Correlation between copy number variations of arm-level result and molecular subtypes
Lung Adenocarcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C1H41QP4
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/C1H41QP4
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 516 patients, 452 significant findings detected with P value < 0.05 and Q value < 0.25.

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

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

  • 2p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 2q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 3q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 4p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • 4q gain cnv correlated to 'RPPA_CHIERARCHICAL' and 'MRNASEQ_CNMF'.

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

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

  • 6p gain cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

  • 8p gain cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

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

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

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

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

  • 11p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 11q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • 13q gain cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

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

  • 15q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 16p gain cnv correlated to 'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

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

  • 17p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

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

  • 18p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 18q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

  • 21q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

  • xp gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • xq gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 1p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

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

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

  • 4q 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'.

  • 5p loss cnv correlated to 'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 6p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

  • 7p loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 7q loss cnv correlated to 'CN_CNMF'.

  • 8p 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'.

  • 8q loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • 9p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 9q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

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

  • 12p loss cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 12q loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

  • 14q loss cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

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

  • 16p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 16q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 17q loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • 18p loss cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 18q loss cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

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

  • 20p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

  • xq loss cnv correlated to 'CN_CNMF',  'METHLYATION_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, 452 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
8q gain 244 (47%) 272 0.0341
(0.0803) 		0.0199
(0.0523) 		1e-05
(9.74e-05) 		1e-05
(9.74e-05) 		0.0472
(0.103) 		0.644
(0.755) 		0.00014
(0.00085) 		2e-05
(0.000171) 		1e-05
(9.74e-05) 		0.00178
(0.00712) 		0.00831
(0.0259) 		1e-05
(9.74e-05)
4q loss 141 (27%) 375 0.00101
(0.00442) 		0.00869
(0.027) 		8e-05
(0.000528) 		1e-05
(9.74e-05) 		0.0172
(0.0467) 		0.0311
(0.0755) 		2e-05
(0.000171) 		1e-05
(9.74e-05) 		1e-05
(9.74e-05) 		1e-05
(9.74e-05) 		0.0837
(0.166) 		0.00014
(0.00085)
8p loss 203 (39%) 313 0.0129
(0.0371) 		0.0943
(0.182) 		1e-05
(9.74e-05) 		0.047
(0.103) 		0.00208
(0.00819) 		0.0169
(0.0462) 		1e-05
(9.74e-05) 		8e-05
(0.000528) 		0.00992
(0.0301) 		0.0429
(0.0967) 		0.0216
(0.0559) 		0.0121
(0.0353)
7p gain 259 (50%) 257 0.746
(0.845) 		0.741
(0.841) 		1e-05
(9.74e-05) 		0.0157
(0.0438) 		0.00342
(0.0122) 		0.00242
(0.00923) 		1e-05
(9.74e-05) 		1e-05
(9.74e-05) 		2e-05
(0.000171) 		9e-05
(0.000586) 		6e-05
(0.000419) 		1e-05
(9.74e-05)
20q gain 192 (37%) 324 0.00429
(0.0148) 		0.0095
(0.029) 		1e-05
(9.74e-05) 		1e-05
(9.74e-05) 		0.0643
(0.131) 		0.00025
(0.00131) 		3e-05
(0.000242) 		1e-05
(9.74e-05) 		2e-05
(0.000171) 		1e-05
(9.74e-05) 		0.0603
(0.125) 		1e-05
(9.74e-05)
2q gain 141 (27%) 375 0.0185
(0.0497) 		0.0447
(0.0994) 		1e-05
(9.74e-05) 		0.00034
(0.0017) 		0.753
(0.851) 		0.973
(1.00) 		0.0398
(0.0911) 		0.0188
(0.0503) 		0.00266
(0.00988) 		0.104
(0.197) 		0.0349
(0.0818) 		0.0109
(0.0325)
10p gain 111 (22%) 405 0.12
(0.219) 		0.0844
(0.167) 		1e-05
(9.74e-05) 		1e-05
(9.74e-05) 		0.00326
(0.0117) 		0.0168
(0.046) 		1e-05
(9.74e-05) 		1e-05
(9.74e-05) 		0.00018
(0.00102) 		0.00012
(0.000743) 		0.323
(0.458) 		0.00112
(0.00485)
12p gain 137 (27%) 379 0.194
(0.312) 		0.0204
(0.0533) 		1e-05
(9.74e-05) 		0.00034
(0.0017) 		0.0321
(0.0764) 		0.0743
(0.149) 		2e-05
(0.000171) 		1e-05
(9.74e-05) 		3e-05
(0.000242) 		1e-05
(9.74e-05) 		0.404
(0.544) 		1e-05
(9.74e-05)
12q gain 130 (25%) 386 0.195
(0.312) 		0.0196
(0.0521) 		1e-05
(9.74e-05) 		3e-05
(0.000242) 		0.0191
(0.0511) 		0.178
(0.293) 		1e-05
(9.74e-05) 		1e-05
(9.74e-05) 		1e-05
(9.74e-05) 		1e-05
(9.74e-05) 		0.222
(0.343) 		1e-05
(9.74e-05)
20p gain 173 (34%) 343 0.0691
(0.14) 		0.137
(0.246) 		0.00011
(0.000685) 		0.00015
(0.000889) 		0.462
(0.591) 		0.0093
(0.0286) 		0.00059
(0.00279) 		2e-05
(0.000171) 		6e-05
(0.000419) 		0.00013
(0.000799) 		0.0456
(0.101) 		0.00011
(0.000685)
4p loss 124 (24%) 392 0.186
(0.3) 		0.382
(0.522) 		0.00101
(0.00442) 		0.00023
(0.00122) 		0.00041
(0.00201) 		0.00462
(0.0157) 		0.026
(0.0656) 		1e-05
(9.74e-05) 		1e-05
(9.74e-05) 		1e-05
(9.74e-05) 		0.16
(0.272) 		8e-05
(0.000528)
5q loss 153 (30%) 363 0.201
(0.322) 		0.208
(0.331) 		1e-05
(9.74e-05) 		8e-05
(0.000528) 		2e-05
(0.000171) 		8e-05
(0.000528) 		3e-05
(0.000242) 		1e-05
(9.74e-05) 		1e-05
(9.74e-05) 		1e-05
(9.74e-05) 		0.663
(0.769) 		1e-05
(9.74e-05)
16p loss 118 (23%) 398 0.289
(0.422) 		1
(1.00) 		0.00089
(0.00398) 		0.00166
(0.00675) 		0.00613
(0.0198) 		0.00387
(0.0136) 		1e-05
(9.74e-05) 		0.00025
(0.00131) 		0.0143
(0.0402) 		0.0239
(0.0605) 		0.602
(0.719) 		0.00931
(0.0286)
16q loss 145 (28%) 371 0.576
(0.696) 		0.639
(0.751) 		0.00037
(0.00183) 		0.00023
(0.00122) 		0.00076
(0.00349) 		0.0282
(0.0698) 		2e-05
(0.000171) 		2e-05
(0.000171) 		0.0225
(0.0576) 		0.0133
(0.0378) 		0.826
(0.903) 		0.00246
(0.00927)
19p loss 248 (48%) 268 0.604
(0.72) 		0.9
(0.954) 		1e-05
(9.74e-05) 		1e-05
(9.74e-05) 		0.00128
(0.00545) 		0.114
(0.211) 		1e-05
(9.74e-05) 		1e-05
(9.74e-05) 		1e-05
(9.74e-05) 		1e-05
(9.74e-05) 		0.0346
(0.0812) 		0.00309
(0.0112)
19q loss 160 (31%) 356 0.345
(0.48) 		0.462
(0.591) 		1e-05
(9.74e-05) 		1e-05
(9.74e-05) 		0.0318
(0.0762) 		0.00456
(0.0155) 		0.00015
(0.000889) 		1e-05
(9.74e-05) 		0.00022
(0.00118) 		1e-05
(9.74e-05) 		0.214
(0.338) 		0.0351
(0.082)
21q loss 167 (32%) 349 0.185
(0.3) 		0.143
(0.254) 		1e-05
(9.74e-05) 		0.00172
(0.00694) 		1e-05
(9.74e-05) 		0.00454
(0.0155) 		1e-05
(9.74e-05) 		1e-05
(9.74e-05) 		1e-05
(9.74e-05) 		4e-05
(0.000307) 		0.533
(0.661) 		0.00026
(0.00135)
22q loss 217 (42%) 299 0.328
(0.463) 		0.658
(0.768) 		1e-05
(9.74e-05) 		1e-05
(9.74e-05) 		0.0179
(0.0484) 		0.00371
(0.0131) 		5e-05
(0.000376) 		1e-05
(9.74e-05) 		0.00016
(0.000921) 		3e-05
(0.000242) 		0.106
(0.2) 		6e-05
(0.000419)
1q gain 310 (60%) 206 0.333
(0.467) 		0.72
(0.822) 		0.0042
(0.0145) 		0.00135
(0.0057) 		0.00022
(0.00118) 		0.00556
(0.0182) 		0.00272
(0.01) 		0.0266
(0.0667) 		0.315
(0.45) 		0.0276
(0.0691) 		0.0321
(0.0764) 		0.218
(0.34)
3q gain 89 (17%) 427 4e-05
(0.000307) 		0.00035
(0.00174) 		0.0116
(0.0341) 		0.148
(0.258) 		2e-05
(0.000171) 		1e-05
(9.74e-05) 		0.00717
(0.0227) 		0.0281
(0.0697) 		0.236
(0.36) 		0.00189
(0.0075)
11q gain 114 (22%) 402 0.00061
(0.00287) 		0.00101
(0.00442) 		1e-05
(9.74e-05) 		0.0435
(0.0974) 		0.475
(0.606) 		0.323
(0.458) 		0.141
(0.25) 		0.00023
(0.00122) 		0.00021
(0.00115) 		1e-05
(9.74e-05) 		0.398
(0.54) 		0.00526
(0.0174)
18q gain 70 (14%) 446 0.45
(0.582) 		0.485
(0.615) 		1e-05
(9.74e-05) 		1e-05
(9.74e-05) 		0.0546
(0.116) 		0.455
(0.585) 		0.00084
(0.00381) 		3e-05
(0.000242) 		0.00701
(0.0223) 		0.00203
(0.00802) 		0.0435
(0.0974) 		0.00323
(0.0116)
10q loss 136 (26%) 380 0.182
(0.297) 		0.0531
(0.113) 		0.00098
(0.00434) 		0.0307
(0.0749) 		0.0503
(0.109) 		0.563
(0.687) 		6e-05
(0.000419) 		1e-05
(9.74e-05) 		0.00519
(0.0173) 		0.0111
(0.0327) 		0.0214
(0.0555) 		0.00234
(0.00899)
13q loss 258 (50%) 258 0.0571
(0.12) 		0.454
(0.585) 		1e-05
(9.74e-05) 		0.0417
(0.0943) 		0.00011
(0.000685) 		0.272
(0.404) 		0.0004
(0.00197) 		1e-05
(9.74e-05) 		0.00689
(0.0219) 		0.0218
(0.0559) 		0.273
(0.404) 		0.0041
(0.0143)
2p gain 153 (30%) 363 0.19
(0.305) 		0.16
(0.272) 		1e-05
(9.74e-05) 		1e-05
(9.74e-05) 		0.532
(0.661) 		0.682
(0.785) 		0.00228
(0.00883) 		0.0003
(0.00153) 		2e-05
(0.000171) 		0.00122
(0.00522) 		0.0529
(0.113) 		0.00016
(0.000921)
11p gain 94 (18%) 422 0.00983
(0.0299) 		0.0109
(0.0324) 		0.00015
(0.000889) 		0.104
(0.197) 		0.249
(0.377) 		0.605
(0.72) 		0.45
(0.582) 		0.00027
(0.00139) 		0.00139
(0.00585) 		2e-05
(0.000171) 		0.22
(0.341) 		0.0158
(0.0439)
14q gain 130 (25%) 386 0.109
(0.204) 		0.265
(0.396) 		1e-05
(9.74e-05) 		0.013
(0.0372) 		0.0379
(0.0875) 		0.293
(0.426) 		0.0497
(0.108) 		1e-05
(9.74e-05) 		0.00016
(0.000921) 		0.00067
(0.00312) 		0.185
(0.3) 		0.116
(0.212)
17q gain 191 (37%) 325 0.533
(0.661) 		1
(1.00) 		1e-05
(9.74e-05) 		1e-05
(9.74e-05) 		0.382
(0.522) 		0.257
(0.387) 		0.00233
(0.00899) 		1e-05
(9.74e-05) 		0.00017
(0.000973) 		7e-05
(0.000482) 		0.478
(0.609) 		0.00044
(0.00213)
3p loss 213 (41%) 303 0.346
(0.481) 		0.114
(0.211) 		5e-05
(0.000376) 		1e-05
(9.74e-05) 		0.344
(0.48) 		0.306
(0.443) 		0.00478
(0.0162) 		8e-05
(0.000528) 		0.017
(0.0464) 		0.0159
(0.044) 		0.221
(0.342) 		0.0317
(0.0762)
15q loss 241 (47%) 275 0.322
(0.458) 		0.431
(0.567) 		1e-05
(9.74e-05) 		0.00246
(0.00927) 		0.115
(0.212) 		0.43
(0.567) 		0.00512
(0.0171) 		1e-05
(9.74e-05) 		7e-05
(0.000482) 		0.0121
(0.0353) 		0.578
(0.696) 		2e-05
(0.000171)
1p gain 150 (29%) 366 0.912
(0.961) 		0.825
(0.903) 		1e-05
(9.74e-05) 		0.542
(0.668) 		0.00047
(0.00227) 		0.0162
(0.0449) 		0.0341
(0.0803) 		0.0103
(0.031) 		0.0364
(0.0844) 		0.168
(0.281) 		0.398
(0.541) 		0.154
(0.265)
3p gain 40 (8%) 476 4e-05
(0.000307) 		0.00237
