 (3%) 511 0.00024
(0.00118) 		0.256
(0.38) 		0.0981
(0.184) 		0.176
(0.285) 		0.00105
(0.00422) 		0.00021
(0.00106) 		0.0193
(0.0517) 		0.0693
(0.144)
10q gain 12 (2%) 516 0.00019
(0.000964) 		0.117
(0.208) 		0.0574
(0.124) 		0.218
(0.337) 		0.0139
(0.0394) 		0.00176
(0.00656) 		0.0152
(0.0427) 		0.215
(0.333)
16q gain 99 (19%) 429 0.232
(0.35) 		0.347
(0.479) 		4e-05
(0.000236) 		0.0874
(0.169) 		0.0521
(0.114) 		0.3
(0.427) 		0.00641
(0.0203) 		0.0167
(0.0456) 		0.0159
(0.0441) 		0.149
(0.252) 		0.182
(0.292) 		0.266
(0.39)
17q gain 33 (6%) 495 0.0694
(0.144) 		0.0254
(0.0647) 		1e-05
(7.08e-05) 		0.233
(0.35) 		0.0837
(0.164) 		0.126
(0.222) 		0.0769
(0.154) 		0.00153
(0.00584) 		0.0771
(0.154) 		0.224
(0.343) 		0.00208
(0.00767) 		0.296
(0.424)
4q loss 65 (12%) 463 0.388
(0.526) 		0.783
(0.923) 		1e-05
(7.08e-05) 		3e-05
(0.000186) 		0.179
(0.288) 		0.0905
(0.173) 		0.00049
(0.00215) 		4e-05
(0.000236) 		0.199
(0.316) 		0.0653
(0.138) 		0.433
(0.57) 		0.0568
(0.123)
5p loss 7 (1%) 521 0.016
(0.0441) 		0.289
(0.418) 		0.465
(0.599) 		0.128
(0.223) 		0.0272
(0.0683) 		0.011
(0.0323) 		0.0411
(0.0945) 		0.0662
(0.139)
8p loss 137 (26%) 391 0.379
(0.516) 		0.163
(0.271) 		2e-05
(0.00013) 		0.277
(0.403) 		0.121
(0.214) 		0.0907
(0.173) 		0.0816
(0.161) 		0.00113
(0.0045) 		0.0431
(0.0982) 		0.0229
(0.0596) 		0.278
(0.403) 		0.244
(0.363)
5p gain 193 (37%) 335 0.881
(1.00) 		0.923
(1.00) 		0.00032
(0.00149) 		0.258
(0.382) 		0.305
(0.434) 		0.337
(0.469) 		0.00889
(0.0273) 		0.0226
(0.059) 		0.0697
(0.145) 		0.153
(0.257) 		0.083
(0.163) 		0.906
(1.00)
3q loss 99 (19%) 429 0.922
(1.00) 		0.515
(0.654) 		0.00133
(0.00515) 		0.405
(0.543) 		0.254
(0.376) 		0.209
(0.326) 		0.13
(0.225) 		0.0189
(0.0507) 		0.649
(0.795) 		0.0278
(0.0692) 		0.802
(0.94) 		0.86
(0.991)
5q loss 6 (1%) 522 0.0452
(0.101) 		0.542
(0.682) 		0.346
(0.479) 		0.395
(0.533) 		0.0455
(0.102) 		0.0158
(0.044) 		0.0723
(0.147) 		0.0929
(0.176)
10p loss 67 (13%) 461 0.172
(0.28) 		0.404
(0.543) 		1e-05
(7.08e-05) 		0.0817
(0.161) 		0.808
(0.946) 		0.068
(0.143) 		0.153
(0.257) 		0.0007
(0.00299) 		0.0174
(0.0474) 		0.108
(0.196) 		0.775
(0.917) 		0.298
(0.426)
11p loss 18 (3%) 510 2e-05
(0.00013) 		0.022
(0.0578) 		0.299
(0.426) 		0.262
(0.385) 		0.172
(0.28) 		0.0277
(0.0692) 		0.169
(0.277) 		0.151
(0.255) 		0.298
(0.426) 		0.306
(0.434)
16q loss 16 (3%) 512 0.0368
(0.0867) 		0.91
(1.00) 		0.182
(0.292) 		0.161
(0.268) 		0.105
(0.194) 		0.0907
(0.173) 		0.0651
(0.138) 		0.00821
(0.0254) 		0.0713
(0.146) 		0.0284
(0.0703)
2p gain 77 (15%) 451 0.704
(0.847) 		0.461
(0.595) 		1e-05
(7.08e-05) 		0.0834
(0.163) 		0.0533
(0.117) 		0.942
(1.00) 		0.232
(0.35) 		0.012
(0.0348) 		0.618
(0.763) 		0.144
(0.246) 		0.231
(0.35) 		0.471
(0.605)
9p gain 13 (2%) 515 0.015
(0.0421) 		0.904
(1.00) 		0.865
(0.995) 		1
(1.00) 		0.249
(0.37) 		0.0177
(0.048) 		1
(1.00) 		0.862
(0.991) 		1
(1.00) 		1
(1.00)
9q gain 12 (2%) 516 0.00125
(0.00488) 		0.91
(1.00) 		0.684
(0.827) 		0.231
(0.35) 		0.242
(0.362) 		0.0272
(0.0683) 		0.53
(0.67) 		0.673
(0.819) 		1
(1.00) 		1
(1.00)
22q gain 40 (8%) 488 0.328
(0.459) 		0.218
(0.337) 		3e-05
(0.000186) 		0.208
(0.326) 		0.418
(0.556) 		0.975
(1.00) 		0.0554
(0.121) 		0.0164
(0.0451) 		0.0632
(0.135) 		0.411
(0.548) 		0.907
(1.00) 		0.306
(0.434)
xq gain 31 (6%) 497 0.388
(0.526) 		0.703
(0.847) 		0.224
(0.343) 		0.291
(0.418) 		0.03
(0.0735) 		0.00802
(0.0249) 		0.153
(0.257) 		0.102
(0.19) 		0.32
(0.45) 		0.605
(0.749) 		0.92
(1.00) 		0.812
(0.95)
7q loss 4 (1%) 524 0.12
(0.213) 		0.347
(0.479) 		0.0858
(0.167) 		0.177
(0.285) 		0.0499
(0.111) 		0.0793
(0.158) 		0.0195
(0.052) 		0.773
(0.916)
20p loss 8 (2%) 520 0.172
(0.28) 		1
(1.00) 		0.0301
(0.0735) 		1
(1.00) 		0.0893
(0.171) 		0.233
(0.35) 		0.0201
(0.0533) 		0.232
(0.35)
5q gain 207 (39%) 321 0.335
(0.466) 		0.626
(0.771) 		0.022
(0.0579) 		0.435
(0.57) 		0.664
(0.811) 		0.447
(0.583) 		0.056
(0.122) 		0.0683
(0.143) 		0.448
(0.583) 		0.208
(0.325) 		0.128
(0.223) 		0.906
(1.00)
6q gain 9 (2%) 519 0.0805
(0.16) 		0.682
(0.826) 		0.0196
(0.0521) 		0.631
(0.777) 		1
(1.00) 		0.912
(1.00) 		1
(1.00) 		0.187
(0.298) 		0.605
(0.749) 		0.78
(0.92)
11p gain 31 (6%) 497 0.232
(0.35) 		0.67
(0.817) 		1e-05
(7.08e-05) 		0.27
(0.394) 		0.0868
(0.169) 		0.0966
(0.182) 		0.152
(0.256) 		0.238
(0.356) 		0.147
(0.251) 		0.279
(0.404) 		0.391
(0.529) 		0.855
(0.99)
11q gain 29 (5%) 499 0.341
(0.474) 		0.907
(1.00) 		0.00018
(0.000927) 		0.526
(0.665) 		0.335
(0.466) 		0.522
(0.662) 		0.426
(0.563) 		0.572
(0.716) 		0.361
(0.495) 		0.186
(0.298) 		0.752
(0.895) 		0.68
(0.825)
13q gain 22 (4%) 506 0.489
(0.624) 		0.034
(0.081) 		0.637
(0.782) 		0.797
(0.937) 		0.0706
(0.146) 		0.123
(0.216) 		0.344
(0.477) 		0.262
(0.385) 		0.29
(0.418) 		0.326
(0.457)
15q gain 26 (5%) 502 1
(1.00) 		0.115
(0.206) 		0.00078
(0.00324) 		0.722
(0.864) 		0.499
(0.636) 		0.466
(0.599) 		0.673
(0.819) 		0.106
(0.195) 		0.705
(0.848) 		0.409
(0.547) 		0.685
(0.827) 		0.826
(0.959)
18p gain 25 (5%) 503 0.313
(0.441) 		0.0768
(0.154) 		0.0734
(0.149) 		0.446
(0.583) 		0.814
(0.951) 		0.0808
(0.16) 		0.191
(0.304) 		0.421
(0.558) 		0.833
(0.965) 		0.453
(0.587) 		0.204
(0.321) 		0.0428
(0.0981)
18q gain 25 (5%) 503 0.312
(0.44) 		0.0767
(0.154) 		0.0669
(0.141) 		0.559
(0.703) 		0.426
(0.563) 		0.213
(0.331) 		0.19
(0.303) 		0.418
(0.556) 		0.965
(1.00) 		0.451
(0.587) 		0.2
(0.316) 		0.0444
(0.1)
8q loss 64 (12%) 464 0.649
(0.795) 		0.127
(0.223) 		0.12
(0.213) 		0.045
(0.101) 		0.161
(0.268) 		0.933
(1.00) 		0.721
(0.864) 		0.19
(0.303) 		0.586
(0.728) 		0.409
(0.547) 		0.683
(0.826) 		0.0893
(0.171)
16p loss 10 (2%) 518 0.2
(0.317) 		0.878
(1.00) 		0.13
(0.225) 		0.0255
(0.0647) 		0.293
(0.42) 		0.0631
(0.135) 		0.0888
(0.171) 		0.114
(0.206) 		0.116
(0.208) 		0.114
(0.205)
19q loss 4 (1%) 524 0.0118
(0.0343) 		0.919
(1.00) 		0.169
(0.277) 		0.434
(0.57) 		0.512
(0.651) 		0.831
(0.965) 		0.0848
(0.166)
20q loss 3 (1%) 525 0.164
(0.272) 		0.106
(0.195) 		0.154
(0.257) 		0.0588
(0.127) 		0.0301
(0.0735)
6p gain 11 (2%) 517 0.152
(0.256) 		0.444
(0.581) 		0.0739
(0.149) 		0.434
(0.57) 		0.794
(0.934) 		0.984
(1.00) 		0.859
(0.991) 		0.113
(0.204) 		0.604
(0.749) 		0.78
(0.92)
7p loss 3 (1%) 525 0.165
(0.273) 		0.106
(0.195) 		0.169
(0.277) 		0.0591
(0.127) 		0.358
(0.491)
12p loss 4 (1%) 524 0.0871
(0.169) 		0.205
(0.321) 		0.471
(0.605) 		0.293
(0.42) 		0.143
(0.245)
12q loss 4 (1%) 524 0.486
(0.621) 		0.378
(0.515) 		0.26
(0.383) 		1
(1.00) 		1
(1.00) 		0.234
(0.35) 		0.613
(0.758)
'1p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S1.  Gene #1: '1p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
1P GAIN MUTATED 2 1 21
1P GAIN WILD-TYPE 236 134 134

Figure S1.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #3: 'CN_CNMF'

'1p gain' versus 'METHLYATION_CNMF'

P value = 0.00074 (Fisher's exact test), Q value = 0.0031

Table S2.  Gene #1: '1p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
1P GAIN MUTATED 0 7 4
1P GAIN WILD-TYPE 128 69 106

Figure S2.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1p gain' versus 'RPPA_CNMF'

P value = 0.00105 (Fisher's exact test), Q value = 0.0042

Table S3.  Gene #1: '1p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
1P GAIN MUTATED 0 7 7 3 4 0
1P GAIN WILD-TYPE 108 55 68 77 75 43

Figure S3.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'1p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0255 (Fisher's exact test), Q value = 0.065

Table S4.  Gene #1: '1p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
1P GAIN MUTATED 6 4 11
1P GAIN WILD-TYPE 115 192 119

Figure S4.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'1p gain' versus 'MRNASEQ_CNMF'

P value = 0.00086 (Fisher's exact test), Q value = 0.0035

Table S5.  Gene #1: '1p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
1P GAIN MUTATED 1 5 17
1P GAIN WILD-TYPE 110 216 176

Figure S5.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00146 (Fisher's exact test), Q value = 0.0056

Table S6.  Gene #1: '1p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
1P GAIN MUTATED 1 1 4 13 4 0
1P GAIN WILD-TYPE 116 32 179 119 31 25

Figure S6.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p gain' versus 'MIRSEQ_CNMF'

P value = 0.00211 (Fisher's exact test), Q value = 0.0077

Table S7.  Gene #1: '1p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
1P GAIN MUTATED 2 5 17
1P GAIN WILD-TYPE 122 199 165

