Correlation between copy number variations of arm-level result and molecular subtypes
Kidney Renal Clear Cell Carcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C17P8XMD
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/C17P8XMD
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, 455 significant findings detected with P value < 0.05 and Q value < 0.25.

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

  • 1q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  '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',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 3p gain cnv correlated to 'CN_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_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

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

  • 5q gain cnv correlated to 'CN_CNMF' and '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',  'RPPA_CHIERARCHICAL',  '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',  'RPPA_CHIERARCHICAL', and 'MRNASEQ_CHIERARCHICAL'.

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

  • 10p gain cnv correlated to 'CN_CNMF',  'RPPA_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' and 'RPPA_CHIERARCHICAL'.

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

  • 16q gain cnv correlated to 'CN_CNMF',  'RPPA_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',  'RPPA_CHIERARCHICAL',  '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',  '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'.

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

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

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

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

  • 5q loss cnv correlated to 'CN_CNMF',  'RPPA_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 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 7p loss cnv correlated to 'RPPA_CNMF' and 'RPPA_CHIERARCHICAL'.

  • 7q loss cnv correlated to 'RPPA_CNMF',  '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',  'RPPA_CHIERARCHICAL',  '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',  'RPPA_CHIERARCHICAL',  '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', and 'MIRSEQ_CHIERARCHICAL'.

  • 15q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  '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 'MIRSEQ_CNMF'.

  • 20q loss cnv correlated to 'MIRSEQ_CHIERARCHICAL'.