(0.00907) 		0.0278
(0.0692) 		0.63
(0.746) 		0.00022
(0.00118) 		0.00129
(0.00547) 		0.154
(0.265) 		0.126
(0.229) 		0.849
(0.922) 		0.0168
(0.046)
5p gain 270 (52%) 246 0.267
(0.399) 		0.405
(0.544) 		1e-05
(9.74e-05) 		0.00806
(0.0252) 		0.785
(0.875) 		0.11
(0.205) 		0.422
(0.558) 		0.00737
(0.0232) 		0.034
(0.0803) 		0.0442
(0.0985) 		0.59
(0.708) 		1e-05
(9.74e-05)
6p gain 143 (28%) 373 0.155
(0.266) 		0.0327
(0.0775) 		0.0025
(0.00939) 		0.0001
(0.000639) 		0.186
(0.3) 		0.808
(0.89) 		0.0978
(0.187) 		0.0183
(0.0493) 		0.0739
(0.149) 		0.00547
(0.018) 		0.578
(0.696) 		0.0135
(0.0382)
7q gain 212 (41%) 304 1
(1.00) 		0.806
(0.89) 		1e-05
(9.74e-05) 		0.109
(0.204) 		0.0761
(0.153) 		0.5
(0.629) 		1e-05
(9.74e-05) 		1e-05
(9.74e-05) 		0.00501
(0.0169) 		0.00074
(0.00342) 		0.0904
(0.176) 		1e-05
(9.74e-05)
18p gain 91 (18%) 425 0.912
(0.961) 		1
(1.00) 		1e-05
(9.74e-05) 		4e-05
(0.000307) 		0.687
(0.789) 		0.933
(0.976) 		0.116
(0.212) 		0.00083
(0.0038) 		0.00935
(0.0287) 		0.00671
(0.0215) 		0.15
(0.26) 		0.0001
(0.000639)
19q gain 76 (15%) 440 0.00043
(0.00209) 		0.00417
(0.0144) 		0.0353
(0.0824) 		0.219
(0.34) 		0.00798
(0.025) 		0.0261
(0.0657) 		0.172
(0.285) 		0.333
(0.467) 		0.53
(0.66) 		0.00118
(0.00507)
9q loss 254 (49%) 262 0.851
(0.922) 		1
(1.00) 		1e-05
(9.74e-05) 		0.00209
(0.00819) 		0.287
(0.42) 		0.132
(0.238) 		0.0565
(0.119) 		0.00088
(0.00395) 		0.00169
(0.00684) 		3e-05
(0.000242) 		0.307
(0.443) 		0.0126
(0.0364)
10p loss 114 (22%) 402 0.184
(0.299) 		0.0526
(0.113) 		0.00053
(0.00252) 		0.255
(0.385) 		0.0313
(0.0758) 		0.755
(0.852) 		0.00102
(0.00444) 		1e-05
(9.74e-05) 		0.00325
(0.0117) 		0.305
(0.442) 		0.0383
(0.088) 		0.063
(0.129)
5q gain 125 (24%) 391 0.355
(0.49) 		0.519
(0.65) 		0.0456
(0.101) 		0.899
(0.954) 		0.148
(0.259) 		0.00602
(0.0195) 		0.0028
(0.0103) 		0.0115
(0.0339) 		0.178
(0.293) 		0.0424
(0.0958) 		0.551
(0.676) 		0.209
(0.332)
6q gain 61 (12%) 455 1
(1.00) 		1
(1.00) 		0.0295
(0.0726) 		0.02
(0.0525) 		0.0911
(0.177) 		0.549
(0.675) 		0.714
(0.818) 		0.0232
(0.0594) 		0.00449
(0.0154) 		0.00686
(0.0219) 		0.98
(1.00) 		0.157
(0.269)
8p gain 129 (25%) 387 0.0466
(0.103) 		0.0631
(0.129) 		1e-05
(9.74e-05) 		0.00394
(0.0138) 		0.222
(0.342) 		0.887
(0.95) 		0.00033
(0.00167) 		0.00256
(0.00958) 		0.432
(0.567) 		0.889
(0.95) 		0.311
(0.446) 		0.57
(0.693)
10q gain 78 (15%) 438 0.00084
(0.00381) 		0.00018
(0.00102) 		0.0412
(0.0935) 		0.728
(0.829) 		1e-05
(9.74e-05) 		1e-05
(9.74e-05) 		0.145
(0.256) 		0.0852
(0.168) 		0.897
(0.954) 		0.0507
(0.109)
16p gain 131 (25%) 385 0.495
(0.624) 		0.787
(0.876) 		0.0502
(0.109) 		0.944
(0.984) 		0.0177
(0.0479) 		0.33
(0.464) 		0.0377
(0.0873) 		0.0106
(0.0317) 		0.0111
(0.0327) 		0.788
(0.876) 		0.0409
(0.0932) 		0.107
(0.201)
5p loss 53 (10%) 463 0.576
(0.696) 		0.416
(0.552) 		0.142
(0.252) 		0.0782
(0.156) 		0.0285
(0.0703) 		0.0122
(0.0354) 		0.0106
(0.0317) 		0.15
(0.26) 		0.166
(0.28) 		0.0204
(0.0533) 		0.806
(0.89) 		0.0208
(0.0539)
9p loss 270 (52%) 246 0.539
(0.666) 		0.898
(0.954) 		1e-05
(9.74e-05) 		0.00184
(0.00733) 		0.725
(0.827) 		0.458
(0.588) 		0.0573
(0.12) 		6e-05
(0.000419) 		0.00663
(0.0213) 		0.00159
(0.0066) 		0.151
(0.261) 		0.0931
(0.18)
11p loss 116 (22%) 400 0.559
(0.685) 		0.308
(0.443) 		0.0002
(0.00111) 		0.0276
(0.0691) 		0.238
(0.362) 		0.0103
(0.031) 		6e-05
(0.000419) 		0.00074
(0.00342) 		0.0982
(0.187) 		0.139
(0.249) 		0.355
(0.49) 		0.146
(0.257)
17p loss 216 (42%) 300 0.635
(0.748) 		0.318
(0.452) 		1e-05
(9.74e-05) 		4e-05
(0.000307) 		0.0613
(0.127) 		0.259
(0.388) 		5e-05
(0.000376) 		0.0002
(0.00111) 		0.426
(0.563) 		0.184
(0.3) 		0.833
(0.908) 		0.0134
(0.0381)
18p loss 178 (34%) 338 0.405
(0.544) 		0.223
(0.343) 		1e-05
(9.74e-05) 		0.673
(0.777) 		0.0207
(0.0539) 		0.0132
(0.0375) 		0.01
(0.0304) 		0.00115
(0.00496) 		0.0795
(0.158) 		0.302
(0.437) 		0.914
(0.961) 		0.665
(0.771)
20p loss 113 (22%) 403 0.407
(0.545) 		0.223
(0.343) 		0.00165
(0.00674) 		0.00919
(0.0284) 		0.0679
(0.138) 		0.0923
(0.179) 		0.00029
(0.00149) 		0.00174
(0.00699) 		1
(1.00) 		0.996
(1.00) 		0.376
(0.514) 		0.0306
(0.0748)
15q gain 38 (7%) 478 0.193
(0.31) 		0.147
(0.258) 		6e-05
(0.000419) 		0.00553
(0.0181) 		0.519
(0.65) 		0.808
(0.89) 		0.0183
(0.0493) 		1e-05
(9.74e-05) 		0.79
(0.876) 		0.655
(0.766) 		0.227
(0.347) 		1
(1.00)
17p gain 83 (16%) 433 1
(1.00) 		0.824
(0.903) 		0.00016
(0.000921) 		0.0029
(0.0106) 		0.171
(0.285) 		0.0196
(0.0521) 		0.442
(0.578) 		0.0529
(0.113) 		0.00518
(0.0173) 		0.0583
(0.122) 		0.759
(0.855) 		0.447
(0.582)
1p loss 83 (16%) 433 0.561
(0.686) 		0.217
(0.34) 		1e-05
(9.74e-05) 		0.0482
(0.105) 		0.317
(0.452) 		0.772
(0.867) 		0.00015
(0.000889) 		6e-05
(0.000419) 		0.853
(0.923) 		0.344
(0.48) 		0.286
(0.419) 		0.731
(0.832)
3q loss 146 (28%) 370 0.404
(0.544) 		0.145
(0.256) 		0.0143
(0.0402) 		0.0259
(0.0656) 		0.45
(0.582) 		0.927
(0.974) 		0.00588
(0.0192) 		0.0234
(0.0596) 		0.22
(0.342) 		0.594
(0.712) 		0.206
(0.329) 		0.856
(0.926)
6p loss 107 (21%) 409 0.0305
(0.0748) 		0.00772
(0.0243) 		0.0889
(0.175) 		0.0321
(0.0764) 		0.486
(0.615) 		0.951
(0.99) 		0.226
(0.346) 		0.363
(0.5) 		0.312
(0.446) 		0.00416
(0.0144) 		0.861
(0.929) 		0.259
(0.388)
6q loss 217 (42%) 299 0.409
(0.546) 		0.347
(0.482) 		0.00259
(0.00965) 		2e-05
(0.000171) 		0.572
(0.694) 		0.715
(0.818) 		0.277
(0.408) 		0.00094
(0.00419) 		0.667
(0.772) 		0.00085
(0.00384) 		0.838
(0.911) 		0.152
(0.262)
7p loss 39 (8%) 477 0.295
(0.428) 		0.473
(0.603) 		0.0002
(0.00111) 		0.268
(0.399) 		0.98
(1.00) 		0.906
(0.958) 		0.0448
(0.0996) 		0.0137
(0.0385) 		0.583
(0.701) 		0.349
(0.483) 		0.00599
(0.0195) 		0.0627
(0.129)
11q loss 91 (18%) 425 0.559
(0.685) 		0.311
(0.446) 		0.00141
(0.0059) 		0.0411
(0.0935) 		0.864
(0.931) 		0.187
(0.302) 		0.00163
(0.00668) 		0.0197
(0.0522) 		0.162
(0.275) 		0.169
(0.282) 		0.158
(0.269) 		0.661
(0.769)
12p loss 114 (22%) 402 0.63
(0.746) 		1
(1.00) 		1e-05
(9.74e-05) 		0.4
(0.542) 		0.0126
(0.0364) 		0.248
(0.376) 		0.00034
(0.0017) 		0.00021
(0.00115) 		0.0561
(0.118) 		0.601
(0.718) 		1
(1.00) 		0.284
(0.417)
14q loss 114 (22%) 402 0.929
(0.974) 		0.412
(0.549) 		6e-05
(0.000419) 		0.102
(0.194) 		0.00244
(0.00927) 		0.18
(0.295) 		0.155
(0.266) 		0.00222
(0.00867) 		0.0316
(0.0762) 		0.166
(0.28) 		0.208
(0.331) 		0.0623
(0.129)
18q loss 212 (41%) 304 0.619
(0.737) 		0.456
(0.586) 		1e-05
(9.74e-05) 		0.895
(0.954) 		0.0316
(0.0762) 		0.15
(0.26) 		0.00067
(0.00312) 		0.0001
(0.000639) 		0.091
(0.177) 		0.535
(0.662) 		0.662
(0.769) 		0.217
(0.34)
xp loss 105 (20%) 411 0.908
(0.96) 		0.784
(0.875) 		9e-05
(0.000586) 		0.038
(0.0875) 		0.0534
(0.113) 		0.0405
(0.0925) 		0.132
(0.238) 		0.00267
(0.00988) 		0.646
(0.757) 		0.393
(0.535) 		0.438
(0.574) 		0.214
(0.338)
4p gain 77 (15%) 439 0.9
(0.954) 		0.405
(0.544) 		6e-05
(0.000419) 		0.0118
(0.0344) 		0.451
(0.582) 		0.106
(0.2) 		0.00522
(0.0173) 		0.0838
(0.166) 		0.131
(0.238) 		0.137
(0.246) 		0.798
(0.884) 		0.131
(0.238)
9p gain 45 (9%) 471 0.00149
(0.00621) 		0.106
(0.2) 		0.68
(0.785) 		0.333
(0.467) 		0.706
(0.81) 		0.00227
(0.00883) 		0.0763
(0.153) 		0.466
(0.596) 		0.0462
(0.102) 		0.137
(0.246)
21q gain 96 (19%) 420 0.171
(0.285) 		0.0553
(0.117) 		0.00016
(0.000921) 		0.965
(1.00) 		0.0547
(0.116) 		0.256
(0.386) 		0.00026
(0.00135) 		0.00053
(0.00252) 		0.764
(0.86) 		0.785
(0.875) 		0.434
(0.569) 		0.569
(0.693)
xp gain 51 (10%) 465 0.401
(0.543) 		0.219
(0.34) 		0.0002
(0.00111) 		0.00289
(0.0106) 		0.452
(0.582) 		0.816
(0.898) 		0.181
(0.296) 		0.0506
(0.109) 		0.0509
(0.109) 		0.0279
(0.0694) 		0.891
(0.951) 		0.273
(0.404)
12q loss 102 (20%) 414 0.774
(0.867) 		0.825
(0.903) 		1e-05
(9.74e-05) 		0.0952
(0.183) 		0.111
(0.205) 		0.213
(0.336) 		1e-05
(9.74e-05) 		4e-05
(0.000307) 		0.0612
(0.127) 		0.186
(0.3) 		0.896
(0.954) 		0.227
(0.347)
xq loss 63 (12%) 453 0.172
(0.285) 		0.255
(0.385) 		0.00353
(0.0125) 		0.00162
(0.00667) 		0.221
(0.342) 		0.272
(0.404) 		0.0828
(0.164) 		0.0579
(0.121) 		0.0899
(0.176) 		0.00375
(0.0132) 		0.514
(0.645) 		0.173
(0.286)
4q gain 44 (9%) 472 0.869
(0.935) 		0.784
(0.875) 		0.0644
(0.131) 		0.872
(0.937) 		0.799
(0.884) 		0.011
(0.0325) 		0.00161
(0.00666) 		0.0668
(0.136) 		0.114
(0.211) 		0.178
(0.293) 		0.408
(0.545) 		0.21
(0.333)
9q gain 32 (6%) 484 0.0666
(0.136) 		0.0318
(0.0762) 		0.273
(0.404) 		0.14
(0.25) 		0.635
(0.748) 		0.0359
(0.0835) 		0.345
(0.48) 		0.662
(0.769) 		0.44
(0.576) 		0.218
(0.34)
13q gain 44 (9%) 472 0.413
(0.551) 		0.544
(0.67) 		0.172
(0.285) 		0.0308
(0.0751) 		0.0807
(0.16) 		0.888
(0.95) 		0.943
(0.984) 		0.0217
(0.0559) 		0.977
(1.00) 		0.369
(0.506) 		0.449
(0.582) 		0.354
(0.49)
16q gain 99 (19%) 417 0.595
(0.712) 		0.309
(0.443) 		0.0391
(0.0897) 		0.88
(0.943) 		0.309
(0.443) 		0.481
(0.611) 		0.0919
(0.178) 		0.14
(0.25) 		0.00504
(0.0169) 		0.14
(0.25) 		0.213
(0.336) 		0.0963
(0.185)
22q gain 62 (12%) 454 0.109
(0.204) 		0.12
(0.219) 		0.00048
(0.0023) 		0.932
(0.975) 		0.859
(0.928) 		0.144
(0.255) 		0.36
(0.497) 		0.0434
(0.0974) 		0.45
(0.582) 		0.564
(0.688) 		0.28
(0.412) 		0.538
(0.665)
xq gain 83 (16%) 433 0.659
(0.768) 		0.247
(0.376) 		0.00011
(0.000685) 		0.073
(0.148) 		0.764
(0.86) 		0.407
(0.545) 		0.172
(0.285) 		0.0163
(0.045) 		0.0501
(0.109) 		0.293
(0.426) 		0.223
(0.343) 		0.161
(0.274)
8q loss 60 (12%) 456 0.0773
(0.155) 		0.0944
(0.182) 		0.0198
(0.0522) 		0.498
(0.628) 		0.131
(0.238) 		0.11
(0.205) 		0.0148
(0.0413) 		0.0624
(0.129) 		0.443
(0.578) 		0.823
(0.903) 		0.167
(0.281) 		0.43
(0.567)
17q loss 57 (11%) 459 0.912
(0.961) 		1
(1.00) 		0.00312
(0.0113) 		0.419
(0.556) 		0.249
(0.378) 		0.929
(0.974) 		0.0468
(0.103) 		0.547
(0.673) 		0.748
(0.848) 		0.288
(0.421) 		1
(1.00) 		0.872
(0.937)
7q loss 47 (9%) 469 0.57
(0.693) 		0.625
(0.742) 		0.0237
(0.0604) 		0.976
(1.00) 		0.366
(0.503) 		0.422
(0.558) 		0.634
(0.748) 		0.414
(0.551) 		0.401
(0.543) 		0.276
(0.407) 		0.531
(0.661) 		0.642
(0.753)
19p gain 30 (6%) 486 0.15
(0.26) 		0.219
(0.34) 		0.109
(0.204) 		0.716
(0.818) 		0.501
(0.629) 		0.635
(0.748) 		0.682
(0.785) 		0.83
(0.907) 		0.875
(0.939) 		0.324
(0.459)
1q loss 33 (6%) 483 0.75
(0.848) 		0.577
(0.696) 		0.571
(0.693) 		0.704
(0.809) 		0.135
(0.243) 		0.344
(0.48) 		0.178
(0.293) 		0.914
(0.961) 		0.327
(0.461) 		0.656
(0.767) 		0.483
(0.613) 		0.521
(0.651)
2p loss 28 (5%) 488 0.777
(0.87) 		0.323
(0.458) 		0.789
(0.876) 		1
(1.00) 		1
(1.00) 		0.669
(0.774) 		0.737
(0.837) 		0.836
(0.91) 		0.164
(0.278) 		0.836
(0.91) 		0.162
(0.275) 		0.279
(0.41)
2q loss 29 (6%) 487 0.492
(0.622) 		0.181
(0.296) 		0.103
(0.196) 		0.635
(0.748) 		0.841
(0.914) 		0.448
(0.582) 		0.291
(0.424) 		0.396
(0.538) 		0.0897
(0.176) 		0.525
(0.654) 		0.494
(0.624) 		0.372
(0.51)
20q loss 69 (13%) 447 0.258
(0.388) 		0.0983
(0.187) 		0.62
(0.737) 		0.968
(1.00) 		0.524
(0.654) 		0.773
(0.867) 		0.581
(0.698) 		0.149
(0.26) 		0.941
(0.983) 		0.823
(0.903) 		0.167
(0.281) 		0.958
(0.997)
'1p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
1P GAIN MUTATED 12 50 19 69
1P GAIN WILD-TYPE 57 178 60 71