Figure S7.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00608 (Fisher's exact test), Q value = 0.019

Table S8.  Gene #1: '1p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
1P GAIN MUTATED 7 9 3 5
1P GAIN WILD-TYPE 137 125 192 32

Figure S8.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0391 (Fisher's exact test), Q value = 0.091

Table S9.  Gene #1: '1p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 56 47
1P GAIN MUTATED 0 4 0
1P GAIN WILD-TYPE 39 52 47

Figure S9.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S10.  Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
1Q GAIN MUTATED 6 2 43
1Q GAIN WILD-TYPE 232 133 112

Figure S10.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

'1q gain' versus 'METHLYATION_CNMF'

P value = 0.0142 (Fisher's exact test), Q value = 0.04

Table S11.  Gene #2: '1q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
1Q GAIN MUTATED 4 10 11
1Q GAIN WILD-TYPE 124 66 99

Figure S11.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1q gain' versus 'RPPA_CNMF'

P value = 0.0279 (Fisher's exact test), Q value = 0.069

Table S12.  Gene #2: '1q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
1Q GAIN MUTATED 7 12 12 6 5 2
1Q GAIN WILD-TYPE 101 50 63 74 74 41

Figure S12.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'1q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.016 (Fisher's exact test), Q value = 0.044

Table S13.  Gene #2: '1q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
1Q GAIN MUTATED 18 11 15
1Q GAIN WILD-TYPE 103 185 115

Figure S13.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'1q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S14.  Gene #2: '1q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
1Q GAIN MUTATED 1 15 33
1Q GAIN WILD-TYPE 110 206 160

Figure S14.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00173 (Fisher's exact test), Q value = 0.0065

Table S15.  Gene #2: '1q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
1Q GAIN MUTATED 4 2 15 22 6 0
1Q GAIN WILD-TYPE 113 31 168 110 29 25

Figure S15.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S16.  Gene #2: '1q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
1Q GAIN MUTATED 3 13 33
1Q GAIN WILD-TYPE 121 191 149

Figure S16.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00545 (Fisher's exact test), Q value = 0.018

Table S17.  Gene #2: '1q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
1Q GAIN MUTATED 11 17 12 9
1Q GAIN WILD-TYPE 133 117 183 28

Figure S17.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S18.  Gene #3: '2p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
2P GAIN MUTATED 15 14 48
2P GAIN WILD-TYPE 223 121 107

Figure S18.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #3: 'CN_CNMF'

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.012 (Fisher's exact test), Q value = 0.035

Table S19.  Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
2P GAIN MUTATED 13 2 29 29 3 0
2P GAIN WILD-TYPE 104 31 154 103 32 25

Figure S19.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S20.  Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
2Q GAIN MUTATED 18 14 47
2Q GAIN WILD-TYPE 220 121 108

Figure S20.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

'2q gain' versus 'RPPA_CNMF'

P value = 0.0432 (Fisher's exact test), Q value = 0.098

Table S21.  Gene #4: '2q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
2Q GAIN MUTATED 11 9 13 19 7 10
2Q GAIN WILD-TYPE 97 53 62 61 72 33

Figure S21.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'2q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0179 (Fisher's exact test), Q value = 0.048

Table S22.  Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
2Q GAIN MUTATED 13 2 32 28 4 0
2Q GAIN WILD-TYPE 104 31 151 104 31 25

Figure S22.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0254 (Fisher's exact test), Q value = 0.065

Table S23.  Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
2Q GAIN MUTATED 25 11 38 4
2Q GAIN WILD-TYPE 119 123 157 33

Figure S23.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3p gain' versus 'CN_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.0016

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
3P GAIN MUTATED 1 9 9
3P GAIN WILD-TYPE 237 126 146

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

'3p gain' versus 'RPPA_CNMF'

P value = 0.0239 (Fisher's exact test), Q value = 0.062

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
3P GAIN MUTATED 1 5 4 6 1 0
3P GAIN WILD-TYPE 107 57 71 74 78 43

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

'3p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00205 (Fisher's exact test), Q value = 0.0076

Table S26.  Gene #5: '3p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
3P GAIN MUTATED 4 2 11
3P GAIN WILD-TYPE 117 194 119

Figure S26.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'3p gain' versus 'MRNASEQ_CNMF'

P value = 0.00914 (Fisher's exact test), Q value = 0.028

Table S27.  Gene #5: '3p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
3P GAIN MUTATED 6 2 11
3P GAIN WILD-TYPE 105 219 182

Figure S27.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.00089

Table S28.  Gene #5: '3p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
3P GAIN MUTATED 0 2 2 9 2 4
3P GAIN WILD-TYPE 117 31 181 123 33 21

Figure S28.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3p gain' versus 'MIRSEQ_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.00079

Table S29.  Gene #5: '3p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
3P GAIN MUTATED 3 1 15
3P GAIN WILD-TYPE 121 203 167

Figure S29.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3q gain' versus 'MRNA_CNMF'

P value = 0.012 (Fisher's exact test), Q value = 0.035

Table S30.  Gene #6: '3q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 24 13
3Q GAIN MUTATED 1 7 2
3Q GAIN WILD-TYPE 32 17 11

Figure S30.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'3q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0315 (Fisher's exact test), Q value = 0.076

Table S31.  Gene #6: '3q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 4 11 13 9 10
3Q GAIN MUTATED 0 2 0 5 0 1 2
3Q GAIN WILD-TYPE 11 10 4 6 13 8 8

Figure S31.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'3q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
3Q GAIN MUTATED 7 15 39
3Q GAIN WILD-TYPE 231 120 116

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

'3q gain' versus 'METHLYATION_CNMF'

P value = 0.00382 (Fisher's exact test), Q value = 0.013

Table S33.  Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
3Q GAIN MUTATED 6 8 20
3Q GAIN WILD-TYPE 122 68 90

Figure S33.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3q gain' versus 'RPPA_CNMF'

P value = 0.00073 (Fisher's exact test), Q value = 0.0031

Table S34.  Gene #6: '3q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
3Q GAIN MUTATED 6 15 8 17 7 2
3Q GAIN WILD-TYPE 102 47 67 63 72 41

Figure S34.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'3q gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S35.  Gene #6: '3q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
3Q GAIN MUTATED 7 12 36
3Q GAIN WILD-TYPE 114 184 94

Figure S35.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'3q gain' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00024

Table S36.  Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
3Q GAIN MUTATED 12 11 38
3Q GAIN WILD-TYPE 99 210 155

Figure S36.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S37.  Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
3Q GAIN MUTATED 8 4 8 30 7 4
3Q GAIN WILD-TYPE 109 29 175 102 28 21

Figure S37.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S38.  Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
3Q GAIN MUTATED 8 10 42
3Q GAIN WILD-TYPE 116 194 140

Figure S38.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00046 (Fisher's exact test), Q value = 0.002

Table S39.  Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
3Q GAIN MUTATED 23 23 9 5
3Q GAIN WILD-TYPE 121 111 186 32

Figure S39.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00158 (Fisher's exact test), Q value = 0.006

Table S40.  Gene #6: '3q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 21 48 35
3Q GAIN MUTATED 3 0 2 10
3Q GAIN WILD-TYPE 35 21 46 25

Figure S40.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4p gain' versus 'RPPA_CHIERARCHICAL'

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

Table S41.  Gene #7: '4p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
4P GAIN MUTATED 1 1 7
4P GAIN WILD-TYPE 120 195 123

Figure S41.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'4p gain' versus 'MRNASEQ_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.0014

Table S42.  Gene #7: '4p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
4P GAIN MUTATED 7 0 5
4P GAIN WILD-TYPE 104 221 188

Figure S42.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00056 (Fisher's exact test), Q value = 0.0024

Table S43.  Gene #7: '4p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
4P GAIN MUTATED 3 0 0 5 0 4
4P GAIN WILD-TYPE 114 33 183 127 35 21

Figure S43.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p gain' versus 'MIRSEQ_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.0016

Table S44.  Gene #7: '4p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
4P GAIN MUTATED 2 0 11
4P GAIN WILD-TYPE 122 204 171

Figure S44.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0435 (Fisher's exact test), Q value = 0.099

Table S45.  Gene #7: '4p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
4P GAIN MUTATED 4 7 1 1
4P GAIN WILD-TYPE 140 127 194 36

Figure S45.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4q gain' versus 'MRNASEQ_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.0018

Table S46.  Gene #8: '4q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
4Q GAIN MUTATED 7 0 5
4Q GAIN WILD-TYPE 104 221 188

Figure S46.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00434 (Fisher's exact test), Q value = 0.015

Table S47.  Gene #8: '4q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
4Q GAIN MUTATED 3 0 1 4 0 4
4Q GAIN WILD-TYPE 114 33 182 128 35 21

Figure S47.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q gain' versus 'MIRSEQ_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.0015

Table S48.  Gene #8: '4q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
4Q GAIN MUTATED 2 0 11
4Q GAIN WILD-TYPE 122 204 171

Figure S48.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.043 (Fisher's exact test), Q value = 0.098

Table S49.  Gene #8: '4q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
4Q GAIN MUTATED 4 7 1 1
4Q GAIN WILD-TYPE 140 127 194 36

Figure S49.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5p gain' versus 'CN_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.0015

Table S50.  Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
5P GAIN MUTATED 73 43 77
5P GAIN WILD-TYPE 165 92 78

Figure S50.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

'5p gain' versus 'MRNASEQ_CNMF'

P value = 0.00889 (Fisher's exact test), Q value = 0.027

Table S51.  Gene #9: '5p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
5P GAIN MUTATED 29 78 84
5P GAIN WILD-TYPE 82 143 109

Figure S51.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0226 (Fisher's exact test), Q value = 0.059

Table S52.  Gene #9: '5p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
5P GAIN MUTATED 44 8 60 60 15 4
5P GAIN WILD-TYPE 73 25 123 72 20 21

Figure S52.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q gain' versus 'CN_CNMF'

P value = 0.022 (Fisher's exact test), Q value = 0.058

Table S53.  Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
5Q GAIN MUTATED 85 47 75
5Q GAIN WILD-TYPE 153 88 80

Figure S53.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'

'6q gain' versus 'RPPA_CNMF'

P value = 0.0196 (Fisher's exact test), Q value = 0.052

Table S54.  Gene #12: '6q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
6Q GAIN MUTATED 1 1 0 5 0 2
6Q GAIN WILD-TYPE 107 61 75 75 79 41

Figure S54.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S55.  Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
7P GAIN MUTATED 39 46 86
7P GAIN WILD-TYPE 199 89 69

Figure S55.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 0.00154 (Fisher's exact test), Q value = 0.0059

Table S56.  Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
7P GAIN MUTATED 26 16 44
7P GAIN WILD-TYPE 102 60 66

Figure S56.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p gain' versus 'RPPA_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.0015

Table S57.  Gene #13: '7p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
7P GAIN MUTATED 23 30 31 35 19 11
7P GAIN WILD-TYPE 85 32 44 45 60 32

Figure S57.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'7p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00541 (Fisher's exact test), Q value = 0.018

Table S58.  Gene #13: '7p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
7P GAIN MUTATED 40 52 57
7P GAIN WILD-TYPE 81 144 73

Figure S58.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00064

Table S59.  Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
7P GAIN MUTATED 31 53 85
7P GAIN WILD-TYPE 80 168 108

Figure S59.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00913 (Fisher's exact test), Q value = 0.028

Table S60.  Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
7P GAIN MUTATED 38 9 45 59 12 6
7P GAIN WILD-TYPE 79 24 138 73 23 19

Figure S60.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_CNMF'

P value = 0.0041 (Fisher's exact test), Q value = 0.014

Table S61.  Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
7P GAIN MUTATED 34 57 77
7P GAIN WILD-TYPE 90 147 105

Figure S61.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0295 (Fisher's exact test), Q value = 0.073

Table S62.  Gene #13: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
7P GAIN MUTATED 42 54 55 17
7P GAIN WILD-TYPE 102 80 140 20

Figure S62.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S63.  Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
7Q GAIN MUTATED 39 47 86
7Q GAIN WILD-TYPE 199 88 69

Figure S63.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 0.00381 (Fisher's exact test), Q value = 0.013

Table S64.  Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
7Q GAIN MUTATED 28 17 44
7Q GAIN WILD-TYPE 100 59 66

Figure S64.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7q gain' versus 'RPPA_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.0011

Table S65.  Gene #14: '7q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
7Q GAIN MUTATED 23 30 31 35 21 10
7Q GAIN WILD-TYPE 85 32 44 45 58 33

Figure S65.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'7q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00243 (Fisher's exact test), Q value = 0.0089

Table S66.  Gene #14: '7q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
7Q GAIN MUTATED 41 51 58
7Q GAIN WILD-TYPE 80 145 72

Figure S66.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00049

Table S67.  Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
7Q GAIN MUTATED 32 53 85
7Q GAIN WILD-TYPE 79 168 108

Figure S67.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00629 (Fisher's exact test), Q value = 0.02

Table S68.  Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
7Q GAIN MUTATED 37 11 44 59 13 6
7Q GAIN WILD-TYPE 80 22 139 73 22 19