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

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

  • xq loss cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  '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, 455 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
(0.0338) 		0.0309
(0.0737) 		1e-05
(6.52e-05) 		0.00365
(0.0122) 		1e-05
(6.52e-05) 		2e-05
(0.000118) 		6e-05
(0.000319) 		2e-05
(0.000118) 		1e-05
(6.52e-05) 		0.0004
(0.00173) 		0.00154
(0.00563) 		0.079
(0.153)
12p gain 121 (23%) 407 0.0131
(0.0365) 		0.0326
(0.0766) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		2e-05
(0.000118) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		0.00149
(0.00549) 		0.104
(0.19)
12q gain 122 (23%) 406 0.0132
(0.0368) 		0.0333
(0.078) 		1e-05
(6.52e-05) 		8e-05
(0.000414) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		0.00288
(0.01) 		0.128
(0.221)
20q gain 115 (22%) 413 0.0429
(0.0957) 		0.0746
(0.147) 		1e-05
(6.52e-05) 		4e-05
(0.000219) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		0.0326
(0.0766)
6p loss 100 (19%) 428 0.0107
(0.0308) 		0.0141
(0.0387) 		1e-05
(6.52e-05) 		6e-05
(0.000319) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		0.0829
(0.158) 		0.0243
(0.06)
9p loss 149 (28%) 379 0.00377
(0.0126) 		0.0365
(0.084) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		0.0164
(0.0437) 		0.0984
(0.181)
9q loss 150 (28%) 378 0.00921
(0.0274) 		0.0585
(0.123) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		0.00357
(0.012) 		0.037
(0.0849)
18q loss 95 (18%) 433 0.0462
(0.101) 		0.22
(0.335) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		0.00336
(0.0114) 		0.0308
(0.0736)
22q loss 39 (7%) 489 0.00982
(0.0287) 		0.00138
(0.0052) 		1e-05
(6.52e-05) 		0.00354
(0.0119) 		0.00037
(0.00163) 		0.0204
(0.0523) 		1e-05
(6.52e-05) 		2e-05
(0.000118) 		1e-05
(6.52e-05) 		0.00341
(0.0115) 		0.0254
(0.0625) 		0.259
(0.376)
3p loss 380 (72%) 148 0.003
(0.0104) 		0.0103
(0.0299) 		1e-05
(6.52e-05) 		0.00068
(0.00276) 		0.0122
(0.0344) 		0.00034
(0.00153) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		0.0227
(0.057) 		0.0086
(0.026) 		0.0916
(0.171) 		0.733
(0.873)
13q loss 71 (13%) 457 0.0033
(0.0113) 		0.0468
(0.102) 		1e-05
(6.52e-05) 		0.00023
(0.00109) 		1e-05
(6.52e-05) 		2e-05
(0.000118) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		0.107
(0.192) 		0.103
(0.189)
14q loss 216 (41%) 312 4e-05
(0.000219) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		0.0139
(0.0385) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		0.0506
(0.109) 		0.88
(1.00)
18p loss 93 (18%) 435 0.0586
(0.123) 		0.459
(0.591) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		0.00025
(0.00115) 		0.0045
(0.0146)
8p gain 31 (6%) 497 1e-05
(6.52e-05) 		0.00042
(0.0018) 		0.00044
(0.00188) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		2e-05
(0.000118) 		1e-05
(6.52e-05) 		0.00477
(0.0154) 		0.0116
(0.033) 		0.105
(0.19)
8q gain 62 (12%) 466 0.227
(0.341) 		0.105
(0.19) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		0.00014
(0.000689) 		0.00047
(0.00198) 		0.408
(0.545)
20p gain 112 (21%) 416 0.117
(0.204) 		0.116
(0.204) 		1e-05
(6.52e-05) 		2e-05
(0.000118) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		2e-05
(0.000118) 		0.053
(0.113)
1p loss 57 (11%) 471 0.00085
(0.00336) 		0.00273
(0.00959) 		1e-05
(6.52e-05) 		0.675
(0.816) 		0.00748
(0.0227) 		0.0193
(0.0497) 		0.116
(0.204) 		4e-05
(0.000219) 		0.00796
(0.0241) 		0.0233
(0.058) 		0.0356
(0.0822) 		0.824
(0.953)
1q loss 36 (7%) 492 0.0102
(0.0296) 		0.0111
(0.0317) 		1e-05
(6.52e-05) 		0.369
(0.502) 		0.0362
(0.0834) 		0.00265
(0.00935) 		0.00449
(0.0146) 		1e-05
(6.52e-05) 		0.00589
(0.0184) 		0.042
(0.0942) 		0.223
(0.338) 		0.708
(0.846)
2p loss 14 (3%) 514 4e-05
(0.000219) 		0.00061
(0.00251) 		1e-05
(6.52e-05) 		0.662
(0.805) 		0.00079
(0.00316) 		0.0002
(0.000969) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		2e-05
(0.000118) 		4e-05
(0.000219) 		0.131
(0.224) 		0.0969
(0.179)
2q loss 14 (3%) 514 0.00028
(0.00128) 		0.00086
(0.00338) 		1e-05
(6.52e-05) 		1
(1.00) 		0.00295
(0.0103) 		0.00024
(0.00112) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		2e-05
(0.000118) 		0.132
(0.225) 		0.0962
(0.178)
6q loss 128 (24%) 400 0.0507
(0.109) 		0.0521
(0.112) 		1e-05
(6.52e-05) 		0.00577
(0.0181) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		0.00025
(0.00115) 		8e-05
(0.000414) 		1e-05
(6.52e-05) 		4e-05
(0.000219) 		0.168
(0.273) 		0.0259
(0.0633)
17p loss 46 (9%) 482 7e-05
(0.000368) 		0.00024
(0.00112) 		1e-05
(6.52e-05) 		0.0886
(0.167) 		0.00045
(0.00191) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		0.00022
(0.00106) 		0.202
(0.315) 		0.0856
(0.163)
21q loss 55 (10%) 473 0.0256
(0.0629) 		0.0885
(0.167) 		1e-05
(6.52e-05) 		0.0137
(0.0379) 		0.00074
(0.003) 		1e-05
(6.52e-05) 		0.00324
(0.0111) 		0.0001
(0.00051) 		0.00694
(0.0213) 		0.0093
(0.0276) 		0.884
(1.00) 		1
(1.00)
7p gain 171 (32%) 357 0.452
(0.586) 		0.859
(0.984) 		1e-05
(6.52e-05) 		0.00147
(0.00544) 		1e-05
(6.52e-05) 		4e-05
(0.000219) 		5e-05
(0.000269) 		0.00953
(0.0281) 		0.00411
(0.0135) 		0.031
(0.0737) 		0.102
(0.187) 		0.766
(0.905)
7q gain 172 (33%) 356 0.451
(0.585) 		0.859
(0.984) 		1e-05
(6.52e-05) 		0.00405
(0.0134) 		3e-05
(0.000173) 		2e-05
(0.000118) 		8e-05
(0.000414) 		0.007
(0.0214) 		0.00516
(0.0165) 		0.0178
(0.0467) 		0.174
(0.279) 		0.589
(0.727)
17q loss 28 (5%) 500 0.00051
(0.00214) 		0.00032
(0.00145) 		1e-05
(6.52e-05) 		0.582
(0.721) 		0.156
(0.257) 		0.00278
(0.00973) 		7e-05
(0.000368) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		0.00512
(0.0164) 		0.456
(0.588) 		0.15
(0.251)
19p loss 11 (2%) 517 2e-05
(0.000118) 		0.0322
(0.0759) 		0.00015
(0.000734) 		0.00177
(0.00636) 		0.168
(0.273) 		0.0108
(0.031) 		0.24
(0.354) 		0.00939
(0.0277) 		0.0335
(0.0782) 		0.0374
(0.0853)
1p gain 24 (5%) 504 0.82
(0.949) 		0.925
(1.00) 		1e-05
(6.52e-05) 		0.00059
(0.00244) 		0.176
(0.281) 		0.393
(0.529) 		0.00088
(0.00345) 		0.00139
(0.0052) 		0.00176
(0.00634) 		0.0065
(0.0202) 		0.752
(0.891) 		0.0391
(0.0885)
19p gain 51 (10%) 477 0.223
(0.338) 		0.484
(0.617) 		1e-05
(6.52e-05) 		5e-05
(0.000269) 		0.00146
(0.00542) 		0.0127
(0.0356) 		0.00163
(0.00594) 		0.00078
(0.00313) 		3e-05
(0.000173) 		0.356
(0.486) 		0.921
(1.00) 		0.626
(0.766)
19q gain 57 (11%) 471 0.103
(0.188) 		0.224
(0.338) 		1e-05
(6.52e-05) 		4e-05
(0.000219) 		2e-05
(0.000118) 		0.00064
(0.00262) 		0.00059
(0.00244) 		9e-05
(0.000461) 		1e-05
(6.52e-05) 		0.17
(0.275) 		0.582
(0.721) 		0.287
(0.409)
11q loss 23 (4%) 505 0.189
(0.297) 		0.374
(0.508) 		1e-05
(6.52e-05) 		0.00553
(0.0176) 		0.162
(0.266) 		0.00966
(0.0284) 		0.014
(0.0385) 		0.00039
(0.0017) 		0.0229
(0.0574) 		0.0378
(0.0861) 		0.3
(0.421) 		0.309
(0.432)
15q loss 36 (7%) 492 0.117
(0.204) 		0.334
(0.461) 		1e-05
(6.52e-05) 		0.00068
(0.00276) 		0.0618
(0.129) 		0.00969
(0.0284) 		1e-05
(6.52e-05) 		1e-05
(6.52e-05) 		0.00089
(0.00348) 		0.016
(0.043) 		0.0703
(0.142) 		0.131
(0.223)
1q gain 51 (10%) 477 0.41
(0.545) 		0.901
(1.00) 		1e-05
(6.52e-05) 		0.0139
(0.0385) 		0.149
(0.25) 		0.207
(0.32) 		1e-05
(6.52e-05) 		0.00175
(0.00633) 		3e-05
(0.000173) 		0.00567
(0.0179) 		0.421
(0.557) 		0.758
(0.898)
4p gain 13 (2%) 515 0.0723
(0.144) 		0.374
(0.508) 		0.0373
(0.0853) 		5e-05
(0.000269) 		0.00038
(0.00166) 		0.00041
(0.00177) 		0.00023
(0.00109) 		0.0448
(0.098)
14q gain 16 (3%) 512 0.77
(0.908) 		0.572
(0.711) 		0.00119
(0.00456) 		0.35
(0.48) 		0.00191
(0.00681) 		0.0334
(0.078) 		0.00694
(0.0213) 		0.00034
(0.00153) 		0.00403
(0.0134) 		0.113
(0.2)
21q gain 50 (9%) 478 0.27
(0.389) 		0.208
(0.32) 		1e-05
(6.52e-05) 		0.00133
(0.00503) 		0.162
(0.266) 		0.0629
(0.13) 		0.00025
(0.00115) 		0.00322
(0.0111) 		0.00315
(0.0109) 		0.0311
(0.0738) 		0.351
(0.48) 		0.474
(0.606)
4p loss 72 (14%) 456 0.532
(0.669) 		0.816
(0.947) 		1e-05
(6.52e-05) 		0.00012
(0.000602) 		0.00058
(0.00242) 		0.0581
(0.122) 		0.00083
(0.00329) 		0.00125
(0.00475) 		0.568
(0.707) 		0.0708
(0.142) 		0.0788
(0.153) 		0.00695
(0.0213)
4q loss 65 (12%) 463 0.386
(0.522) 		0.785
(0.919) 		1e-05
(6.52e-05) 		2e-05
(0.000118) 		0.00036
(0.0016) 		0.017
(0.045) 		0.00038
(0.00166) 		3e-05
(0.000173) 		0.198
(0.31) 		0.0641
(0.132) 		0.429
(0.566) 		0.0565
(0.12)
10q loss 89 (17%) 439 0.331
(0.458) 		0.4
(0.536) 		1e-05
(6.52e-05) 		0.00421
(0.0138) 		0.819
(0.949) 		0.0222
(0.0563) 		0.122
(0.212) 		0.00198
(0.00703) 		0.0383
(0.0869) 		0.0005
(0.0021) 		0.804
(0.937) 		0.436
(0.572)
xq loss 46 (9%) 482 0.0241
(0.0597) 		0.0628
(0.13) 		1e-05
(6.52e-05) 		0.00897
(0.0268) 		0.597
(0.736) 		0.0508
(0.109) 		0.0914
(0.171) 		0.0281
(0.0674) 		0.018
(0.0471) 		0.00334
(0.0114) 		0.229
(0.343) 		0.175
(0.279)
3p gain 19 (4%) 509 0.0542
(0.116) 		0.433
(0.569) 		0.00037
(0.00163) 		0.579
(0.719) 		0.178
(0.284) 		0.00045
(0.00191) 		0.009
(0.0268) 		0.00014
(0.000689) 		0.00014
(0.000689) 		0.125
(0.217) 		0.392
(0.528) 		0.736
(0.875)
4q gain 13 (2%) 515 0.214
(0.327) 		0.456
(0.588) 		0.272
(0.39) 		0.0015
(0.00551) 		0.00032
(0.00145) 		0.00435
(0.0142) 		0.00021
(0.00101) 		0.0442
(0.0971)
10p gain 17 (3%) 511 0.00024
(0.00112) 		0.255
(0.373) 		0.0239
(0.0594) 		0.0784
(0.153) 		0.00091
(0.00353) 		0.00017
(0.000828) 		0.0186
(0.0483) 		0.0682
(0.139)
16p gain 107 (20%) 421 0.273
(0.391) 		0.379
(0.514) 		9e-05
(0.000461) 		0.168
(0.273) 		0.0215
(0.0549) 		0.181
(0.286) 		0.00671
(0.0208) 		0.00438
(0.0143) 		0.0603
(0.126) 		0.0259
(0.0633) 		0.129
(0.221) 		0.394
(0.529)
16q gain 99 (19%) 429 0.234
(0.347) 		0.351
(0.48) 		4e-05
(0.000219) 		0.0881
(0.167) 		0.00558
(0.0177) 		0.0922
(0.171) 		0.00626
(0.0195) 		0.016
(0.043) 		0.0162
(0.0434) 		0.147
(0.247) 		0.18
(0.286) 		0.266
(0.385)
17p gain 26 (5%) 502 0.0181
(0.0472) 		0.00532
(0.0169) 		2e-05
(0.000118) 		0.816
(0.947) 		0.135
(0.229) 		0.101
(0.186) 		0.15
(0.251) 		0.00497
(0.016) 		0.147
(0.247) 		0.263
(0.381) 		0.0346
(0.08) 		0.735
(0.874)
xp gain 32 (6%) 496 1
(1.00) 		0.527
(0.664) 		0.00586
(0.0184) 		0.225
(0.339) 		0.00012
(0.000602) 		0.0011
(0.00423) 		0.016
(0.043) 		0.00091
(0.00353) 		0.128
(0.22) 		0.142
(0.241) 		0.556
(0.695) 		0.901
(1.00)
5p loss 7 (1%) 521 0.0163
(0.0436) 		0.287
(0.409) 		0.0102
(0.0296) 		0.0783
(0.153) 		0.0265
(0.0642) 		0.011
(0.0316) 		0.0423
(0.0945) 		0.0656
(0.134)
xp loss 46 (9%) 482 0.0433
(0.0961) 		0.0663
(0.135) 		0.00013
(0.000649) 		0.0718
(0.143) 		0.464
(0.595) 		0.24
(0.354) 		0.207
(0.32) 		0.0123
(0.0345) 		0.0398
(0.0899) 		0.00094
(0.00363) 		0.109
(0.195) 		0.161
(0.264)
5p gain 193 (37%) 335 0.883
(1.00) 		0.924
(1.00) 		0.00036
(0.0016) 		0.259
(0.377) 		0.0186
(0.0483) 		0.891
(1.00) 		0.00864
(0.026) 		0.0217
(0.0554) 		0.0689
(0.139) 		0.152
(0.252) 		0.0829
(0.158) 		0.906
(1.00)
10q gain 12 (2%) 516 0.00012
(0.000602) 		0.117
(0.204) 		0.0573
(0.121) 		0.0923
(0.171) 		0.014
(0.0385) 		0.00182
(0.00651) 		0.0154
(0.0419) 		0.213
(0.327)
17q gain 33 (6%) 495 0.0703
(0.142) 		0.026
(0.0633) 		1e-05
(6.52e-05) 		0.238
(0.353) 		0.115
(0.204) 		0.223
(0.338) 		0.076
(0.149) 		0.00167
(0.00606) 		0.0786
(0.153) 		0.222
(0.338) 		0.0021
(0.00743) 		0.297
(0.419)
5q loss 6 (1%) 522 0.0432
(0.096) 		0.542
(0.679) 		0.0432
(0.096) 		0.224
(0.339) 		0.0458
(0.0999) 		0.0151
(0.0411) 		0.0728
(0.144) 		0.0947
(0.175)
8p loss 137 (26%) 391 0.381
(0.515) 		0.165
(0.269) 		1e-05
(6.52e-05) 		0.28
(0.4) 		0.0729
(0.144) 		0.977
(1.00) 		0.0829
(0.158) 		0.00124
(0.00473) 		0.0417
(0.094) 		0.0231
(0.0578) 		0.274
(0.392) 		0.243
(0.357)
10p loss 67 (13%) 461 0.175
(0.279) 		0.404
(0.54) 		1e-05
(6.52e-05) 		0.0808
(0.156) 		0.461
(0.592) 		0.0226
(0.0569) 		0.153
(0.254) 		0.0008
(0.00319) 		0.017
(0.045) 		0.109
(0.195) 		0.776
(0.913) 		0.296
(0.418)
2q gain 79 (15%) 449 0.562
(0.701) 		0.267
(0.386) 		1e-05
(6.52e-05) 		0.165
(0.27) 		0.18
(0.286) 		0.668
(0.812) 		0.23
(0.344) 		0.0173
(0.0456) 		0.708
(0.846) 		0.0252
(0.0622) 		0.32
(0.445) 		0.652
(0.794)
9p gain 13 (2%) 515 0.0152
(0.0412) 		0.902
(1.00) 		0.51
(0.648) 		0.0342
(0.0795) 		0.248
(0.363) 		0.0176
(0.0463) 		1
(1.00) 		0.861
(0.985) 		1
(1.00) 		1
(1.00)
9q gain 12 (2%) 516 0.00139
(0.0052) 		0.909
(1.00) 		0.25
(0.365) 		0.0316
(0.0747) 		0.241
(0.354) 		0.0262
(0.0638) 		0.531
(0.669) 		0.67
(0.813) 		1
(1.00) 		1
(1.00)
3q loss 99 (19%) 429 0.923
(1.00) 		0.513
(0.65) 		0.00143
(0.00533) 		0.403
(0.54) 		0.19
(0.299) 		0.174
(0.279) 		0.129
(0.221) 		0.0192
(0.0497) 		0.651
(0.794) 		0.0273
(0.0659) 		0.802
(0.937) 		0.863
(0.986)
7q loss 4 (1%) 524 0.122
(0.212) 		0.344
(0.473) 		0.0107
(0.0308) 		0.0563
(0.12) 		0.0495
(0.107) 		0.0788
(0.153) 		0.0193
(0.0497) 		0.773
(0.912)
11p loss 18 (3%) 510 1e-05
(6.52e-05) 		0.0223
(0.0565) 		0.434
(0.57) 		0.105
(0.19) 		0.171
(0.275) 		0.0273
(0.0659) 		0.171
(0.275) 		0.149
(0.25) 		0.3
(0.421) 		0.31
(0.433)
16q loss 16 (3%) 512 0.0379
(0.0861) 		0.909
(1.00) 		0.295
(0.417) 		0.432
(0.568) 		0.106
(0.192) 		0.0898
(0.169) 		0.0648
(0.133) 		0.00867
(0.026) 		0.0707
(0.142) 		0.028
(0.0674)
2p gain 77 (15%) 451 0.701
(0.841) 		0.458
(0.59) 		1e-05
(6.52e-05) 		0.0824
(0.158) 		0.0736
(0.146) 		0.777
(0.913) 		0.232
(0.346) 		0.0118
(0.0334) 		0.621
(0.76) 		0.143
(0.242) 		0.229
(0.343) 		0.47
(0.601)
5q gain 207 (39%) 321 0.334
(0.461) 		0.626
(0.766) 		0.0225
(0.0568) 		0.439
(0.573) 		0.00708
(0.0216) 		0.797
(0.932) 		0.0567
(0.12) 		0.0686
(0.139) 		0.448
(0.583) 		0.207
(0.32) 		0.129
(0.221) 		0.906
(1.00)
15q gain 26 (5%) 502 1
(1.00) 		0.117
(0.204) 		0.00077
(0.00311) 		0.724
(0.864) 		0.0914
(0.171) 		0.00385
(0.0128) 		0.672
(0.813) 		0.106
(0.191) 		0.706
(0.846) 		0.412
(0.547) 		0.684
(0.822) 		0.827
(0.955)
22q gain 40 (8%) 488 0.327
(0.454) 		0.219
(0.335) 		2e-05
(0.000118) 		0.209
(0.321) 		0.534
(0.67) 		0.292
(0.414) 		0.0547
(0.117) 		0.0164
(0.0436) 		0.0621
(0.129) 		0.412
(0.547) 		0.91
(1.00) 		0.306
(0.43)
7p loss 3 (1%) 525 0.166
(0.271) 		0.0445
(0.0976) 		0.042
(0.0942) 		0.107
(0.193) 		0.169
(0.273) 		0.0574
(0.121) 		0.355
(0.485)
11p gain 31 (6%) 497 0.231
(0.345) 		0.671
(0.813) 		1e-05
(6.52e-05) 		0.271
(0.39) 		0.0726
(0.144) 		0.514
(0.65) 		0.152
(0.253) 		0.239
(0.353) 		0.146
(0.246) 		0.281
(0.401) 		0.392
(0.528) 		0.854
(0.982)
11q gain 29 (5%) 499 0.342
(0.471) 		0.906
(1.00) 		0.00023
(0.00109) 		0.528
(0.666) 		0.138
(0.234) 		0.828
(0.956) 		0.422
(0.557) 		0.573
(0.712) 		0.364
(0.496) 		0.186
(0.293) 		0.751
(0.891) 		0.679
(0.819)
13q gain 22 (4%) 506 0.487
(0.62) 		0.0344
(0.0798) 		0.227
(0.342) 		0.431
(0.568) 		0.0707
(0.142) 		0.12
(0.21) 		0.345
(0.474) 		0.263
(0.381) 		0.285
(0.406) 		0.323
(0.449)
18p gain 25 (5%) 503 0.313
(0.436) 		0.0765
(0.15) 		0.0749
(0.147) 		0.448
(0.583) 		0.904
(1.00) 		0.522
(0.66) 		0.191
(0.299) 		0.421
(0.557) 		0.835
(0.961) 		0.454
(0.588) 		0.202
(0.315) 		0.0442
(0.0971)
18q gain 25 (5%) 503 0.313
(0.436) 		0.076
(0.149) 		0.0678
(0.138) 		0.558
(0.697) 		0.764
(0.904) 		0.549
(0.688) 		0.188
(0.297) 		0.42
(0.557) 		0.965
(1.00) 		0.452
(0.585) 		0.202
(0.315) 		0.0441
(0.0971)
xq gain 31 (6%) 497 0.39
(0.526) 		0.701
(0.841) 		0.222
(0.338) 		0.292
(0.414) 		0.0226
(0.0569) 		0.0692
(0.14) 		0.154
(0.255) 		0.102
(0.188) 		0.323
(0.449) 		0.6
(0.739) 		0.918
(1.00) 		0.811
(0.944)
8q loss 64 (12%) 464 0.647
(0.79) 		0.126
(0.219) 		0.122
(0.212) 		0.0439
(0.0971) 		0.0649
(0.133) 		0.439
(0.573) 		0.722
(0.862) 		0.19
(0.298) 		0.589
(0.727) 		0.409
(0.545) 		0.682
(0.821) 		0.0893
(0.168)
16p loss 10 (2%) 518 0.204
(0.318) 		0.877
(1.00) 		0.127
(0.219) 		0.0487
(0.105) 		0.293
(0.415) 		0.0624
(0.129) 		0.0918
(0.171) 		0.116
(0.204) 		0.117
(0.204) 		0.116
(0.204)
19q loss 4 (1%) 524 0.0118
(0.0334) 		0.262
(0.38) 		0.256
(0.374) 		0.437
(0.572) 		0.513
(0.65) 		0.833
(0.96) 		0.082
(0.158)
20p loss 8 (2%) 520 0.172
(0.276) 		1
(1.00) 		0.257
(0.374) 		0.499
(0.634) 		0.0904
(0.17) 		0.233
(0.346) 		0.0193
(0.0497) 		0.233
(0.346)
20q loss 3 (1%) 525 0.165
(0.269) 		0.108
(0.194) 		0.154
(0.255) 		0.0592
(0.124) 		0.0294
(0.0704)
6p gain 11 (2%) 517 0.152
(0.253) 		0.445
(0.58) 		0.217
(0.332) 		0.951
(1.00) 		0.794
(0.929) 		0.984
(1.00) 		0.859
(0.984) 		0.111
(0.199) 		0.606
(0.744) 		0.78
(0.915)
6q gain 9 (2%) 519 0.0837
(0.16) 		0.679
(0.819) 		0.109
(0.195) 		0.806
(0.939) 		1
(1.00) 		0.911
(1.00) 		1
(1.00) 		0.183
(0.289) 		0.603
(0.742) 		0.779
(0.915)
12p loss 4 (1%) 524 0.0858
(0.163) 		0.206
(0.32) 		0.469
(0.601) 		0.295
(0.417) 		0.144
(0.243)
12q loss 4 (1%) 524 0.483
(0.617) 		0.209
(0.322) 		0.88
(1.00) 		1
(1.00) 		1
(1.00) 		0.233
(0.346) 		0.613
(0.752)
'1p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.5e-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 = 0.00059 (Fisher's exact test), Q value = 0.0024