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

'1p gain' versus 'RPPA_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.0023

Table S2.  Gene #1: '1p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
1P GAIN MUTATED 43 6 20 22 20
1P GAIN WILD-TYPE 48 16 46 53 89

Figure S2.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'1p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0162 (Fisher's exact test), Q value = 0.045

Table S3.  Gene #1: '1p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
1P GAIN MUTATED 57 44 10
1P GAIN WILD-TYPE 110 89 53

Figure S3.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'1p gain' versus 'MRNASEQ_CNMF'

P value = 0.0341 (Fisher's exact test), Q value = 0.08

Table S4.  Gene #1: '1p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
1P GAIN MUTATED 44 70 36
1P GAIN WILD-TYPE 122 125 115

Figure S4.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0103 (Fisher's exact test), Q value = 0.031

Table S5.  Gene #1: '1p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
1P GAIN MUTATED 20 40 39 8 9 14 20
1P GAIN WILD-TYPE 58 70 58 40 44 35 57

Figure S5.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p gain' versus 'MIRSEQ_CNMF'

P value = 0.0364 (Fisher's exact test), Q value = 0.084

Table S6.  Gene #1: '1p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
1P GAIN MUTATED 45 67 36
1P GAIN WILD-TYPE 144 161 57

Figure S6.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1q gain' versus 'CN_CNMF'

P value = 0.0042 (Fisher's exact test), Q value = 0.015

Table S7.  Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
1Q GAIN MUTATED 50 121 44 95
1Q GAIN WILD-TYPE 19 107 35 45

Figure S7.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

'1q gain' versus 'METHLYATION_CNMF'

P value = 0.00135 (Fisher's exact test), Q value = 0.0057

Table S8.  Gene #2: '1q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
1Q GAIN MUTATED 70 98 109
1Q GAIN WILD-TYPE 74 51 53

Figure S8.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1q gain' versus 'RPPA_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.0012

Table S9.  Gene #2: '1q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
1Q GAIN MUTATED 59 16 52 40 51
1Q GAIN WILD-TYPE 32 6 14 35 58

Figure S9.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'1q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00556 (Fisher's exact test), Q value = 0.018

Table S10.  Gene #2: '1q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
1Q GAIN MUTATED 115 71 32
1Q GAIN WILD-TYPE 52 62 31

Figure S10.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'1q gain' versus 'MRNASEQ_CNMF'

P value = 0.00272 (Fisher's exact test), Q value = 0.01

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
1Q GAIN MUTATED 97 103 107
1Q GAIN WILD-TYPE 69 92 44

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

'1q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0266 (Fisher's exact test), Q value = 0.067

Table S12.  Gene #2: '1q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
1Q GAIN MUTATED 49 61 53 37 38 30 39
1Q GAIN WILD-TYPE 29 49 44 11 15 19 38

Figure S12.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0276 (Fisher's exact test), Q value = 0.069

Table S13.  Gene #2: '1q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
1Q GAIN MUTATED 50 126 72 58
1Q GAIN WILD-TYPE 21 72 69 42

Figure S13.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0321 (Fisher's exact test), Q value = 0.076

Table S14.  Gene #2: '1q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 198 91
1Q GAIN MUTATED 90 130 45
1Q GAIN WILD-TYPE 55 68 46

Figure S14.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'2p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
2P GAIN MUTATED 28 35 37 53
2P GAIN WILD-TYPE 41 193 42 87

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

'2p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S16.  Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
2P GAIN MUTATED 20 60 49
2P GAIN WILD-TYPE 124 89 113

Figure S16.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2p gain' versus 'MRNASEQ_CNMF'

P value = 0.00228 (Fisher's exact test), Q value = 0.0088

Table S17.  Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
2P GAIN MUTATED 33 66 54
2P GAIN WILD-TYPE 133 129 97

Figure S17.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.0015

Table S18.  Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
2P GAIN MUTATED 16 31 34 8 25 23 16
2P GAIN WILD-TYPE 62 79 63 40 28 26 61

Figure S18.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00017

Table S19.  Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
2P GAIN MUTATED 40 93 19
2P GAIN WILD-TYPE 149 135 74

Figure S19.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00122 (Fisher's exact test), Q value = 0.0052

Table S20.  Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
2P GAIN MUTATED 14 67 30 41
2P GAIN WILD-TYPE 57 131 111 59

Figure S20.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.00092

Table S21.  Gene #3: '2p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
2P GAIN MUTATED 16 91 19
2P GAIN WILD-TYPE 87 157 64

Figure S21.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q gain' versus 'MRNA_CNMF'

P value = 0.0185 (Fisher's exact test), Q value = 0.05

Table S22.  Gene #4: '2q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 5 9 12 6
2Q GAIN MUTATED 0 2 3 5
2Q GAIN WILD-TYPE 5 7 9 1

Figure S22.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'2q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0447 (Fisher's exact test), Q value = 0.099

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 11 7
2Q GAIN MUTATED 3 2 5
2Q GAIN WILD-TYPE 11 9 2

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

'2q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S24.  Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
2Q GAIN MUTATED 25 36 35 45
2Q GAIN WILD-TYPE 44 192 44 95

Figure S24.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

'2q gain' versus 'METHLYATION_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.0017

Table S25.  Gene #4: '2q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
2Q GAIN MUTATED 21 50 49
2Q GAIN WILD-TYPE 123 99 113

Figure S25.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2q gain' versus 'MRNASEQ_CNMF'

P value = 0.0398 (Fisher's exact test), Q value = 0.091

Table S26.  Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
2Q GAIN MUTATED 35 55 51
2Q GAIN WILD-TYPE 131 140 100

Figure S26.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0188 (Fisher's exact test), Q value = 0.05

Table S27.  Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
2Q GAIN MUTATED 15 28 33 12 18 21 14
2Q GAIN WILD-TYPE 63 82 64 36 35 28 63

Figure S27.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_CNMF'

P value = 0.00266 (Fisher's exact test), Q value = 0.0099

Table S28.  Gene #4: '2q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
2Q GAIN MUTATED 41 80 19
2Q GAIN WILD-TYPE 148 148 74

Figure S28.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0349 (Fisher's exact test), Q value = 0.082

Table S29.  Gene #4: '2q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 198 91
2Q GAIN MUTATED 38 61 15
2Q GAIN WILD-TYPE 107 137 76

Figure S29.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'2q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0109 (Fisher's exact test), Q value = 0.032

Table S30.  Gene #4: '2q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
2Q GAIN MUTATED 17 78 19
2Q GAIN WILD-TYPE 86 170 64

Figure S30.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3p gain' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00031

Table S31.  Gene #5: '3p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
3P GAIN MUTATED 10 5 7 18
3P GAIN WILD-TYPE 59 223 72 122

Figure S31.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #3: 'CN_CNMF'

'3p gain' versus 'METHLYATION_CNMF'

P value = 0.00237 (Fisher's exact test), Q value = 0.0091

Table S32.  Gene #5: '3p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
3P GAIN MUTATED 3 14 19
3P GAIN WILD-TYPE 141 135 143

Figure S32.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3p gain' versus 'RPPA_CNMF'

P value = 0.0278 (Fisher's exact test), Q value = 0.069

Table S33.  Gene #5: '3p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
3P GAIN MUTATED 7 3 4 11 3
3P GAIN WILD-TYPE 84 19 62 64 106

Figure S33.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'3p gain' versus 'MRNASEQ_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.0012

Table S34.  Gene #5: '3p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
3P GAIN MUTATED 4 27 9
3P GAIN WILD-TYPE 162 168 142

Figure S34.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00129 (Fisher's exact test), Q value = 0.0055

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
3P GAIN MUTATED 3 13 17 1 2 2 2
3P GAIN WILD-TYPE 75 97 80 47 51 47 75

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

'3p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0168 (Fisher's exact test), Q value = 0.046

Table S36.  Gene #5: '3p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
3P GAIN MUTATED 2 24 9
3P GAIN WILD-TYPE 101 224 74

Figure S36.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q gain' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00031

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
3Q GAIN MUTATED 13 20 23 33
3Q GAIN WILD-TYPE 56 208 56 107

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

'3q gain' versus 'METHLYATION_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.0017

Table S38.  Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
3Q GAIN MUTATED 12 38 29
3Q GAIN WILD-TYPE 132 111 133

Figure S38.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3q gain' versus 'RPPA_CNMF'

P value = 0.0116 (Fisher's exact test), Q value = 0.034

Table S39.  Gene #6: '3q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
3Q GAIN MUTATED 14 5 9 23 12
3Q GAIN WILD-TYPE 77 17 57 52 97

Figure S39.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'3q gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00017

Table S40.  Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
3Q GAIN MUTATED 13 51 25
3Q GAIN WILD-TYPE 153 144 126

Figure S40.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S41.  Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
3Q GAIN MUTATED 4 22 41 2 6 8 6
3Q GAIN WILD-TYPE 74 88 56 46 47 41 71

Figure S41.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_CNMF'

P value = 0.00717 (Fisher's exact test), Q value = 0.023

Table S42.  Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
3Q GAIN MUTATED 26 53 10
3Q GAIN WILD-TYPE 163 175 83

Figure S42.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0281 (Fisher's exact test), Q value = 0.07

Table S43.  Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
3Q GAIN MUTATED 8 37 18 26
3Q GAIN WILD-TYPE 63 161 123 74

Figure S43.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00189 (Fisher's exact test), Q value = 0.0075

Table S44.  Gene #6: '3q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
3Q GAIN MUTATED 8 57 13
3Q GAIN WILD-TYPE 95 191 70

Figure S44.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p gain' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00042

Table S45.  Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
4P GAIN MUTATED 10 17 20 30
4P GAIN WILD-TYPE 59 211 59 110

Figure S45.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

'4p gain' versus 'METHLYATION_CNMF'

P value = 0.0118 (Fisher's exact test), Q value = 0.034

Table S46.  Gene #7: '4p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
4P GAIN MUTATED 13 32 25
4P GAIN WILD-TYPE 131 117 137

Figure S46.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p gain' versus 'MRNASEQ_CNMF'

P value = 0.00522 (Fisher's exact test), Q value = 0.017

Table S47.  Gene #7: '4p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
4P GAIN MUTATED 16 42 19
4P GAIN WILD-TYPE 150 153 132

Figure S47.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.011 (Fisher's exact test), Q value = 0.033

Table S48.  Gene #8: '4q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
4Q GAIN MUTATED 6 17 5
4Q GAIN WILD-TYPE 161 116 58

Figure S48.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'4q gain' versus 'MRNASEQ_CNMF'

P value = 0.00161 (Fisher's exact test), Q value = 0.0067

Table S49.  Gene #8: '4q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
4Q GAIN MUTATED 12 27 5
4Q GAIN WILD-TYPE 154 168 146

Figure S49.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
5P GAIN MUTATED 43 90 37 100
5P GAIN WILD-TYPE 26 138 42 40

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

'5p gain' versus 'METHLYATION_CNMF'

P value = 0.00806 (Fisher's exact test), Q value = 0.025

Table S51.  Gene #9: '5p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
5P GAIN MUTATED 62 90 91
5P GAIN WILD-TYPE 82 59 71

Figure S51.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00737 (Fisher's exact test), Q value = 0.023

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
5P GAIN MUTATED 42 64 58 16 32 26 30
5P GAIN WILD-TYPE 36 46 39 32 21 23 47

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

'5p gain' versus 'MIRSEQ_CNMF'

P value = 0.034 (Fisher's exact test), Q value = 0.08

Table S53.  Gene #9: '5p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
5P GAIN MUTATED 86 133 49
5P GAIN WILD-TYPE 103 95 44

Figure S53.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0442 (Fisher's exact test), Q value = 0.099

Table S54.  Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
5P GAIN MUTATED 36 111 61 60
5P GAIN WILD-TYPE 35 87 80 40

Figure S54.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S55.  Gene #9: '5p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
5P GAIN MUTATED 36 152 48
5P GAIN WILD-TYPE 67 96 35

Figure S55.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q gain' versus 'CN_CNMF'

P value = 0.0456 (Fisher's exact test), Q value = 0.1

Table S56.  Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
5Q GAIN MUTATED 16 55 11 43
5Q GAIN WILD-TYPE 53 173 68 97

Figure S56.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'

'5q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00602 (Fisher's exact test), Q value = 0.019

Table S57.  Gene #10: '5q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
5Q GAIN MUTATED 46 21 22
5Q GAIN WILD-TYPE 121 112 41

Figure S57.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'5q gain' versus 'MRNASEQ_CNMF'

P value = 0.0028 (Fisher's exact test), Q value = 0.01

Table S58.  Gene #10: '5q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
5Q GAIN MUTATED 55 42 26
5Q GAIN WILD-TYPE 111 153 125

Figure S58.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0115 (Fisher's exact test), Q value = 0.034

Table S59.  Gene #10: '5q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
5Q GAIN MUTATED 32 20 26 10 12 10 13
5Q GAIN WILD-TYPE 46 90 71 38 41 39 64

Figure S59.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0424 (Fisher's exact test), Q value = 0.096

Table S60.  Gene #10: '5q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
5Q GAIN MUTATED 26 41 37 20
5Q GAIN WILD-TYPE 45 157 104 80

Figure S60.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0327 (Fisher's exact test), Q value = 0.077

Table S61.  Gene #11: '6p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 11 7
6P GAIN MUTATED 4 1 5
6P GAIN WILD-TYPE 10 10 2

Figure S61.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6p gain' versus 'CN_CNMF'

P value = 0.0025 (Fisher's exact test), Q value = 0.0094

Table S62.  Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
6P GAIN MUTATED 29 47 22 45
6P GAIN WILD-TYPE 40 181 57 95

Figure S62.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

'6p gain' versus 'METHLYATION_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00064

Table S63.  Gene #11: '6p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
6P GAIN MUTATED 22 56 46
6P GAIN WILD-TYPE 122 93 116

Figure S63.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6p gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S64.  Gene #11: '6p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
6P GAIN MUTATED 17 25 38 18 17 14 14
6P GAIN WILD-TYPE 61 85 59 30 36 35 63

Figure S64.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00547 (Fisher's exact test), Q value = 0.018

Table S65.  Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
6P GAIN MUTATED 15 64 26 35
6P GAIN WILD-TYPE 56 134 115 65

Figure S65.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0135 (Fisher's exact test), Q value = 0.038

Table S66.  Gene #11: '6p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
6P GAIN MUTATED 17 78 23
6P GAIN WILD-TYPE 86 170 60

Figure S66.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q gain' versus 'CN_CNMF'

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

Table S67.  Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
6Q GAIN MUTATED 10 17 10 24
6Q GAIN WILD-TYPE 59 211 69 116

Figure S67.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

'6q gain' versus 'METHLYATION_CNMF'

P value = 0.02 (Fisher's exact test), Q value = 0.052

Table S68.  Gene #12: '6q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
6Q GAIN MUTATED 10 26 17
6Q GAIN WILD-TYPE 134 123 145

Figure S68.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0232 (Fisher's exact test), Q value = 0.059