Figure S68.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_CNMF'

P value = 0.00532 (Fisher's exact test), Q value = 0.018

Table S69.  Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
7Q GAIN MUTATED 34 58 77
7Q GAIN WILD-TYPE 90 146 105

Figure S69.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0183 (Fisher's exact test), Q value = 0.049

Table S70.  Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
7Q GAIN MUTATED 44 55 53 17
7Q GAIN WILD-TYPE 100 79 142 20

Figure S70.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S71.  Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
8P GAIN MUTATED 1 8 22
8P GAIN WILD-TYPE 237 127 133

Figure S71.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

'8p gain' versus 'METHLYATION_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.0016

Table S72.  Gene #15: '8p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
8P GAIN MUTATED 2 4 16
8P GAIN WILD-TYPE 126 72 94

Figure S72.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p gain' versus 'RPPA_CNMF'

P value = 0.0102 (Fisher's exact test), Q value = 0.031

Table S73.  Gene #15: '8p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
8P GAIN MUTATED 2 9 8 4 3 1
8P GAIN WILD-TYPE 106 53 67 76 76 42

Figure S73.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'8p gain' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00019

Table S74.  Gene #15: '8p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
8P GAIN MUTATED 4 3 24
8P GAIN WILD-TYPE 107 218 169

Figure S74.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00029

Table S75.  Gene #15: '8p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
8P GAIN MUTATED 6 2 1 19 2 1
8P GAIN WILD-TYPE 111 31 182 113 33 24

Figure S75.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S76.  Gene #15: '8p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
8P GAIN MUTATED 3 3 25
8P GAIN WILD-TYPE 121 201 157

Figure S76.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00511 (Fisher's exact test), Q value = 0.017

Table S77.  Gene #15: '8p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
8P GAIN MUTATED 10 12 4 5
8P GAIN WILD-TYPE 134 122 191 32

Figure S77.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0117 (Fisher's exact test), Q value = 0.034

Table S78.  Gene #15: '8p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 21 48 35
8P GAIN MUTATED 1 0 0 5
8P GAIN WILD-TYPE 37 21 48 30

Figure S78.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S79.  Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
8Q GAIN MUTATED 3 13 46
8Q GAIN WILD-TYPE 235 122 109

Figure S79.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S80.  Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
8Q GAIN MUTATED 3 11 26
8Q GAIN WILD-TYPE 125 65 84

Figure S80.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8q gain' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S81.  Gene #16: '8q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
8Q GAIN MUTATED 3 18 14 11 7 2
8Q GAIN WILD-TYPE 105 44 61 69 72 41

Figure S81.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'8q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00037 (Fisher's exact test), Q value = 0.0017

Table S82.  Gene #16: '8q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
8Q GAIN MUTATED 14 13 28
8Q GAIN WILD-TYPE 107 183 102

Figure S82.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S83.  Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
8Q GAIN MUTATED 5 6 50
8Q GAIN WILD-TYPE 106 215 143

Figure S83.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S84.  Gene #16: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
8Q GAIN MUTATED 8 2 4 42 4 1
8Q GAIN WILD-TYPE 109 31 179 90 31 24

Figure S84.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S85.  Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
8Q GAIN MUTATED 8 7 45
8Q GAIN WILD-TYPE 116 197 137

Figure S85.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.00059

Table S86.  Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
8Q GAIN MUTATED 20 22 9 9
8Q GAIN WILD-TYPE 124 112 186 28

Figure S86.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.0015

Table S87.  Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 21 48 35
8Q GAIN MUTATED 3 0 1 10
8Q GAIN WILD-TYPE 35 21 47 25

Figure S87.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9p gain' versus 'CN_CNMF'

P value = 0.015 (Fisher's exact test), Q value = 0.042

Table S88.  Gene #17: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
9P GAIN MUTATED 4 8 1
9P GAIN WILD-TYPE 234 127 154

Figure S88.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'

'9p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0177 (Fisher's exact test), Q value = 0.048

Table S89.  Gene #17: '9p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
9P GAIN MUTATED 0 0 7 2 1 3
9P GAIN WILD-TYPE 117 33 176 130 34 22

Figure S89.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q gain' versus 'CN_CNMF'

P value = 0.00125 (Fisher's exact test), Q value = 0.0049

Table S90.  Gene #18: '9q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
9Q GAIN MUTATED 2 9 1
9Q GAIN WILD-TYPE 236 126 154

Figure S90.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #3: 'CN_CNMF'

'9q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0272 (Fisher's exact test), Q value = 0.068

Table S91.  Gene #18: '9q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
9Q GAIN MUTATED 0 0 4 4 1 3
9Q GAIN WILD-TYPE 117 33 179 128 34 22

Figure S91.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p gain' versus 'CN_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.0012

Table S92.  Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
10P GAIN MUTATED 1 4 12
10P GAIN WILD-TYPE 237 131 143

Figure S92.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

'10p gain' versus 'MRNASEQ_CNMF'

P value = 0.00105 (Fisher's exact test), Q value = 0.0042

Table S93.  Gene #19: '10p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
10P GAIN MUTATED 3 1 13
10P GAIN WILD-TYPE 108 220 180

Figure S93.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.0011

Table S94.  Gene #19: '10p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
10P GAIN MUTATED 2 1 0 12 2 0
10P GAIN WILD-TYPE 115 32 183 120 33 25

Figure S94.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p gain' versus 'MIRSEQ_CNMF'

P value = 0.0193 (Fisher's exact test), Q value = 0.052

Table S95.  Gene #19: '10p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
10P GAIN MUTATED 4 2 11
10P GAIN WILD-TYPE 120 202 171

Figure S95.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10q gain' versus 'CN_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.00096

Table S96.  Gene #20: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
10Q GAIN MUTATED 0 3 9
10Q GAIN WILD-TYPE 238 132 146

Figure S96.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

'10q gain' versus 'MRNASEQ_CNMF'

P value = 0.0139 (Fisher's exact test), Q value = 0.039

Table S97.  Gene #20: '10q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
10Q GAIN MUTATED 2 1 9
10Q GAIN WILD-TYPE 109 220 184

Figure S97.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00176 (Fisher's exact test), Q value = 0.0066

Table S98.  Gene #20: '10q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
10Q GAIN MUTATED 1 1 0 9 1 0
10Q GAIN WILD-TYPE 116 32 183 123 34 25

Figure S98.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q gain' versus 'MIRSEQ_CNMF'

P value = 0.0152 (Fisher's exact test), Q value = 0.043

Table S99.  Gene #20: '10q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
10Q GAIN MUTATED 2 1 9
10Q GAIN WILD-TYPE 122 203 173

Figure S99.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S100.  Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
11P GAIN MUTATED 2 12 17
11P GAIN WILD-TYPE 236 123 138

Figure S100.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

'11q gain' versus 'CN_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.00093

Table S101.  Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
11Q GAIN MUTATED 3 12 14
11Q GAIN WILD-TYPE 235 123 141

Figure S101.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'MRNA_CNMF'

P value = 0.0133 (Fisher's exact test), Q value = 0.038

Table S102.  Gene #23: '12p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 24 13
12P GAIN MUTATED 3 10 2
12P GAIN WILD-TYPE 30 14 11

Figure S102.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'12p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0322 (Fisher's exact test), Q value = 0.078

Table S103.  Gene #23: '12p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 4 11 13 9 10
12P GAIN MUTATED 0 4 0 6 1 2 2
12P GAIN WILD-TYPE 11 8 4 5 12 7 8

Figure S103.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'12p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S104.  Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
12P GAIN MUTATED 22 34 65
12P GAIN WILD-TYPE 216 101 90

Figure S104.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00013

Table S105.  Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
12P GAIN MUTATED 16 18 42
12P GAIN WILD-TYPE 112 58 68

Figure S105.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p gain' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S106.  Gene #23: '12p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
12P GAIN MUTATED 7 31 28 17 15 6
12P GAIN WILD-TYPE 101 31 47 63 64 37

Figure S106.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'12p gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S107.  Gene #23: '12p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
12P GAIN MUTATED 26 27 51
12P GAIN WILD-TYPE 95 169 79

Figure S107.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S108.  Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
12P GAIN MUTATED 18 24 78
12P GAIN WILD-TYPE 93 197 115

Figure S108.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S109.  Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
12P GAIN MUTATED 22 5 19 58 11 5
12P GAIN WILD-TYPE 95 28 164 74 24 20

Figure S109.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S110.  Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
12P GAIN MUTATED 20 24 75
12P GAIN WILD-TYPE 104 180 107

Figure S110.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S111.  Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
12P GAIN MUTATED 33 46 24 16
12P GAIN WILD-TYPE 111 88 171 21

Figure S111.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00164 (Fisher's exact test), Q value = 0.0062

Table S112.  Gene #23: '12p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 21 48 35
12P GAIN MUTATED 4 4 5 15
12P GAIN WILD-TYPE 34 17 43 20

Figure S112.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12q gain' versus 'MRNA_CNMF'

P value = 0.0132 (Fisher's exact test), Q value = 0.038

Table S113.  Gene #24: '12q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 24 13
12Q GAIN MUTATED 3 10 2
12Q GAIN WILD-TYPE 30 14 11

Figure S113.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'12q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0333 (Fisher's exact test), Q value = 0.08

Table S114.  Gene #24: '12q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 4 11 13 9 10
12Q GAIN MUTATED 0 4 0 6 1 2 2
12Q GAIN WILD-TYPE 11 8 4 5 12 7 8

Figure S114.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'12q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S115.  Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
12Q GAIN MUTATED 22 34 66
12Q GAIN WILD-TYPE 216 101 89

Figure S115.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

'12q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S116.  Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
12Q GAIN MUTATED 16 18 42
12Q GAIN WILD-TYPE 112 58 68

Figure S116.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12q gain' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S117.  Gene #24: '12q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
12Q GAIN MUTATED 7 33 28 17 14 6
12Q GAIN WILD-TYPE 101 29 47 63 65 37

Figure S117.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'12q gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S118.  Gene #24: '12q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
12Q GAIN MUTATED 26 26 53
12Q GAIN WILD-TYPE 95 170 77

Figure S118.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'12q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S119.  Gene #24: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
12Q GAIN MUTATED 19 24 78
12Q GAIN WILD-TYPE 92 197 115

Figure S119.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S120.  Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
12Q GAIN MUTATED 22 5 19 59 11 5
12Q GAIN WILD-TYPE 95 28 164 73 24 20

Figure S120.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S121.  Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
12Q GAIN MUTATED 19 24 77
12Q GAIN WILD-TYPE 105 180 105

Figure S121.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S122.  Gene #24: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
12Q GAIN MUTATED 32 48 24 16
12Q GAIN WILD-TYPE 112 86 171 21

Figure S122.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00312 (Fisher's exact test), Q value = 0.011

Table S123.  Gene #24: '12q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 21 48 35
12Q GAIN MUTATED 5 4 5 15
12Q GAIN WILD-TYPE 33 17 43 20

Figure S123.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'13q gain' versus 'METHLYATION_CNMF'

P value = 0.034 (Fisher's exact test), Q value = 0.081

Table S124.  Gene #25: '13q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
13Q GAIN MUTATED 6 1 11
13Q GAIN WILD-TYPE 122 75 99

Figure S124.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q gain' versus 'CN_CNMF'

P value = 0.00123 (Fisher's exact test), Q value = 0.0048

Table S125.  Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
14Q GAIN MUTATED 1 8 7
14Q GAIN WILD-TYPE 237 127 148

Figure S125.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

'14q gain' versus 'RPPA_CNMF'

P value = 0.00593 (Fisher's exact test), Q value = 0.019

Table S126.  Gene #26: '14q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
14Q GAIN MUTATED 0 3 1 7 2 0
14Q GAIN WILD-TYPE 108 59 74 73 77 43

Figure S126.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'14q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0407 (Fisher's exact test), Q value = 0.094

Table S127.  Gene #26: '14q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
14Q GAIN MUTATED 1 4 8
14Q GAIN WILD-TYPE 120 192 122

Figure S127.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'14q gain' versus 'MRNASEQ_CNMF'

P value = 0.00689 (Fisher's exact test), Q value = 0.022

Table S128.  Gene #26: '14q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
14Q GAIN MUTATED 8 2 6
14Q GAIN WILD-TYPE 103 219 187

Figure S128.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.0014

Table S129.  Gene #26: '14q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
14Q GAIN MUTATED 3 0 1 7 0 5
14Q GAIN WILD-TYPE 114 33 182 125 35 20

Figure S129.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_CNMF'

P value = 0.00378 (Fisher's exact test), Q value = 0.013

Table S130.  Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
14Q GAIN MUTATED 3 1 11
14Q GAIN WILD-TYPE 121 203 171

Figure S130.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'15q gain' versus 'CN_CNMF'

P value = 0.00078 (Fisher's exact test), Q value = 0.0032

Table S131.  Gene #27: '15q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
15Q GAIN MUTATED 3 11 12
15Q GAIN WILD-TYPE 235 124 143

Figure S131.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #3: 'CN_CNMF'

'16p gain' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00034

Table S132.  Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
16P GAIN MUTATED 30 29 48
16P GAIN WILD-TYPE 208 106 107