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 'MRNASEQ_CNMF'

P value = 0.00088 (Fisher's exact test), Q value = 0.0034

Table S3.  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 S3.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00139 (Fisher's exact test), Q value = 0.0052

Table S4.  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 S4.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p gain' versus 'MIRSEQ_CNMF'

P value = 0.00176 (Fisher's exact test), Q value = 0.0063

Table S5.  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 S5.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0065 (Fisher's exact test), Q value = 0.02

Table S6.  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 S6.  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 = 0.088

Table S7.  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 S7.  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 = 6.5e-05

Table S8.  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 S8.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

'1q gain' versus 'METHLYATION_CNMF'

P value = 0.0139 (Fisher's exact test), Q value = 0.038

Table S9.  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 S9.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.5e-05

Table S10.  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 S10.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00175 (Fisher's exact test), Q value = 0.0063

Table S11.  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 S11.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00017

Table S12.  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 S12.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00567 (Fisher's exact test), Q value = 0.018

Table S13.  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 S13.  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 = 6.5e-05

Table S14.  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 S14.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #3: 'CN_CNMF'

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0118 (Fisher's exact test), Q value = 0.033

Table S15.  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 S15.  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 = 6.5e-05

Table S16.  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 S16.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

'2q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0173 (Fisher's exact test), Q value = 0.046

Table S17.  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 S17.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0252 (Fisher's exact test), Q value = 0.062