Table S69.  Gene #12: '6q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
6Q GAIN MUTATED 11 7 20 5 8 6 4
6Q GAIN WILD-TYPE 67 103 77 43 45 43 73

Figure S69.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6q gain' versus 'MIRSEQ_CNMF'

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

Table S70.  Gene #12: '6q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
6Q GAIN MUTATED 12 38 10
6Q GAIN WILD-TYPE 177 190 83

Figure S70.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00686 (Fisher's exact test), Q value = 0.022

Table S71.  Gene #12: '6q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
6Q GAIN MUTATED 3 30 10 17
6Q GAIN WILD-TYPE 68 168 131 83

Figure S71.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S72.  Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
7P GAIN MUTATED 26 79 43 111
7P GAIN WILD-TYPE 43 149 36 29

Figure S72.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 0.0157 (Fisher's exact test), Q value = 0.044

Table S73.  Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
7P GAIN MUTATED 60 72 94
7P GAIN WILD-TYPE 84 77 68

Figure S73.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p gain' versus 'RPPA_CNMF'

P value = 0.00342 (Fisher's exact test), Q value = 0.012

Table S74.  Gene #13: '7p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
7P GAIN MUTATED 57 10 24 46 49
7P GAIN WILD-TYPE 34 12 42 29 60

Figure S74.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'7p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00242 (Fisher's exact test), Q value = 0.0092

Table S75.  Gene #13: '7p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
7P GAIN MUTATED 75 84 27
7P GAIN WILD-TYPE 92 49 36

Figure S75.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S76.  Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
7P GAIN MUTATED 71 131 54
7P GAIN WILD-TYPE 95 64 97

Figure S76.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S77.  Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
7P GAIN MUTATED 31 78 58 8 22 28 31
7P GAIN WILD-TYPE 47 32 39 40 31 21 46

Figure S77.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00017

Table S78.  Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
7P GAIN MUTATED 69 126 61
7P GAIN WILD-TYPE 120 102 32

Figure S78.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00059

Table S79.  Gene #13: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
7P GAIN MUTATED 21 118 62 55
7P GAIN WILD-TYPE 50 80 79 45

Figure S79.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00042

Table S80.  Gene #13: '7p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 198 91
7P GAIN MUTATED 59 101 64
7P GAIN WILD-TYPE 86 97 27

Figure S80.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S81.  Gene #13: '7p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
7P GAIN MUTATED 28 146 50
7P GAIN WILD-TYPE 75 102 33

Figure S81.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S82.  Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
7Q GAIN MUTATED 18 67 35 92
7Q GAIN WILD-TYPE 51 161 44 48

Figure S82.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S83.  Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
7Q GAIN MUTATED 59 107 43
7Q GAIN WILD-TYPE 107 88 108

Figure S83.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S84.  Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
7Q GAIN MUTATED 25 69 43 6 17 23 26
7Q GAIN WILD-TYPE 53 41 54 42 36 26 51

Figure S84.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_CNMF'

P value = 0.00501 (Fisher's exact test), Q value = 0.017

Table S85.  Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
7Q GAIN MUTATED 61 101 47
7Q GAIN WILD-TYPE 128 127 46

Figure S85.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00074 (Fisher's exact test), Q value = 0.0034

Table S86.  Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
7Q GAIN MUTATED 18 99 48 44
7Q GAIN WILD-TYPE 53 99 93 56

Figure S86.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S87.  Gene #14: '7q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
7Q GAIN MUTATED 21 119 40
7Q GAIN WILD-TYPE 82 129 43

Figure S87.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p gain' versus 'MRNA_CNMF'

P value = 0.0466 (Fisher's exact test), Q value = 0.1

Table S88.  Gene #15: '8p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 5 9 12 6
8P GAIN MUTATED 0 1 2 4
8P GAIN WILD-TYPE 5 8 10 2

Figure S88.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'8p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S89.  Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
8P GAIN MUTATED 39 38 22 30
8P GAIN WILD-TYPE 30 190 57 110

Figure S89.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

'8p gain' versus 'METHLYATION_CNMF'

P value = 0.00394 (Fisher's exact test), Q value = 0.014

Table S90.  Gene #15: '8p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
8P GAIN MUTATED 25 51 38
8P GAIN WILD-TYPE 119 98 124

Figure S90.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p gain' versus 'MRNASEQ_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.0017

Table S91.  Gene #15: '8p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
8P GAIN MUTATED 34 37 56
8P GAIN WILD-TYPE 132 158 95

Figure S91.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00256 (Fisher's exact test), Q value = 0.0096

Table S92.  Gene #15: '8p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
8P GAIN MUTATED 15 23 21 15 25 15 13
8P GAIN WILD-TYPE 63 87 76 33 28 34 64

Figure S92.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'MRNA_CNMF'

P value = 0.0341 (Fisher's exact test), Q value = 0.08

Table S93.  Gene #16: '8q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 5 9 12 6
8Q GAIN MUTATED 3 3 2 5
8Q GAIN WILD-TYPE 2 6 10 1

Figure S93.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'8q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0199 (Fisher's exact test), Q value = 0.052

Table S94.  Gene #16: '8q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 11 7
8Q GAIN MUTATED 3 4 6
8Q GAIN WILD-TYPE 11 7 1

Figure S94.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'8q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S95.  Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
8Q GAIN MUTATED 61 66 47 70
8Q GAIN WILD-TYPE 8 162 32 70

Figure S95.  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 = 9.7e-05

Table S96.  Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
8Q GAIN MUTATED 43 86 87
8Q GAIN WILD-TYPE 101 63 75

Figure S96.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8q gain' versus 'RPPA_CNMF'

P value = 0.0472 (Fisher's exact test), Q value = 0.1

Table S97.  Gene #16: '8q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
8Q GAIN MUTATED 39 8 35 46 46
8Q GAIN WILD-TYPE 52 14 31 29 63

Figure S97.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00085

Table S98.  Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
8Q GAIN MUTATED 59 92 90
8Q GAIN WILD-TYPE 107 103 61

Figure S98.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00017

Table S99.  Gene #16: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
8Q GAIN MUTATED 30 51 49 20 43 26 22
8Q GAIN WILD-TYPE 48 59 48 28 10 23 55

Figure S99.  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 = 9.7e-05

Table S100.  Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
8Q GAIN MUTATED 63 131 48
8Q GAIN WILD-TYPE 126 97 45

Figure S100.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00178 (Fisher's exact test), Q value = 0.0071

Table S101.  Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
8Q GAIN MUTATED 26 108 53 55
8Q GAIN WILD-TYPE 45 90 88 45

Figure S101.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00831 (Fisher's exact test), Q value = 0.026

Table S102.  Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 198 91
8Q GAIN MUTATED 56 110 45
8Q GAIN WILD-TYPE 89 88 46

Figure S102.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S103.  Gene #16: '8q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
8Q GAIN MUTATED 31 143 37
8Q GAIN WILD-TYPE 72 105 46

Figure S103.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p gain' versus 'CN_CNMF'

P value = 0.00149 (Fisher's exact test), Q value = 0.0062

Table S104.  Gene #17: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
9P GAIN MUTATED 13 10 6 16
9P GAIN WILD-TYPE 56 218 73 124

Figure S104.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'

'9p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00227 (Fisher's exact test), Q value = 0.0088

Table S105.  Gene #17: '9p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
9P GAIN MUTATED 1 11 13 2 10 1 6
9P GAIN WILD-TYPE 77 99 84 46 43 48 71

Figure S105.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p gain' versus 'MIRSEQ_MATURE_CNMF'

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

Table S106.  Gene #17: '9p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 198 91
9P GAIN MUTATED 9 27 6
9P GAIN WILD-TYPE 136 171 85

Figure S106.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9q gain' versus 'METHLYATION_CNMF'

P value = 0.0318 (Fisher's exact test), Q value = 0.076

Table S107.  Gene #18: '9q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
9Q GAIN MUTATED 7 17 7
9Q GAIN WILD-TYPE 137 132 155

Figure S107.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0359 (Fisher's exact test), Q value = 0.084

Table S108.  Gene #18: '9q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
9Q GAIN MUTATED 1 5 12 2 6 2 3
9Q GAIN WILD-TYPE 77 105 85 46 47 47 74

Figure S108.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S109.  Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
10P GAIN MUTATED 29 25 23 34
10P GAIN WILD-TYPE 40 203 56 106

Figure S109.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

'10p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S110.  Gene #19: '10p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
10P GAIN MUTATED 10 45 44
10P GAIN WILD-TYPE 134 104 118

Figure S110.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p gain' versus 'RPPA_CNMF'

P value = 0.00326 (Fisher's exact test), Q value = 0.012

Table S111.  Gene #19: '10p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
10P GAIN MUTATED 11 2 19 23 33
10P GAIN WILD-TYPE 80 20 47 52 76

Figure S111.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'10p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0168 (Fisher's exact test), Q value = 0.046

Table S112.  Gene #19: '10p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
10P GAIN MUTATED 30 36 22
10P GAIN WILD-TYPE 137 97 41

Figure S112.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'10p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S113.  Gene #19: '10p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
10P GAIN MUTATED 15 40 55
10P GAIN WILD-TYPE 151 155 96

Figure S113.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S114.  Gene #19: '10p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
10P GAIN MUTATED 5 19 20 14 25 18 9
10P GAIN WILD-TYPE 73 91 77 34 28 31 68

Figure S114.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p gain' versus 'MIRSEQ_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.001

Table S115.  Gene #19: '10p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
10P GAIN MUTATED 25 67 17
10P GAIN WILD-TYPE 164 161 76

Figure S115.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.00074

Table S116.  Gene #19: '10p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
10P GAIN MUTATED 12 56 14 27
10P GAIN WILD-TYPE 59 142 127 73

Figure S116.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00112 (Fisher's exact test), Q value = 0.0049

Table S117.  Gene #19: '10p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
10P GAIN MUTATED 11 70 16
10P GAIN WILD-TYPE 92 178 67

Figure S117.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q gain' versus 'CN_CNMF'

P value = 0.00084 (Fisher's exact test), Q value = 0.0038

Table S118.  Gene #20: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
10Q GAIN MUTATED 20 22 16 20
10Q GAIN WILD-TYPE 49 206 63 120

Figure S118.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

'10q gain' versus 'METHLYATION_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.001

Table S119.  Gene #20: '10q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
10Q GAIN MUTATED 8 29 32
10Q GAIN WILD-TYPE 136 120 130

Figure S119.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q gain' versus 'RPPA_CNMF'

P value = 0.0412 (Fisher's exact test), Q value = 0.093

Table S120.  Gene #20: '10q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
10Q GAIN MUTATED 8 1 16 14 20
10Q GAIN WILD-TYPE 83 21 50 61 89

Figure S120.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'10q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S121.  Gene #20: '10q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
10Q GAIN MUTATED 11 25 41
10Q GAIN WILD-TYPE 155 170 110

Figure S121.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S122.  Gene #20: '10q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
10Q GAIN MUTATED 3 15 8 13 18 14 6
10Q GAIN WILD-TYPE 75 95 89 35 35 35 71

Figure S122.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11p gain' versus 'MRNA_CNMF'

P value = 0.00983 (Fisher's exact test), Q value = 0.03

Table S123.  Gene #21: '11p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 5 9 12 6
11P GAIN MUTATED 0 0 2 4
11P GAIN WILD-TYPE 5 9 10 2

Figure S123.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'11p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0109 (Fisher's exact test), Q value = 0.032

Table S124.  Gene #21: '11p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 11 7
11P GAIN MUTATED 2 0 4
11P GAIN WILD-TYPE 12 11 3

Figure S124.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'11p gain' versus 'CN_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.00089

Table S125.  Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
11P GAIN MUTATED 18 23 15 38
11P GAIN WILD-TYPE 51 205 64 102

Figure S125.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

'11p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 0.0014

Table S126.  Gene #21: '11p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
11P GAIN MUTATED 18 17 29 2 14 7 7
11P GAIN WILD-TYPE 60 93 68 46 39 42 70

Figure S126.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11p gain' versus 'MIRSEQ_CNMF'

P value = 0.00139 (Fisher's exact test), Q value = 0.0058

Table S127.  Gene #21: '11p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
11P GAIN MUTATED 20 50 23
11P GAIN WILD-TYPE 169 178 70

Figure S127.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00017

Table S128.  Gene #21: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
11P GAIN MUTATED 4 40 16 33
11P GAIN WILD-TYPE 67 158 125 67

Figure S128.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0158 (Fisher's exact test), Q value = 0.044

Table S129.  Gene #21: '11p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
11P GAIN MUTATED 10 47 21
11P GAIN WILD-TYPE 93 201 62

Figure S129.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q gain' versus 'MRNA_CNMF'

P value = 0.00061 (Fisher's exact test), Q value = 0.0029

Table S130.  Gene #22: '11q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 5 9 12 6
11Q GAIN MUTATED 0 0 2 5
11Q GAIN WILD-TYPE 5 9 10 1

Figure S130.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'11q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00101 (Fisher's exact test), Q value = 0.0044

Table S131.  Gene #22: '11q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 11 7
11Q GAIN MUTATED 2 0 5
11Q GAIN WILD-TYPE 12 11 2

Figure S131.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'11q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S132.  Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
11Q GAIN MUTATED 16 26 18 54
11Q GAIN WILD-TYPE 53 202 61 86

Figure S132.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

'11q gain' versus 'METHLYATION_CNMF'

P value = 0.0435 (Fisher's exact test), Q value = 0.097

Table S133.  Gene #22: '11q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
11Q GAIN MUTATED 23 32 45
11Q GAIN WILD-TYPE 121 117 117

Figure S133.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.0012

Table S134.  Gene #22: '11q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
11Q GAIN MUTATED 19 30 28 1 16 10 10
11Q GAIN WILD-TYPE 59 80 69 47 37 39 67

Figure S134.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_CNMF'

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

Table S135.  Gene #22: '11q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
11Q GAIN MUTATED 24 59 28
11Q GAIN WILD-TYPE 165 169 65

Figure S135.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S136.  Gene #22: '11q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
11Q GAIN MUTATED 4 51 22 34
11Q GAIN WILD-TYPE 67 147 119 66

Figure S136.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00526 (Fisher's exact test), Q value = 0.017

Table S137.  Gene #22: '11q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
11Q GAIN MUTATED 12 62 24
11Q GAIN WILD-TYPE 91 186 59

Figure S137.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0204 (Fisher's exact test), Q value = 0.053

Table S138.  Gene #23: '12p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 11 7
12P GAIN MUTATED 1 1 4
12P GAIN WILD-TYPE 13 10 3

Figure S138.  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 = 9.7e-05

Table S139.  Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
12P GAIN MUTATED 22 33 50 32
12P GAIN WILD-TYPE 47 195 29 108

Figure S139.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.0017

Table S140.  Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
12P GAIN MUTATED 24 56 41
12P GAIN WILD-TYPE 120 93 121

Figure S140.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p gain' versus 'RPPA_CNMF'

P value = 0.0321 (Fisher's exact test), Q value = 0.076

Table S141.  Gene #23: '12p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
12P GAIN MUTATED 20 2 19 28 23
12P GAIN WILD-TYPE 71 20 47 47 86

Figure S141.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00017

Table S142.  Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
12P GAIN MUTATED 21 61 55
12P GAIN WILD-TYPE 145 134 96

Figure S142.  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 = 9.7e-05

Table S143.  Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
12P GAIN MUTATED 8 27 30 4 29 26 13
12P GAIN WILD-TYPE 70 83 67 44 24 23 64

Figure S143.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00024

Table S144.  Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
12P GAIN MUTATED 30 83 22
12P GAIN WILD-TYPE 159 145 71

Figure S144.  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 = 9.7e-05

Table S145.  Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
12P GAIN MUTATED 10 56 22 47
12P GAIN WILD-TYPE 61 142 119 53

Figure S145.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S146.  Gene #23: '12p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
12P GAIN MUTATED 10 89 19
12P GAIN WILD-TYPE 93 159 64

