Correlation between copy number variations of arm-level result and molecular subtypes
Stomach and Esophageal carcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C1ZW1K78
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/C1ZW1K78
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 10 molecular subtypes across 625 patients, 425 significant findings detected with P value < 0.05 and Q value < 0.25.

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

  • 1q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 2q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 3p gain cnv correlated to 'CN_CNMF'.

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

  • 4p gain cnv correlated to 'CN_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 4q gain cnv correlated to 'CN_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 5p 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'.

  • 5q gain cnv correlated to 'CN_CNMF'.

  • 6p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 6q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 7q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CNMF'.

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

  • 8q gain cnv correlated to 'METHLYATION_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 9q gain cnv correlated to 'CN_CNMF'.

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

  • 10q gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • 11p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 11q gain cnv correlated to 'CN_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 12q gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.

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

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

  • 15q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

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

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

  • 18q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 19p gain cnv correlated to 'CN_CNMF'.

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

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

  • 20q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 21q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

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

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

  • 2p loss cnv correlated to 'CN_CNMF',  'RPPA_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 2q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 3q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 4p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

  • 6p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 6q loss cnv correlated to 'CN_CNMF'.

  • 7p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 7q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.

  • 8p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

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

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

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

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

  • 12p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

  • 15q loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

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

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

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

  • 17q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

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

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

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

  • 20p loss cnv correlated to 'CN_CNMF'.

  • 20q loss cnv correlated to 'MIRSEQ_CNMF'.

  • 21q loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • xp loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • xq loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_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 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 425 significant findings detected.