Table S18.  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 S18.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3p gain' versus 'CN_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.0016

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

'3p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00045 (Fisher's exact test), Q value = 0.0019

Table S20.  Gene #5: '3p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
3P GAIN MUTATED 1 3 10 3
3P GAIN WILD-TYPE 134 109 75 136

Figure S20.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'3p gain' versus 'MRNASEQ_CNMF'

P value = 0.009 (Fisher's exact test), Q value = 0.027

Table S21.  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 S21.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.00069

Table S22.  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 S22.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3p gain' versus 'MIRSEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00069

Table S23.  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 S23.  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 = 0.034

Table S24.  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 S24.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'3q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0309 (Fisher's exact test), Q value = 0.074

Table S25.  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 S25.  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 = 6.5e-05

Table S26.  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 S26.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #3: 'CN_CNMF'

'3q gain' versus 'METHLYATION_CNMF'

P value = 0.00365 (Fisher's exact test), Q value = 0.012

Table S27.  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 S27.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3q gain' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.5e-05

Table S28.  Gene #6: '3q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
3Q GAIN MUTATED 16 5 24 4 7 0
3Q GAIN WILD-TYPE 72 81 66 78 85 33

Figure S28.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'3q gain' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
3Q GAIN MUTATED 8 14 25 9
3Q GAIN WILD-TYPE 127 98 60 130

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

'3q gain' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00032

Table S30.  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 S30.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

Table S31.  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 S31.  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 = 6.5e-05

Table S32.  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 S32.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-04 (Fisher's exact test), Q value = 0.0017

Table S33.  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 S33.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00154 (Fisher's exact test), Q value = 0.0056

Table S34.  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 S34.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4p gain' versus 'RPPA_CNMF'

P value = 0.0373 (Fisher's exact test), Q value = 0.085

Table S35.  Gene #7: '4p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
4P GAIN MUTATED 3 1 5 0 0 0
4P GAIN WILD-TYPE 85 85 85 82 92 33

Figure S35.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'4p gain' versus 'RPPA_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00027

Table S36.  Gene #7: '4p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
4P GAIN MUTATED 0 2 7 0
4P GAIN WILD-TYPE 135 110 78 139

Figure S36.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'4p gain' versus 'MRNASEQ_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.0017

Table S37.  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 S37.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00041 (Fisher's exact test), Q value = 0.0018

Table S38.  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 S38.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p gain' versus 'MIRSEQ_CNMF'

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

Table S39.  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 S39.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0448 (Fisher's exact test), Q value = 0.098

Table S40.  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 S40.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0015 (Fisher's exact test), Q value = 0.0055

Table S41.  Gene #8: '4q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
4Q GAIN MUTATED 1 2 6 0
4Q GAIN WILD-TYPE 134 110 79 139

Figure S41.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'4q gain' versus 'MRNASEQ_CNMF'

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

Table S42.  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 S42.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00435 (Fisher's exact test), Q value = 0.014

Table S43.  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 S43.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q gain' versus 'MIRSEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.001

Table S44.  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 S44.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0442 (Fisher's exact test), Q value = 0.097

Table S45.  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 S45.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5p gain' versus 'CN_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.0016

Table S46.  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 S46.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

'5p gain' versus 'RPPA_CNMF'

P value = 0.0186 (Fisher's exact test), Q value = 0.048

Table S47.  Gene #9: '5p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
5P GAIN MUTATED 31 20 40 37 37 9
5P GAIN WILD-TYPE 57 66 50 45 55 24

Figure S47.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'5p gain' versus 'MRNASEQ_CNMF'

P value = 0.00864 (Fisher's exact test), Q value = 0.026

Table S48.  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 S48.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0217 (Fisher's exact test), Q value = 0.055

Table S49.  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 S49.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q gain' versus 'CN_CNMF'

P value = 0.0225 (Fisher's exact test), Q value = 0.057

Table S50.  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 S50.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'

'5q gain' versus 'RPPA_CNMF'

P value = 0.00708 (Fisher's exact test), Q value = 0.022

Table S51.  Gene #10: '5q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
5Q GAIN MUTATED 35 20 38 41 42 11
5Q GAIN WILD-TYPE 53 66 52 41 50 22

Figure S51.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.5e-05

Table S52.  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 S52.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 0.00147 (Fisher's exact test), Q value = 0.0054

Table S53.  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 S53.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p gain' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.5e-05

Table S54.  Gene #13: '7p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
7P GAIN MUTATED 32 21 50 23 22 5
7P GAIN WILD-TYPE 56 65 40 59 70 28

Figure S54.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'7p gain' versus 'RPPA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00022

Table S55.  Gene #13: '7p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
7P GAIN MUTATED 34 48 41 30
7P GAIN WILD-TYPE 101 64 44 109

Figure S55.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00027

Table S56.  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 S56.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00953 (Fisher's exact test), Q value = 0.028

Table S57.  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 S57.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_CNMF'

P value = 0.00411 (Fisher's exact test), Q value = 0.014

Table S58.  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 S58.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.031 (Fisher's exact test), Q value = 0.074

Table S59.  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 S59.  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 = 6.5e-05

Table S60.  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 S60.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 0.00405 (Fisher's exact test), Q value = 0.013

Table S61.  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 S61.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7q gain' versus 'RPPA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00017

Table S62.  Gene #14: '7q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
7Q GAIN MUTATED 32 21 50 24 23 4
7Q GAIN WILD-TYPE 56 65 40 58 69 29

Figure S62.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'7q gain' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

Table S63.  Gene #14: '7q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
7Q GAIN MUTATED 35 49 41 29
7Q GAIN WILD-TYPE 100 63 44 110

Figure S63.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00041

Table S64.  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 S64.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.007 (Fisher's exact test), Q value = 0.021

Table S65.  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 S65.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_CNMF'

P value = 0.00516 (Fisher's exact test), Q value = 0.016

Table S66.  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 S66.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0178 (Fisher's exact test), Q value = 0.047

Table S67.  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 S67.  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 = 6.5e-05

Table S68.  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 S68.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

'8p gain' versus 'METHLYATION_CNMF'

P value = 0.00042 (Fisher's exact test), Q value = 0.0018

Table S69.  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 S69.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p gain' versus 'RPPA_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.0019

Table S70.  Gene #15: '8p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
8P GAIN MUTATED 3 2 16 4 4 0
8P GAIN WILD-TYPE 85 84 74 78 88 33

Figure S70.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'8p gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.5e-05

Table S71.  Gene #15: '8p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
8P GAIN MUTATED 1 18 7 3
8P GAIN WILD-TYPE 134 94 78 136

Figure S71.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'8p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.5e-05

Table S72.  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 S72.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

Table S73.  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 S73.  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 = 6.5e-05

Table S74.  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 S74.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00477 (Fisher's exact test), Q value = 0.015

Table S75.  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 S75.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0116 (Fisher's exact test), Q value = 0.033

Table S76.  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 S76.  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 = 6.5e-05

Table S77.  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 S77.  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 = 6.5e-05

Table S78.  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 S78.  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 = 6.5e-05

Table S79.  Gene #16: '8q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
8Q GAIN MUTATED 10 3 30 6 8 1
8Q GAIN WILD-TYPE 78 83 60 76 84 32

Figure S79.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'8q gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.5e-05

Table S80.  Gene #16: '8q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
8Q GAIN MUTATED 5 29 17 7
8Q GAIN WILD-TYPE 130 83 68 132

Figure S80.  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 = 6.5e-05

Table S81.  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 S81.  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 = 6.5e-05

Table S82.  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 S82.  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 = 6.5e-05

Table S83.  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 S83.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.00069

Table S84.  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 S84.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.002

Table S85.  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 S85.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9p gain' versus 'CN_CNMF'

P value = 0.0152 (Fisher's exact test), Q value = 0.041

Table S86.  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 S86.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'

'9p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0342 (Fisher's exact test), Q value = 0.079

Table S87.  Gene #17: '9p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
9P GAIN MUTATED 1 0 3 6
9P GAIN WILD-TYPE 134 112 82 133

Figure S87.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'9p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0176 (Fisher's exact test), Q value = 0.046

Table S88.  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 S88.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q gain' versus 'CN_CNMF'

P value = 0.00139 (Fisher's exact test), Q value = 0.0052

Table S89.  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 S89.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #3: 'CN_CNMF'

'9q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0316 (Fisher's exact test), Q value = 0.075

Table S90.  Gene #18: '9q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
9Q GAIN MUTATED 0 1 4 4
9Q GAIN WILD-TYPE 135 111 81 135

Figure S90.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'9q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0262 (Fisher's exact test), Q value = 0.064

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 = 0.0011

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 'RPPA_CNMF'

P value = 0.0239 (Fisher's exact test), Q value = 0.059

Table S93.  Gene #19: '10p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
10P GAIN MUTATED 1 1 9 2 2 1
10P GAIN WILD-TYPE 87 85 81 80 90 32

Figure S93.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'10p gain' versus 'MRNASEQ_CNMF'

P value = 0.00091 (Fisher's exact test), Q value = 0.0035

Table S94.  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 S94.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.00083

Table S95.  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 S95.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p gain' versus 'MIRSEQ_CNMF'

P value = 0.0186 (Fisher's exact test), Q value = 0.048

Table S96.  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 S96.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10q gain' versus 'CN_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 6e-04

Table S97.  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 S97.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

'10q gain' versus 'MRNASEQ_CNMF'

P value = 0.014 (Fisher's exact test), Q value = 0.039

Table S98.  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 S98.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00182 (Fisher's exact test), Q value = 0.0065

Table S99.  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 S99.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q gain' versus 'MIRSEQ_CNMF'

P value = 0.0154 (Fisher's exact test), Q value = 0.042

Table S100.  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 S100.  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 = 6.5e-05

Table S101.  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 S101.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