Figure S146.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q gain' versus 'MRNA_CHIERARCHICAL'

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

Table S147.  Gene #24: '12q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 11 7
12Q GAIN MUTATED 1 1 4
12Q GAIN WILD-TYPE 13 10 3

Figure S147.  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 = 9.7e-05

Table S148.  Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
12Q GAIN MUTATED 26 30 50 24
12Q GAIN WILD-TYPE 43 198 29 116

Figure S148.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

'12q gain' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00024

Table S149.  Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
12Q GAIN MUTATED 20 56 38
12Q GAIN WILD-TYPE 124 93 124

Figure S149.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12q gain' versus 'RPPA_CNMF'

P value = 0.0191 (Fisher's exact test), Q value = 0.051

Table S150.  Gene #24: '12q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
12Q GAIN MUTATED 18 3 19 30 24
12Q GAIN WILD-TYPE 73 19 47 45 85

Figure S150.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'12q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S151.  Gene #24: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
12Q GAIN MUTATED 16 50 64
12Q GAIN WILD-TYPE 150 145 87

Figure S151.  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 = 9.7e-05

Table S152.  Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
12Q GAIN MUTATED 9 25 25 4 33 27 7
12Q GAIN WILD-TYPE 69 85 72 44 20 22 70

Figure S152.  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 = 9.7e-05

Table S153.  Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
12Q GAIN MUTATED 28 81 19
12Q GAIN WILD-TYPE 161 147 74

Figure S153.  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 = 9.7e-05

Table S154.  Gene #24: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
12Q GAIN MUTATED 12 58 15 43
12Q GAIN WILD-TYPE 59 140 126 57

Figure S154.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S155.  Gene #24: '12q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
12Q GAIN MUTATED 8 85 19
12Q GAIN WILD-TYPE 95 163 64

Figure S155.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q gain' versus 'METHLYATION_CNMF'

P value = 0.0308 (Fisher's exact test), Q value = 0.075

Table S156.  Gene #25: '13q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
13Q GAIN MUTATED 5 17 13
13Q GAIN WILD-TYPE 139 132 149

Figure S156.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0217 (Fisher's exact test), Q value = 0.056

Table S157.  Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
13Q GAIN MUTATED 8 4 10 8 3 8 3
13Q GAIN WILD-TYPE 70 106 87 40 50 41 74

Figure S157.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S158.  Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
14Q GAIN MUTATED 35 36 15 44
14Q GAIN WILD-TYPE 34 192 64 96

Figure S158.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

'14q gain' versus 'METHLYATION_CNMF'

P value = 0.013 (Fisher's exact test), Q value = 0.037

Table S159.  Gene #26: '14q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
14Q GAIN MUTATED 27 50 38
14Q GAIN WILD-TYPE 117 99 124

Figure S159.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q gain' versus 'RPPA_CNMF'

P value = 0.0379 (Fisher's exact test), Q value = 0.088

Table S160.  Gene #26: '14q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
14Q GAIN MUTATED 15 4 16 28 30
14Q GAIN WILD-TYPE 76 18 50 47 79

Figure S160.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'14q gain' versus 'MRNASEQ_CNMF'

P value = 0.0497 (Fisher's exact test), Q value = 0.11

Table S161.  Gene #26: '14q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
14Q GAIN MUTATED 31 53 45
14Q GAIN WILD-TYPE 135 142 106

Figure S161.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S162.  Gene #26: '14q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
14Q GAIN MUTATED 16 23 43 8 23 7 9
14Q GAIN WILD-TYPE 62 87 54 40 30 42 68

Figure S162.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.00092

Table S163.  Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
14Q GAIN MUTATED 28 65 33
14Q GAIN WILD-TYPE 161 163 60

Figure S163.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'14q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00067 (Fisher's exact test), Q value = 0.0031

Table S164.  Gene #26: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
14Q GAIN MUTATED 12 61 21 32
14Q GAIN WILD-TYPE 59 137 120 68

Figure S164.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'15q gain' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00042

Table S165.  Gene #27: '15q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
15Q GAIN MUTATED 2 12 17 7
15Q GAIN WILD-TYPE 67 216 62 133

Figure S165.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #3: 'CN_CNMF'

'15q gain' versus 'METHLYATION_CNMF'

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

Table S166.  Gene #27: '15q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
15Q GAIN MUTATED 7 18 5
15Q GAIN WILD-TYPE 137 131 157

Figure S166.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'15q gain' versus 'MRNASEQ_CNMF'

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

Table S167.  Gene #27: '15q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
15Q GAIN MUTATED 10 9 19
15Q GAIN WILD-TYPE 156 186 132

Figure S167.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S168.  Gene #27: '15q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
15Q GAIN MUTATED 2 1 4 3 5 16 7
15Q GAIN WILD-TYPE 76 109 93 45 48 33 70

Figure S168.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'RPPA_CNMF'

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

Table S169.  Gene #28: '16p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
16P GAIN MUTATED 33 7 19 16 18
16P GAIN WILD-TYPE 58 15 47 59 91

Figure S169.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 0.0377 (Fisher's exact test), Q value = 0.087

Table S170.  Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
16P GAIN MUTATED 54 46 31
16P GAIN WILD-TYPE 112 149 120

Figure S170.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0106 (Fisher's exact test), Q value = 0.032

Table S171.  Gene #28: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
16P GAIN MUTATED 32 25 31 9 9 10 15
16P GAIN WILD-TYPE 46 85 66 39 44 39 62

Figure S171.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_CNMF'

P value = 0.0111 (Fisher's exact test), Q value = 0.033

Table S172.  Gene #28: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
16P GAIN MUTATED 40 55 35
16P GAIN WILD-TYPE 149 173 58

Figure S172.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0409 (Fisher's exact test), Q value = 0.093

Table S173.  Gene #28: '16p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 198 91
16P GAIN MUTATED 42 39 29
16P GAIN WILD-TYPE 103 159 62

Figure S173.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16q gain' versus 'CN_CNMF'

P value = 0.0391 (Fisher's exact test), Q value = 0.09

Table S174.  Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
16Q GAIN MUTATED 13 32 19 35
16Q GAIN WILD-TYPE 56 196 60 105

Figure S174.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

'16q gain' versus 'MIRSEQ_CNMF'

P value = 0.00504 (Fisher's exact test), Q value = 0.017

Table S175.  Gene #29: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
16Q GAIN MUTATED 26 44 28
16Q GAIN WILD-TYPE 163 184 65

Figure S175.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17p gain' versus 'CN_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.00092

Table S176.  Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
17P GAIN MUTATED 20 21 19 23
17P GAIN WILD-TYPE 49 207 60 117

Figure S176.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

'17p gain' versus 'METHLYATION_CNMF'

P value = 0.0029 (Fisher's exact test), Q value = 0.011

Table S177.  Gene #30: '17p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
17P GAIN MUTATED 12 34 25
17P GAIN WILD-TYPE 132 115 137

Figure S177.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17p gain' versus 'RPPA_CHIERARCHICAL'

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

Table S178.  Gene #30: '17p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
17P GAIN MUTATED 30 24 3
17P GAIN WILD-TYPE 137 109 60

Figure S178.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_CNMF'

P value = 0.00518 (Fisher's exact test), Q value = 0.017

Table S179.  Gene #30: '17p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
17P GAIN MUTATED 19 49 13
17P GAIN WILD-TYPE 170 179 80

Figure S179.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S180.  Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
17Q GAIN MUTATED 30 48 36 77
17Q GAIN WILD-TYPE 39 180 43 63

Figure S180.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S181.  Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
17Q GAIN MUTATED 31 58 77
17Q GAIN WILD-TYPE 113 91 85

Figure S181.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 0.00233 (Fisher's exact test), Q value = 0.009

Table S182.  Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
17Q GAIN MUTATED 50 91 49
17Q GAIN WILD-TYPE 116 104 102

Figure S182.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S183.  Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
17Q GAIN MUTATED 29 52 45 5 27 13 19
17Q GAIN WILD-TYPE 49 58 52 43 26 36 58

Figure S183.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.00097

Table S184.  Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
17Q GAIN MUTATED 50 106 33
17Q GAIN WILD-TYPE 139 122 60

Figure S184.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00048

Table S185.  Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
17Q GAIN MUTATED 19 86 35 49
17Q GAIN WILD-TYPE 52 112 106 51

Figure S185.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00044 (Fisher's exact test), Q value = 0.0021

Table S186.  Gene #31: '17q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
17Q GAIN MUTATED 22 106 34
17Q GAIN WILD-TYPE 81 142 49

Figure S186.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S187.  Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
18P GAIN MUTATED 24 20 13 34
18P GAIN WILD-TYPE 45 208 66 106

Figure S187.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00031

Table S188.  Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
18P GAIN MUTATED 9 39 33
18P GAIN WILD-TYPE 135 110 129

Figure S188.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00083 (Fisher's exact test), Q value = 0.0038

Table S189.  Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
18P GAIN MUTATED 10 15 26 4 19 6 10
18P GAIN WILD-TYPE 68 95 71 44 34 43 67

Figure S189.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_CNMF'

P value = 0.00935 (Fisher's exact test), Q value = 0.029

Table S190.  Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
18P GAIN MUTATED 21 50 19
18P GAIN WILD-TYPE 168 178 74

Figure S190.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00671 (Fisher's exact test), Q value = 0.022

Table S191.  Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
18P GAIN MUTATED 6 40 18 26
18P GAIN WILD-TYPE 65 158 123 74

Figure S191.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00064

Table S192.  Gene #32: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
18P GAIN MUTATED 5 58 16
18P GAIN WILD-TYPE 98 190 67

Figure S192.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S193.  Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
18Q GAIN MUTATED 18 12 18 22
18Q GAIN WILD-TYPE 51 216 61 118

Figure S193.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

'18q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S194.  Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
18Q GAIN MUTATED 5 36 20
18Q GAIN WILD-TYPE 139 113 142

Figure S194.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q gain' versus 'MRNASEQ_CNMF'

P value = 0.00084 (Fisher's exact test), Q value = 0.0038

Table S195.  Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
18Q GAIN MUTATED 12 24 33
18Q GAIN WILD-TYPE 154 171 118

Figure S195.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00024

Table S196.  Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
18Q GAIN MUTATED 5 9 18 6 20 5 6
18Q GAIN WILD-TYPE 73 101 79 42 33 44 71

Figure S196.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_CNMF'

P value = 0.00701 (Fisher's exact test), Q value = 0.022

Table S197.  Gene #33: '18q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
18Q GAIN MUTATED 15 42 12
18Q GAIN WILD-TYPE 174 186 81

Figure S197.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00203 (Fisher's exact test), Q value = 0.008

Table S198.  Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
18Q GAIN MUTATED 4 30 12 23
18Q GAIN WILD-TYPE 67 168 129 77

Figure S198.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0435 (Fisher's exact test), Q value = 0.097

Table S199.  Gene #33: '18q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 198 91
18Q GAIN MUTATED 14 36 9
18Q GAIN WILD-TYPE 131 162 82

Figure S199.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00323 (Fisher's exact test), Q value = 0.012

Table S200.  Gene #33: '18q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
18Q GAIN MUTATED 5 44 10
18Q GAIN WILD-TYPE 98 204 73

Figure S200.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q gain' versus 'CN_CNMF'

P value = 0.00043 (Fisher's exact test), Q value = 0.0021

Table S201.  Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
19Q GAIN MUTATED 15 22 22 17
19Q GAIN WILD-TYPE 54 206 57 123

Figure S201.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

'19q gain' versus 'METHLYATION_CNMF'

P value = 0.00417 (Fisher's exact test), Q value = 0.014

Table S202.  Gene #35: '19q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
19Q GAIN MUTATED 17 36 19
19Q GAIN WILD-TYPE 127 113 143

Figure S202.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q gain' versus 'RPPA_CNMF'

P value = 0.0353 (Fisher's exact test), Q value = 0.082

Table S203.  Gene #35: '19q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
19Q GAIN MUTATED 10 2 10 21 14
19Q GAIN WILD-TYPE 81 20 56 54 95

Figure S203.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 0.00798 (Fisher's exact test), Q value = 0.025

Table S204.  Gene #35: '19q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
19Q GAIN MUTATED 14 29 31
19Q GAIN WILD-TYPE 152 166 120

Figure S204.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0261 (Fisher's exact test), Q value = 0.066

Table S205.  Gene #35: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
19Q GAIN MUTATED 5 12 17 11 9 12 8
19Q GAIN WILD-TYPE 73 98 80 37 44 37 69

Figure S205.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00118 (Fisher's exact test), Q value = 0.0051

Table S206.  Gene #35: '19q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
19Q GAIN MUTATED 14 51 4
19Q GAIN WILD-TYPE 89 197 79

Figure S206.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00069

Table S207.  Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
20P GAIN MUTATED 36 56 33 48
20P GAIN WILD-TYPE 33 172 46 92

Figure S207.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.00089

Table S208.  Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
20P GAIN MUTATED 35 69 47
20P GAIN WILD-TYPE 109 80 115

Figure S208.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0093 (Fisher's exact test), Q value = 0.029

Table S209.  Gene #36: '20p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
20P GAIN MUTATED 44 57 19
20P GAIN WILD-TYPE 123 76 44

Figure S209.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 0.00059 (Fisher's exact test), Q value = 0.0028

Table S210.  Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
20P GAIN MUTATED 37 71 62
20P GAIN WILD-TYPE 129 124 89

Figure S210.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00017

Table S211.  Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
20P GAIN MUTATED 12 35 52 14 26 16 15
20P GAIN WILD-TYPE 66 75 45 34 27 33 62

Figure S211.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00042

Table S212.  Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
20P GAIN MUTATED 41 92 38
20P GAIN WILD-TYPE 148 136 55

Figure S212.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 8e-04

Table S213.  Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
20P GAIN MUTATED 17 75 32 47
20P GAIN WILD-TYPE 54 123 109 53

Figure S213.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0456 (Fisher's exact test), Q value = 0.1

Table S214.  Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 198 91
20P GAIN MUTATED 37 74 34
20P GAIN WILD-TYPE 108 124 57

Figure S214.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.00069

Table S215.  Gene #36: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
20P GAIN MUTATED 19 101 25
20P GAIN WILD-TYPE 84 147 58

Figure S215.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q gain' versus 'MRNA_CNMF'

P value = 0.00429 (Fisher's exact test), Q value = 0.015

Table S216.  Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 5 9 12 6
20Q GAIN MUTATED 0 1 2 5
20Q GAIN WILD-TYPE 5 8 10 1

Figure S216.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0095 (Fisher's exact test), Q value = 0.029

Table S217.  Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 11 7
20Q GAIN MUTATED 2 1 5
20Q GAIN WILD-TYPE 12 10 2

Figure S217.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S218.  Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
20Q GAIN MUTATED 36 54 41 61
20Q GAIN WILD-TYPE 33 174 38 79

Figure S218.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S219.  Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
20Q GAIN MUTATED 33 77 58
20Q GAIN WILD-TYPE 111 72 104

Figure S219.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00025 (Fisher's exact test), Q value = 0.0013

Table S220.  Gene #37: '20q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
20Q GAIN MUTATED 46 67 23
20Q GAIN WILD-TYPE 121 66 40

Figure S220.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00024

Table S221.  Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
20Q GAIN MUTATED 38 85 66
20Q GAIN WILD-TYPE 128 110 85

Figure S221.  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 = 9.7e-05

Table S222.  Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
20Q GAIN MUTATED 12 44 58 14 28 18 15
20Q GAIN WILD-TYPE 66 66 39 34 25 31 62

Figure S222.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00017

Table S223.  Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
20Q GAIN MUTATED 45 106 37
20Q GAIN WILD-TYPE 144 122 56

Figure S223.  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 = 9.7e-05

Table S224.  Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
20Q GAIN MUTATED 16 84 37 51
20Q GAIN WILD-TYPE 55 114 104 49

Figure S224.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S225.  Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
20Q GAIN MUTATED 16 117 28
20Q GAIN WILD-TYPE 87 131 55

Figure S225.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q gain' versus 'CN_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.00092