Clinical
Features 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
5p gain 177 (28%) 448 1e-05
(5.16e-05) 		1e-05
(5.16e-05) 		0.557
(0.649) 		0.0175
(0.0397) 		0.0148
(0.0345) 		0.00874
(0.0215) 		1e-05
(5.16e-05) 		1e-05
(5.16e-05) 		1e-05
(5.16e-05) 		1e-05
(5.16e-05)
6p gain 117 (19%) 508 1e-05
(5.16e-05) 		1e-05
(5.16e-05) 		0.0241
(0.0518) 		0.0302
(0.0632) 		0.668
(0.742) 		0.406
(0.504) 		0.00401
(0.0111) 		1e-05
(5.16e-05) 		0.00503
(0.0135) 		0.00018
(0.000734)
12p gain 148 (24%) 477 1e-05
(5.16e-05) 		1e-05
(5.16e-05) 		0.913
(0.942) 		0.17
(0.252) 		0.00407
(0.0112) 		0.00287
(0.00838) 		0.00018
(0.000734) 		0.00036
(0.00138) 		0.00109
(0.00358) 		5e-05
(0.000233)
14q gain 75 (12%) 550 1e-05
(5.16e-05) 		1e-05
(5.16e-05) 		0.53
(0.626) 		0.187
(0.27) 		0.0302
(0.0632) 		0.0156
(0.0358) 		1e-05
(5.16e-05) 		1e-05
(5.16e-05) 		0.00026
(0.00103) 		1e-05
(5.16e-05)
16p gain 99 (16%) 526 1e-05
(5.16e-05) 		0.00088
(0.00295) 		0.045
(0.089) 		0.662
(0.737) 		0.0195
(0.0435) 		0.00349
(0.00983) 		0.00833
(0.0208) 		6e-05
(0.000278) 		0.103
(0.172) 		0.00018
(0.000734)
16q gain 86 (14%) 539 1e-05
(5.16e-05) 		0.00126
(0.00405) 		0.0865
(0.15) 		0.414
(0.513) 		0.00346
(0.00978) 		0.00937
(0.0229) 		9e-05
(0.000397) 		1e-05
(5.16e-05) 		0.00186
(0.00582) 		1e-05
(5.16e-05)
22q gain 64 (10%) 561 1e-05
(5.16e-05) 		1e-05
(5.16e-05) 		0.942
(0.956) 		0.619
(0.704) 		1e-05
(5.16e-05) 		1e-05
(5.16e-05) 		1e-05
(5.16e-05) 		1e-05
(5.16e-05) 		1e-05
(5.16e-05) 		1e-05
(5.16e-05)
3p loss 187 (30%) 438 1e-05
(5.16e-05) 		1e-05
(5.16e-05) 		0.867
(0.911) 		0.139
(0.22) 		0.0001
(0.000432) 		1e-05
(5.16e-05) 		1e-05
(5.16e-05) 		1e-05
(5.16e-05) 		1e-05
(5.16e-05) 		1e-05
(5.16e-05)
5p loss 112 (18%) 513 1e-05
(5.16e-05) 		1e-05
(5.16e-05) 		0.18
(0.264) 		0.451
(0.548) 		0.0001
(0.000432) 		0.00011
(0.00047) 		0.0003
(0.00118) 		1e-05
(5.16e-05) 		0.0462
(0.0907) 		0.00013
(0.000547)
10p loss 117 (19%) 508 1e-05
(5.16e-05) 		1e-05
(5.16e-05) 		0.869
(0.911) 		0.714
(0.787) 		0.0225
(0.0491) 		0.015
(0.0347) 		0.00206
(0.0063) 		1e-05
(5.16e-05) 		0.00038
(0.00142) 		1e-05
(5.16e-05)
10q loss 117 (19%) 508 1e-05
(5.16e-05) 		1e-05
(5.16e-05) 		0.363
(0.463) 		0.563
(0.652) 		0.00859
(0.0212) 		0.00226
(0.00684) 		0.00078
(0.00265) 		1e-05
(5.16e-05) 		0.00109
(0.00358) 		1e-05
(5.16e-05)
11q loss 120 (19%) 505 1e-05
(5.16e-05) 		1e-05
(5.16e-05) 		0.553
(0.647) 		0.472
(0.568) 		0.0306
(0.0638) 		0.0365
(0.0748) 		1e-05
(5.16e-05) 		1e-05
(5.16e-05) 		1e-05
(5.16e-05) 		3e-05
(0.000143)
16p loss 156 (25%) 469 1e-05
(5.16e-05) 		0.00308
(0.00883) 		0.16
(0.243) 		0.373
(0.471) 		0.00048
(0.00174) 		9e-05
(0.000397) 		0.0152
(0.0351) 		1e-05
(5.16e-05) 		0.00793
(0.0199) 		1e-05
(5.16e-05)
xq loss 96 (15%) 529 1e-05
(5.16e-05) 		0.00656
(0.0168) 		0.0354
(0.0728) 		0.0223
(0.0487) 		0.257
(0.354) 		0.0957
(0.163) 		0.00039
(0.00144) 		0.00031
(0.0012) 		0.015
(0.0347) 		0.00192
(0.00592)
17p gain 62 (10%) 563 1e-05
(5.16e-05) 		0.00067
(0.00235) 		0.569
(0.656) 		0.19
(0.274) 		0.0483
(0.0939) 		0.0515
(0.0979) 		2e-05
(9.76e-05) 		0.00949
(0.0231) 		0.00303
(0.00872) 		0.00039
(0.00144)
18p gain 137 (22%) 488 1e-05
(5.16e-05) 		1e-05
(5.16e-05) 		0.608
(0.694) 		0.0132
(0.031) 		0.239
(0.332) 		0.469
(0.565) 		0.00057
(0.00202) 		8e-05
(0.000366) 		0.00073
(0.0025) 		0.00078
(0.00265)
2q loss 51 (8%) 574 2e-05
(9.76e-05) 		0.012
(0.0285) 		0.718
(0.79) 		0.153
(0.236) 		0.12
(0.195) 		0.0333
(0.0687) 		0.0379
(0.0767) 		0.00474
(0.0127) 		0.0222
(0.0487) 		0.0221
(0.0487)
5q loss 195 (31%) 430 1e-05
(5.16e-05) 		1e-05
(5.16e-05) 		0.0298
(0.0627) 		0.59
(0.677) 		0.148
(0.232) 		0.0789
(0.138) 		2e-05
(9.76e-05) 		1e-05
(5.16e-05) 		0.00013
(0.000547) 		2e-05
(9.76e-05)
8p loss 153 (24%) 472 1e-05
(5.16e-05) 		0.00559
(0.0148) 		0.145
(0.228) 		0.0345
(0.0711) 		0.449
(0.546) 		0.523
(0.619) 		4e-05
(0.00019) 		1e-05
(5.16e-05) 		0.00055
(0.00197) 		1e-05
(5.16e-05)
12p loss 95 (15%) 530 1e-05
(5.16e-05) 		0.00621
(0.0161) 		0.168
(0.249) 		0.897
(0.932) 		0.00061
(0.00216) 		0.00145
(0.00459) 		0.076
(0.133) 		1e-05
(5.16e-05) 		0.0468
(0.0917) 		0.00982
(0.0238)
13q loss 102 (16%) 523 1e-05
(5.16e-05) 		1e-05
(5.16e-05) 		0.961
(0.973) 		0.0539
(0.101) 		0.132
(0.211) 		0.0432
(0.0857) 		1e-05
(5.16e-05) 		1e-05
(5.16e-05) 		1e-05
(5.16e-05) 		1e-05
(5.16e-05)
16q loss 168 (27%) 457 1e-05
(5.16e-05) 		0.0455
(0.0896) 		0.867
(0.911) 		0.167
(0.249) 		1e-05
(5.16e-05) 		1e-05
(5.16e-05) 		0.214
(0.303) 		1e-05
(5.16e-05) 		0.0103
(0.0247) 		1e-05
(5.16e-05)
17p loss 236 (38%) 389 1e-05
(5.16e-05) 		0.00051
(0.00184) 		0.173
(0.255) 		0.237
(0.33) 		0.00189
(0.00587) 		0.00083
(0.00279) 		0.00662
(0.0169) 		1e-05
(5.16e-05) 		0.166
(0.247) 		3e-05
(0.000143)
18q loss 256 (41%) 369 1e-05
(5.16e-05) 		0.025
(0.0535) 		0.928
(0.949) 		0.183
(0.267) 		0.00514
(0.0137) 		0.0263
(0.0559) 		0.0232
(0.0503) 		0.00073
(0.0025) 		0.039
(0.0787) 		0.0651
(0.117)
19q loss 136 (22%) 489 1e-05
(5.16e-05) 		1e-05
(5.16e-05) 		0.199
(0.284) 		0.229
(0.321) 		0.321
(0.418) 		0.00428
(0.0117) 		1e-05
(5.16e-05) 		1e-05
(5.16e-05) 		1e-05
(5.16e-05) 		0.00011
(0.00047)
xp loss 122 (20%) 503 1e-05
(5.16e-05) 		5e-05
(0.000233) 		0.312
(0.41) 		0.0166
(0.0378) 		0.374
(0.472) 		0.805
(0.863) 		1e-05
(5.16e-05) 		1e-05
(5.16e-05) 		0.0131
(0.0307) 		0.00016
(0.000666)
1q gain 167 (27%) 458 1e-05
(5.16e-05) 		1e-05