Figure S132.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

'16p gain' versus 'RPPA_CNMF'

P value = 0.0377 (Fisher's exact test), Q value = 0.088

Table S133.  Gene #28: '16p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
16P GAIN MUTATED 17 12 23 22 12 5
16P GAIN WILD-TYPE 91 50 52 58 67 38

Figure S133.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 0.00735 (Fisher's exact test), Q value = 0.023

Table S134.  Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
16P GAIN MUTATED 23 32 52
16P GAIN WILD-TYPE 88 189 141

Figure S134.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00419 (Fisher's exact test), Q value = 0.014

Table S135.  Gene #28: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
16P GAIN MUTATED 26 13 23 34 6 5
16P GAIN WILD-TYPE 91 20 160 98 29 20

Figure S135.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0251 (Fisher's exact test), Q value = 0.064

Table S136.  Gene #28: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
16P GAIN MUTATED 26 40 32 8
16P GAIN WILD-TYPE 118 94 163 29

Figure S136.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16q gain' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00024

Table S137.  Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
16Q GAIN MUTATED 26 29 44
16Q GAIN WILD-TYPE 212 106 111

Figure S137.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

'16q gain' versus 'MRNASEQ_CNMF'

P value = 0.00641 (Fisher's exact test), Q value = 0.02

Table S138.  Gene #29: '16q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
16Q GAIN MUTATED 21 29 49
16Q GAIN WILD-TYPE 90 192 144

Figure S138.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0167 (Fisher's exact test), Q value = 0.046

Table S139.  Gene #29: '16q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
16Q GAIN MUTATED 23 11 22 33 6 4
16Q GAIN WILD-TYPE 94 22 161 99 29 21

Figure S139.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_CNMF'

P value = 0.0159 (Fisher's exact test), Q value = 0.044

Table S140.  Gene #29: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
16Q GAIN MUTATED 24 28 46
16Q GAIN WILD-TYPE 100 176 136

Figure S140.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17p gain' versus 'MRNA_CNMF'

P value = 0.0176 (Fisher's exact test), Q value = 0.048

Table S141.  Gene #30: '17p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 24 13
17P GAIN MUTATED 1 0 3
17P GAIN WILD-TYPE 32 24 10

Figure S141.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'17p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00554 (Fisher's exact test), Q value = 0.018

Table S142.  Gene #30: '17p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 4 11 13 9 10
17P GAIN MUTATED 0 0 2 0 0 1 1
17P GAIN WILD-TYPE 11 12 2 11 13 8 9

Figure S142.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S143.  Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
17P GAIN MUTATED 1 10 15
17P GAIN WILD-TYPE 237 125 140

Figure S143.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

'17p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00484 (Fisher's exact test), Q value = 0.016

Table S144.  Gene #30: '17p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
17P GAIN MUTATED 2 6 5 10 2 1
17P GAIN WILD-TYPE 115 27 178 122 33 24

Figure S144.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0365 (Fisher's exact test), Q value = 0.086

Table S145.  Gene #30: '17p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 21 48 35
17P GAIN MUTATED 1 0 0 4
17P GAIN WILD-TYPE 37 21 48 31

Figure S145.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'17q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0254 (Fisher's exact test), Q value = 0.065

Table S146.  Gene #31: '17q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 4 11 13 9 10
17Q GAIN MUTATED 0 0 2 1 0 1 1
17Q GAIN WILD-TYPE 11 12 2 10 13 8 9

Figure S146.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S147.  Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
17Q GAIN MUTATED 3 11 19
17Q GAIN WILD-TYPE 235 124 136

Figure S147.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00153 (Fisher's exact test), Q value = 0.0058

Table S148.  Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
17Q GAIN MUTATED 3 7 6 13 3 1
17Q GAIN WILD-TYPE 114 26 177 119 32 24

Figure S148.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00208 (Fisher's exact test), Q value = 0.0077

Table S149.  Gene #31: '17q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 21 48 35
17Q GAIN MUTATED 1 0 0 6
17Q GAIN WILD-TYPE 37 21 48 29

Figure S149.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0428 (Fisher's exact test), Q value = 0.098

Table S150.  Gene #32: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 56 47
18P GAIN MUTATED 1 1 6
18P GAIN WILD-TYPE 38 55 41

Figure S150.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0444 (Fisher's exact test), Q value = 0.1

Table S151.  Gene #33: '18q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 56 47
18Q GAIN MUTATED 1 1 6
18Q GAIN WILD-TYPE 38 55 41

Figure S151.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S152.  Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
19P GAIN MUTATED 4 19 28
19P GAIN WILD-TYPE 234 116 127

Figure S152.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

'19p gain' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00029

Table S153.  Gene #34: '19p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
19P GAIN MUTATED 7 3 24
19P GAIN WILD-TYPE 121 73 86

Figure S153.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p gain' versus 'RPPA_CNMF'

P value = 0.00383 (Fisher's exact test), Q value = 0.013

Table S154.  Gene #34: '19p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
19P GAIN MUTATED 6 8 14 13 4 1
19P GAIN WILD-TYPE 102 54 61 67 75 42

Figure S154.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'19p gain' versus 'MRNASEQ_CNMF'

P value = 0.00145 (Fisher's exact test), Q value = 0.0056

Table S155.  Gene #34: '19p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
19P GAIN MUTATED 14 10 27
19P GAIN WILD-TYPE 97 211 166

Figure S155.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00078 (Fisher's exact test), Q value = 0.0032

Table S156.  Gene #34: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
19P GAIN MUTATED 10 2 8 24 2 5
19P GAIN WILD-TYPE 107 31 175 108 33 20

Figure S156.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00029

Table S157.  Gene #34: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
19P GAIN MUTATED 10 8 32
19P GAIN WILD-TYPE 114 196 150

Figure S157.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S158.  Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
19Q GAIN MUTATED 4 19 34
19Q GAIN WILD-TYPE 234 116 121

Figure S158.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

'19q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S159.  Gene #35: '19q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
19Q GAIN MUTATED 7 3 27
19Q GAIN WILD-TYPE 121 73 83

Figure S159.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q gain' versus 'RPPA_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.0011

Table S160.  Gene #35: '19q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
19Q GAIN MUTATED 6 13 15 13 4 1
19Q GAIN WILD-TYPE 102 49 60 67 75 42

Figure S160.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'19q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0132 (Fisher's exact test), Q value = 0.038

Table S161.  Gene #35: '19q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
19Q GAIN MUTATED 13 15 24
19Q GAIN WILD-TYPE 108 181 106

Figure S161.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 0.00066 (Fisher's exact test), Q value = 0.0028

Table S162.  Gene #35: '19q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
19Q GAIN MUTATED 14 11 31
19Q GAIN WILD-TYPE 97 210 162

Figure S162.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00049

Table S163.  Gene #35: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
19Q GAIN MUTATED 11 2 8 28 2 5
19Q GAIN WILD-TYPE 106 31 175 104 33 20

Figure S163.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00024

Table S164.  Gene #35: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
19Q GAIN MUTATED 10 9 36
19Q GAIN WILD-TYPE 114 195 146

Figure S164.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S165.  Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
20P GAIN MUTATED 10 39 63
20P GAIN WILD-TYPE 228 96 92

Figure S165.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00034

Table S166.  Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
20P GAIN MUTATED 12 16 37
20P GAIN WILD-TYPE 116 60 73

Figure S166.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p gain' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S167.  Gene #36: '20p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
20P GAIN MUTATED 7 30 17 20 18 6
20P GAIN WILD-TYPE 101 32 58 60 61 37

Figure S167.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'20p gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S168.  Gene #36: '20p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
20P GAIN MUTATED 19 28 51
20P GAIN WILD-TYPE 102 168 79

Figure S168.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S169.  Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
20P GAIN MUTATED 18 18 76
20P GAIN WILD-TYPE 93 203 117

Figure S169.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S170.  Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
20P GAIN MUTATED 20 4 13 66 3 6
20P GAIN WILD-TYPE 97 29 170 66 32 19

Figure S170.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S171.  Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
20P GAIN MUTATED 25 18 68
20P GAIN WILD-TYPE 99 186 114

Figure S171.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S172.  Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
20P GAIN MUTATED 36 33 22 20
20P GAIN WILD-TYPE 108 101 173 17

Figure S172.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S173.  Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 21 48 35
20P GAIN MUTATED 6 3 3 18
20P GAIN WILD-TYPE 32 18 45 17

Figure S173.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'MRNA_CNMF'

P value = 0.0409 (Fisher's exact test), Q value = 0.094

Table S174.  Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 24 13
20Q GAIN MUTATED 3 8 4
20Q GAIN WILD-TYPE 30 16 9

Figure S174.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S175.  Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
20Q GAIN MUTATED 10 38 67
20Q GAIN WILD-TYPE 228 97 88

Figure S175.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00019

Table S176.  Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
20Q GAIN MUTATED 12 16 37
20Q GAIN WILD-TYPE 116 60 73

Figure S176.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q gain' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S177.  Gene #37: '20q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
20Q GAIN MUTATED 7 32 19 20 17 6
20Q GAIN WILD-TYPE 101 30 56 60 62 37

Figure S177.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'20q gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S178.  Gene #37: '20q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
20Q GAIN MUTATED 20 28 53
20Q GAIN WILD-TYPE 101 168 77

Figure S178.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S179.  Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
20Q GAIN MUTATED 17 18 80
20Q GAIN WILD-TYPE 94 203 113

Figure S179.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S180.  Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
20Q GAIN MUTATED 20 4 13 69 3 6
20Q GAIN WILD-TYPE 97 29 170 63 32 19

Figure S180.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S181.  Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
20Q GAIN MUTATED 25 18 71
20Q GAIN WILD-TYPE 99 186 111

Figure S181.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S182.  Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
20Q GAIN MUTATED 38 34 22 20
20Q GAIN WILD-TYPE 106 100 173 17

Figure S182.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S183.  Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 21 48 35
20Q GAIN MUTATED 6 3 3 19
20Q GAIN WILD-TYPE 32 18 45 16

Figure S183.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0323 (Fisher's exact test), Q value = 0.078

Table S184.  Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 56 47
20Q GAIN MUTATED 8 18 5
20Q GAIN WILD-TYPE 31 38 42

Figure S184.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S185.  Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
21Q GAIN MUTATED 12 7 31
21Q GAIN WILD-TYPE 226 128 124

Figure S185.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

'21q gain' versus 'METHLYATION_CNMF'

P value = 0.00121 (Fisher's exact test), Q value = 0.0048

Table S186.  Gene #38: '21q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
21Q GAIN MUTATED 6 4 20
21Q GAIN WILD-TYPE 122 72 90

Figure S186.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'21q gain' versus 'RPPA_CNMF'

P value = 0.00184 (Fisher's exact test), Q value = 0.0068

Table S187.  Gene #38: '21q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
21Q GAIN MUTATED 3 12 12 6 5 6
21Q GAIN WILD-TYPE 105 50 63 74 74 37

Figure S187.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'21q gain' versus 'MRNASEQ_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.0014

Table S188.  Gene #38: '21q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
21Q GAIN MUTATED 7 11 32
21Q GAIN WILD-TYPE 104 210 161

Figure S188.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00262 (Fisher's exact test), Q value = 0.0095

Table S189.  Gene #38: '21q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
21Q GAIN MUTATED 10 2 9 25 3 1
21Q GAIN WILD-TYPE 107 31 174 107 32 24

Figure S189.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'21q gain' versus 'MIRSEQ_CNMF'

P value = 0.00294 (Fisher's exact test), Q value = 0.011

Table S190.  Gene #38: '21q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
21Q GAIN MUTATED 9 12 29
21Q GAIN WILD-TYPE 115 192 153

Figure S190.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'21q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0324 (Fisher's exact test), Q value = 0.078

Table S191.  Gene #38: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
21Q GAIN MUTATED 11 17 14 8
21Q GAIN WILD-TYPE 133 117 181 29

Figure S191.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q gain' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00019

Table S192.  Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
22Q GAIN MUTATED 5 13 22
22Q GAIN WILD-TYPE 233 122 133

Figure S192.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

'22q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0164 (Fisher's exact test), Q value = 0.045

Table S193.  Gene #39: '22q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
22Q GAIN MUTATED 5 1 10 17 2 5
22Q GAIN WILD-TYPE 112 32 173 115 33 20

Figure S193.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xp gain' versus 'CN_CNMF'

P value = 0.00582 (Fisher's exact test), Q value = 0.019

Table S194.  Gene #40: 'xp gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
XP GAIN MUTATED 7 8 17
XP GAIN WILD-TYPE 231 127 138

Figure S194.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #3: 'CN_CNMF'

'xp gain' versus 'RPPA_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.0015

Table S195.  Gene #40: 'xp gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
XP GAIN MUTATED 0 5 5 11 4 0
XP GAIN WILD-TYPE 108 57 70 69 75 43

Figure S195.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'xp gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00068 (Fisher's exact test), Q value = 0.0029

Table S196.  Gene #40: 'xp gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
XP GAIN MUTATED 2 7 16
XP GAIN WILD-TYPE 119 189 114