Table S226.  Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
21Q GAIN MUTATED 8 35 9 44
21Q GAIN WILD-TYPE 61 193 70 96

Figure S226.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

'21q gain' versus 'MRNASEQ_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.0013

Table S227.  Gene #38: '21q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
21Q GAIN MUTATED 41 42 13
21Q GAIN WILD-TYPE 125 153 138

Figure S227.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00053 (Fisher's exact test), Q value = 0.0025

Table S228.  Gene #38: '21q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
21Q GAIN MUTATED 24 24 25 3 4 7 9
21Q GAIN WILD-TYPE 54 86 72 45 49 42 68

Figure S228.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q gain' versus 'CN_CNMF'

P value = 0.00048 (Fisher's exact test), Q value = 0.0023

Table S229.  Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
22Q GAIN MUTATED 3 18 13 28
22Q GAIN WILD-TYPE 66 210 66 112

Figure S229.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

'22q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0434 (Fisher's exact test), Q value = 0.097

Table S230.  Gene #39: '22q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
22Q GAIN MUTATED 7 12 19 2 4 10 7
22Q GAIN WILD-TYPE 71 98 78 46 49 39 70

Figure S230.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xp gain' versus 'CN_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.0011

Table S231.  Gene #40: 'xp gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
XP GAIN MUTATED 13 10 7 21
XP GAIN WILD-TYPE 56 218 72 119

Figure S231.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #3: 'CN_CNMF'

'xp gain' versus 'METHLYATION_CNMF'

P value = 0.00289 (Fisher's exact test), Q value = 0.011

Table S232.  Gene #40: 'xp gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
XP GAIN MUTATED 5 21 19
XP GAIN WILD-TYPE 139 128 143

Figure S232.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xp gain' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S233.  Gene #40: 'xp gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
XP GAIN MUTATED 6 27 6 11
XP GAIN WILD-TYPE 65 171 135 89

Figure S233.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'xq gain' versus 'CN_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00069

Table S234.  Gene #41: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
XQ GAIN MUTATED 14 22 9 38
XQ GAIN WILD-TYPE 55 206 70 102

Figure S234.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

'xq gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0163 (Fisher's exact test), Q value = 0.045

Table S235.  Gene #41: 'xq gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
XQ GAIN MUTATED 13 22 26 5 5 4 8
XQ GAIN WILD-TYPE 65 88 71 43 48 45 69

Figure S235.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S236.  Gene #42: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
1P LOSS MUTATED 22 35 18 8
1P LOSS WILD-TYPE 47 193 61 132

Figure S236.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 0.0482 (Fisher's exact test), Q value = 0.11

Table S237.  Gene #42: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
1P LOSS MUTATED 15 31 25
1P LOSS WILD-TYPE 129 118 137

Figure S237.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.00089

Table S238.  Gene #42: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
1P LOSS MUTATED 15 27 39
1P LOSS WILD-TYPE 151 168 112

Figure S238.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00042

Table S239.  Gene #42: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
1P LOSS MUTATED 9 16 8 10 21 11 6
1P LOSS WILD-TYPE 69 94 89 38 32 38 71

Figure S239.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00038

Table S240.  Gene #46: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
3P LOSS MUTATED 36 69 42 66
3P LOSS WILD-TYPE 33 159 37 74

Figure S240.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S241.  Gene #46: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
3P LOSS MUTATED 40 84 62
3P LOSS WILD-TYPE 104 65 100

Figure S241.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 0.00478 (Fisher's exact test), Q value = 0.016

Table S242.  Gene #46: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
3P LOSS MUTATED 57 75 78
3P LOSS WILD-TYPE 109 120 73

Figure S242.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00053

Table S243.  Gene #46: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
3P LOSS MUTATED 28 37 51 19 33 24 18
3P LOSS WILD-TYPE 50 73 46 29 20 25 59

Figure S243.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CNMF'

P value = 0.017 (Fisher's exact test), Q value = 0.046

Table S244.  Gene #46: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
3P LOSS MUTATED 63 100 46
3P LOSS WILD-TYPE 126 128 47

Figure S244.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S245.  Gene #46: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
3P LOSS MUTATED 28 80 47 54
3P LOSS WILD-TYPE 43 118 94 46

Figure S245.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0317 (Fisher's exact test), Q value = 0.076

Table S246.  Gene #46: '3p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
3P LOSS MUTATED 33 116 32
3P LOSS WILD-TYPE 70 132 51

Figure S246.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

P value = 0.0143 (Fisher's exact test), Q value = 0.04

Table S247.  Gene #47: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
3Q LOSS MUTATED 29 51 23 43
3Q LOSS WILD-TYPE 40 177 56 97

Figure S247.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

'3q loss' versus 'METHLYATION_CNMF'

P value = 0.0259 (Fisher's exact test), Q value = 0.066

Table S248.  Gene #47: '3q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
3Q LOSS MUTATED 29 50 49
3Q LOSS WILD-TYPE 115 99 113

Figure S248.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3q loss' versus 'MRNASEQ_CNMF'

P value = 0.00588 (Fisher's exact test), Q value = 0.019

Table S249.  Gene #47: '3q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
3Q LOSS MUTATED 45 42 56
3Q LOSS WILD-TYPE 121 153 95

Figure S249.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0234 (Fisher's exact test), Q value = 0.06

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 CLUS_7
ALL 78 110 97 48 53 49 77
3Q LOSS MUTATED 24 28 21 18 23 15 14
3Q LOSS WILD-TYPE 54 82 76 30 30 34 63

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

'4p loss' versus 'CN_CNMF'

P value = 0.00101 (Fisher's exact test), Q value = 0.0044

Table S251.  Gene #48: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
4P LOSS MUTATED 22 36 22 44
4P LOSS WILD-TYPE 47 192 57 96

Figure S251.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.0012

Table S252.  Gene #48: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
4P LOSS MUTATED 24 52 29
4P LOSS WILD-TYPE 120 97 133

Figure S252.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p loss' versus 'RPPA_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.002

Table S253.  Gene #48: '4p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
4P LOSS MUTATED 21 7 10 34 22
4P LOSS WILD-TYPE 70 15 56 41 87

Figure S253.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'4p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00462 (Fisher's exact test), Q value = 0.016

Table S254.  Gene #48: '4p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
4P LOSS MUTATED 41 45 8
4P LOSS WILD-TYPE 126 88 55

Figure S254.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 0.026 (Fisher's exact test), Q value = 0.066

Table S255.  Gene #48: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
4P LOSS MUTATED 28 50 44
4P LOSS WILD-TYPE 138 145 107

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

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

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 CLUS_7
ALL 78 110 97 48 53 49 77
4P LOSS MUTATED 13 18 40 2 22 14 13
4P LOSS WILD-TYPE 65 92 57 46 31 35 64

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

'4p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S257.  Gene #48: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
4P LOSS MUTATED 23 76 23
4P LOSS WILD-TYPE 166 152 70

Figure S257.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S258.  Gene #48: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
4P LOSS MUTATED 6 56 23 37
4P LOSS WILD-TYPE 65 142 118 63

Figure S258.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00053

Table S259.  Gene #48: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
4P LOSS MUTATED 13 77 12
4P LOSS WILD-TYPE 90 171 71

Figure S259.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'MRNA_CNMF'

P value = 0.00101 (Fisher's exact test), Q value = 0.0044

Table S260.  Gene #49: '4q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 5 9 12 6
4Q LOSS MUTATED 2 2 0 5
4Q LOSS WILD-TYPE 3 7 12 1

Figure S260.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'4q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00869 (Fisher's exact test), Q value = 0.027

Table S261.  Gene #49: '4q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 11 7
4Q LOSS MUTATED 1 3 5
4Q LOSS WILD-TYPE 13 8 2

Figure S261.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00053

Table S262.  Gene #49: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
4Q LOSS MUTATED 29 40 27 45
4Q LOSS WILD-TYPE 40 188 52 95

Figure S262.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S263.  Gene #49: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
4Q LOSS MUTATED 25 64 31
4Q LOSS WILD-TYPE 119 85 131

Figure S263.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q loss' versus 'RPPA_CNMF'

P value = 0.0172 (Fisher's exact test), Q value = 0.047

Table S264.  Gene #49: '4q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
4Q LOSS MUTATED 27 6 12 33 29
4Q LOSS WILD-TYPE 64 16 54 42 80

Figure S264.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'4q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0311 (Fisher's exact test), Q value = 0.075

Table S265.  Gene #49: '4q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
4Q LOSS MUTATED 46 49 12
4Q LOSS WILD-TYPE 121 84 51

Figure S265.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00017

Table S266.  Gene #49: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
4Q LOSS MUTATED 26 55 58
4Q LOSS WILD-TYPE 140 140 93

Figure S266.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S267.  Gene #49: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
4Q LOSS MUTATED 11 18 43 5 29 20 13
4Q LOSS WILD-TYPE 67 92 54 43 24 29 64

Figure S267.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S268.  Gene #49: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
4Q LOSS MUTATED 27 86 26
4Q LOSS WILD-TYPE 162 142 67

Figure S268.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S269.  Gene #49: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
4Q LOSS MUTATED 8 63 22 46
4Q LOSS WILD-TYPE 63 135 119 54

Figure S269.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.00085

Table S270.  Gene #49: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
4Q LOSS MUTATED 15 85 16
4Q LOSS WILD-TYPE 88 163 67

Figure S270.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p loss' versus 'RPPA_CNMF'

P value = 0.0285 (Fisher's exact test), Q value = 0.07

Table S271.  Gene #50: '5p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
5P LOSS MUTATED 10 1 3 15 8
5P LOSS WILD-TYPE 81 21 63 60 101

Figure S271.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'5p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0122 (Fisher's exact test), Q value = 0.035

Table S272.  Gene #50: '5p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
5P LOSS MUTATED 11 22 4
5P LOSS WILD-TYPE 156 111 59

Figure S272.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'5p loss' versus 'MRNASEQ_CNMF'

P value = 0.0106 (Fisher's exact test), Q value = 0.032

Table S273.  Gene #50: '5p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
5P LOSS MUTATED 8 21 22
5P LOSS WILD-TYPE 158 174 129

Figure S273.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0204 (Fisher's exact test), Q value = 0.053

Table S274.  Gene #50: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
5P LOSS MUTATED 3 19 11 18
5P LOSS WILD-TYPE 68 179 130 82

Figure S274.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0208 (Fisher's exact test), Q value = 0.054

Table S275.  Gene #50: '5p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
5P LOSS MUTATED 4 28 3
5P LOSS WILD-TYPE 99 220 80

Figure S275.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S276.  Gene #51: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
5Q LOSS MUTATED 27 41 35 50
5Q LOSS WILD-TYPE 42 187 44 90

Figure S276.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00053

Table S277.  Gene #51: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
5Q LOSS MUTATED 23 57 53
5Q LOSS WILD-TYPE 121 92 109

Figure S277.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5q loss' versus 'RPPA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00017

Table S278.  Gene #51: '5q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
5Q LOSS MUTATED 34 6 12 37 20
5Q LOSS WILD-TYPE 57 16 54 38 89

Figure S278.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'5q loss' versus 'RPPA_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00053

Table S279.  Gene #51: '5q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
5Q LOSS MUTATED 40 58 11
5Q LOSS WILD-TYPE 127 75 52

Figure S279.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00024

Table S280.  Gene #51: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
5Q LOSS MUTATED 28 66 57
5Q LOSS WILD-TYPE 138 129 94

Figure S280.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S281.  Gene #51: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
5Q LOSS MUTATED 7 41 36 8 22 18 19
5Q LOSS WILD-TYPE 71 69 61 40 31 31 58

Figure S281.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S282.  Gene #51: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
5Q LOSS MUTATED 33 91 26
5Q LOSS WILD-TYPE 156 137 67

Figure S282.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S283.  Gene #51: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
5Q LOSS MUTATED 10 68 25 47
5Q LOSS WILD-TYPE 61 130 116 53

Figure S283.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S284.  Gene #51: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
5Q LOSS MUTATED 13 94 19
5Q LOSS WILD-TYPE 90 154 64

Figure S284.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p loss' versus 'MRNA_CNMF'

P value = 0.0305 (Fisher's exact test), Q value = 0.075

Table S285.  Gene #52: '6p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 5 9 12 6
6P LOSS MUTATED 1 5 1 0
6P LOSS WILD-TYPE 4 4 11 6

Figure S285.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'6p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00772 (Fisher's exact test), Q value = 0.024

Table S286.  Gene #52: '6p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 11 7
6P LOSS MUTATED 1 6 0
6P LOSS WILD-TYPE 13 5 7

Figure S286.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6p loss' versus 'METHLYATION_CNMF'

P value = 0.0321 (Fisher's exact test), Q value = 0.076

Table S287.  Gene #52: '6p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
6P LOSS MUTATED 27 24 45
6P LOSS WILD-TYPE 117 125 117

Figure S287.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00416 (Fisher's exact test), Q value = 0.014

Table S288.  Gene #52: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
6P LOSS MUTATED 15 52 29 9
6P LOSS WILD-TYPE 56 146 112 91

Figure S288.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6q loss' versus 'CN_CNMF'

P value = 0.00259 (Fisher's exact test), Q value = 0.0097

Table S289.  Gene #53: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
6Q LOSS MUTATED 42 81 36 58
6Q LOSS WILD-TYPE 27 147 43 82

Figure S289.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

'6q loss' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00017

Table S290.  Gene #53: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
6Q LOSS MUTATED 45 57 92
6Q LOSS WILD-TYPE 99 92 70

Figure S290.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00094 (Fisher's exact test), Q value = 0.0042

Table S291.  Gene #53: '6q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
6Q LOSS MUTATED 29 56 28 28 29 18 26
6Q LOSS WILD-TYPE 49 54 69 20 24 31 51

Figure S291.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00085 (Fisher's exact test), Q value = 0.0038

Table S292.  Gene #53: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
6Q LOSS MUTATED 32 102 52 29
6Q LOSS WILD-TYPE 39 96 89 71

Figure S292.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7p loss' versus 'CN_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.0011

Table S293.  Gene #54: '7p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
7P LOSS MUTATED 10 16 11 2
7P LOSS WILD-TYPE 59 212 68 138

Figure S293.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #3: 'CN_CNMF'

'7p loss' versus 'MRNASEQ_CNMF'

P value = 0.0448 (Fisher's exact test), Q value = 0.1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
7P LOSS MUTATED 8 12 18
7P LOSS WILD-TYPE 158 183 133

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

'7p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0137 (Fisher's exact test), Q value = 0.039

Table S295.  Gene #54: '7p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
7P LOSS MUTATED 2 6 7 7 8 6 2
7P LOSS WILD-TYPE 76 104 90 41 45 43 75

Figure S295.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00599 (Fisher's exact test), Q value = 0.019

Table S296.  Gene #54: '7p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 198 91
7P LOSS MUTATED 16 10 1
7P LOSS WILD-TYPE 129 188 90

Figure S296.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7q loss' versus 'CN_CNMF'

P value = 0.0237 (Fisher's exact test), Q value = 0.06

Table S297.  Gene #55: '7q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
7Q LOSS MUTATED 11 18 11 7
7Q LOSS WILD-TYPE 58 210 68 133

Figure S297.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'MRNA_CNMF'

P value = 0.0129 (Fisher's exact test), Q value = 0.037

Table S298.  Gene #56: '8p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 5 9 12 6
8P LOSS MUTATED 4 7 2 2
8P LOSS WILD-TYPE 1 2 10 4

Figure S298.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'8p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S299.  Gene #56: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
8P LOSS MUTATED 21 60 38 84
8P LOSS WILD-TYPE 48 168 41 56

Figure S299.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 0.047 (Fisher's exact test), Q value = 0.1

Table S300.  Gene #56: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
8P LOSS MUTATED 47 57 75
8P LOSS WILD-TYPE 97 92 87

Figure S300.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p loss' versus 'RPPA_CNMF'