(5.16e-05) 		0.872
(0.913) 		0.125
(0.202) 		0.832
(0.883) 		0.425
(0.523) 		0.00197
(0.00605) 		1e-05
(5.16e-05) 		0.00079
(0.00268) 		0.00136
(0.00432)
2p gain 137 (22%) 488 1e-05
(5.16e-05) 		1e-05
(5.16e-05) 		0.52
(0.616) 		0.598
(0.684) 		0.104
(0.173) 		0.106
(0.176) 		2e-05
(9.76e-05) 		1e-05
(5.16e-05) 		1e-05
(5.16e-05) 		1e-05
(5.16e-05)
2q gain 111 (18%) 514 1e-05
(5.16e-05) 		0.00013
(0.000547) 		0.997
(1.00) 		0.834
(0.883) 		0.654
(0.734) 		0.0989
(0.166) 		0.0186
(0.0418) 		0.00368
(0.0103) 		0.00119
(0.00386) 		0.0222
(0.0487)
3q gain 170 (27%) 455 1e-05
(5.16e-05) 		1e-05
(5.16e-05) 		0.158
(0.24) 		0.921
(0.946) 		0.275
(0.375) 		0.0869
(0.15) 		0.0001
(0.000432) 		1e-05
(5.16e-05) 		1e-05
(5.16e-05) 		1e-05
(5.16e-05)
6q gain 100 (16%) 525 1e-05
(5.16e-05) 		0.00022
(0.00088) 		0.0418
(0.084) 		0.0376
(0.0764) 		0.721
(0.792) 		0.296
(0.396) 		0.0709
(0.126) 		1e-05
(5.16e-05) 		0.0673
(0.12) 		1e-05
(5.16e-05)
7p gain 306 (49%) 319 1e-05
(5.16e-05) 		1e-05
(5.16e-05) 		0.625
(0.706) 		0.46
(0.556) 		0.0514
(0.0979) 		0.183
(0.267) 		0.00207
(0.00631) 		0.00032
(0.00124) 		0.00091
(0.00303) 		0.00625
(0.0162)
13q gain 197 (32%) 428 1e-05
(5.16e-05) 		0.102
(0.171) 		0.113
(0.186) 		0.782
(0.844) 		0.0001
(0.000432) 		1e-05
(5.16e-05) 		0.0114
(0.0272) 		1e-05
(5.16e-05) 		0.186
(0.269) 		1e-05
(5.16e-05)
17q gain 106 (17%) 519 1e-05
(5.16e-05) 		0.00102
(0.00339) 		0.881
(0.92) 		0.94
(0.956) 		0.538
(0.633) 		0.0489
(0.0944) 		0.00444
(0.0121) 		0.0776
(0.136) 		0.0239
(0.0516) 		0.00248
(0.00737)
20p gain 349 (56%) 276 1e-05
(5.16e-05) 		0.00678
(0.0173) 		0.134
(0.213) 		0.0736
(0.13) 		0.36
(0.46) 		0.334
(0.431) 		0.0154
(0.0353) 		1e-05
(5.16e-05) 		0.0294
(0.062) 		0.0105
(0.0251)
21q gain 36 (6%) 589 1e-05
(5.16e-05) 		1e-05
(5.16e-05) 		0.875
(0.916) 		0.369
(0.468) 		0.279
(0.377) 		0.113
(0.186) 		0.0215
(0.0477) 		0.00031
(0.0012) 		0.0241
(0.0518) 		0.0376
(0.0764)
4p loss 271 (43%) 354 1e-05
(5.16e-05) 		1e-05
(5.16e-05) 		0.83
(0.883) 		0.905
(0.937) 		0.0966
(0.164) 		0.203
(0.289) 		1e-05
(5.16e-05) 		1e-05
(5.16e-05) 		1e-05
(5.16e-05) 		1e-05
(5.16e-05)
4q loss 251 (40%) 374 1e-05
(5.16e-05) 		9e-05
(0.000397) 		0.309
(0.409) 		0.335
(0.432) 		0.0589
(0.108) 		0.145
(0.228) 		0.00507
(0.0135) 		1e-05
(5.16e-05) 		0.00073
(0.0025) 		0.00289
(0.0084)
6p loss 93 (15%) 532 1e-05
(5.16e-05) 		0.00469
(0.0127) 		0.158
(0.24) 		0.281
(0.379) 		0.426
(0.524) 		0.843
(0.891) 		0.00638
(0.0165) 		0.00019
(0.000771) 		0.0121
(0.0286) 		0.00271
(0.00802)
9p loss 250 (40%) 375 1e-05
(5.16e-05) 		0.00017
(0.000704) 		0.795
(0.854) 		0.185
(0.269) 		0.191
(0.274) 		0.149
(0.232) 		0.00022
(0.00088) 		1e-05
(5.16e-05) 		0.00608
(0.0158) 		0.00036
(0.00138)
9q loss 175 (28%) 450 1e-05
(5.16e-05) 		9e-05
(0.000397) 		0.563
(0.652) 		0.421
(0.52) 		0.29
(0.39) 		0.326
(0.423) 		9e-05
(0.000397) 		1e-05
(5.16e-05) 		0.00039
(0.00144) 		0.0023
(0.00691)
11p loss 118 (19%) 507 1e-05
(5.16e-05) 		1e-05
(5.16e-05) 		0.44
(0.537) 		0.119
(0.194) 		0.911
(0.941) 		0.972
(0.982) 		9e-05
(0.000397) 		3e-05
(0.000143) 		0.00037
(0.0014) 		0.00853
(0.0211)
14q loss 158 (25%) 467 1e-05
(5.16e-05) 		0.0129
(0.0304) 		0.486
(0.582) 		0.278
(0.377) 		0.0056
(0.0148) 		0.0173
(0.0393) 		0.504
(0.6) 		1e-05
(5.16e-05) 		0.432
(0.529) 		0.00227
(0.00684)
19p loss 177 (28%) 448 1e-05
(5.16e-05) 		1e-05
(5.16e-05) 		0.315
(0.413) 		0.215
(0.304) 		0.523
(0.618) 		0.37
(0.469) 		1e-05
(5.16e-05) 		1e-05
(5.16e-05) 		1e-05
(5.16e-05) 		0.00063
(0.00222)
21q loss 289 (46%) 336 1e-05
(5.16e-05) 		0.0578
(0.107) 		0.918
(0.944) 		0.848
(0.895) 		0.0423
(0.0848) 		0.0987
(0.166) 		0.00299
(0.00866) 		2e-05
(9.76e-05) 		0.003
(0.00866) 		0.0258
(0.0549)
22q loss 218 (35%) 407 1e-05
(5.16e-05) 		0.0624
(0.113) 		0.613
(0.699) 		0.452
(0.549) 		0.00056
(0.002) 		7e-05
(0.000322) 		0.00282
(0.00826) 		1e-05
(5.16e-05) 		0.165
(0.247) 		0.00026
(0.00103)
15q gain 67 (11%) 558 2e-05
(9.76e-05) 		0.0312
(0.065) 		0.199
(0.284) 		0.192
(0.275) 		0.36
(0.46) 		0.0504
(0.0966) 		0.00335
(0.00951) 		0.0706
(0.126) 		0.00595
(0.0155) 		0.00449
(0.0122)
19q gain 117 (19%) 508 1e-05
(5.16e-05) 		0.406
(0.504) 		0.00641
(0.0165) 		0.0164
(0.0376) 		0.46
(0.556) 		0.157
(0.239) 		0.634
(0.714) 		0.00037
(0.0014) 		0.0566
(0.105) 		0.0178
(0.0402)
20q gain 395 (63%) 230 1e-05
(5.16e-05) 		0.0738
(0.13) 		0.475
(0.57) 		0.163
(0.246) 		0.00828
(0.0207) 		0.0038
(0.0106) 		0.223
(0.315) 		1e-05
(5.16e-05) 		0.292
(0.392) 		2e-05
(9.76e-05)
xq gain 91 (15%) 534 0.0002
(0.000808) 		0.0016
(0.00505) 		0.575
(0.66) 		0.153
(0.235) 		0.156
(0.239) 		0.0832
(0.144) 		0.00054
(0.00194) 		0.00131
(0.00418) 		0.118
(0.193) 		0.00236
(0.00704)
1p loss 95 (15%) 530 1e-05
(5.16e-05) 		0.00047
(0.00171) 		0.373
(0.471) 		0.658
(0.735) 		0.0375
(0.0764) 		0.0816
(0.142) 		0.0131
(0.0307) 		0.0007
(0.00243) 		0.0508
(0.0971) 		0.0592
(0.108)
3q loss 90 (14%) 535 1e-05
(5.16e-05) 		0.0017
(0.00534) 		0.0329
(0.0683) 		0.0666
(0.119) 		0.511
(0.608) 		0.752
(0.819) 		0.0137
(0.0319) 		1e-05
(5.16e-05) 		0.0616
(0.112) 		0.309
(0.409)
12q loss 82 (13%) 543 1e-05
(5.16e-05) 		0.0666
(0.119) 		0.235
(0.329) 		0.927
(0.949) 		0.00916
(0.0225) 		0.00575
(0.0151) 		0.0746
(0.131) 		5e-05
(0.000233) 		0.139
(0.22) 		0.0372
(0.0761)
1p gain 82 (13%) 543 1e-05
(5.16e-05) 		0.00279
(0.0082) 		0.797
(0.855) 		0.237
(0.33) 		0.886