'11q gain' versus 'CN_CNMF'

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

Table S102.  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 S102.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'MRNA_CNMF'

P value = 0.0131 (Fisher's exact test), Q value = 0.036

Table S103.  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 S103.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'12p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0326 (Fisher's exact test), Q value = 0.077

Table S104.  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 S104.  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 = 6.5e-05

Table S105.  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 S105.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.5e-05

Table S106.  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 S106.  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 = 6.5e-05

Table S107.  Gene #23: '12p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
12P GAIN MUTATED 16 3 47 20 19 2
12P GAIN WILD-TYPE 72 83 43 62 73 31

Figure S107.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'12p gain' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

Table S108.  Gene #23: '12p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
12P GAIN MUTATED 21 37 31 18
12P GAIN WILD-TYPE 114 75 54 121

Figure S108.  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 = 6.5e-05

Table S109.  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 S109.  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 = 6.5e-05

Table S110.  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 S110.  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 = 6.5e-05

Table S111.  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 S111.  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 = 6.5e-05

Table S112.  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 S112.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00149 (Fisher's exact test), Q value = 0.0055

Table S113.  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 S113.  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 = 0.037

Table S114.  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 S114.  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 = 0.078

Table S115.  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 S115.  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 = 6.5e-05

Table S116.  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 S116.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

'12q gain' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00041

Table S117.  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 S117.  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 = 6.5e-05

Table S118.  Gene #24: '12q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
12Q GAIN MUTATED 16 3 49 20 18 2
12Q GAIN WILD-TYPE 72 83 41 62 74 31

Figure S118.  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 = 6.5e-05

Table S119.  Gene #24: '12q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
12Q GAIN MUTATED 21 38 31 18
12Q GAIN WILD-TYPE 114 74 54 121

Figure S119.  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 = 6.5e-05

Table S120.  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 S120.  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 = 6.5e-05

Table S121.  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 S121.  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 = 6.5e-05

Table S122.  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 S122.  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 = 6.5e-05

Table S123.  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 S123.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00288 (Fisher's exact test), Q value = 0.01

Table S124.  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 S124.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'13q gain' versus 'METHLYATION_CNMF'

P value = 0.0344 (Fisher's exact test), Q value = 0.08

Table S125.  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 S125.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q gain' versus 'CN_CNMF'

P value = 0.00119 (Fisher's exact test), Q value = 0.0046

Table S126.  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 S126.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

'14q gain' versus 'RPPA_CNMF'

P value = 0.00191 (Fisher's exact test), Q value = 0.0068

Table S127.  Gene #26: '14q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
14Q GAIN MUTATED 5 0 7 1 0 0
14Q GAIN WILD-TYPE 83 86 83 81 92 33

Figure S127.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'14q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0334 (Fisher's exact test), Q value = 0.078

Table S128.  Gene #26: '14q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
14Q GAIN MUTATED 1 4 6 2
14Q GAIN WILD-TYPE 134 108 79 137

Figure S128.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'14q gain' versus 'MRNASEQ_CNMF'

P value = 0.00694 (Fisher's exact test), Q value = 0.021

Table S129.  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 S129.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00034 (Fisher's exact test), Q value = 0.0015

Table S130.  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 S130.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_CNMF'

P value = 0.00403 (Fisher's exact test), Q value = 0.013

Table S131.  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 S131.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'15q gain' versus 'CN_CNMF'

P value = 0.00077 (Fisher's exact test), Q value = 0.0031

Table S132.  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 S132.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #3: 'CN_CNMF'

'15q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00385 (Fisher's exact test), Q value = 0.013

Table S133.  Gene #27: '15q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
15Q GAIN MUTATED 0 7 6 9
15Q GAIN WILD-TYPE 135 105 79 130

Figure S133.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'16p gain' versus 'CN_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00046

Table S134.  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 S134.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

'16p gain' versus 'RPPA_CNMF'

P value = 0.0215 (Fisher's exact test), Q value = 0.055

Table S135.  Gene #28: '16p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
16P GAIN MUTATED 23 10 23 22 13 4
16P GAIN WILD-TYPE 65 76 67 60 79 29

Figure S135.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 0.00671 (Fisher's exact test), Q value = 0.021

Table S136.  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 S136.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00438 (Fisher's exact test), Q value = 0.014

Table S137.  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 S137.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0259 (Fisher's exact test), Q value = 0.063

Table S138.  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 S138.  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 = 0.00022

Table S139.  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 S139.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

'16q gain' versus 'RPPA_CNMF'

P value = 0.00558 (Fisher's exact test), Q value = 0.018

Table S140.  Gene #29: '16q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
16Q GAIN MUTATED 23 7 23 18 12 4
16Q GAIN WILD-TYPE 65 79 67 64 80 29

Figure S140.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'16q gain' versus 'MRNASEQ_CNMF'

P value = 0.00626 (Fisher's exact test), Q value = 0.019

Table S141.  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 S141.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.016 (Fisher's exact test), Q value = 0.043

Table S142.  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 S142.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_CNMF'

P value = 0.0162 (Fisher's exact test), Q value = 0.043

Table S143.  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 S143.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17p gain' versus 'MRNA_CNMF'

P value = 0.0181 (Fisher's exact test), Q value = 0.047

Table S144.  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 S144.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'17p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00532 (Fisher's exact test), Q value = 0.017

Table S145.  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 S145.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17p gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

Table S146.  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 S146.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

'17p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00497 (Fisher's exact test), Q value = 0.016

Table S147.  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 S147.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0346 (Fisher's exact test), Q value = 0.08

Table S148.  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 S148.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'17q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.026 (Fisher's exact test), Q value = 0.063

Table S149.  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 S149.  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 = 6.5e-05

Table S150.  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 S150.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00167 (Fisher's exact test), Q value = 0.0061

Table S151.  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 S151.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0021 (Fisher's exact test), Q value = 0.0074

Table S152.  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 S152.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0442 (Fisher's exact test), Q value = 0.097

Table S153.  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 S153.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0441 (Fisher's exact test), Q value = 0.097

Table S154.  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 S154.  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 = 6.5e-05

Table S155.  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 S155.  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 = 0.00027

Table S156.  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 S156.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p gain' versus 'RPPA_CNMF'

P value = 0.00146 (Fisher's exact test), Q value = 0.0054

Table S157.  Gene #34: '19p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
19P GAIN MUTATED 13 3 17 7 6 0
19P GAIN WILD-TYPE 75 83 73 75 86 33

Figure S157.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'19p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0127 (Fisher's exact test), Q value = 0.036

Table S158.  Gene #34: '19p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
19P GAIN MUTATED 6 17 12 11
19P GAIN WILD-TYPE 129 95 73 128

Figure S158.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'19p gain' versus 'MRNASEQ_CNMF'

P value = 0.00163 (Fisher's exact test), Q value = 0.0059

Table S159.  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 S159.  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 = 0.0031

Table S160.  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 S160.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00017

Table S161.  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 S161.  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 = 6.5e-05

Table S162.  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 S162.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

'19q gain' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00022

Table S163.  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 S163.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q gain' versus 'RPPA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

Table S164.  Gene #35: '19q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
19Q GAIN MUTATED 13 3 23 7 6 0
19Q GAIN WILD-TYPE 75 83 67 75 86 33

Figure S164.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'19q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00064 (Fisher's exact test), Q value = 0.0026

Table S165.  Gene #35: '19q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
19Q GAIN MUTATED 6 20 15 11
19Q GAIN WILD-TYPE 129 92 70 128

Figure S165.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 0.00059 (Fisher's exact test), Q value = 0.0024

Table S166.  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 S166.  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 = 0.00046

Table S167.  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 S167.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.5e-05

Table S168.  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 S168.  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 = 6.5e-05

Table S169.  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 S169.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

Table S170.  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 S170.  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 = 6.5e-05

Table S171.  Gene #36: '20p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
20P GAIN MUTATED 19 5 45 11 19 2
20P GAIN WILD-TYPE 69 81 45 71 73 31

Figure S171.  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 = 6.5e-05

Table S172.  Gene #36: '20p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
20P GAIN MUTATED 18 35 34 14
20P GAIN WILD-TYPE 117 77 51 125

Figure S172.  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 = 6.5e-05

Table S173.  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 S173.  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 = 6.5e-05

Table S174.  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 S174.  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 = 6.5e-05

Table S175.  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 S175.  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 = 6.5e-05

Table S176.  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 S176.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

Table S177.  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 S177.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'MRNA_CNMF'

P value = 0.0429 (Fisher's exact test), Q value = 0.096

Table S178.  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 S178.  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 = 6.5e-05

Table S179.  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 S179.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00022

Table S180.  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 S180.  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 = 6.5e-05

Table S181.  Gene #37: '20q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
20Q GAIN MUTATED 19 5 47 12 19 2
20Q GAIN WILD-TYPE 69 81 43 70 73 31

Figure S181.  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 = 6.5e-05

Table S182.  Gene #37: '20q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
20Q GAIN MUTATED 18 38 34 14
20Q GAIN WILD-TYPE 117 74 51 125

Figure S182.  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 = 6.5e-05

Table S183.  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 S183.  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 = 6.5e-05

Table S184.  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 S184.  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 = 6.5e-05

Table S185.  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 S185.  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 = 6.5e-05

Table S186.  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 S186.  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 = 6.5e-05

Table S187.  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 S187.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0326 (Fisher's exact test), Q value = 0.077

Table S188.  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 S188.  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 = 6.5e-05

Table S189.  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 S189.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

'21q gain' versus 'METHLYATION_CNMF'

P value = 0.00133 (Fisher's exact test), Q value = 0.005

Table S190.  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 S190.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'21q gain' versus 'MRNASEQ_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.0011

Table S191.  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 S191.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00322 (Fisher's exact test), Q value = 0.011