Figure S196.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'xp gain' versus 'MRNASEQ_CNMF'

P value = 0.0154 (Fisher's exact test), Q value = 0.043

Table S197.  Gene #40: 'xp gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
XP GAIN MUTATED 9 6 17
XP GAIN WILD-TYPE 102 215 176

Figure S197.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'xp gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00096 (Fisher's exact test), Q value = 0.0039

Table S198.  Gene #40: 'xp gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
XP GAIN MUTATED 3 4 6 18 1 0
XP GAIN WILD-TYPE 114 29 177 114 34 25

Figure S198.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xq gain' versus 'RPPA_CNMF'

P value = 0.03 (Fisher's exact test), Q value = 0.074

Table S199.  Gene #41: 'xq gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
XQ GAIN MUTATED 2 5 5 9 3 0
XQ GAIN WILD-TYPE 106 57 70 71 76 43

Figure S199.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'xq gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00802 (Fisher's exact test), Q value = 0.025

Table S200.  Gene #41: 'xq gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
XQ GAIN MUTATED 3 7 14
XQ GAIN WILD-TYPE 118 189 116

Figure S200.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'1p loss' versus 'MRNA_CNMF'

P value = 0.00092 (Fisher's exact test), Q value = 0.0037

Table S201.  Gene #42: '1p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 24 13
1P LOSS MUTATED 2 3 7
1P LOSS WILD-TYPE 31 21 6

Figure S201.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'1p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00276 (Fisher's exact test), Q value = 0.01

Table S202.  Gene #42: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 4 11 13 9 10
1P LOSS MUTATED 0 1 2 1 1 1 6
1P LOSS WILD-TYPE 11 11 2 10 12 8 4

Figure S202.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S203.  Gene #42: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
1P LOSS MUTATED 5 27 25
1P LOSS WILD-TYPE 233 108 130

Figure S203.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'RPPA_CNMF'

P value = 0.00131 (Fisher's exact test), Q value = 0.0051

Table S204.  Gene #42: '1p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
1P LOSS MUTATED 9 5 8 19 2 5
1P LOSS WILD-TYPE 99 57 67 61 77 38

Figure S204.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00019

Table S205.  Gene #42: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
1P LOSS MUTATED 9 5 15 14 2 12
1P LOSS WILD-TYPE 108 28 168 118 33 13

Figure S205.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_CNMF'

P value = 0.00784 (Fisher's exact test), Q value = 0.024

Table S206.  Gene #42: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
1P LOSS MUTATED 8 18 31
1P LOSS WILD-TYPE 116 186 151

Figure S206.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0218 (Fisher's exact test), Q value = 0.058

Table S207.  Gene #42: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
1P LOSS MUTATED 11 25 18 3
1P LOSS WILD-TYPE 133 109 177 34

Figure S207.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0367 (Fisher's exact test), Q value = 0.087

Table S208.  Gene #42: '1p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 21 48 35
1P LOSS MUTATED 5 0 2 7
1P LOSS WILD-TYPE 33 21 46 28

Figure S208.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'1q loss' versus 'MRNA_CNMF'

P value = 0.0107 (Fisher's exact test), Q value = 0.031

Table S209.  Gene #43: '1q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 24 13
1Q LOSS MUTATED 2 1 5
1Q LOSS WILD-TYPE 31 23 8

Figure S209.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'1q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0114 (Fisher's exact test), Q value = 0.033

Table S210.  Gene #43: '1q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 4 11 13 9 10
1Q LOSS MUTATED 0 1 0 0 1 1 5
1Q LOSS WILD-TYPE 11 11 4 11 12 8 5

Figure S210.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'1q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S211.  Gene #43: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
1Q LOSS MUTATED 1 23 12
1Q LOSS WILD-TYPE 237 112 143

Figure S211.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

'1q loss' versus 'RPPA_CNMF'

P value = 0.0283 (Fisher's exact test), Q value = 0.07

Table S212.  Gene #43: '1q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
1Q LOSS MUTATED 6 5 4 12 1 3
1Q LOSS WILD-TYPE 102 57 71 68 78 40

Figure S212.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'1q loss' versus 'MRNASEQ_CNMF'

P value = 0.00416 (Fisher's exact test), Q value = 0.014

Table S213.  Gene #43: '1q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
1Q LOSS MUTATED 16 10 10
1Q LOSS WILD-TYPE 95 211 183

Figure S213.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S214.  Gene #43: '1q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
1Q LOSS MUTATED 5 1 7 10 2 11
1Q LOSS WILD-TYPE 112 32 176 122 33 14

Figure S214.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1q loss' versus 'MIRSEQ_CNMF'

P value = 0.00585 (Fisher's exact test), Q value = 0.019

Table S215.  Gene #43: '1q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
1Q LOSS MUTATED 5 9 22
1Q LOSS WILD-TYPE 119 195 160

Figure S215.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0418 (Fisher's exact test), Q value = 0.096

Table S216.  Gene #43: '1q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
1Q LOSS MUTATED 8 17 9 2
1Q LOSS WILD-TYPE 136 117 186 35

Figure S216.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2p loss' versus 'MRNA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00024

Table S217.  Gene #44: '2p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 24 13
2P LOSS MUTATED 0 1 6
2P LOSS WILD-TYPE 33 23 7

Figure S217.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'2p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00046 (Fisher's exact test), Q value = 0.002

Table S218.  Gene #44: '2p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 4 11 13 9 10
2P LOSS MUTATED 0 1 1 0 0 0 5
2P LOSS WILD-TYPE 11 11 3 11 13 9 5

Figure S218.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'2p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S219.  Gene #44: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
2P LOSS MUTATED 0 12 2
2P LOSS WILD-TYPE 238 123 153

Figure S219.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

'2p loss' versus 'RPPA_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.00096

Table S220.  Gene #44: '2p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
2P LOSS MUTATED 0 2 0 7 0 0
2P LOSS WILD-TYPE 108 60 75 73 79 43

Figure S220.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'2p loss' versus 'RPPA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00024

Table S221.  Gene #44: '2p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
2P LOSS MUTATED 0 0 9
2P LOSS WILD-TYPE 121 196 121

Figure S221.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'2p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S222.  Gene #44: '2p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
2P LOSS MUTATED 12 0 2
2P LOSS WILD-TYPE 99 221 191

Figure S222.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S223.  Gene #44: '2p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
2P LOSS MUTATED 0 2 1 2 0 9
2P LOSS WILD-TYPE 117 31 182 130 35 16

Figure S223.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00013

Table S224.  Gene #44: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
2P LOSS MUTATED 1 0 13
2P LOSS WILD-TYPE 123 204 169

Figure S224.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00029

Table S225.  Gene #44: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
2P LOSS MUTATED 1 12 1 0
2P LOSS WILD-TYPE 143 122 194 37

Figure S225.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2q loss' versus 'MRNA_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.0015

Table S226.  Gene #45: '2q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 24 13
2Q LOSS MUTATED 0 1 5
2Q LOSS WILD-TYPE 33 23 8

Figure S226.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'2q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00078 (Fisher's exact test), Q value = 0.0032

Table S227.  Gene #45: '2q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 4 11 13 9 10
2Q LOSS MUTATED 0 1 0 0 0 0 5
2Q LOSS WILD-TYPE 11 11 4 11 13 9 5

Figure S227.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'2q loss' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00019

Table S228.  Gene #45: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
2Q LOSS MUTATED 0 11 3
2Q LOSS WILD-TYPE 238 124 152

Figure S228.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

'2q loss' versus 'RPPA_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.0016

Table S229.  Gene #45: '2q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
2Q LOSS MUTATED 0 3 0 6 0 0
2Q LOSS WILD-TYPE 108 59 75 74 79 43

Figure S229.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'2q loss' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00013

Table S230.  Gene #45: '2q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
2Q LOSS MUTATED 0 0 9
2Q LOSS WILD-TYPE 121 196 121

Figure S230.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'2q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S231.  Gene #45: '2q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
2Q LOSS MUTATED 12 0 2
2Q LOSS WILD-TYPE 99 221 191

Figure S231.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S232.  Gene #45: '2q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
2Q LOSS MUTATED 0 1 1 3 0 9
2Q LOSS WILD-TYPE 117 32 182 129 35 16

Figure S232.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S233.  Gene #45: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
2Q LOSS MUTATED 0 0 14
2Q LOSS WILD-TYPE 124 204 168

Figure S233.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S234.  Gene #45: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
2Q LOSS MUTATED 1 13 0 0
2Q LOSS WILD-TYPE 143 121 195 37

Figure S234.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'MRNA_CNMF'

P value = 0.00381 (Fisher's exact test), Q value = 0.013

Table S235.  Gene #46: '3p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 24 13
3P LOSS MUTATED 22 19 3
3P LOSS WILD-TYPE 11 5 10

Figure S235.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'3p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0104 (Fisher's exact test), Q value = 0.031

Table S236.  Gene #46: '3p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 4 11 13 9 10
3P LOSS MUTATED 8 9 1 10 7 7 2
3P LOSS WILD-TYPE 3 3 3 1 6 2 8

Figure S236.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'3p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S237.  Gene #46: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
3P LOSS MUTATED 203 41 136
3P LOSS WILD-TYPE 35 94 19

Figure S237.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 0.00053 (Fisher's exact test), Q value = 0.0023

Table S238.  Gene #46: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
3P LOSS MUTATED 104 43 85
3P LOSS WILD-TYPE 24 33 25

Figure S238.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3p loss' versus 'RPPA_CNMF'

P value = 0.0338 (Fisher's exact test), Q value = 0.081

Table S239.  Gene #46: '3p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
3P LOSS MUTATED 88 42 57 51 51 34
3P LOSS WILD-TYPE 20 20 18 29 28 9

Figure S239.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'3p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0445 (Fisher's exact test), Q value = 0.1

Table S240.  Gene #46: '3p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
3P LOSS MUTATED 95 144 84
3P LOSS WILD-TYPE 26 52 46

Figure S240.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S241.  Gene #46: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
3P LOSS MUTATED 54 183 141
3P LOSS WILD-TYPE 57 38 52

Figure S241.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S242.  Gene #46: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
3P LOSS MUTATED 93 14 148 96 25 2
3P LOSS WILD-TYPE 24 19 35 36 10 23

Figure S242.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CNMF'

P value = 0.0226 (Fisher's exact test), Q value = 0.059

Table S243.  Gene #46: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
3P LOSS MUTATED 84 160 122
3P LOSS WILD-TYPE 40 44 60

Figure S243.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00856 (Fisher's exact test), Q value = 0.026

Table S244.  Gene #46: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
3P LOSS MUTATED 91 92 154 29
3P LOSS WILD-TYPE 53 42 41 8

Figure S244.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

P value = 0.00133 (Fisher's exact test), Q value = 0.0052

Table S245.  Gene #47: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
3Q LOSS MUTATED 46 13 40
3Q LOSS WILD-TYPE 192 122 115

Figure S245.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

'3q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0189 (Fisher's exact test), Q value = 0.051

Table S246.  Gene #47: '3q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
3Q LOSS MUTATED 33 5 28 28 4 1
3Q LOSS WILD-TYPE 84 28 155 104 31 24

Figure S246.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0278 (Fisher's exact test), Q value = 0.069

Table S247.  Gene #47: '3q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
3Q LOSS MUTATED 19 27 38 13
3Q LOSS WILD-TYPE 125 107 157 24

Figure S247.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S248.  Gene #48: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
4P LOSS MUTATED 9 16 47
4P LOSS WILD-TYPE 229 119 108

Figure S248.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.00084

Table S249.  Gene #48: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
4P LOSS MUTATED 11 8 31
4P LOSS WILD-TYPE 117 68 79

Figure S249.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 0.00082 (Fisher's exact test), Q value = 0.0034

Table S250.  Gene #48: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
4P LOSS MUTATED 6 26 39
4P LOSS WILD-TYPE 105 195 154

Figure S250.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00116 (Fisher's exact test), Q value = 0.0046

Table S251.  Gene #48: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
4P LOSS MUTATED 16 1 19 31 4 0
4P LOSS WILD-TYPE 101 32 164 101 31 25

Figure S251.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00723 (Fisher's exact test), Q value = 0.023

Table S252.  Gene #48: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 56 47
4P LOSS MUTATED 1 13 4
4P LOSS WILD-TYPE 38 43 43

Figure S252.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S253.  Gene #49: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
4Q LOSS MUTATED 5 14 46
4Q LOSS WILD-TYPE 233 121 109

Figure S253.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00019

Table S254.  Gene #49: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
4Q LOSS MUTATED 9 6 30
4Q LOSS WILD-TYPE 119 70 80

Figure S254.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.0022

Table S255.  Gene #49: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
4Q LOSS MUTATED 6 21 38
4Q LOSS WILD-TYPE 105 200 155

Figure S255.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00024

Table S256.  Gene #49: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
4Q LOSS MUTATED 15 0 14 32 4 0
4Q LOSS WILD-TYPE 102 33 169 100 31 25

Figure S256.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5p loss' versus 'CN_CNMF'