(0.924) 		0.925
(0.948) 		0.0459
(0.0903) 		0.00103
(0.00341) 		0.18
(0.264) 		0.0938
(0.16)
11p gain 99 (16%) 526 1e-05
(5.16e-05) 		0.0107
(0.0257) 		0.661
(0.737) 		0.363
(0.463) 		0.738
(0.806) 		0.664
(0.738) 		0.0664
(0.119) 		0.00829
(0.0207) 		0.0075
(0.019) 		0.297
(0.397)
11q gain 104 (17%) 521 1e-05
(5.16e-05) 		0.0975
(0.165) 		0.298
(0.397) 		0.157
(0.239) 		0.117
(0.192) 		0.149
(0.232) 		0.108
(0.18) 		0.00131
(0.00418) 		0.00187
(0.00583) 		0.0331
(0.0685)
18q gain 82 (13%) 543 0.00225
(0.00683) 		0.00448
(0.0122) 		0.922
(0.946) 		0.256
(0.354) 		0.321
(0.418) 		0.79
(0.851) 		0.0276
(0.0585) 		0.0474
(0.0924) 		0.0647
(0.117) 		0.0592
(0.108)
7p loss 33 (5%) 592 0.00117
(0.00381) 		0.00037
(0.0014) 		0.321
(0.418) 		0.305
(0.405) 		0.27
(0.37) 		0.64
(0.72) 		0.0486
(0.0942) 		0.0441
(0.0874) 		0.157
(0.239) 		0.17
(0.251)
17q loss 99 (16%) 526 1e-05
(5.16e-05) 		0.0206
(0.0458) 		0.359
(0.46) 		0.144
(0.227) 		0.982
(0.988) 		1
(1.00) 		0.0288
(0.0609) 		0.00014
(0.000586) 		0.327
(0.424) 		0.256
(0.354)
18p loss 187 (30%) 438 1e-05
(5.16e-05) 		0.124
(0.2) 		0.0425
(0.085) 		0.783
(0.844) 		0.00121
(0.00391) 		0.00326
(0.00931) 		0.655
(0.734) 		0.0981
(0.165) 		0.738
(0.806) 		0.662
(0.737)
4p gain 39 (6%) 586 0.00081
(0.00273) 		0.424
(0.523) 		0.0885
(0.153) 		0.938
(0.955) 		0.623
(0.706) 		0.69
(0.762) 		0.389
(0.487) 		0.00399
(0.0111) 		0.0585
(0.108) 		0.0236
(0.051)
4q gain 33 (5%) 592 0.00279
(0.0082) 		0.432
(0.529) 		0.131
(0.21) 		0.247
(0.343) 		0.193
(0.277) 		0.123
(0.2) 		0.117
(0.191) 		0.00027
(0.00106) 		0.15
(0.233) 		0.00392
(0.0109)
7q gain 257 (41%) 368 1e-05
(5.16e-05) 		0.00043
(0.00158) 		0.729
(0.798) 		0.519
(0.615) 		0.602
(0.688) 		0.239
(0.332) 		0.152
(0.234) 		0.128
(0.205) 		0.00354
(0.00994) 		0.133
(0.212)
8p gain 248 (40%) 377 0.0054
(0.0143) 		0.0489
(0.0944) 		0.907
(0.938) 		0.28
(0.378) 		0.455
(0.551) 		0.0431
(0.0857) 		0.0527
(0.0993) 		0.4
(0.498) 		0.269
(0.37) 		0.63
(0.711)
8q gain 338 (54%) 287 0.634
(0.714) 		0.0189
(0.0423) 		0.49
(0.585) 		0.624
(0.706) 		0.474
(0.57) 		0.424
(0.523) 		0.0204
(0.0454) 		0.0144
(0.0335) 		0.337
(0.434) 		0.721
(0.792)
10p gain 135 (22%) 490 1e-05
(5.16e-05) 		0.184
(0.268) 		0.916
(0.943) 		0.826
(0.879) 		0.0176
(0.0397) 		0.0527
(0.0993) 		0.856
(0.903) 		0.00068
(0.00237) 		0.514
(0.611) 		0.276
(0.375)
xp gain 71 (11%) 554 0.0033
(0.0094) 		0.0101
(0.0244) 		0.898
(0.932) 		0.165
(0.247) 		0.428
(0.525) 		0.726
(0.796) 		0.0522
(0.0989) 		0.00944
(0.023) 		0.0804
(0.14) 		0.0501
(0.0965)
1q loss 47 (8%) 578 1e-05
(5.16e-05) 		0.0216
(0.0477) 		0.532
(0.627) 		0.109
(0.18) 		0.308
(0.409) 		0.0385
(0.0779) 		0.101
(0.169) 		0.0585
(0.108) 		0.0623
(0.113) 		0.173
(0.255)
2p loss 38 (6%) 587 3e-05
(0.000143) 		0.166
(0.247) 		0.023
(0.05) 		0.0735
(0.13) 		0.388
(0.487) 		0.283
(0.38) 		0.227
(0.32) 		0.00766
(0.0194) 		0.0928
(0.159) 		0.19
(0.274)
7q loss 51 (8%) 574 9e-05
(0.000397) 		0.00838
(0.0208) 		0.161
(0.244) 		0.539
(0.633) 		0.818
(0.873) 		0.672
(0.745) 		0.00981
(0.0238) 		0.0929
(0.159) 		0.329
(0.426) 		0.128
(0.205)
10q gain 98 (16%) 527 0.00038
(0.00142) 		0.557
(0.649) 		0.764
(0.83) 		0.769
(0.833) 		0.0548
(0.102) 		0.0586
(0.108) 		0.657
(0.735) 		0.0472
(0.0921) 		0.38
(0.479) 		0.196
(0.28)
12q gain 115 (18%) 510 0.00114
(0.00372) 		0.152
(0.234) 		0.965
(0.975) 		0.169
(0.251) 		0.4
(0.498) 		0.623
(0.706) 		0.165
(0.247) 		0.16
(0.242) 		0.0258
(0.0549) 		0.208
(0.295)
8q loss 57 (9%) 568 1e-05
(5.16e-05) 		0.365
(0.465) 		0.893
(0.929) 		0.115
(0.189) 		0.981
(0.988) 		0.196
(0.28) 		0.314
(0.412) 		0.271
(0.371) 		0.147
(0.23) 		0.00768
(0.0194)
15q loss 149 (24%) 476 1e-05
(5.16e-05) 		0.366
(0.466) 		0.299
(0.398) 		0.388
(0.487) 		0.137
(0.217) 		0.0504
(0.0966) 		0.227
(0.319) 		0.00047
(0.00171) 		0.321
(0.418) 		0.556
(0.649)
3p gain 83 (13%) 542 0.00405
(0.0111) 		0.0538
(0.101) 		0.294
(0.394) 		0.175
(0.257) 		0.863
(0.908) 		0.273
(0.373) 		0.388
(0.487) 		0.236
(0.33) 		0.0551
(0.103) 		0.262
(0.36)
5q gain 63 (10%) 562 0.00233
(0.00697) 		0.783
(0.844) 		0.891
(0.928) 		0.406
(0.504) 		0.0925
(0.159) 		0.754
(0.819) 		0.566
(0.655) 		0.489
(0.584) 		0.561
(0.652) 		0.181
(0.265)
9q gain 109 (17%) 516 0.043
(0.0857) 		0.71
(0.784) 		0.311
(0.41) 		0.836
(0.884) 		0.618
(0.704) 		0.753
(0.819) 		0.641
(0.72) 		0.563
(0.652) 		0.574
(0.66) 		0.937
(0.955)
19p gain 83 (13%) 542 2e-05
(9.76e-05) 		0.324
(0.421) 		0.122
(0.199) 		0.0597
(0.109) 		0.817
(0.872) 		0.831
(0.883) 		0.961
(0.973) 		0.34
(0.437) 		0.397
(0.496) 		0.44
(0.537)
6q loss 110 (18%) 515 1e-05
(5.16e-05) 		0.0519
(0.0985) 		0.567
(0.655) 		0.276
(0.375) 		0.767
(0.832) 		0.814
(0.871) 		0.0898
(0.154) 		0.0774
(0.136) 		0.163
(0.246) 		0.0951
(0.162)
20p loss 41 (7%) 584 0.0019
(0.00588) 		0.124
(0.2) 		0.0642
(0.116) 		0.309
(0.409) 		0.816
(0.872) 		0.151
(0.234) 		0.977
(0.985) 		0.232
(0.325) 		0.316
(0.414) 		0.556
(0.649)
20q loss 8 (1%) 617 0.163
(0.246) 		0.0536
(0.101) 		0.0586
(0.108) 		0.55
(0.646) 		1
(1.00) 		1
(1.00) 		0.00574
(0.0151) 		0.143
(0.225) 		0.127
(0.204) 		0.0979
(0.165)
9p gain 77 (12%) 548 0.481
(0.576) 		0.935
(0.955) 		0.772
(0.835) 		0.449
(0.546) 		0.275
(0.375) 		1
(1.00) 		0.575
(0.66) 		0.68
(0.752) 		0.94
(0.956) 		0.901
(0.934)
'1p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
1P GAIN MUTATED 28 45 9
1P GAIN WILD-TYPE 138 165 240