P value = 0.00208 (Fisher's exact test), Q value = 0.0082

Table S301.  Gene #56: '8p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
8P LOSS MUTATED 44 11 20 39 31
8P LOSS WILD-TYPE 47 11 46 36 78

Figure S301.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'8p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0169 (Fisher's exact test), Q value = 0.046

Table S302.  Gene #56: '8p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
8P LOSS MUTATED 58 66 21
8P LOSS WILD-TYPE 109 67 42

Figure S302.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S303.  Gene #56: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
8P LOSS MUTATED 52 106 43
8P LOSS WILD-TYPE 114 89 108

Figure S303.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00053

Table S304.  Gene #56: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
8P LOSS MUTATED 30 56 51 8 16 15 25
8P LOSS WILD-TYPE 48 54 46 40 37 34 52

Figure S304.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_CNMF'

P value = 0.00992 (Fisher's exact test), Q value = 0.03

Table S305.  Gene #56: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
8P LOSS MUTATED 59 104 38
8P LOSS WILD-TYPE 130 124 55

Figure S305.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0429 (Fisher's exact test), Q value = 0.097

Table S306.  Gene #56: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
8P LOSS MUTATED 23 89 45 44
8P LOSS WILD-TYPE 48 109 96 56

Figure S306.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0216 (Fisher's exact test), Q value = 0.056

Table S307.  Gene #56: '8p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 198 91
8P LOSS MUTATED 44 86 41
8P LOSS WILD-TYPE 101 112 50

Figure S307.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0121 (Fisher's exact test), Q value = 0.035

Table S308.  Gene #56: '8p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
8P LOSS MUTATED 28 109 34
8P LOSS WILD-TYPE 75 139 49

Figure S308.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q loss' versus 'CN_CNMF'

P value = 0.0198 (Fisher's exact test), Q value = 0.052

Table S309.  Gene #57: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
8Q LOSS MUTATED 3 26 6 25
8Q LOSS WILD-TYPE 66 202 73 115

Figure S309.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'

'8q loss' versus 'MRNASEQ_CNMF'

P value = 0.0148 (Fisher's exact test), Q value = 0.041

Table S310.  Gene #57: '8q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
8Q LOSS MUTATED 19 31 9
8Q LOSS WILD-TYPE 147 164 142

Figure S310.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S311.  Gene #58: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
9P LOSS MUTATED 33 94 61 82
9P LOSS WILD-TYPE 36 134 18 58

Figure S311.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 0.00184 (Fisher's exact test), Q value = 0.0073

Table S312.  Gene #58: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
9P LOSS MUTATED 62 94 79
9P LOSS WILD-TYPE 82 55 83

Figure S312.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00042

Table S313.  Gene #58: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
9P LOSS MUTATED 40 51 61 20 25 39 32
9P LOSS WILD-TYPE 38 59 36 28 28 10 45

Figure S313.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_CNMF'

P value = 0.00663 (Fisher's exact test), Q value = 0.021

Table S314.  Gene #58: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
9P LOSS MUTATED 89 115 62
9P LOSS WILD-TYPE 100 113 31

Figure S314.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00159 (Fisher's exact test), Q value = 0.0066

Table S315.  Gene #58: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
9P LOSS MUTATED 32 100 65 69
9P LOSS WILD-TYPE 39 98 76 31

Figure S315.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S316.  Gene #59: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
9Q LOSS MUTATED 36 84 56 78
9Q LOSS WILD-TYPE 33 144 23 62

Figure S316.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 0.00209 (Fisher's exact test), Q value = 0.0082

Table S317.  Gene #59: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
9Q LOSS MUTATED 57 88 72
9Q LOSS WILD-TYPE 87 61 90

Figure S317.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00088 (Fisher's exact test), Q value = 0.004

Table S318.  Gene #59: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
9Q LOSS MUTATED 37 50 59 14 30 32 30
9Q LOSS WILD-TYPE 41 60 38 34 23 17 47

Figure S318.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_CNMF'

P value = 0.00169 (Fisher's exact test), Q value = 0.0068

Table S319.  Gene #59: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
9Q LOSS MUTATED 75 118 57
9Q LOSS WILD-TYPE 114 110 36

Figure S319.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00024

Table S320.  Gene #59: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
9Q LOSS MUTATED 29 94 57 70
9Q LOSS WILD-TYPE 42 104 84 30

Figure S320.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0126 (Fisher's exact test), Q value = 0.036

Table S321.  Gene #59: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
9Q LOSS MUTATED 37 132 40
9Q LOSS WILD-TYPE 66 116 43

Figure S321.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 0.00053 (Fisher's exact test), Q value = 0.0025

Table S322.  Gene #60: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
10P LOSS MUTATED 11 39 15 49
10P LOSS WILD-TYPE 58 189 64 91

Figure S322.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

'10p loss' versus 'RPPA_CNMF'

P value = 0.0313 (Fisher's exact test), Q value = 0.076

Table S323.  Gene #60: '10p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
10P LOSS MUTATED 30 6 12 17 16
10P LOSS WILD-TYPE 61 16 54 58 93

Figure S323.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 0.00102 (Fisher's exact test), Q value = 0.0044

Table S324.  Gene #60: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
10P LOSS MUTATED 34 58 20
10P LOSS WILD-TYPE 132 137 131

Figure S324.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S325.  Gene #60: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
10P LOSS MUTATED 18 29 38 0 10 3 14
10P LOSS WILD-TYPE 60 81 59 48 43 46 63

Figure S325.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_CNMF'

P value = 0.00325 (Fisher's exact test), Q value = 0.012

Table S326.  Gene #60: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
10P LOSS MUTATED 31 48 32
10P LOSS WILD-TYPE 158 180 61

Figure S326.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0383 (Fisher's exact test), Q value = 0.088

Table S327.  Gene #60: '10p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 198 91
10P LOSS MUTATED 21 49 23
10P LOSS WILD-TYPE 124 149 68

Figure S327.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10q loss' versus 'CN_CNMF'

P value = 0.00098 (Fisher's exact test), Q value = 0.0043

Table S328.  Gene #61: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
10Q LOSS MUTATED 16 44 22 54
10Q LOSS WILD-TYPE 53 184 57 86

Figure S328.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 0.0307 (Fisher's exact test), Q value = 0.075

Table S329.  Gene #61: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
10Q LOSS MUTATED 27 48 43
10Q LOSS WILD-TYPE 117 101 119

Figure S329.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00042

Table S330.  Gene #61: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
10Q LOSS MUTATED 36 72 26
10Q LOSS WILD-TYPE 130 123 125

Figure S330.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S331.  Gene #61: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
10Q LOSS MUTATED 21 33 49 0 10 8 13
10Q LOSS WILD-TYPE 57 77 48 48 43 41 64

Figure S331.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_CNMF'

P value = 0.00519 (Fisher's exact test), Q value = 0.017

Table S332.  Gene #61: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
10Q LOSS MUTATED 36 63 34
10Q LOSS WILD-TYPE 153 165 59

Figure S332.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0111 (Fisher's exact test), Q value = 0.033

Table S333.  Gene #61: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
10Q LOSS MUTATED 10 56 32 35
10Q LOSS WILD-TYPE 61 142 109 65

Figure S333.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0214 (Fisher's exact test), Q value = 0.056

Table S334.  Gene #61: '10q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 198 91
10Q LOSS MUTATED 27 63 23
10Q LOSS WILD-TYPE 118 135 68

Figure S334.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00234 (Fisher's exact test), Q value = 0.009

Table S335.  Gene #61: '10q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
10Q LOSS MUTATED 14 76 23
10Q LOSS WILD-TYPE 89 172 60

Figure S335.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.0011

Table S336.  Gene #62: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
11P LOSS MUTATED 19 31 24 42
11P LOSS WILD-TYPE 50 197 55 98

Figure S336.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 0.0276 (Fisher's exact test), Q value = 0.069

Table S337.  Gene #62: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
11P LOSS MUTATED 24 44 34
11P LOSS WILD-TYPE 120 105 128

Figure S337.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0103 (Fisher's exact test), Q value = 0.031

Table S338.  Gene #62: '11p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
11P LOSS MUTATED 28 42 13
11P LOSS WILD-TYPE 139 91 50

Figure S338.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'11p loss' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00042

Table S339.  Gene #62: '11p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
11P LOSS MUTATED 18 57 38
11P LOSS WILD-TYPE 148 138 113

Figure S339.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00074 (Fisher's exact test), Q value = 0.0034

Table S340.  Gene #62: '11p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
11P LOSS MUTATED 7 31 26 8 13 18 10
11P LOSS WILD-TYPE 71 79 71 40 40 31 67

Figure S340.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

P value = 0.00141 (Fisher's exact test), Q value = 0.0059

Table S341.  Gene #63: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
11Q LOSS MUTATED 19 25 20 27
11Q LOSS WILD-TYPE 50 203 59 113

Figure S341.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

P value = 0.0411 (Fisher's exact test), Q value = 0.093

Table S342.  Gene #63: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
11Q LOSS MUTATED 19 36 26
11Q LOSS WILD-TYPE 125 113 136

Figure S342.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11q loss' versus 'MRNASEQ_CNMF'

P value = 0.00163 (Fisher's exact test), Q value = 0.0067

Table S343.  Gene #63: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
11Q LOSS MUTATED 15 39 34
11Q LOSS WILD-TYPE 151 156 117

Figure S343.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0197 (Fisher's exact test), Q value = 0.052

Table S344.  Gene #63: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
11Q LOSS MUTATED 6 19 19 7 15 13 9
11Q LOSS WILD-TYPE 72 91 78 41 38 36 68

Figure S344.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S345.  Gene #64: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
12P LOSS MUTATED 14 42 7 51
12P LOSS WILD-TYPE 55 186 72 89

Figure S345.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

'12p loss' versus 'RPPA_CNMF'

P value = 0.0126 (Fisher's exact test), Q value = 0.036

Table S346.  Gene #64: '12p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
12P LOSS MUTATED 28 10 16 13 18
12P LOSS WILD-TYPE 63 12 50 62 91

Figure S346.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'12p loss' versus 'MRNASEQ_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.0017

Table S347.  Gene #64: '12p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
12P LOSS MUTATED 47 48 17
12P LOSS WILD-TYPE 119 147 134

Figure S347.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12p loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S348.  Gene #64: '12p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
12P LOSS MUTATED 19 25 33 11 3 3 18
12P LOSS WILD-TYPE 59 85 64 37 50 46 59

Figure S348.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S349.  Gene #65: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
12Q LOSS MUTATED 9 39 4 50
12Q LOSS WILD-TYPE 60 189 75 90

Figure S349.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

'12q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S350.  Gene #65: '12q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
12Q LOSS MUTATED 42 48 10
12Q LOSS WILD-TYPE 124 147 141

Figure S350.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00031

Table S351.  Gene #65: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
12Q LOSS MUTATED 17 25 27 10 1 2 18
12Q LOSS WILD-TYPE 61 85 70 38 52 47 59

Figure S351.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S352.  Gene #66: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
13Q LOSS MUTATED 48 72 39 99
13Q LOSS WILD-TYPE 21 156 40 41

Figure S352.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

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

Table S353.  Gene #66: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
13Q LOSS MUTATED 60 80 89
13Q LOSS WILD-TYPE 84 69 73

Figure S353.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q loss' versus 'RPPA_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00069

Table S354.  Gene #66: '13q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
13Q LOSS MUTATED 57 8 29 50 41
13Q LOSS WILD-TYPE 34 14 37 25 68

Figure S354.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.002

Table S355.  Gene #66: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
13Q LOSS MUTATED 63 114 78
13Q LOSS WILD-TYPE 103 81 73

Figure S355.  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 = 9.7e-05

Table S356.  Gene #66: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
13Q LOSS MUTATED 34 72 55 11 37 18 28
13Q LOSS WILD-TYPE 44 38 42 37 16 31 49

Figure S356.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_CNMF'

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

Table S357.  Gene #66: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
13Q LOSS MUTATED 78 122 55
13Q LOSS WILD-TYPE 111 106 38

Figure S357.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'13q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0218 (Fisher's exact test), Q value = 0.056

Table S358.  Gene #66: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
13Q LOSS MUTATED 33 113 57 52
13Q LOSS WILD-TYPE 38 85 84 48

Figure S358.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S359.  Gene #66: '13q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
13Q LOSS MUTATED 38 139 44
13Q LOSS WILD-TYPE 65 109 39

Figure S359.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00042

Table S360.  Gene #67: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
14Q LOSS MUTATED 9 38 33 34
14Q LOSS WILD-TYPE 60 190 46 106

Figure S360.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

'14q loss' versus 'RPPA_CNMF'

P value = 0.00244 (Fisher's exact test), Q value = 0.0093

Table S361.  Gene #67: '14q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
14Q LOSS MUTATED 23 2 16 26 13
14Q LOSS WILD-TYPE 68 20 50 49 96

Figure S361.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00222 (Fisher's exact test), Q value = 0.0087

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 CLUS_7
ALL 78 110 97 48 53 49 77
14Q LOSS MUTATED 11 26 20 10 11 23 12
14Q LOSS WILD-TYPE 67 84 77 38 42 26 65

Figure S362.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_CNMF'

P value = 0.0316 (Fisher's exact test), Q value = 0.076

Table S363.  Gene #67: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
14Q LOSS MUTATED 36 63 15
14Q LOSS WILD-TYPE 153 165 78

Figure S363.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'15q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S364.  Gene #68: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
15Q LOSS MUTATED 44 76 30 91
15Q LOSS WILD-TYPE 25 152 49 49

Figure S364.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 0.00246 (Fisher's exact test), Q value = 0.0093

Table S365.  Gene #68: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
15Q LOSS MUTATED 50 74 87
15Q LOSS WILD-TYPE 94 75 75

Figure S365.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 0.00512 (Fisher's exact test), Q value = 0.017

Table S366.  Gene #68: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
15Q LOSS MUTATED 68 108 61
15Q LOSS WILD-TYPE 98 87 90

Figure S366.  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 = 9.7e-05

Table S367.  Gene #68: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
15Q LOSS MUTATED 34 66 55 8 35 8 31
15Q LOSS WILD-TYPE 44 44 42 40 18 41 46

Figure S367.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00048

Table S368.  Gene #68: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
15Q LOSS MUTATED 65 121 52
15Q LOSS WILD-TYPE 124 107 41

Figure S368.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0121 (Fisher's exact test), Q value = 0.035

Table S369.  Gene #68: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
15Q LOSS MUTATED 25 103 56 54
15Q LOSS WILD-TYPE 46 95 85 46

Figure S369.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00017

Table S370.  Gene #68: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
15Q LOSS MUTATED 29 131 46
15Q LOSS WILD-TYPE 74 117 37

Figure S370.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p loss' versus 'CN_CNMF'

P value = 0.00089 (Fisher's exact test), Q value = 0.004

Table S371.  Gene #69: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
16P LOSS MUTATED 24 34 22 38
16P LOSS WILD-TYPE 45 194 57 102

Figure S371.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

'16p loss' versus 'METHLYATION_CNMF'

P value = 0.00166 (Fisher's exact test), Q value = 0.0067

Table S372.  Gene #69: '16p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
16P LOSS MUTATED 19 43 44
16P LOSS WILD-TYPE 125 106 118

Figure S372.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16p loss' versus 'RPPA_CNMF'

P value = 0.00613 (Fisher's exact test), Q value = 0.02

Table S373.  Gene #69: '16p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
16P LOSS MUTATED 23 5 10 30 20
16P LOSS WILD-TYPE 68 17 56 45 89

Figure S373.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'16p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00387 (Fisher's exact test), Q value = 0.014

Table S374.  Gene #69: '16p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
16P LOSS MUTATED 34 45 9
16P LOSS WILD-TYPE 133 88 54

Figure S374.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'16p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S375.  Gene #69: '16p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
16P LOSS MUTATED 18 65 35
16P LOSS WILD-TYPE 148 130 116