P value = 0.016 (Fisher's exact test), Q value = 0.044

Table S257.  Gene #50: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
5P LOSS MUTATED 0 4 3
5P LOSS WILD-TYPE 238 131 152

Figure S257.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

'5p loss' versus 'MRNASEQ_CNMF'

P value = 0.0272 (Fisher's exact test), Q value = 0.068

Table S258.  Gene #50: '5p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
5P LOSS MUTATED 3 0 4
5P LOSS WILD-TYPE 108 221 189

Figure S258.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.011 (Fisher's exact test), Q value = 0.032

Table S259.  Gene #50: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
5P LOSS MUTATED 0 0 0 5 1 1
5P LOSS WILD-TYPE 117 33 183 127 34 24

Figure S259.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_CNMF'

P value = 0.0411 (Fisher's exact test), Q value = 0.094

Table S260.  Gene #50: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
5P LOSS MUTATED 2 0 5
5P LOSS WILD-TYPE 122 204 177

Figure S260.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5q loss' versus 'CN_CNMF'

P value = 0.0452 (Fisher's exact test), Q value = 0.1

Table S261.  Gene #51: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
5Q LOSS MUTATED 0 3 3
5Q LOSS WILD-TYPE 238 132 152

Figure S261.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 0.0455 (Fisher's exact test), Q value = 0.1

Table S262.  Gene #51: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
5Q LOSS MUTATED 3 0 3
5Q LOSS WILD-TYPE 108 221 190

Figure S262.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0158 (Fisher's exact test), Q value = 0.044

Table S263.  Gene #51: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
5Q LOSS MUTATED 0 0 0 5 0 1
5Q LOSS WILD-TYPE 117 33 183 127 35 24

Figure S263.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6p loss' versus 'MRNA_CNMF'

P value = 0.0109 (Fisher's exact test), Q value = 0.032

Table S264.  Gene #52: '6p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 24 13
6P LOSS MUTATED 4 10 6
6P LOSS WILD-TYPE 29 14 7

Figure S264.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'6p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0142 (Fisher's exact test), Q value = 0.04

Table S265.  Gene #52: '6p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 4 11 13 9 10
6P LOSS MUTATED 2 7 0 3 1 1 6
6P LOSS WILD-TYPE 9 5 4 8 12 8 4

Figure S265.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S266.  Gene #52: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
6P LOSS MUTATED 11 26 63
6P LOSS WILD-TYPE 227 109 92

Figure S266.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

'6p loss' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00029

Table S267.  Gene #52: '6p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
6P LOSS MUTATED 9 12 31
6P LOSS WILD-TYPE 119 64 79

Figure S267.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6p loss' versus 'RPPA_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00044

Table S268.  Gene #52: '6p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
6P LOSS MUTATED 17 26 15 18 7 5
6P LOSS WILD-TYPE 91 36 60 62 72 38

Figure S268.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'6p loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S269.  Gene #52: '6p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
6P LOSS MUTATED 22 20 46
6P LOSS WILD-TYPE 99 176 84

Figure S269.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'6p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S270.  Gene #52: '6p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
6P LOSS MUTATED 17 20 61
6P LOSS WILD-TYPE 94 201 132

Figure S270.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S271.  Gene #52: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
6P LOSS MUTATED 19 1 12 51 6 9
6P LOSS WILD-TYPE 98 32 171 81 29 16

Figure S271.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S272.  Gene #52: '6p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
6P LOSS MUTATED 14 17 65
6P LOSS WILD-TYPE 110 187 117

Figure S272.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S273.  Gene #52: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
6P LOSS MUTATED 26 40 14 16
6P LOSS WILD-TYPE 118 94 181 21

Figure S273.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0246 (Fisher's exact test), Q value = 0.063

Table S274.  Gene #52: '6p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 56 47
6P LOSS MUTATED 4 14 3
6P LOSS WILD-TYPE 35 42 44

Figure S274.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q loss' versus 'MRNA_CNMF'

P value = 0.0495 (Fisher's exact test), Q value = 0.11

Table S275.  Gene #53: '6q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 24 13
6Q LOSS MUTATED 7 11 7
6Q LOSS WILD-TYPE 26 13 6

Figure S275.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'6q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S276.  Gene #53: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
6Q LOSS MUTATED 27 26 75
6Q LOSS WILD-TYPE 211 109 80

Figure S276.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

'6q loss' versus 'METHLYATION_CNMF'

P value = 0.00576 (Fisher's exact test), Q value = 0.019

Table S277.  Gene #53: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
6Q LOSS MUTATED 19 14 35
6Q LOSS WILD-TYPE 109 62 75

Figure S277.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6q loss' versus 'RPPA_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00039

Table S278.  Gene #53: '6q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
6Q LOSS MUTATED 28 28 21 20 7 7
6Q LOSS WILD-TYPE 80 34 54 60 72 36

Figure S278.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'6q loss' versus 'RPPA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00019

Table S279.  Gene #53: '6q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
6Q LOSS MUTATED 33 30 48
6Q LOSS WILD-TYPE 88 166 82

Figure S279.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'6q loss' versus 'MRNASEQ_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.0011

Table S280.  Gene #53: '6q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
6Q LOSS MUTATED 19 41 66
6Q LOSS WILD-TYPE 92 180 127

Figure S280.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S281.  Gene #53: '6q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
6Q LOSS MUTATED 22 5 29 53 8 9
6Q LOSS WILD-TYPE 95 28 154 79 27 16

Figure S281.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S282.  Gene #53: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
6Q LOSS MUTATED 20 33 71
6Q LOSS WILD-TYPE 104 171 111

Figure S282.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00013

Table S283.  Gene #53: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
6Q LOSS MUTATED 31 46 30 17
6Q LOSS WILD-TYPE 113 88 165 20

Figure S283.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0259 (Fisher's exact test), Q value = 0.066

Table S284.  Gene #53: '6q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 56 47
6Q LOSS MUTATED 5 18 6
6Q LOSS WILD-TYPE 34 38 41

Figure S284.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q loss' versus 'MRNASEQ_CNMF'

P value = 0.0499 (Fisher's exact test), Q value = 0.11

Table S285.  Gene #55: '7q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
7Q LOSS MUTATED 0 0 4
7Q LOSS WILD-TYPE 111 221 189

Figure S285.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7q loss' versus 'MIRSEQ_CNMF'

P value = 0.0195 (Fisher's exact test), Q value = 0.052

Table S286.  Gene #55: '7q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
7Q LOSS MUTATED 0 0 4
7Q LOSS WILD-TYPE 124 204 178

Figure S286.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8p loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00013

Table S287.  Gene #56: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
8P LOSS MUTATED 43 30 64
8P LOSS WILD-TYPE 195 105 91

Figure S287.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00113 (Fisher's exact test), Q value = 0.0045

Table S288.  Gene #56: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
8P LOSS MUTATED 28 3 47 50 4 4
8P LOSS WILD-TYPE 89 30 136 82 31 21

Figure S288.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_CNMF'

P value = 0.0431 (Fisher's exact test), Q value = 0.098

Table S289.  Gene #56: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
8P LOSS MUTATED 32 43 59
8P LOSS WILD-TYPE 92 161 123

Figure S289.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0229 (Fisher's exact test), Q value = 0.06

Table S290.  Gene #56: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
8P LOSS MUTATED 44 33 41 16
8P LOSS WILD-TYPE 100 101 154 21

Figure S290.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8q loss' versus 'METHLYATION_CNMF'

P value = 0.045 (Fisher's exact test), Q value = 0.1

Table S291.  Gene #57: '8q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
8Q LOSS MUTATED 17 3 16
8Q LOSS WILD-TYPE 111 73 94

Figure S291.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p loss' versus 'MRNA_CNMF'

P value = 0.00388 (Fisher's exact test), Q value = 0.013

Table S292.  Gene #58: '9p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 24 13
9P LOSS MUTATED 5 12 1
9P LOSS WILD-TYPE 28 12 12

Figure S292.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'9p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0362 (Fisher's exact test), Q value = 0.086

Table S293.  Gene #58: '9p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 4 11 13 9 10
9P LOSS MUTATED 2 7 0 5 1 2 1
9P LOSS WILD-TYPE 9 5 4 6 12 7 9

Figure S293.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S294.  Gene #58: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
9P LOSS MUTATED 10 32 107
9P LOSS WILD-TYPE 228 103 48

Figure S294.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S295.  Gene #58: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
9P LOSS MUTATED 6 20 67
9P LOSS WILD-TYPE 122 56 43

Figure S295.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S296.  Gene #58: '9p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
9P LOSS MUTATED 18 36 29 21 20 10
9P LOSS WILD-TYPE 90 26 46 59 59 33

Figure S296.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'9p loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00054

Table S297.  Gene #58: '9p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
9P LOSS MUTATED 33 43 58
9P LOSS WILD-TYPE 88 153 72

Figure S297.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S298.  Gene #58: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
9P LOSS MUTATED 16 26 106
9P LOSS WILD-TYPE 95 195 87

Figure S298.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S299.  Gene #58: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
9P LOSS MUTATED 31 2 16 82 13 4
9P LOSS WILD-TYPE 86 31 167 50 22 21

Figure S299.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S300.  Gene #58: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
9P LOSS MUTATED 27 26 91
9P LOSS WILD-TYPE 97 178 91

Figure S300.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S301.  Gene #58: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
9P LOSS MUTATED 43 53 24 24
9P LOSS WILD-TYPE 101 81 171 13

Figure S301.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0161 (Fisher's exact test), Q value = 0.044

Table S302.  Gene #58: '9p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 21 48 35
9P LOSS MUTATED 8 4 5 14
9P LOSS WILD-TYPE 30 17 43 21

Figure S302.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9q loss' versus 'MRNA_CNMF'

P value = 0.0104 (Fisher's exact test), Q value = 0.031

Table S303.  Gene #59: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 24 13
9Q LOSS MUTATED 5 12 2
9Q LOSS WILD-TYPE 28 12 11

Figure S303.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'9q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S304.  Gene #59: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
9Q LOSS MUTATED 11 32 107
9Q LOSS WILD-TYPE 227 103 48

Figure S304.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S305.  Gene #59: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
9Q LOSS MUTATED 6 21 64
9Q LOSS WILD-TYPE 122 55 46

Figure S305.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S306.  Gene #59: '9q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
9Q LOSS MUTATED 17 36 32 21 20 10
9Q LOSS WILD-TYPE 91 26 43 59 59 33

Figure S306.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'9q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.00064

Table S307.  Gene #59: '9q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
9Q LOSS MUTATED 36 43 57
9Q LOSS WILD-TYPE 85 153 73

Figure S307.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S308.  Gene #59: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
9Q LOSS MUTATED 16 26 107
9Q LOSS WILD-TYPE 95 195 86

Figure S308.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S309.  Gene #59: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
9Q LOSS MUTATED 32 3 15 82 13 4
9Q LOSS WILD-TYPE 85 30 168 50 22 21

Figure S309.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S310.  Gene #59: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
9Q LOSS MUTATED 26 25 93
9Q LOSS WILD-TYPE 98 179 89

Figure S310.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S311.  Gene #59: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
9Q LOSS MUTATED 42 55 23 24
9Q LOSS WILD-TYPE 102 79 172 13

Figure S311.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00372 (Fisher's exact test), Q value = 0.013

Table S312.  Gene #59: '9q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 21 48 35
9Q LOSS MUTATED 6 4 6 16
9Q LOSS WILD-TYPE 32 17 42 19

Figure S312.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0365 (Fisher's exact test), Q value = 0.086

Table S313.  Gene #59: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 56 47
9Q LOSS MUTATED 6 19 7
9Q LOSS WILD-TYPE 33 37 40

Figure S313.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S314.  Gene #60: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
10P LOSS MUTATED 9 23 35
10P LOSS WILD-TYPE 229 112 120

Figure S314.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-04 (Fisher's exact test), Q value = 0.003

Table S315.  Gene #60: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
10P LOSS MUTATED 16 3 13 24 2 9
10P LOSS WILD-TYPE 101 30 170 108 33 16

Figure S315.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_CNMF'

P value = 0.0174 (Fisher's exact test), Q value = 0.047

Table S316.  Gene #60: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
10P LOSS MUTATED 15 17 33
10P LOSS WILD-TYPE 109 187 149

Figure S316.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S317.  Gene #61: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
10Q LOSS MUTATED 17 27 45
10Q LOSS WILD-TYPE 221 108 110

Figure S317.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 0.00425 (Fisher's exact test), Q value = 0.014

Table S318.  Gene #61: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
10Q LOSS MUTATED 17 8 30
10Q LOSS WILD-TYPE 111 68 80

Figure S318.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0209 (Fisher's exact test), Q value = 0.055

Table S319.  Gene #61: '10q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
10Q LOSS MUTATED 20 26 33
10Q LOSS WILD-TYPE 101 170 97

Figure S319.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00214 (Fisher's exact test), Q value = 0.0078

Table S320.  Gene #61: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
10Q LOSS MUTATED 22 3 20 32 3 9
10Q LOSS WILD-TYPE 95 30 163 100 32 16