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

'1p gain' versus 'METHLYATION_CNMF'

P value = 0.00279 (Fisher's exact test), Q value = 0.0082

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
1P GAIN MUTATED 33 31 12
1P GAIN WILD-TYPE 215 126 160

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

'1p gain' versus 'MIRSEQ_CNMF'

P value = 0.0459 (Fisher's exact test), Q value = 0.09

Table S3.  Gene #1: '1p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
1P GAIN MUTATED 29 42 10
1P GAIN WILD-TYPE 134 286 116

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

'1p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00103 (Fisher's exact test), Q value = 0.0034

Table S4.  Gene #1: '1p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
1P GAIN MUTATED 26 21 10 17 7
1P GAIN WILD-TYPE 101 122 154 77 82

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

'1q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S5.  Gene #2: '1q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
1Q GAIN MUTATED 64 79 24
1Q GAIN WILD-TYPE 102 131 225

Figure S5.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #1: 'CN_CNMF'

'1q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S6.  Gene #2: '1q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
1Q GAIN MUTATED 65 66 26
1Q GAIN WILD-TYPE 183 91 146

Figure S6.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1q gain' versus 'MIRSEQ_CNMF'

P value = 0.00197 (Fisher's exact test), Q value = 0.0061

Table S7.  Gene #2: '1q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
1Q GAIN MUTATED 60 79 25
1Q GAIN WILD-TYPE 103 249 101

Figure S7.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'1q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S8.  Gene #2: '1q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
1Q GAIN MUTATED 48 43 18 37 18
1Q GAIN WILD-TYPE 79 100 146 57 71

Figure S8.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00079 (Fisher's exact test), Q value = 0.0027

Table S9.  Gene #2: '1q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
1Q GAIN MUTATED 56 52 33
1Q GAIN WILD-TYPE 89 153 136

Figure S9.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'1q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00136 (Fisher's exact test), Q value = 0.0043

Table S10.  Gene #2: '1q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
1Q GAIN MUTATED 61 23 21 36
1Q GAIN WILD-TYPE 137 107 78 56

Figure S10.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S11.  Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
2P GAIN MUTATED 48 73 16
2P GAIN WILD-TYPE 118 137 233

Figure S11.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

'2p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
2P GAIN MUTATED 56 59 16
2P GAIN WILD-TYPE 192 98 156

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

'2p gain' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9.8e-05

Table S13.  Gene #3: '2p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
2P GAIN MUTATED 57 65 14
2P GAIN WILD-TYPE 106 263 112

Figure S13.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'2p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S14.  Gene #3: '2p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
2P GAIN MUTATED 35 33 22 37 9
2P GAIN WILD-TYPE 92 110 142 57 80

Figure S14.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S15.  Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
2P GAIN MUTATED 53 45 19
2P GAIN WILD-TYPE 92 160 150

Figure S15.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'2p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S16.  Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
2P GAIN MUTATED 53 18 11 35
2P GAIN WILD-TYPE 145 112 88 57

Figure S16.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S17.  Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
2Q GAIN MUTATED 43 54 14
2Q GAIN WILD-TYPE 123 156 235

Figure S17.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

'2q gain' versus 'METHLYATION_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00055

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
2Q GAIN MUTATED 51 40 15
2Q GAIN WILD-TYPE 197 117 157

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

'2q gain' versus 'MIRSEQ_CNMF'

P value = 0.0186 (Fisher's exact test), Q value = 0.042

Table S19.  Gene #4: '2q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
2Q GAIN MUTATED 41 52 17
2Q GAIN WILD-TYPE 122 276 109

Figure S19.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'2q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00368 (Fisher's exact test), Q value = 0.01

Table S20.  Gene #4: '2q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
2Q GAIN MUTATED 30 28 19 24 9
2Q GAIN WILD-TYPE 97 115 145 70 80

Figure S20.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00119 (Fisher's exact test), Q value = 0.0039

Table S21.  Gene #4: '2q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
2Q GAIN MUTATED 41 37 20
2Q GAIN WILD-TYPE 104 168 149

Figure S21.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'2q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0222 (Fisher's exact test), Q value = 0.049

Table S22.  Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
2Q GAIN MUTATED 44 17 13 24
2Q GAIN WILD-TYPE 154 113 86 68

Figure S22.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3p gain' versus 'CN_CNMF'

P value = 0.00405 (Fisher's exact test), Q value = 0.011

Table S23.  Gene #5: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
3P GAIN MUTATED 25 38 20
3P GAIN WILD-TYPE 141 172 229

Figure S23.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'

'3q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S24.  Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
3Q GAIN MUTATED 37 99 34
3Q GAIN WILD-TYPE 129 111 215

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

'3q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S25.  Gene #6: '3q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
3Q GAIN MUTATED 60 69 29
3Q GAIN WILD-TYPE 188 88 143

Figure S25.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3q gain' versus 'MIRSEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00043

Table S26.  Gene #6: '3q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
3Q GAIN MUTATED 65 79 23
3Q GAIN WILD-TYPE 98 249 103

Figure S26.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S27.  Gene #6: '3q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
3Q GAIN MUTATED 38 29 40 46 14
3Q GAIN WILD-TYPE 89 114 124 48 75

Figure S27.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S28.  Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
3Q GAIN MUTATED 61 48 28
3Q GAIN WILD-TYPE 84 157 141

Figure S28.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'3q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S29.  Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
3Q GAIN MUTATED 53 26 13 45
3Q GAIN WILD-TYPE 145 104 86 47

Figure S29.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p gain' versus 'CN_CNMF'

P value = 0.00081 (Fisher's exact test), Q value = 0.0027

Table S30.  Gene #7: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
4P GAIN MUTATED 10 23 6
4P GAIN WILD-TYPE 156 187 243

Figure S30.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

'4p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00399 (Fisher's exact test), Q value = 0.011

Table S31.  Gene #7: '4p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
4P GAIN MUTATED 4 13 8 12 1
4P GAIN WILD-TYPE 123 130 156 82 88

Figure S31.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0236 (Fisher's exact test), Q value = 0.051

Table S32.  Gene #7: '4p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
4P GAIN MUTATED 13 7 2 12
4P GAIN WILD-TYPE 185 123 97 80

Figure S32.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q gain' versus 'CN_CNMF'

P value = 0.00279 (Fisher's exact test), Q value = 0.0082

Table S33.  Gene #8: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
4Q GAIN MUTATED 7 20 6
4Q GAIN WILD-TYPE 159 190 243

Figure S33.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

'4q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 0.0011

Table S34.  Gene #8: '4q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
4Q GAIN MUTATED 2 11 8 12 0
4Q GAIN WILD-TYPE 125 132 156 82 89

Figure S34.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00392 (Fisher's exact test), Q value = 0.011

Table S35.  Gene #8: '4q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
4Q GAIN MUTATED 11 5 1 12
4Q GAIN WILD-TYPE 187 125 98 80

Figure S35.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S36.  Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
5P GAIN MUTATED 64 89 24
5P GAIN WILD-TYPE 102 121 225

Figure S36.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S37.  Gene #9: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
5P GAIN MUTATED 50 81 32
5P GAIN WILD-TYPE 198 76 140

Figure S37.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0175 (Fisher's exact test), Q value = 0.04

Table S38.  Gene #9: '5p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 110 99
5P GAIN MUTATED 88 23 20
5P GAIN WILD-TYPE 185 87 79

Figure S38.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'5p gain' versus 'MRNASEQ_CNMF'

P value = 0.0148 (Fisher's exact test), Q value = 0.034

Table S39.  Gene #9: '5p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
5P GAIN MUTATED 25 37 12 3
5P GAIN WILD-TYPE 56 32 10 8

Figure S39.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00874 (Fisher's exact test), Q value = 0.022

Table S40.  Gene #9: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
5P GAIN MUTATED 23 4 50
5P GAIN WILD-TYPE 44 16 46