Table S192.  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 S192.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'21q gain' versus 'MIRSEQ_CNMF'

P value = 0.00315 (Fisher's exact test), Q value = 0.011

Table S193.  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 S193.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'21q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0311 (Fisher's exact test), Q value = 0.074

Table S194.  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 S194.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

Table S195.  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 S195.  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 = 0.044

Table S196.  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 S196.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xp gain' versus 'CN_CNMF'

P value = 0.00586 (Fisher's exact test), Q value = 0.018

Table S197.  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 S197.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #3: 'CN_CNMF'

'xp gain' versus 'RPPA_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 6e-04

Table S198.  Gene #40: 'xp gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
XP GAIN MUTATED 12 0 10 2 3 0
XP GAIN WILD-TYPE 76 86 80 80 89 33

Figure S198.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'xp gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0011 (Fisher's exact test), Q value = 0.0042

Table S199.  Gene #40: 'xp gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
XP GAIN MUTATED 5 6 13 3
XP GAIN WILD-TYPE 130 106 72 136

Figure S199.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'xp gain' versus 'MRNASEQ_CNMF'

P value = 0.016 (Fisher's exact test), Q value = 0.043

Table S200.  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 S200.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'xp gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00091 (Fisher's exact test), Q value = 0.0035

Table S201.  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 S201.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xq gain' versus 'RPPA_CNMF'

P value = 0.0226 (Fisher's exact test), Q value = 0.057

Table S202.  Gene #41: 'xq gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
XQ GAIN MUTATED 9 1 9 4 3 0
XQ GAIN WILD-TYPE 79 85 81 78 89 33

Figure S202.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'1p loss' versus 'MRNA_CNMF'

P value = 0.00085 (Fisher's exact test), Q value = 0.0034

Table S203.  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 S203.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'1p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00273 (Fisher's exact test), Q value = 0.0096

Table S204.  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 S204.  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 = 6.5e-05

Table S205.  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 S205.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'RPPA_CNMF'

P value = 0.00748 (Fisher's exact test), Q value = 0.023

Table S206.  Gene #42: '1p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
1P LOSS MUTATED 18 6 9 9 3 4
1P LOSS WILD-TYPE 70 80 81 73 89 29

Figure S206.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'1p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0193 (Fisher's exact test), Q value = 0.05

Table S207.  Gene #42: '1p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
1P LOSS MUTATED 6 12 14 17
1P LOSS WILD-TYPE 129 100 71 122

Figure S207.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00022

Table S208.  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 S208.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_CNMF'

P value = 0.00796 (Fisher's exact test), Q value = 0.024

Table S209.  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 S209.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0233 (Fisher's exact test), Q value = 0.058

Table S210.  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 S210.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0356 (Fisher's exact test), Q value = 0.082

Table S211.  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 S211.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'1q loss' versus 'MRNA_CNMF'

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

Table S212.  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 S212.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'1q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0111 (Fisher's exact test), Q value = 0.032

Table S213.  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 S213.  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 = 6.5e-05

Table S214.  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 S214.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

'1q loss' versus 'RPPA_CNMF'

P value = 0.0362 (Fisher's exact test), Q value = 0.083

Table S215.  Gene #43: '1q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
1Q LOSS MUTATED 12 4 8 3 2 2
1Q LOSS WILD-TYPE 76 82 82 79 90 31

Figure S215.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'1q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00265 (Fisher's exact test), Q value = 0.0093

Table S216.  Gene #43: '1q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
1Q LOSS MUTATED 3 10 12 6
1Q LOSS WILD-TYPE 132 102 73 133

Figure S216.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'1q loss' versus 'MRNASEQ_CNMF'

P value = 0.00449 (Fisher's exact test), Q value = 0.015

Table S217.  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 S217.  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 = 6.5e-05

Table S218.  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 S218.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1q loss' versus 'MIRSEQ_CNMF'

P value = 0.00589 (Fisher's exact test), Q value = 0.018

Table S219.  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 S219.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.042 (Fisher's exact test), Q value = 0.094

Table S220.  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 S220.  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 = 0.00022

Table S221.  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 S221.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'2p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00061 (Fisher's exact test), Q value = 0.0025

Table S222.  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 S222.  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 = 6.5e-05

Table S223.  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 S223.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

'2p loss' versus 'RPPA_CNMF'

P value = 0.00079 (Fisher's exact test), Q value = 0.0032

Table S224.  Gene #44: '2p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
2P LOSS MUTATED 7 0 2 0 0 0
2P LOSS WILD-TYPE 81 86 88 82 92 33

Figure S224.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'2p loss' versus 'RPPA_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.00097

Table S225.  Gene #44: '2p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
2P LOSS MUTATED 0 1 7 1
2P LOSS WILD-TYPE 135 111 78 138

Figure S225.  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 = 6.5e-05

Table S226.  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 S226.  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 = 6.5e-05

Table S227.  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 S227.  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 = 0.00012

Table S228.  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 S228.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00022

Table S229.  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 S229.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2q loss' versus 'MRNA_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.0013

Table S230.  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 S230.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'2q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00086 (Fisher's exact test), Q value = 0.0034

Table S231.  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 S231.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'2q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.5e-05

Table S232.  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 S232.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

'2q loss' versus 'RPPA_CNMF'

P value = 0.00295 (Fisher's exact test), Q value = 0.01

Table S233.  Gene #45: '2q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
2Q LOSS MUTATED 6 0 3 0 0 0
2Q LOSS WILD-TYPE 82 86 87 82 92 33

Figure S233.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'2q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.0011

Table S234.  Gene #45: '2q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
2Q LOSS MUTATED 0 1 7 1
2Q LOSS WILD-TYPE 135 111 78 138

Figure S234.  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 = 6.5e-05

Table S235.  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 S235.  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 = 6.5e-05

Table S236.  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 S236.  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 = 6.5e-05

Table S237.  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 S237.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

Table S238.  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 S238.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'MRNA_CNMF'

P value = 0.003 (Fisher's exact test), Q value = 0.01

Table S239.  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 S239.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'3p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0103 (Fisher's exact test), Q value = 0.03

Table S240.  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 S240.  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 = 6.5e-05

Table S241.  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 S241.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 0.00068 (Fisher's exact test), Q value = 0.0028

Table S242.  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 S242.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3p loss' versus 'RPPA_CNMF'

P value = 0.0122 (Fisher's exact test), Q value = 0.034

Table S243.  Gene #46: '3p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
3P LOSS MUTATED 52 70 64 65 62 26
3P LOSS WILD-TYPE 36 16 26 17 30 7

Figure S243.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'3p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00034 (Fisher's exact test), Q value = 0.0015

Table S244.  Gene #46: '3p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
3P LOSS MUTATED 95 90 46 108
3P LOSS WILD-TYPE 40 22 39 31

Figure S244.  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 = 6.5e-05

Table S245.  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 S245.  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 = 6.5e-05

Table S246.  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 S246.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CNMF'

P value = 0.0227 (Fisher's exact test), Q value = 0.057

Table S247.  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 S247.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0086 (Fisher's exact test), Q value = 0.026

Table S248.  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 S248.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

P value = 0.00143 (Fisher's exact test), Q value = 0.0053

Table S249.  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 S249.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

'3q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0192 (Fisher's exact test), Q value = 0.05

Table S250.  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 S250.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0273 (Fisher's exact test), Q value = 0.066

Table S251.  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 S251.  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 = 6.5e-05

Table S252.  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 S252.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 6e-04

Table S253.  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 S253.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p loss' versus 'RPPA_CNMF'

P value = 0.00058 (Fisher's exact test), Q value = 0.0024

Table S254.  Gene #48: '4p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
4P LOSS MUTATED 6 11 26 10 15 1
4P LOSS WILD-TYPE 82 75 64 72 77 32

Figure S254.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 0.00083 (Fisher's exact test), Q value = 0.0033

Table S255.  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 S255.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00125 (Fisher's exact test), Q value = 0.0047

Table S256.  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 S256.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00695 (Fisher's exact test), Q value = 0.021

Table S257.  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 S257.  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 = 6.5e-05

Table S258.  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 S258.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

Table S259.  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 S259.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q loss' versus 'RPPA_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.0016

Table S260.  Gene #49: '4q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
4Q LOSS MUTATED 7 8 26 9 12 1
4Q LOSS WILD-TYPE 81 78 64 73 80 32

Figure S260.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'4q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.017 (Fisher's exact test), Q value = 0.045

Table S261.  Gene #49: '4q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
4Q LOSS MUTATED 12 21 17 13
4Q LOSS WILD-TYPE 123 91 68 126

Figure S261.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.0017

Table S262.  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 S262.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00017

Table S263.  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 S263.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5p loss' versus 'CN_CNMF'

P value = 0.0163 (Fisher's exact test), Q value = 0.044

Table S264.  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 S264.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

'5p loss' versus 'RPPA_CNMF'

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

Table S265.  Gene #50: '5p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
5P LOSS MUTATED 0 0 5 0 1 0
5P LOSS WILD-TYPE 88 86 85 82 91 33

Figure S265.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'5p loss' versus 'MRNASEQ_CNMF'

P value = 0.0265 (Fisher's exact test), Q value = 0.064

Table S266.  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 S266.  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 S267.  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 S267.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_CNMF'

P value = 0.0423 (Fisher's exact test), Q value = 0.095

Table S268.  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 S268.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5q loss' versus 'CN_CNMF'

P value = 0.0432 (Fisher's exact test), Q value = 0.096

Table S269.  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 S269.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

'5q loss' versus 'RPPA_CNMF'

P value = 0.0432 (Fisher's exact test), Q value = 0.096

Table S270.  Gene #51: '5q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
5Q LOSS MUTATED 0 0 4 0 1 0
5Q LOSS WILD-TYPE 88 86 86 82 91 33