Figure S320.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_CNMF'

P value = 0.0387 (Fisher's exact test), Q value = 0.091

Table S321.  Gene #61: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
10Q LOSS MUTATED 20 26 41
10Q LOSS WILD-TYPE 104 178 141

Figure S321.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00055 (Fisher's exact test), Q value = 0.0024

Table S322.  Gene #61: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
10Q LOSS MUTATED 20 32 22 13
10Q LOSS WILD-TYPE 124 102 173 24

Figure S322.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00013

Table S323.  Gene #62: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
11P LOSS MUTATED 0 5 13
11P LOSS WILD-TYPE 238 130 142

Figure S323.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 0.022 (Fisher's exact test), Q value = 0.058

Table S324.  Gene #62: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
11P LOSS MUTATED 1 3 8
11P LOSS WILD-TYPE 127 73 102

Figure S324.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0277 (Fisher's exact test), Q value = 0.069

Table S325.  Gene #62: '11p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
11P LOSS MUTATED 3 1 2 11 1 0
11P LOSS WILD-TYPE 114 32 181 121 34 25

Figure S325.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S326.  Gene #63: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
11Q LOSS MUTATED 0 5 18
11Q LOSS WILD-TYPE 238 130 137

Figure S326.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

P value = 0.00594 (Fisher's exact test), Q value = 0.019

Table S327.  Gene #63: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
11Q LOSS MUTATED 1 4 10
11Q LOSS WILD-TYPE 127 72 100

Figure S327.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11q loss' versus 'MRNASEQ_CNMF'

P value = 0.0141 (Fisher's exact test), Q value = 0.04

Table S328.  Gene #63: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
11Q LOSS MUTATED 4 4 15
11Q LOSS WILD-TYPE 107 217 178

Figure S328.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00032 (Fisher's exact test), Q value = 0.0015

Table S329.  Gene #63: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
11Q LOSS MUTATED 3 1 2 16 1 0
11Q LOSS WILD-TYPE 114 32 181 116 34 25

Figure S329.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_CNMF'

P value = 0.023 (Fisher's exact test), Q value = 0.06

Table S330.  Gene #63: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
11Q LOSS MUTATED 5 4 14
11Q LOSS WILD-TYPE 119 200 168

Figure S330.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.037 (Fisher's exact test), Q value = 0.087

Table S331.  Gene #63: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
11Q LOSS MUTATED 9 8 3 3
11Q LOSS WILD-TYPE 135 126 192 34

Figure S331.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'13q loss' versus 'MRNA_CNMF'

P value = 0.00339 (Fisher's exact test), Q value = 0.012

Table S332.  Gene #66: '13q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 24 13
13Q LOSS MUTATED 0 6 3
13Q LOSS WILD-TYPE 33 18 10

Figure S332.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'13q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0466 (Fisher's exact test), Q value = 0.1

Table S333.  Gene #66: '13q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 4 11 13 9 10
13Q LOSS MUTATED 0 3 0 3 0 0 3
13Q LOSS WILD-TYPE 11 9 4 8 13 9 7

Figure S333.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S334.  Gene #66: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
13Q LOSS MUTATED 7 23 41
13Q LOSS WILD-TYPE 231 112 114

Figure S334.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.0013

Table S335.  Gene #66: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
13Q LOSS MUTATED 7 15 24
13Q LOSS WILD-TYPE 121 61 86

Figure S335.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q loss' versus 'RPPA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00024

Table S336.  Gene #66: '13q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
13Q LOSS MUTATED 3 19 13 14 9 4
13Q LOSS WILD-TYPE 105 43 62 66 70 39

Figure S336.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'13q loss' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00013

Table S337.  Gene #66: '13q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
13Q LOSS MUTATED 14 14 34
13Q LOSS WILD-TYPE 107 182 96

Figure S337.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00013

Table S338.  Gene #66: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
13Q LOSS MUTATED 13 14 44
13Q LOSS WILD-TYPE 98 207 149

Figure S338.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S339.  Gene #66: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
13Q LOSS MUTATED 6 2 10 40 6 7
13Q LOSS WILD-TYPE 111 31 173 92 29 18

Figure S339.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S340.  Gene #66: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
13Q LOSS MUTATED 12 12 45
13Q LOSS WILD-TYPE 112 192 137

Figure S340.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'13q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S341.  Gene #66: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
13Q LOSS MUTATED 17 31 9 12
13Q LOSS WILD-TYPE 127 103 186 25

Figure S341.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00013

Table S342.  Gene #67: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 24 13
14Q LOSS MUTATED 9 19 2
14Q LOSS WILD-TYPE 24 5 11

Figure S342.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'14q loss' versus 'MRNA_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00034

Table S343.  Gene #67: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 4 11 13 9 10
14Q LOSS MUTATED 4 7 1 11 5 0 2
14Q LOSS WILD-TYPE 7 5 3 0 8 9 8

Figure S343.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S344.  Gene #67: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
14Q LOSS MUTATED 63 45 108
14Q LOSS WILD-TYPE 175 90 47

Figure S344.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S345.  Gene #67: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
14Q LOSS MUTATED 25 34 64
14Q LOSS WILD-TYPE 103 42 46

Figure S345.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S346.  Gene #67: '14q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
14Q LOSS MUTATED 34 40 55 27 24 12
14Q LOSS WILD-TYPE 74 22 20 53 55 31

Figure S346.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'14q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S347.  Gene #67: '14q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
14Q LOSS MUTATED 67 59 66
14Q LOSS WILD-TYPE 54 137 64

Figure S347.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S348.  Gene #67: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
14Q LOSS MUTATED 17 69 127
14Q LOSS WILD-TYPE 94 152 66

Figure S348.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S349.  Gene #67: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
14Q LOSS MUTATED 41 7 52 79 32 2
14Q LOSS WILD-TYPE 76 26 131 53 3 23

Figure S349.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S350.  Gene #67: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
14Q LOSS MUTATED 34 61 115
14Q LOSS WILD-TYPE 90 143 67

Figure S350.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'14q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S351.  Gene #67: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
14Q LOSS MUTATED 49 80 58 23
14Q LOSS WILD-TYPE 95 54 137 14

Figure S351.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0499 (Fisher's exact test), Q value = 0.11

Table S352.  Gene #67: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 21 48 35
14Q LOSS MUTATED 11 5 14 19
14Q LOSS WILD-TYPE 27 16 34 16

Figure S352.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'15q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S353.  Gene #68: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
15Q LOSS MUTATED 1 6 29
15Q LOSS WILD-TYPE 237 129 126

Figure S353.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 0.00075 (Fisher's exact test), Q value = 0.0032

Table S354.  Gene #68: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
15Q LOSS MUTATED 3 3 16
15Q LOSS WILD-TYPE 125 73 94

Figure S354.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'15q loss' versus 'RPPA_CNMF'

P value = 0.0299 (Fisher's exact test), Q value = 0.074

Table S355.  Gene #68: '15q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
15Q LOSS MUTATED 2 8 8 9 4 3
15Q LOSS WILD-TYPE 106 54 67 71 75 40

Figure S355.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S356.  Gene #68: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
15Q LOSS MUTATED 2 7 27
15Q LOSS WILD-TYPE 109 214 166

Figure S356.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00013

Table S357.  Gene #68: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
15Q LOSS MUTATED 5 0 5 24 2 0
15Q LOSS WILD-TYPE 112 33 178 108 33 25

Figure S357.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_CNMF'

P value = 0.00083 (Fisher's exact test), Q value = 0.0034

Table S358.  Gene #68: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
15Q LOSS MUTATED 7 6 23
15Q LOSS WILD-TYPE 117 198 159

Figure S358.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0164 (Fisher's exact test), Q value = 0.045

Table S359.  Gene #68: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
15Q LOSS MUTATED 14 11 6 5
15Q LOSS WILD-TYPE 130 123 189 32

Figure S359.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0255 (Fisher's exact test), Q value = 0.065

Table S360.  Gene #69: '16p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
16P LOSS MUTATED 0 3 6
16P LOSS WILD-TYPE 121 193 124

Figure S360.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'16q loss' versus 'CN_CNMF'

P value = 0.0368 (Fisher's exact test), Q value = 0.087

Table S361.  Gene #70: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
16Q LOSS MUTATED 3 4 9
16Q LOSS WILD-TYPE 235 131 146

Figure S361.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

'16q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00821 (Fisher's exact test), Q value = 0.025

Table S362.  Gene #70: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
16Q LOSS MUTATED 4 3 3 5
16Q LOSS WILD-TYPE 140 131 192 32

Figure S362.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0284 (Fisher's exact test), Q value = 0.07

Table S363.  Gene #70: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 56 47
16Q LOSS MUTATED 1 6 0
16Q LOSS WILD-TYPE 38 50 47

Figure S363.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'MRNA_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.00093

Table S364.  Gene #71: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 24 13
17P LOSS MUTATED 0 5 6
17P LOSS WILD-TYPE 33 19 7

Figure S364.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.0012

Table S365.  Gene #71: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 4 11 13 9 10
17P LOSS MUTATED 0 5 1 0 0 0 5
17P LOSS WILD-TYPE 11 7 3 11 13 9 5

Figure S365.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S366.  Gene #71: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
17P LOSS MUTATED 2 16 28
17P LOSS WILD-TYPE 236 119 127

Figure S366.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

'17p loss' versus 'RPPA_CNMF'

P value = 0.0094 (Fisher's exact test), Q value = 0.028

Table S367.  Gene #71: '17p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
17P LOSS MUTATED 4 10 4 13 5 2
17P LOSS WILD-TYPE 104 52 71 67 74 41

Figure S367.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'17p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00039 (Fisher's exact test), Q value = 0.0018

Table S368.  Gene #71: '17p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
17P LOSS MUTATED 5 11 22
17P LOSS WILD-TYPE 116 185 108

Figure S368.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S369.  Gene #71: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
17P LOSS MUTATED 15 3 28
17P LOSS WILD-TYPE 96 218 165

Figure S369.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S370.  Gene #71: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
17P LOSS MUTATED 6 3 3 23 2 9
17P LOSS WILD-TYPE 111 30 180 109 33 16

Figure S370.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S371.  Gene #71: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
17P LOSS MUTATED 9 4 33
17P LOSS WILD-TYPE 115 200 149

Figure S371.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.00079

Table S372.  Gene #71: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
17P LOSS MUTATED 13 20 6 7
17P LOSS WILD-TYPE 131 114 189 30

Figure S372.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17q loss' versus 'MRNA_CNMF'

P value = 0.00073 (Fisher's exact test), Q value = 0.0031

Table S373.  Gene #72: '17q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 24 13
17Q LOSS MUTATED 0 4 5
17Q LOSS WILD-TYPE 33 20 8

Figure S373.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00042 (Fisher's exact test), Q value = 0.0019

Table S374.  Gene #72: '17q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 4 11 13 9 10
17Q LOSS MUTATED 0 4 0 0 0 0 5
17Q LOSS WILD-TYPE 11 8 4 11 13 9 5

Figure S374.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S375.  Gene #72: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
17Q LOSS MUTATED 1 13 14
17Q LOSS WILD-TYPE 237 122 141

Figure S375.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

'17q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00775 (Fisher's exact test), Q value = 0.024

Table S376.  Gene #72: '17q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
17Q LOSS MUTATED 2 7 13
17Q LOSS WILD-TYPE 119 189 117

Figure S376.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'17q loss' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00024

Table S377.  Gene #72: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
17Q LOSS MUTATED 12 2 14
17Q LOSS WILD-TYPE 99 219 179

Figure S377.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S378.  Gene #72: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
17Q LOSS MUTATED 4 1 2 11 1 9
17Q LOSS WILD-TYPE 113 32 181 121 34 16

Figure S378.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00013

Table S379.  Gene #72: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
17Q LOSS MUTATED 4 2 22
17Q LOSS WILD-TYPE 120 202 160

Figure S379.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00512 (Fisher's exact test), Q value = 0.017

Table S380.  Gene #72: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
17Q LOSS MUTATED 5 15 5 3
17Q LOSS WILD-TYPE 139 119 190 34

Figure S380.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S381.  Gene #73: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
18P LOSS MUTATED 12 25 56
18P LOSS WILD-TYPE 226 110 99

Figure S381.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S382.  Gene #73: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
18P LOSS MUTATED 6 19 32
18P LOSS WILD-TYPE 122 57 78

Figure S382.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S383.  Gene #73: '18p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
18P LOSS MUTATED 7 24 20 16 13 3
18P LOSS WILD-TYPE 101 38 55 64 66 40

Figure S383.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'18p loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S384.  Gene #73: '18p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
18P LOSS MUTATED 21 20 42
18P LOSS WILD-TYPE 100 176 88

Figure S384.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'18p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S385.  Gene #73: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
18P LOSS MUTATED 9 11 72
18P LOSS WILD-TYPE 102 210 121

Figure S385.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S386.  Gene #73: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
18P LOSS MUTATED 10 5 9 55 10 3
18P LOSS WILD-TYPE 107 28 174 77 25 22