Figure S40.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S41.  Gene #9: '5p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
5P GAIN MUTATED 74 79 23
5P GAIN WILD-TYPE 89 249 103

Figure S41.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'5p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S42.  Gene #9: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
5P GAIN MUTATED 51 29 34 50 12
5P GAIN WILD-TYPE 76 114 130 44 77

Figure S42.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S43.  Gene #9: '5p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
5P GAIN MUTATED 69 54 30
5P GAIN WILD-TYPE 76 151 139

Figure S43.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'5p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S44.  Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
5P GAIN MUTATED 56 33 14 50
5P GAIN WILD-TYPE 142 97 85 42

Figure S44.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q gain' versus 'CN_CNMF'

P value = 0.00233 (Fisher's exact test), Q value = 0.007

Table S45.  Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
5Q GAIN MUTATED 20 30 13
5Q GAIN WILD-TYPE 146 180 236

Figure S45.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

'6p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S46.  Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
6P GAIN MUTATED 62 36 19
6P GAIN WILD-TYPE 104 174 230

Figure S46.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

'6p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S47.  Gene #11: '6p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
6P GAIN MUTATED 37 49 19
6P GAIN WILD-TYPE 211 108 153

Figure S47.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p gain' versus 'RPPA_CNMF'

P value = 0.0241 (Fisher's exact test), Q value = 0.052

Table S48.  Gene #11: '6p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 137 136 64
6P GAIN MUTATED 26 33 15 15
6P GAIN WILD-TYPE 119 104 121 49

Figure S48.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'6p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0302 (Fisher's exact test), Q value = 0.063

Table S49.  Gene #11: '6p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 110 99
6P GAIN MUTATED 53 26 10
6P GAIN WILD-TYPE 220 84 89

Figure S49.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_CNMF'

P value = 0.00401 (Fisher's exact test), Q value = 0.011

Table S50.  Gene #11: '6p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
6P GAIN MUTATED 43 59 14
6P GAIN WILD-TYPE 120 269 112

Figure S50.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'6p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S51.  Gene #11: '6p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
6P GAIN MUTATED 49 27 16 17 7
6P GAIN WILD-TYPE 78 116 148 77 82

Figure S51.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00503 (Fisher's exact test), Q value = 0.013

Table S52.  Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
6P GAIN MUTATED 39 36 21
6P GAIN WILD-TYPE 106 169 148

Figure S52.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'6p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.00073

Table S53.  Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
6P GAIN MUTATED 55 13 11 17
6P GAIN WILD-TYPE 143 117 88 75

Figure S53.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S54.  Gene #12: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
6Q GAIN MUTATED 51 32 17
6Q GAIN WILD-TYPE 115 178 232

Figure S54.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

'6q gain' versus 'METHLYATION_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.00088

Table S55.  Gene #12: '6q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
6Q GAIN MUTATED 37 38 14
6Q GAIN WILD-TYPE 211 119 158

Figure S55.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q gain' versus 'RPPA_CNMF'

P value = 0.0418 (Fisher's exact test), Q value = 0.084

Table S56.  Gene #12: '6q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 137 136 64
6Q GAIN MUTATED 23 28 13 14
6Q GAIN WILD-TYPE 122 109 123 50

Figure S56.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'6q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0376 (Fisher's exact test), Q value = 0.076

Table S57.  Gene #12: '6q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 110 99
6Q GAIN MUTATED 49 21 8
6Q GAIN WILD-TYPE 224 89 91

Figure S57.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'6q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S58.  Gene #12: '6q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
6Q GAIN MUTATED 37 28 13 15 6
6Q GAIN WILD-TYPE 90 115 151 79 83

Figure S58.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S59.  Gene #12: '6q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
6Q GAIN MUTATED 50 8 9 15
6Q GAIN WILD-TYPE 148 122 90 77

Figure S59.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S60.  Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
7P GAIN MUTATED 105 126 75
7P GAIN WILD-TYPE 61 84 174

Figure S60.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S61.  Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
7P GAIN MUTATED 137 90 59
7P GAIN WILD-TYPE 111 67 113

Figure S61.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p gain' versus 'MIRSEQ_CNMF'

P value = 0.00207 (Fisher's exact test), Q value = 0.0063

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
7P GAIN MUTATED 89 167 44
7P GAIN WILD-TYPE 74 161 82

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

'7p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00032 (Fisher's exact test), Q value = 0.0012

Table S63.  Gene #13: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
7P GAIN MUTATED 70 82 69 51 28
7P GAIN WILD-TYPE 57 61 95 43 61

Figure S63.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00091 (Fisher's exact test), Q value = 0.003

Table S64.  Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
7P GAIN MUTATED 87 104 66
7P GAIN WILD-TYPE 58 101 103

Figure S64.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'7p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00625 (Fisher's exact test), Q value = 0.016

Table S65.  Gene #13: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
7P GAIN MUTATED 112 59 36 50
7P GAIN WILD-TYPE 86 71 63 42

Figure S65.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S66.  Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
7Q GAIN MUTATED 84 103 70
7Q GAIN WILD-TYPE 82 107 179

Figure S66.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 0.00043 (Fisher's exact test), Q value = 0.0016

Table S67.  Gene #14: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
7Q GAIN MUTATED 114 73 49
7Q GAIN WILD-TYPE 134 84 123

Figure S67.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00354 (Fisher's exact test), Q value = 0.0099

Table S68.  Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
7Q GAIN MUTATED 75 80 56
7Q GAIN WILD-TYPE 70 125 113

Figure S68.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'8p gain' versus 'CN_CNMF'

P value = 0.0054 (Fisher's exact test), Q value = 0.014

Table S69.  Gene #15: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
8P GAIN MUTATED 63 68 117
8P GAIN WILD-TYPE 103 142 132

Figure S69.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

'8p gain' versus 'METHLYATION_CNMF'

P value = 0.0489 (Fisher's exact test), Q value = 0.094

Table S70.  Gene #15: '8p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
8P GAIN MUTATED 110 55 58
8P GAIN WILD-TYPE 138 102 114

Figure S70.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0431 (Fisher's exact test), Q value = 0.086

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
8P GAIN MUTATED 30 3 34
8P GAIN WILD-TYPE 37 17 62

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

'8q gain' versus 'METHLYATION_CNMF'

P value = 0.0189 (Fisher's exact test), Q value = 0.042

Table S72.  Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
8Q GAIN MUTATED 141 90 76
8Q GAIN WILD-TYPE 107 67 96

Figure S72.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8q gain' versus 'MIRSEQ_CNMF'

P value = 0.0204 (Fisher's exact test), Q value = 0.045

Table S73.  Gene #16: '8q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
8Q GAIN MUTATED 93 186 54
8Q GAIN WILD-TYPE 70 142 72

Figure S73.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'8q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0144 (Fisher's exact test), Q value = 0.033

Table S74.  Gene #16: '8q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
8Q GAIN MUTATED 74 91 76 51 41
8Q GAIN WILD-TYPE 53 52 88 43 48

Figure S74.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'9q gain' versus 'CN_CNMF'

P value = 0.043 (Fisher's exact test), Q value = 0.086

Table S75.  Gene #18: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
9Q GAIN MUTATED 33 44 32
9Q GAIN WILD-TYPE 133 166 217

Figure S75.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

'10p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S76.  Gene #19: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
10P GAIN MUTATED 55 55 25
10P GAIN WILD-TYPE 111 155 224

Figure S76.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

'10p gain' versus 'MRNASEQ_CNMF'

P value = 0.0176 (Fisher's exact test), Q value = 0.04

Table S77.  Gene #19: '10p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
10P GAIN MUTATED 26 10 5 0
10P GAIN WILD-TYPE 55 59 17 11