Figure S270.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 0.0458 (Fisher's exact test), Q value = 0.1

Table S271.  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 S271.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0151 (Fisher's exact test), Q value = 0.041

Table S272.  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 S272.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6p loss' versus 'MRNA_CNMF'

P value = 0.0107 (Fisher's exact test), Q value = 0.031

Table S273.  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 S273.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'6p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0141 (Fisher's exact test), Q value = 0.039

Table S274.  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 S274.  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 = 6.5e-05

Table S275.  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 S275.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

'6p loss' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00032

Table S276.  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 S276.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6p loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.5e-05

Table S277.  Gene #52: '6p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
6P LOSS MUTATED 16 9 37 17 7 4
6P LOSS WILD-TYPE 72 77 53 65 85 29

Figure S277.  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 = 6.5e-05

Table S278.  Gene #52: '6p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
6P LOSS MUTATED 10 40 27 13
6P LOSS WILD-TYPE 125 72 58 126

Figure S278.  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 = 6.5e-05

Table S279.  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 S279.  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 = 6.5e-05

Table S280.  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 S280.  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 = 6.5e-05

Table S281.  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 S281.  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 = 6.5e-05

Table S282.  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 S282.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0243 (Fisher's exact test), Q value = 0.06

Table S283.  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 S283.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.5e-05

Table S284.  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 S284.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

'6q loss' versus 'METHLYATION_CNMF'

P value = 0.00577 (Fisher's exact test), Q value = 0.018

Table S285.  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 S285.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6q loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.5e-05

Table S286.  Gene #53: '6q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
6Q LOSS MUTATED 18 21 39 25 7 5
6Q LOSS WILD-TYPE 70 65 51 57 85 28

Figure S286.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'6q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.5e-05

Table S287.  Gene #53: '6q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
6Q LOSS MUTATED 13 45 29 28
6Q LOSS WILD-TYPE 122 67 56 111

Figure S287.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'6q loss' versus 'MRNASEQ_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.0011

Table S288.  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 S288.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00041

Table S289.  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 S289.  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 = 6.5e-05

Table S290.  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 S290.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00022

Table S291.  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 S291.  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 = 0.063

Table S292.  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 S292.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7p loss' versus 'RPPA_CNMF'

P value = 0.0445 (Fisher's exact test), Q value = 0.098

Table S293.  Gene #54: '7p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
7P LOSS MUTATED 0 0 3 0 0 0
7P LOSS WILD-TYPE 88 86 87 82 92 33

Figure S293.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'7p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.042 (Fisher's exact test), Q value = 0.094

Table S294.  Gene #54: '7p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
7P LOSS MUTATED 0 1 2 0
7P LOSS WILD-TYPE 135 111 83 139

Figure S294.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'7q loss' versus 'RPPA_CNMF'

P value = 0.0107 (Fisher's exact test), Q value = 0.031

Table S295.  Gene #55: '7q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
7Q LOSS MUTATED 0 0 4 0 0 0
7Q LOSS WILD-TYPE 88 86 86 82 92 33

Figure S295.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'7q loss' versus 'MRNASEQ_CNMF'

P value = 0.0495 (Fisher's exact test), Q value = 0.11

Table S296.  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 S296.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7q loss' versus 'MIRSEQ_CNMF'

P value = 0.0193 (Fisher's exact test), Q value = 0.05

Table S297.  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 S297.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.5e-05

Table S298.  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 S298.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00124 (Fisher's exact test), Q value = 0.0047

Table S299.  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 S299.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_CNMF'

P value = 0.0417 (Fisher's exact test), Q value = 0.094

Table S300.  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 S300.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0231 (Fisher's exact test), Q value = 0.058

Table S301.  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 S301.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8q loss' versus 'METHLYATION_CNMF'

P value = 0.0439 (Fisher's exact test), Q value = 0.097

Table S302.  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 S302.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p loss' versus 'MRNA_CNMF'

P value = 0.00377 (Fisher's exact test), Q value = 0.013

Table S303.  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 S303.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'9p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0365 (Fisher's exact test), Q value = 0.084

Table S304.  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 S304.  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 = 6.5e-05

Table S305.  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 S305.  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 = 6.5e-05

Table S306.  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 S306.  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 = 6.5e-05

Table S307.  Gene #58: '9p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
9P LOSS MUTATED 16 15 54 22 25 6
9P LOSS WILD-TYPE 72 71 36 60 67 27

Figure S307.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'9p loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.5e-05

Table S308.  Gene #58: '9p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
9P LOSS MUTATED 25 52 36 25
9P LOSS WILD-TYPE 110 60 49 114

Figure S308.  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 = 6.5e-05

Table S309.  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 S309.  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 = 6.5e-05

Table S310.  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 S310.  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 = 6.5e-05

Table S311.  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 S311.  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 = 6.5e-05

Table S312.  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 S312.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0164 (Fisher's exact test), Q value = 0.044

Table S313.  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 S313.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9q loss' versus 'MRNA_CNMF'

P value = 0.00921 (Fisher's exact test), Q value = 0.027

Table S314.  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 S314.  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 = 6.5e-05

Table S315.  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 S315.  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 = 6.5e-05

Table S316.  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 S316.  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 = 6.5e-05

Table S317.  Gene #59: '9q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
9Q LOSS MUTATED 18 14 52 24 26 5
9Q LOSS WILD-TYPE 70 72 38 58 66 28

Figure S317.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'9q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.5e-05

Table S318.  Gene #59: '9q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
9Q LOSS MUTATED 26 52 36 25
9Q LOSS WILD-TYPE 109 60 49 114

Figure S318.  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 = 6.5e-05

Table S319.  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 S319.  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 = 6.5e-05

Table S320.  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 S320.  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 = 6.5e-05

Table S321.  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 S321.  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 = 6.5e-05

Table S322.  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 S322.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00357 (Fisher's exact test), Q value = 0.012

Table S323.  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 S323.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.037 (Fisher's exact test), Q value = 0.085

Table S324.  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 S324.  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 = 6.5e-05

Table S325.  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 S325.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

'10p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0226 (Fisher's exact test), Q value = 0.057

Table S326.  Gene #60: '10p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
10P LOSS MUTATED 9 17 17 16
10P LOSS WILD-TYPE 126 95 68 123

Figure S326.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-04 (Fisher's exact test), Q value = 0.0032

Table S327.  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 S327.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_CNMF'

P value = 0.017 (Fisher's exact test), Q value = 0.045

Table S328.  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 S328.  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 = 6.5e-05

Table S329.  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 S329.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 0.00421 (Fisher's exact test), Q value = 0.014

Table S330.  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 S330.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0222 (Fisher's exact test), Q value = 0.056

Table S331.  Gene #61: '10q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
10Q LOSS MUTATED 14 24 21 22
10Q LOSS WILD-TYPE 121 88 64 117

Figure S331.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00198 (Fisher's exact test), Q value = 0.007

Table S332.  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 S332.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_CNMF'

P value = 0.0383 (Fisher's exact test), Q value = 0.087

Table S333.  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 S333.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-04 (Fisher's exact test), Q value = 0.0021

Table S334.  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 S334.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.5e-05

Table S335.  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 S335.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 0.0223 (Fisher's exact test), Q value = 0.057

Table S336.  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 S336.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0273 (Fisher's exact test), Q value = 0.066

Table S337.  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 S337.  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 = 6.5e-05

Table S338.  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 S338.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

P value = 0.00553 (Fisher's exact test), Q value = 0.018

Table S339.  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 S339.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00966 (Fisher's exact test), Q value = 0.028

Table S340.  Gene #63: '11q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
11Q LOSS MUTATED 2 10 6 3
11Q LOSS WILD-TYPE 133 102 79 136

Figure S340.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'11q loss' versus 'MRNASEQ_CNMF'

P value = 0.014 (Fisher's exact test), Q value = 0.039

Table S341.  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 S341.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00039 (Fisher's exact test), Q value = 0.0017

Table S342.  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 S342.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_CNMF'

P value = 0.0229 (Fisher's exact test), Q value = 0.057

Table S343.  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 S343.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0378 (Fisher's exact test), Q value = 0.086

Table S344.  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 S344.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'13q loss' versus 'MRNA_CNMF'

P value = 0.0033 (Fisher's exact test), Q value = 0.011

Table S345.  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 S345.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'13q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0468 (Fisher's exact test), Q value = 0.1

Table S346.  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 S346.  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 = 6.5e-05

Table S347.  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 S347.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

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

Table S348.  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 S348.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.5e-05

Table S349.  Gene #66: '13q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
13Q LOSS MUTATED 11 2 30 9 9 2
13Q LOSS WILD-TYPE 77 84 60 73 83 31

Figure S349.  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 = 0.00012

Table S350.  Gene #66: '13q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
13Q LOSS MUTATED 9 22 22 10
13Q LOSS WILD-TYPE 126 90 63 129

Figure S350.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.5e-05

Table S351.  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 S351.  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 = 6.5e-05

Table S352.  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 S352.  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 = 6.5e-05

Table S353.  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 S353.  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 = 6.5e-05

Table S354.  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 S354.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'MRNA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00022

Table S355.  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 S355.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'14q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.5e-05

Table S356.  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 S356.  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 = 6.5e-05

Table S357.  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 S357.  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 = 6.5e-05

Table S358.  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 S358.  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 = 6.5e-05

Table S359.  Gene #67: '14q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
14Q LOSS MUTATED 29 22 57 53 31 6
14Q LOSS WILD-TYPE 59 64 33 29 61 27

Figure S359.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'14q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0139 (Fisher's exact test), Q value = 0.038

Table S360.  Gene #67: '14q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
14Q LOSS MUTATED 45 54 45 54
14Q LOSS WILD-TYPE 90 58 40 85