Figure S386.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S387.  Gene #73: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
18P LOSS MUTATED 21 11 61
18P LOSS WILD-TYPE 103 193 121

Figure S387.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S388.  Gene #73: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
18P LOSS MUTATED 29 40 9 15
18P LOSS WILD-TYPE 115 94 186 22

Figure S388.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.0012

Table S389.  Gene #73: '18p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 21 48 35
18P LOSS MUTATED 7 4 0 10
18P LOSS WILD-TYPE 31 17 48 25

Figure S389.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00403 (Fisher's exact test), Q value = 0.014

Table S390.  Gene #73: '18p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 56 47
18P LOSS MUTATED 7 13 1
18P LOSS WILD-TYPE 32 43 46

Figure S390.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q loss' versus 'MRNA_CNMF'

P value = 0.0452 (Fisher's exact test), Q value = 0.1

Table S391.  Gene #74: '18q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 24 13
18Q LOSS MUTATED 2 7 3
18Q LOSS WILD-TYPE 31 17 10

Figure S391.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S392.  Gene #74: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
18Q LOSS MUTATED 13 25 57
18Q LOSS WILD-TYPE 225 110 98

Figure S392.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S393.  Gene #74: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
18Q LOSS MUTATED 7 19 31
18Q LOSS WILD-TYPE 121 57 79

Figure S393.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q loss' versus 'RPPA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00013

Table S394.  Gene #74: '18q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
18Q LOSS MUTATED 7 24 20 17 13 5
18Q LOSS WILD-TYPE 101 38 55 63 66 38

Figure S394.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'18q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00054

Table S395.  Gene #74: '18q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
18Q LOSS MUTATED 20 24 42
18Q LOSS WILD-TYPE 101 172 88

Figure S395.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S396.  Gene #74: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
18Q LOSS MUTATED 10 12 72
18Q LOSS WILD-TYPE 101 209 121

Figure S396.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S397.  Gene #74: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
18Q LOSS MUTATED 10 6 10 55 10 3
18Q LOSS WILD-TYPE 107 27 173 77 25 22

Figure S397.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S398.  Gene #74: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
18Q LOSS MUTATED 22 12 61
18Q LOSS WILD-TYPE 102 192 121

Figure S398.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S399.  Gene #74: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
18Q LOSS MUTATED 28 41 10 16
18Q LOSS WILD-TYPE 116 93 185 21

Figure S399.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00299 (Fisher's exact test), Q value = 0.011

Table S400.  Gene #74: '18q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 21 48 35
18Q LOSS MUTATED 7 3 1 10
18Q LOSS WILD-TYPE 31 18 47 25

Figure S400.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0312 (Fisher's exact test), Q value = 0.076

Table S401.  Gene #74: '18q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 56 47
18Q LOSS MUTATED 7 12 2
18Q LOSS WILD-TYPE 32 44 45

Figure S401.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S402.  Gene #75: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
19P LOSS MUTATED 0 1 10
19P LOSS WILD-TYPE 238 134 145

Figure S402.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

P value = 0.0317 (Fisher's exact test), Q value = 0.077

Table S403.  Gene #75: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
19P LOSS MUTATED 0 2 5
19P LOSS WILD-TYPE 128 74 105

Figure S403.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p loss' versus 'RPPA_CNMF'

P value = 0.00517 (Fisher's exact test), Q value = 0.017

Table S404.  Gene #75: '19p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
19P LOSS MUTATED 1 6 1 0 2 0
19P LOSS WILD-TYPE 107 56 74 80 77 43

Figure S404.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'19p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00041 (Fisher's exact test), Q value = 0.0018

Table S405.  Gene #75: '19p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
19P LOSS MUTATED 2 0 8
19P LOSS WILD-TYPE 119 196 122

Figure S405.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0106 (Fisher's exact test), Q value = 0.031

Table S406.  Gene #75: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
19P LOSS MUTATED 1 0 1 9 0 0
19P LOSS WILD-TYPE 116 33 182 123 35 25

Figure S406.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0096 (Fisher's exact test), Q value = 0.029

Table S407.  Gene #75: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
19P LOSS MUTATED 5 4 0 2
19P LOSS WILD-TYPE 139 130 195 35

Figure S407.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.034 (Fisher's exact test), Q value = 0.081

Table S408.  Gene #75: '19p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 21 48 35
19P LOSS MUTATED 0 1 0 3
19P LOSS WILD-TYPE 38 20 48 32

Figure S408.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.039 (Fisher's exact test), Q value = 0.091

Table S409.  Gene #75: '19p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 56 47
19P LOSS MUTATED 0 4 0
19P LOSS WILD-TYPE 39 52 47

Figure S409.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 0.0118 (Fisher's exact test), Q value = 0.034

Table S410.  Gene #76: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
19Q LOSS MUTATED 0 0 4
19Q LOSS WILD-TYPE 238 135 151

Figure S410.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

'20p loss' versus 'RPPA_CNMF'

P value = 0.0301 (Fisher's exact test), Q value = 0.074

Table S411.  Gene #77: '20p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
20P LOSS MUTATED 0 3 1 0 1 2
20P LOSS WILD-TYPE 108 59 74 80 78 41

Figure S411.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'20p loss' versus 'MIRSEQ_CNMF'

P value = 0.0201 (Fisher's exact test), Q value = 0.053

Table S412.  Gene #77: '20p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
20P LOSS MUTATED 2 0 6
20P LOSS WILD-TYPE 122 204 176

Figure S412.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0301 (Fisher's exact test), Q value = 0.074

Table S413.  Gene #78: '20q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
20Q LOSS MUTATED 0 2 0 1
20Q LOSS WILD-TYPE 144 132 195 36

Figure S413.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'21q loss' versus 'MRNA_CNMF'

P value = 0.0265 (Fisher's exact test), Q value = 0.067

Table S414.  Gene #79: '21q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 24 13
21Q LOSS MUTATED 1 2 4
21Q LOSS WILD-TYPE 32 22 9

Figure S414.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S415.  Gene #79: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
21Q LOSS MUTATED 6 26 23
21Q LOSS WILD-TYPE 232 109 132

Figure S415.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

'21q loss' versus 'METHLYATION_CNMF'

P value = 0.0133 (Fisher's exact test), Q value = 0.038

Table S416.  Gene #79: '21q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
21Q LOSS MUTATED 7 9 19
21Q LOSS WILD-TYPE 121 67 91

Figure S416.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'21q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00109 (Fisher's exact test), Q value = 0.0044

Table S417.  Gene #79: '21q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
21Q LOSS MUTATED 11 11 24
21Q LOSS WILD-TYPE 110 185 106

Figure S417.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'21q loss' versus 'MRNASEQ_CNMF'

P value = 0.00294 (Fisher's exact test), Q value = 0.011

Table S418.  Gene #79: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
21Q LOSS MUTATED 20 13 20
21Q LOSS WILD-TYPE 91 208 173

Figure S418.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.00064

Table S419.  Gene #79: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
21Q LOSS MUTATED 10 4 10 17 2 10
21Q LOSS WILD-TYPE 107 29 173 115 33 15

Figure S419.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_CNMF'

P value = 0.00678 (Fisher's exact test), Q value = 0.021

Table S420.  Gene #79: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
21Q LOSS MUTATED 10 14 30
21Q LOSS WILD-TYPE 114 190 152

Figure S420.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'21q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00906 (Fisher's exact test), Q value = 0.028

Table S421.  Gene #79: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
21Q LOSS MUTATED 14 24 12 4
21Q LOSS WILD-TYPE 130 110 183 33

Figure S421.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'MRNA_CNMF'

P value = 0.0103 (Fisher's exact test), Q value = 0.031

Table S422.  Gene #80: '22q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 24 13
22Q LOSS MUTATED 0 5 2
22Q LOSS WILD-TYPE 33 19 11

Figure S422.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'22q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00146 (Fisher's exact test), Q value = 0.0056

Table S423.  Gene #80: '22q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 4 11 13 9 10
22Q LOSS MUTATED 0 0 2 4 0 0 1
22Q LOSS WILD-TYPE 11 12 2 7 13 9 9

Figure S423.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S424.  Gene #80: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
22Q LOSS MUTATED 2 13 24
22Q LOSS WILD-TYPE 236 122 131

Figure S424.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 0.00378 (Fisher's exact test), Q value = 0.013

Table S425.  Gene #80: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
22Q LOSS MUTATED 3 6 15
22Q LOSS WILD-TYPE 125 70 95

Figure S425.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q loss' versus 'RPPA_CNMF'

P value = 0.0012 (Fisher's exact test), Q value = 0.0047

Table S426.  Gene #80: '22q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
22Q LOSS MUTATED 2 12 8 8 3 3
22Q LOSS WILD-TYPE 106 50 67 72 76 40

Figure S426.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S427.  Gene #80: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
22Q LOSS MUTATED 4 5 30
22Q LOSS WILD-TYPE 107 216 163

Figure S427.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00019

Table S428.  Gene #80: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
22Q LOSS MUTATED 6 6 3 21 3 0
22Q LOSS WILD-TYPE 111 27 180 111 32 25

Figure S428.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S429.  Gene #80: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
22Q LOSS MUTATED 2 7 30
22Q LOSS WILD-TYPE 122 197 152

Figure S429.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00343 (Fisher's exact test), Q value = 0.012

Table S430.  Gene #80: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
22Q LOSS MUTATED 10 15 7 7
22Q LOSS WILD-TYPE 134 119 188 30

Figure S430.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.025 (Fisher's exact test), Q value = 0.064

Table S431.  Gene #80: '22q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 21 48 35
22Q LOSS MUTATED 0 0 2 5
22Q LOSS WILD-TYPE 38 21 46 30

Figure S431.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'xp loss' versus 'MRNA_CNMF'

P value = 0.0407 (Fisher's exact test), Q value = 0.094

Table S432.  Gene #81: 'xp loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 24 13
XP LOSS MUTATED 3 2 5
XP LOSS WILD-TYPE 30 22 8

Figure S432.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'xp loss' versus 'CN_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.00096

Table S433.  Gene #81: 'xp loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
XP LOSS MUTATED 10 10 26
XP LOSS WILD-TYPE 228 125 129

Figure S433.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #3: 'CN_CNMF'

'xp loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00277 (Fisher's exact test), Q value = 0.01

Table S434.  Gene #81: 'xp loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
XP LOSS MUTATED 14 7 17
XP LOSS WILD-TYPE 107 189 113

Figure S434.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'xp loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0127 (Fisher's exact test), Q value = 0.037

Table S435.  Gene #81: 'xp loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
XP LOSS MUTATED 9 1 12 11 6 7
XP LOSS WILD-TYPE 108 32 171 121 29 18

Figure S435.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_CNMF'

P value = 0.0389 (Fisher's exact test), Q value = 0.091

Table S436.  Gene #81: 'xp loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
XP LOSS MUTATED 7 14 24
XP LOSS WILD-TYPE 117 190 158

Figure S436.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xp loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00082 (Fisher's exact test), Q value = 0.0034

Table S437.  Gene #81: 'xp loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
XP LOSS MUTATED 6 23 12 4
XP LOSS WILD-TYPE 138 111 183 33

Figure S437.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'xq loss' versus 'MRNA_CNMF'

P value = 0.0235 (Fisher's exact test), Q value = 0.061

Table S438.  Gene #82: 'xq loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 24 13
XQ LOSS MUTATED 2 4 5
XQ LOSS WILD-TYPE 31 20 8

Figure S438.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'xq loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7.1e-05

Table S439.  Gene #82: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
XQ LOSS MUTATED 7 9 30
XQ LOSS WILD-TYPE 231 126 125

Figure S439.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 0.00904 (Fisher's exact test), Q value = 0.028

Table S440.  Gene #82: 'xq loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
XQ LOSS MUTATED 6 3 16
XQ LOSS WILD-TYPE 122 73 94

Figure S440.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xq loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00169 (Fisher's exact test), Q value = 0.0063

Table S441.  Gene #82: 'xq loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
XQ LOSS MUTATED 13 7 18
XQ LOSS WILD-TYPE 108 189 112

Figure S441.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'xq loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0276 (Fisher's exact test), Q value = 0.069

Table S442.  Gene #82: 'xq loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
XQ LOSS MUTATED 8 2 10 15 5 6
XQ LOSS WILD-TYPE 109 31 173 117 30 19

Figure S442.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_CNMF'

P value = 0.0186 (Fisher's exact test), Q value = 0.05

Table S443.  Gene #82: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
XQ LOSS MUTATED 8 12 25
XQ LOSS WILD-TYPE 116 192 157

Figure S443.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xq loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00328 (Fisher's exact test), Q value = 0.012

Table S444.  Gene #82: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
XQ LOSS MUTATED 9 22 10 4
XQ LOSS WILD-TYPE 135 112 185 33

Figure S444.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_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/KIRC-TP/15087101/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/KIRC-TP/15107132/KIRC-TP.transferedmergedcluster.txt

  • Number of patients = 528

  • Number of significantly arm-level cnvs = 82

  • Number of molecular subtypes = 12

  • Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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