Figure S77.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00068 (Fisher's exact test), Q value = 0.0024

Table S78.  Gene #19: '10p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
10P GAIN MUTATED 43 33 23 14 19
10P GAIN WILD-TYPE 84 110 141 80 70

Figure S78.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'10q gain' versus 'CN_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.0014

Table S79.  Gene #20: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
10Q GAIN MUTATED 33 43 22
10Q GAIN WILD-TYPE 133 167 227

Figure S79.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

'10q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0472 (Fisher's exact test), Q value = 0.092

Table S80.  Gene #20: '10q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
10Q GAIN MUTATED 30 23 21 9 12
10Q GAIN WILD-TYPE 97 120 143 85 77

Figure S80.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'11p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S81.  Gene #21: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
11P GAIN MUTATED 44 39 16
11P GAIN WILD-TYPE 122 171 233

Figure S81.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

'11p gain' versus 'METHLYATION_CNMF'

P value = 0.0107 (Fisher's exact test), Q value = 0.026

Table S82.  Gene #21: '11p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
11P GAIN MUTATED 36 37 20
11P GAIN WILD-TYPE 212 120 152

Figure S82.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00829 (Fisher's exact test), Q value = 0.021

Table S83.  Gene #21: '11p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
11P GAIN MUTATED 30 22 20 17 6
11P GAIN WILD-TYPE 97 121 144 77 83

Figure S83.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'11p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0075 (Fisher's exact test), Q value = 0.019

Table S84.  Gene #21: '11p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
11P GAIN MUTATED 32 33 16
11P GAIN WILD-TYPE 113 172 153

Figure S84.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'11q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S85.  Gene #22: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
11Q GAIN MUTATED 51 35 18
11Q GAIN WILD-TYPE 115 175 231

Figure S85.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

'11q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00131 (Fisher's exact test), Q value = 0.0042

Table S86.  Gene #22: '11q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
11Q GAIN MUTATED 33 26 25 12 5
11Q GAIN WILD-TYPE 94 117 139 82 84

Figure S86.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00187 (Fisher's exact test), Q value = 0.0058

Table S87.  Gene #22: '11q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
11Q GAIN MUTATED 28 42 14
11Q GAIN WILD-TYPE 117 163 155

Figure S87.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'11q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0331 (Fisher's exact test), Q value = 0.068

Table S88.  Gene #22: '11q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
11Q GAIN MUTATED 43 20 9 12
11Q GAIN WILD-TYPE 155 110 90 80

Figure S88.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S89.  Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
12P GAIN MUTATED 32 81 35
12P GAIN WILD-TYPE 134 129 214

Figure S89.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S90.  Gene #23: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
12P GAIN MUTATED 48 63 32
12P GAIN WILD-TYPE 200 94 140

Figure S90.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 0.00407 (Fisher's exact test), Q value = 0.011

Table S91.  Gene #23: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
12P GAIN MUTATED 15 28 11 4
12P GAIN WILD-TYPE 66 41 11 7

Figure S91.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00287 (Fisher's exact test), Q value = 0.0084

Table S92.  Gene #23: '12p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
12P GAIN MUTATED 14 3 41
12P GAIN WILD-TYPE 53 17 55

Figure S92.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.00073

Table S93.  Gene #23: '12p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
12P GAIN MUTATED 58 66 22
12P GAIN WILD-TYPE 105 262 104

Figure S93.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'12p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00036 (Fisher's exact test), Q value = 0.0014

Table S94.  Gene #23: '12p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
12P GAIN MUTATED 28 31 36 39 12
12P GAIN WILD-TYPE 99 112 128 55 77

Figure S94.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00109 (Fisher's exact test), Q value = 0.0036

Table S95.  Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
12P GAIN MUTATED 50 49 28
12P GAIN WILD-TYPE 95 156 141

Figure S95.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'12p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00023

Table S96.  Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
12P GAIN MUTATED 45 31 12 39
12P GAIN WILD-TYPE 153 99 87 53

Figure S96.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q gain' versus 'CN_CNMF'

P value = 0.00114 (Fisher's exact test), Q value = 0.0037

Table S97.  Gene #24: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
12Q GAIN MUTATED 25 56 34
12Q GAIN WILD-TYPE 141 154 215

Figure S97.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

'12q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0258 (Fisher's exact test), Q value = 0.055

Table S98.  Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
12Q GAIN MUTATED 35 37 21
12Q GAIN WILD-TYPE 110 168 148

Figure S98.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'13q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S99.  Gene #25: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
13Q GAIN MUTATED 109 36 52
13Q GAIN WILD-TYPE 57 174 197

Figure S99.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

'13q gain' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00043

Table S100.  Gene #25: '13q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
13Q GAIN MUTATED 33 8 2 2
13Q GAIN WILD-TYPE 48 61 20 9

Figure S100.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'13q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S101.  Gene #25: '13q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
13Q GAIN MUTATED 24 11 10
13Q GAIN WILD-TYPE 43 9 86

Figure S101.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'13q gain' versus 'MIRSEQ_CNMF'

P value = 0.0114 (Fisher's exact test), Q value = 0.027

Table S102.  Gene #25: '13q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
13Q GAIN MUTATED 43 119 30
13Q GAIN WILD-TYPE 120 209 96

Figure S102.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'13q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S103.  Gene #25: '13q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
13Q GAIN MUTATED 62 68 29 9 24
13Q GAIN WILD-TYPE 65 75 135 85 65

Figure S103.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'13q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S104.  Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
13Q GAIN MUTATED 81 37 30 9
13Q GAIN WILD-TYPE 117 93 69 83

Figure S104.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S105.  Gene #26: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
14Q GAIN MUTATED 19 46 10
14Q GAIN WILD-TYPE 147 164 239

Figure S105.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

'14q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S106.  Gene #26: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
14Q GAIN MUTATED 22 38 12
14Q GAIN WILD-TYPE 226 119 160

Figure S106.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'14q gain' versus 'MRNASEQ_CNMF'

P value = 0.0302 (Fisher's exact test), Q value = 0.063

Table S107.  Gene #26: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
14Q GAIN MUTATED 13 24 8 2
14Q GAIN WILD-TYPE 68 45 14 9

Figure S107.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0156 (Fisher's exact test), Q value = 0.036

Table S108.  Gene #26: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
14Q GAIN MUTATED 12 2 33
14Q GAIN WILD-TYPE 55 18 63

Figure S108.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S109.  Gene #26: '14q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
14Q GAIN MUTATED 41 25 8
14Q GAIN WILD-TYPE 122 303 118

Figure S109.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'14q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S110.  Gene #26: '14q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
14Q GAIN MUTATED 10 17 7 33 7
14Q GAIN WILD-TYPE 117 126 157 61 82

Figure S110.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.001

Table S111.  Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
14Q GAIN MUTATED 33 16 18
14Q GAIN WILD-TYPE 112 189 151

Figure S111.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'14q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S112.  Gene #26: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
14Q GAIN MUTATED 22 6 6 33
14Q GAIN WILD-TYPE 176 124 93 59

Figure S112.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9.8e-05

Table S113.  Gene #27: '15q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
15Q GAIN MUTATED 25 33 9
15Q GAIN WILD-TYPE 141 177 240

Figure S113.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #1: 'CN_CNMF'

'15q gain' versus 'METHLYATION_CNMF'

P value = 0.0312 (Fisher's exact test), Q value = 0.065

Table S114.  Gene #27: '15q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
15Q GAIN MUTATED 28 24 11
15Q GAIN WILD-TYPE 220 133 161