Figure S375.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00025 (Fisher's exact test), Q value = 0.0013

Table S376.  Gene #69: '16p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
16P LOSS MUTATED 9 40 27 8 15 10 9
16P LOSS WILD-TYPE 69 70 70 40 38 39 68

Figure S376.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_CNMF'

P value = 0.0143 (Fisher's exact test), Q value = 0.04

Table S377.  Gene #69: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
16P LOSS MUTATED 32 66 20
16P LOSS WILD-TYPE 157 162 73

Figure S377.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0239 (Fisher's exact test), Q value = 0.061

Table S378.  Gene #69: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
16P LOSS MUTATED 13 54 22 29
16P LOSS WILD-TYPE 58 144 119 71

Figure S378.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00931 (Fisher's exact test), Q value = 0.029

Table S379.  Gene #69: '16p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
16P LOSS MUTATED 14 70 17
16P LOSS WILD-TYPE 89 178 66

Figure S379.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q loss' versus 'CN_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.0018

Table S380.  Gene #70: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
16Q LOSS MUTATED 27 43 26 49
16Q LOSS WILD-TYPE 42 185 53 91

Figure S380.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.0012

Table S381.  Gene #70: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
16Q LOSS MUTATED 22 50 54
16Q LOSS WILD-TYPE 122 99 108

Figure S381.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16q loss' versus 'RPPA_CNMF'

P value = 0.00076 (Fisher's exact test), Q value = 0.0035

Table S382.  Gene #70: '16q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
16Q LOSS MUTATED 30 7 10 35 26
16Q LOSS WILD-TYPE 61 15 56 40 83

Figure S382.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'16q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0282 (Fisher's exact test), Q value = 0.07

Table S383.  Gene #70: '16q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
16Q LOSS MUTATED 41 51 16
16Q LOSS WILD-TYPE 126 82 47

Figure S383.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00017

Table S384.  Gene #70: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
16Q LOSS MUTATED 25 78 42
16Q LOSS WILD-TYPE 141 117 109

Figure S384.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00017

Table S385.  Gene #70: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
16Q LOSS MUTATED 13 51 32 9 17 11 12
16Q LOSS WILD-TYPE 65 59 65 39 36 38 65

Figure S385.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_CNMF'

P value = 0.0225 (Fisher's exact test), Q value = 0.058

Table S386.  Gene #70: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
16Q LOSS MUTATED 41 77 27
16Q LOSS WILD-TYPE 148 151 66

Figure S386.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16q loss' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S387.  Gene #70: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
16Q LOSS MUTATED 19 62 27 37
16Q LOSS WILD-TYPE 52 136 114 63

Figure S387.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00246 (Fisher's exact test), Q value = 0.0093

Table S388.  Gene #70: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
16Q LOSS MUTATED 17 84 20
16Q LOSS WILD-TYPE 86 164 63

Figure S388.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S389.  Gene #71: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
17P LOSS MUTATED 28 62 35 91
17P LOSS WILD-TYPE 41 166 44 49

Figure S389.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00031

Table S390.  Gene #71: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
17P LOSS MUTATED 41 61 88
17P LOSS WILD-TYPE 103 88 74

Figure S390.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00038

Table S391.  Gene #71: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
17P LOSS MUTATED 56 106 52
17P LOSS WILD-TYPE 110 89 99

Figure S391.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.0011

Table S392.  Gene #71: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
17P LOSS MUTATED 29 62 46 8 22 20 27
17P LOSS WILD-TYPE 49 48 51 40 31 29 50

Figure S392.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0134 (Fisher's exact test), Q value = 0.038

Table S393.  Gene #71: '17p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
17P LOSS MUTATED 31 115 38
17P LOSS WILD-TYPE 72 133 45

Figure S393.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

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

Table S394.  Gene #72: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
17Q LOSS MUTATED 9 13 11 24
17Q LOSS WILD-TYPE 60 215 68 116

Figure S394.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

'17q loss' versus 'MRNASEQ_CNMF'

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

Table S395.  Gene #72: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
17Q LOSS MUTATED 12 30 15
17Q LOSS WILD-TYPE 154 165 136

Figure S395.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S396.  Gene #73: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
18P LOSS MUTATED 16 59 34 69
18P LOSS WILD-TYPE 53 169 45 71

Figure S396.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

'18p loss' versus 'RPPA_CNMF'

P value = 0.0207 (Fisher's exact test), Q value = 0.054

Table S397.  Gene #73: '18p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
18P LOSS MUTATED 29 8 22 39 31
18P LOSS WILD-TYPE 62 14 44 36 78

Figure S397.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'18p loss' versus 'RPPA_CHIERARCHICAL'

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

Table S398.  Gene #73: '18p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
18P LOSS MUTATED 48 60 21
18P LOSS WILD-TYPE 119 73 42

Figure S398.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'18p loss' versus 'MRNASEQ_CNMF'

P value = 0.01 (Fisher's exact test), Q value = 0.03

Table S399.  Gene #73: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
18P LOSS MUTATED 49 83 44
18P LOSS WILD-TYPE 117 112 107

Figure S399.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00115 (Fisher's exact test), Q value = 0.005

Table S400.  Gene #73: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
18P LOSS MUTATED 30 49 35 9 12 23 18
18P LOSS WILD-TYPE 48 61 62 39 41 26 59

Figure S400.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S401.  Gene #74: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
18Q LOSS MUTATED 17 73 36 86
18Q LOSS WILD-TYPE 52 155 43 54

Figure S401.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

'18q loss' versus 'RPPA_CNMF'

P value = 0.0316 (Fisher's exact test), Q value = 0.076

Table S402.  Gene #74: '18q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
18Q LOSS MUTATED 43 10 26 40 34
18Q LOSS WILD-TYPE 48 12 40 35 75

Figure S402.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 0.00067 (Fisher's exact test), Q value = 0.0031

Table S403.  Gene #74: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
18Q LOSS MUTATED 62 100 48
18Q LOSS WILD-TYPE 104 95 103

Figure S403.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00064

Table S404.  Gene #74: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
18Q LOSS MUTATED 38 55 45 8 13 23 28
18Q LOSS WILD-TYPE 40 55 52 40 40 26 49

Figure S404.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S405.  Gene #75: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
19P LOSS MUTATED 44 69 60 75
19P LOSS WILD-TYPE 25 159 19 65

Figure S405.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S406.  Gene #75: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
19P LOSS MUTATED 41 99 73
19P LOSS WILD-TYPE 103 50 89

Figure S406.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p loss' versus 'RPPA_CNMF'

P value = 0.00128 (Fisher's exact test), Q value = 0.0055

Table S407.  Gene #75: '19p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
19P LOSS MUTATED 38 13 40 48 42
19P LOSS WILD-TYPE 53 9 26 27 67

Figure S407.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'19p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S408.  Gene #75: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
19P LOSS MUTATED 48 100 98
19P LOSS WILD-TYPE 118 95 53

Figure S408.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S409.  Gene #75: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
19P LOSS MUTATED 22 47 57 33 35 34 18
19P LOSS WILD-TYPE 56 63 40 15 18 15 59

Figure S409.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S410.  Gene #75: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
19P LOSS MUTATED 66 137 39
19P LOSS WILD-TYPE 123 91 54

Figure S410.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S411.  Gene #75: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
19P LOSS MUTATED 31 98 45 68
19P LOSS WILD-TYPE 40 100 96 32

Figure S411.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0346 (Fisher's exact test), Q value = 0.081

Table S412.  Gene #75: '19p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 198 91
19P LOSS MUTATED 67 104 33
19P LOSS WILD-TYPE 78 94 58

Figure S412.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00309 (Fisher's exact test), Q value = 0.011

Table S413.  Gene #75: '19p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
19P LOSS MUTATED 40 134 30
19P LOSS WILD-TYPE 63 114 53

Figure S413.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S414.  Gene #76: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
19Q LOSS MUTATED 27 41 32 60
19Q LOSS WILD-TYPE 42 187 47 80

Figure S414.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S415.  Gene #76: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
19Q LOSS MUTATED 22 63 52
19Q LOSS WILD-TYPE 122 86 110

Figure S415.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q loss' versus 'RPPA_CNMF'

P value = 0.0318 (Fisher's exact test), Q value = 0.076

Table S416.  Gene #76: '19q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
19Q LOSS MUTATED 24 8 29 31 28
19Q LOSS WILD-TYPE 67 14 37 44 81

Figure S416.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'19q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00456 (Fisher's exact test), Q value = 0.016

Table S417.  Gene #76: '19q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
19Q LOSS MUTATED 55 54 11
19Q LOSS WILD-TYPE 112 79 52

Figure S417.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'19q loss' versus 'MRNASEQ_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.00089

Table S418.  Gene #76: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
19Q LOSS MUTATED 31 70 58
19Q LOSS WILD-TYPE 135 125 93

Figure S418.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S419.  Gene #76: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
19Q LOSS MUTATED 15 33 40 18 22 22 9
19Q LOSS WILD-TYPE 63 77 57 30 31 27 68

Figure S419.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.0012

Table S420.  Gene #76: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
19Q LOSS MUTATED 39 89 27
19Q LOSS WILD-TYPE 150 139 66

Figure S420.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S421.  Gene #76: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
19Q LOSS MUTATED 19 63 25 48
19Q LOSS WILD-TYPE 52 135 116 52

Figure S421.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0351 (Fisher's exact test), Q value = 0.082

Table S422.  Gene #76: '19q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
19Q LOSS MUTATED 23 87 21
19Q LOSS WILD-TYPE 80 161 62

Figure S422.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p loss' versus 'CN_CNMF'

P value = 0.00165 (Fisher's exact test), Q value = 0.0067

Table S423.  Gene #77: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
20P LOSS MUTATED 12 35 23 43
20P LOSS WILD-TYPE 57 193 56 97

Figure S423.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

'20p loss' versus 'METHLYATION_CNMF'

P value = 0.00919 (Fisher's exact test), Q value = 0.028

Table S424.  Gene #77: '20p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
20P LOSS MUTATED 25 25 48
20P LOSS WILD-TYPE 119 124 114

Figure S424.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p loss' versus 'MRNASEQ_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.0015

Table S425.  Gene #77: '20p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
20P LOSS MUTATED 39 56 17
20P LOSS WILD-TYPE 127 139 134

Figure S425.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00174 (Fisher's exact test), Q value = 0.007

Table S426.  Gene #77: '20p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
20P LOSS MUTATED 24 35 14 5 7 14 13
20P LOSS WILD-TYPE 54 75 83 43 46 35 64

Figure S426.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0306 (Fisher's exact test), Q value = 0.075

Table S427.  Gene #77: '20p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
20P LOSS MUTATED 13 54 23
20P LOSS WILD-TYPE 90 194 60

Figure S427.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S428.  Gene #79: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
21Q LOSS MUTATED 38 50 45 34
21Q LOSS WILD-TYPE 31 178 34 106

Figure S428.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

'21q loss' versus 'METHLYATION_CNMF'

P value = 0.00172 (Fisher's exact test), Q value = 0.0069

Table S429.  Gene #79: '21q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
21Q LOSS MUTATED 29 58 53
21Q LOSS WILD-TYPE 115 91 109

Figure S429.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'21q loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S430.  Gene #79: '21q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
21Q LOSS MUTATED 16 3 18 41 35
21Q LOSS WILD-TYPE 75 19 48 34 74

Figure S430.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'21q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00454 (Fisher's exact test), Q value = 0.016

Table S431.  Gene #79: '21q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
21Q LOSS MUTATED 38 53 22
21Q LOSS WILD-TYPE 129 80 41

Figure S431.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'21q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S432.  Gene #79: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
21Q LOSS MUTATED 24 65 75
21Q LOSS WILD-TYPE 142 130 76

Figure S432.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S433.  Gene #79: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
21Q LOSS MUTATED 11 30 36 13 34 24 16
21Q LOSS WILD-TYPE 67 80 61 35 19 25 61

Figure S433.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S434.  Gene #79: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
21Q LOSS MUTATED 39 97 27
21Q LOSS WILD-TYPE 150 131 66

Figure S434.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'21q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00031

Table S435.  Gene #79: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
21Q LOSS MUTATED 15 66 32 50
21Q LOSS WILD-TYPE 56 132 109 50

Figure S435.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.0013

Table S436.  Gene #79: '21q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
21Q LOSS MUTATED 20 97 20
21Q LOSS WILD-TYPE 83 151 63

Figure S436.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S437.  Gene #80: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
22Q LOSS MUTATED 47 59 39 72
22Q LOSS WILD-TYPE 22 169 40 68

Figure S437.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S438.  Gene #80: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
22Q LOSS MUTATED 29 86 78
22Q LOSS WILD-TYPE 115 63 84

Figure S438.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q loss' versus 'RPPA_CNMF'

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

Table S439.  Gene #80: '22q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
22Q LOSS MUTATED 38 5 23 43 44
22Q LOSS WILD-TYPE 53 17 43 32 65

Figure S439.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'22q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00371 (Fisher's exact test), Q value = 0.013

Table S440.  Gene #80: '22q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
22Q LOSS MUTATED 56 70 27
22Q LOSS WILD-TYPE 111 63 36

Figure S440.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00038

Table S441.  Gene #80: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
22Q LOSS MUTATED 46 95 73
22Q LOSS WILD-TYPE 120 100 78

Figure S441.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S442.  Gene #80: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
22Q LOSS MUTATED 24 56 46 15 34 23 16
22Q LOSS WILD-TYPE 54 54 51 33 19 26 61

Figure S442.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.00092

Table S443.  Gene #80: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
22Q LOSS MUTATED 58 116 38
22Q LOSS WILD-TYPE 131 112 55

Figure S443.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00024

Table S444.  Gene #80: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
22Q LOSS MUTATED 20 98 40 54
22Q LOSS WILD-TYPE 51 100 101 46

Figure S444.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00042

Table S445.  Gene #80: '22q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
22Q LOSS MUTATED 28 127 31
22Q LOSS WILD-TYPE 75 121 52

Figure S445.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xp loss' versus 'CN_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00059

Table S446.  Gene #81: 'xp loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
XP LOSS MUTATED 14 29 16 46
XP LOSS WILD-TYPE 55 199 63 94

Figure S446.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #3: 'CN_CNMF'

'xp loss' versus 'METHLYATION_CNMF'

P value = 0.038 (Fisher's exact test), Q value = 0.088

Table S447.  Gene #81: 'xp loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
XP LOSS MUTATED 19 33 39
XP LOSS WILD-TYPE 125 116 123

Figure S447.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xp loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0405 (Fisher's exact test), Q value = 0.093

Table S448.  Gene #81: 'xp loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
XP LOSS MUTATED 25 35 10
XP LOSS WILD-TYPE 142 98 53

Figure S448.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'xp loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00267 (Fisher's exact test), Q value = 0.0099

Table S449.  Gene #81: 'xp loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
XP LOSS MUTATED 19 36 22 6 6 7 9
XP LOSS WILD-TYPE 59 74 75 42 47 42 68

Figure S449.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xq loss' versus 'CN_CNMF'

P value = 0.00353 (Fisher's exact test), Q value = 0.013

Table S450.  Gene #82: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
XQ LOSS MUTATED 10 15 14 24
XQ LOSS WILD-TYPE 59 213 65 116

Figure S450.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 0.00162 (Fisher's exact test), Q value = 0.0067

Table S451.  Gene #82: 'xq loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
XQ LOSS MUTATED 7 26 23
XQ LOSS WILD-TYPE 137 123 139

Figure S451.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xq loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00375 (Fisher's exact test), Q value = 0.013

Table S452.  Gene #82: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
XQ LOSS MUTATED 11 34 7 11
XQ LOSS WILD-TYPE 60 164 134 89

Figure S452.  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/LUAD-TP/19782226/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LUAD-TP/20140677/LUAD-TP.transferedmergedcluster.txt

  • Number of patients = 516

  • 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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