Figure S360.  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 = 6.5e-05

Table S361.  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 S361.  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 = 6.5e-05

Table S362.  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 S362.  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 = 6.5e-05

Table S363.  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 S363.  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 = 6.5e-05

Table S364.  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 S364.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.5e-05

Table S365.  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 S365.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 0.00068 (Fisher's exact test), Q value = 0.0028

Table S366.  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 S366.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'15q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00969 (Fisher's exact test), Q value = 0.028

Table S367.  Gene #68: '15q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
15Q LOSS MUTATED 5 15 9 6
15Q LOSS WILD-TYPE 130 97 76 133

Figure S367.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.5e-05

Table S368.  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 S368.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.5e-05

Table S369.  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 S369.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_CNMF'

P value = 0.00089 (Fisher's exact test), Q value = 0.0035

Table S370.  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 S370.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.016 (Fisher's exact test), Q value = 0.043

Table S371.  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 S371.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0487 (Fisher's exact test), Q value = 0.11

Table S372.  Gene #69: '16p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
16P LOSS MUTATED 0 3 4 2
16P LOSS WILD-TYPE 135 109 81 137

Figure S372.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'16q loss' versus 'CN_CNMF'

P value = 0.0379 (Fisher's exact test), Q value = 0.086

Table S373.  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 S373.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

'16q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00867 (Fisher's exact test), Q value = 0.026

Table S374.  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 S374.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.028 (Fisher's exact test), Q value = 0.067

Table S375.  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 S375.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'MRNA_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00037

Table S376.  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 S376.  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 = 0.0011

Table S377.  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 S377.  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 = 6.5e-05

Table S378.  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 S378.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

'17p loss' versus 'RPPA_CNMF'

P value = 0.00045 (Fisher's exact test), Q value = 0.0019

Table S379.  Gene #71: '17p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
17P LOSS MUTATED 13 2 16 3 5 1
17P LOSS WILD-TYPE 75 84 74 79 87 32

Figure S379.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'17p loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.5e-05

Table S380.  Gene #71: '17p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
17P LOSS MUTATED 6 11 19 4
17P LOSS WILD-TYPE 129 101 66 135

Figure S380.  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 = 6.5e-05

Table S381.  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 S381.  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 = 6.5e-05

Table S382.  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 S382.  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 = 6.5e-05

Table S383.  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 S383.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S384.  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 S384.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17q loss' versus 'MRNA_CNMF'

P value = 0.00051 (Fisher's exact test), Q value = 0.0021

Table S385.  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 S385.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17q loss' versus 'MRNA_CHIERARCHICAL'

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

Table S386.  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 S386.  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 = 6.5e-05

Table S387.  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 S387.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

'17q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00278 (Fisher's exact test), Q value = 0.0097

Table S388.  Gene #72: '17q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
17Q LOSS MUTATED 3 5 11 3
17Q LOSS WILD-TYPE 132 107 74 136

Figure S388.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'17q loss' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00037

Table S389.  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 S389.  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 = 6.5e-05

Table S390.  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 S390.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.5e-05

Table S391.  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 S391.  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 = 0.016

Table S392.  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 S392.  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 = 6.5e-05

Table S393.  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 S393.  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 = 6.5e-05

Table S394.  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 S394.  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 = 6.5e-05

Table S395.  Gene #73: '18p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
18P LOSS MUTATED 13 4 37 15 11 3
18P LOSS WILD-TYPE 75 82 53 67 81 30

Figure S395.  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 = 6.5e-05

Table S396.  Gene #73: '18p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
18P LOSS MUTATED 10 33 25 15
18P LOSS WILD-TYPE 125 79 60 124

Figure S396.  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 = 6.5e-05

Table S397.  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 S397.  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 = 6.5e-05

Table S398.  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 S398.  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 = 6.5e-05

Table S399.  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 S399.  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 = 6.5e-05

Table S400.  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 S400.  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 = 0.0011

Table S401.  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 S401.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0045 (Fisher's exact test), Q value = 0.015

Table S402.  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 S402.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q loss' versus 'MRNA_CNMF'

P value = 0.0462 (Fisher's exact test), Q value = 0.1

Table S403.  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 S403.  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 = 6.5e-05

Table S404.  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 S404.  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 = 6.5e-05

Table S405.  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 S405.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.5e-05

Table S406.  Gene #74: '18q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
18Q LOSS MUTATED 14 6 37 14 12 3
18Q LOSS WILD-TYPE 74 80 53 68 80 30

Figure S406.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'18q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.5e-05

Table S407.  Gene #74: '18q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
18Q LOSS MUTATED 12 33 25 16
18Q LOSS WILD-TYPE 123 79 60 123

Figure S407.  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 = 6.5e-05

Table S408.  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 S408.  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 = 6.5e-05

Table S409.  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 S409.  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 = 6.5e-05

Table S410.  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 S410.  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 = 6.5e-05

Table S411.  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 S411.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00336 (Fisher's exact test), Q value = 0.011

Table S412.  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 S412.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0308 (Fisher's exact test), Q value = 0.074

Table S413.  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 S413.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

Table S414.  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 S414.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

P value = 0.0322 (Fisher's exact test), Q value = 0.076

Table S415.  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 S415.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p loss' versus 'RPPA_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.00073

Table S416.  Gene #75: '19p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
19P LOSS MUTATED 0 0 8 2 0 0
19P LOSS WILD-TYPE 88 86 82 80 92 33

Figure S416.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'19p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00177 (Fisher's exact test), Q value = 0.0064

Table S417.  Gene #75: '19p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
19P LOSS MUTATED 0 3 6 1
19P LOSS WILD-TYPE 135 109 79 138

Figure S417.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0108 (Fisher's exact test), Q value = 0.031

Table S418.  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 S418.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S419.  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 S419.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0335 (Fisher's exact test), Q value = 0.078

Table S420.  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 S420.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0374 (Fisher's exact test), Q value = 0.085

Table S421.  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 S421.  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 = 0.033

Table S422.  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 S422.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

'20p loss' versus 'MIRSEQ_CNMF'

P value = 0.0193 (Fisher's exact test), Q value = 0.05

Table S423.  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 S423.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0294 (Fisher's exact test), Q value = 0.07

Table S424.  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 S424.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'21q loss' versus 'MRNA_CNMF'

P value = 0.0256 (Fisher's exact test), Q value = 0.063

Table S425.  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 S425.  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 = 6.5e-05

Table S426.  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 S426.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

'21q loss' versus 'METHLYATION_CNMF'

P value = 0.0137 (Fisher's exact test), Q value = 0.038

Table S427.  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 S427.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'21q loss' versus 'RPPA_CNMF'

P value = 0.00074 (Fisher's exact test), Q value = 0.003

Table S428.  Gene #79: '21q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
21Q LOSS MUTATED 11 7 19 8 3 0
21Q LOSS WILD-TYPE 77 79 71 74 89 33

Figure S428.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'21q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.5e-05

Table S429.  Gene #79: '21q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
21Q LOSS MUTATED 4 12 21 11
21Q LOSS WILD-TYPE 131 100 64 128

Figure S429.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'21q loss' versus 'MRNASEQ_CNMF'

P value = 0.00324 (Fisher's exact test), Q value = 0.011

Table S430.  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 S430.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00051

Table S431.  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 S431.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_CNMF'

P value = 0.00694 (Fisher's exact test), Q value = 0.021

Table S432.  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 S432.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'21q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0093 (Fisher's exact test), Q value = 0.028

Table S433.  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 S433.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'MRNA_CNMF'

P value = 0.00982 (Fisher's exact test), Q value = 0.029

Table S434.  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 S434.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'22q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00138 (Fisher's exact test), Q value = 0.0052

Table S435.  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 S435.  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 = 6.5e-05

Table S436.  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 S436.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 0.00354 (Fisher's exact test), Q value = 0.012

Table S437.  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 S437.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q loss' versus 'RPPA_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.0016

Table S438.  Gene #80: '22q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
22Q LOSS MUTATED 6 4 19 3 4 1
22Q LOSS WILD-TYPE 82 82 71 79 88 32

Figure S438.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'22q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0204 (Fisher's exact test), Q value = 0.052

Table S439.  Gene #80: '22q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
22Q LOSS MUTATED 5 15 9 8
22Q LOSS WILD-TYPE 130 97 76 131

Figure S439.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.5e-05

Table S440.  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 S440.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

Table S441.  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 S441.  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 = 6.5e-05

Table S442.  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 S442.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00341 (Fisher's exact test), Q value = 0.012

Table S443.  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 S443.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0254 (Fisher's exact test), Q value = 0.062

Table S444.  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 S444.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'xp loss' versus 'MRNA_CNMF'

P value = 0.0433 (Fisher's exact test), Q value = 0.096

Table S445.  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 S445.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'xp loss' versus 'CN_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00065

Table S446.  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 S446.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #3: 'CN_CNMF'

'xp loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0123 (Fisher's exact test), Q value = 0.035

Table S447.  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 S447.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_CNMF'

P value = 0.0398 (Fisher's exact test), Q value = 0.09

Table S448.  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 S448.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xp loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00094 (Fisher's exact test), Q value = 0.0036

Table S449.  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 S449.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'xq loss' versus 'MRNA_CNMF'

P value = 0.0241 (Fisher's exact test), Q value = 0.06

Table S450.  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 S450.  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 = 6.5e-05

Table S451.  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 S451.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 0.00897 (Fisher's exact test), Q value = 0.027

Table S452.  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 S452.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xq loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0281 (Fisher's exact test), Q value = 0.067

Table S453.  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 S453.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_CNMF'

P value = 0.018 (Fisher's exact test), Q value = 0.047

Table S454.  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 S454.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xq loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00334 (Fisher's exact test), Q value = 0.011

Table S455.  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 S455.  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/20146401/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/KIRC-TP/20125734/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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