Figure S114.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'15q gain' versus 'MIRSEQ_CNMF'

P value = 0.00335 (Fisher's exact test), Q value = 0.0095

Table S115.  Gene #27: '15q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
15Q GAIN MUTATED 26 34 5
15Q GAIN WILD-TYPE 137 294 121

Figure S115.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'15q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00595 (Fisher's exact test), Q value = 0.016

Table S116.  Gene #27: '15q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
15Q GAIN MUTATED 25 22 10
15Q GAIN WILD-TYPE 120 183 159

Figure S116.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'15q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00449 (Fisher's exact test), Q value = 0.012

Table S117.  Gene #27: '15q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
15Q GAIN MUTATED 30 11 3 13
15Q GAIN WILD-TYPE 168 119 96 79

Figure S117.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S118.  Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
16P GAIN MUTATED 20 59 20
16P GAIN WILD-TYPE 146 151 229

Figure S118.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

'16p gain' versus 'METHLYATION_CNMF'

P value = 0.00088 (Fisher's exact test), Q value = 0.0029

Table S119.  Gene #28: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
16P GAIN MUTATED 25 38 27
16P GAIN WILD-TYPE 223 119 145

Figure S119.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p gain' versus 'RPPA_CNMF'

P value = 0.045 (Fisher's exact test), Q value = 0.089

Table S120.  Gene #28: '16p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 137 136 64
16P GAIN MUTATED 17 16 27 15
16P GAIN WILD-TYPE 128 121 109 49

Figure S120.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 0.0195 (Fisher's exact test), Q value = 0.043

Table S121.  Gene #28: '16p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
16P GAIN MUTATED 11 23 6 1
16P GAIN WILD-TYPE 70 46 16 10

Figure S121.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00349 (Fisher's exact test), Q value = 0.0098

Table S122.  Gene #28: '16p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
16P GAIN MUTATED 12 0 29
16P GAIN WILD-TYPE 55 20 67

Figure S122.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_CNMF'

P value = 0.00833 (Fisher's exact test), Q value = 0.021

Table S123.  Gene #28: '16p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
16P GAIN MUTATED 37 39 21
16P GAIN WILD-TYPE 126 289 105

Figure S123.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00028

Table S124.  Gene #28: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
16P GAIN MUTATED 23 11 22 30 11
16P GAIN WILD-TYPE 104 132 142 64 78

Figure S124.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.00073

Table S125.  Gene #28: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
16P GAIN MUTATED 20 21 10 28
16P GAIN WILD-TYPE 178 109 89 64

Figure S125.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S126.  Gene #29: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
16Q GAIN MUTATED 18 50 18
16Q GAIN WILD-TYPE 148 160 231

Figure S126.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16q gain' versus 'METHLYATION_CNMF'

P value = 0.00126 (Fisher's exact test), Q value = 0.0041

Table S127.  Gene #29: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
16Q GAIN MUTATED 23 35 21
16Q GAIN WILD-TYPE 225 122 151

Figure S127.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q gain' versus 'MRNASEQ_CNMF'

P value = 0.00346 (Fisher's exact test), Q value = 0.0098

Table S128.  Gene #29: '16q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
16Q GAIN MUTATED 9 24 5 1
16Q GAIN WILD-TYPE 72 45 17 10

Figure S128.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00937 (Fisher's exact test), Q value = 0.023

Table S129.  Gene #29: '16q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
16Q GAIN MUTATED 8 2 29
16Q GAIN WILD-TYPE 59 18 67

Figure S129.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 4e-04

Table S130.  Gene #29: '16q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
16Q GAIN MUTATED 38 29 17
16Q GAIN WILD-TYPE 125 299 109

Figure S130.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S131.  Gene #29: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
16Q GAIN MUTATED 15 13 17 30 9
16Q GAIN WILD-TYPE 112 130 147 64 80

Figure S131.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00186 (Fisher's exact test), Q value = 0.0058

Table S132.  Gene #29: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
16Q GAIN MUTATED 31 17 20
16Q GAIN WILD-TYPE 114 188 149

Figure S132.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S133.  Gene #29: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
16Q GAIN MUTATED 15 18 7 28
16Q GAIN WILD-TYPE 183 112 92 64

Figure S133.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S134.  Gene #30: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
17P GAIN MUTATED 18 39 5
17P GAIN WILD-TYPE 148 171 244

Figure S134.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

'17p gain' versus 'METHLYATION_CNMF'

P value = 0.00067 (Fisher's exact test), Q value = 0.0023

Table S135.  Gene #30: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
17P GAIN MUTATED 21 28 9
17P GAIN WILD-TYPE 227 129 163

Figure S135.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p gain' versus 'MRNASEQ_CNMF'

P value = 0.0483 (Fisher's exact test), Q value = 0.094

Table S136.  Gene #30: '17p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
17P GAIN MUTATED 12 19 2 0
17P GAIN WILD-TYPE 69 50 20 11

Figure S136.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17p gain' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9.8e-05

Table S137.  Gene #30: '17p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
17P GAIN MUTATED 31 25 5
17P GAIN WILD-TYPE 132 303 121

Figure S137.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00949 (Fisher's exact test), Q value = 0.023

Table S138.  Gene #30: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
17P GAIN MUTATED 14 10 13 19 5
17P GAIN WILD-TYPE 113 133 151 75 84

Figure S138.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00303 (Fisher's exact test), Q value = 0.0087

Table S139.  Gene #30: '17p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
17P GAIN MUTATED 25 17 10
17P GAIN WILD-TYPE 120 188 159

Figure S139.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00039 (Fisher's exact test), Q value = 0.0014

Table S140.  Gene #30: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
17P GAIN MUTATED 17 12 3 20
17P GAIN WILD-TYPE 181 118 96 72

Figure S140.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S141.  Gene #31: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
17Q GAIN MUTATED 33 57 16
17Q GAIN WILD-TYPE 133 153 233

Figure S141.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 0.00102 (Fisher's exact test), Q value = 0.0034

Table S142.  Gene #31: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
17Q GAIN MUTATED 48 37 16
17Q GAIN WILD-TYPE 200 120 156

Figure S142.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0489 (Fisher's exact test), Q value = 0.094

Table S143.  Gene #31: '17q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
17Q GAIN MUTATED 21 1 24
17Q GAIN WILD-TYPE 46 19 72

Figure S143.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_CNMF'

P value = 0.00444 (Fisher's exact test), Q value = 0.012

Table S144.  Gene #31: '17q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
17Q GAIN MUTATED 41 48 15
17Q GAIN WILD-TYPE 122 280 111

Figure S144.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0239 (Fisher's exact test), Q value = 0.052

Table S145.  Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
17Q GAIN MUTATED 34 33 20
17Q GAIN WILD-TYPE 111 172 149

Figure S145.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00248 (Fisher's exact test), Q value = 0.0074

Table S146.  Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
17Q GAIN MUTATED 34 24 6 23
17Q GAIN WILD-TYPE 164 106 93 69

Figure S146.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S147.  Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
18P GAIN MUTATED 46 66 25
18P GAIN WILD-TYPE 120 144 224

Figure S147.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S148.  Gene #32: '18p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
18P GAIN MUTATED 38 65 25
18P GAIN WILD-TYPE 210 92 147

Figure S148.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0132 (Fisher's exact test), Q value = 0.031

Table S149.  Gene #32: '18p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 110 99
18P GAIN MUTATED 70 15 16
18P GAIN WILD-TYPE 203 95 83

Figure S149.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_CNMF'

P value = 0.00057 (Fisher's exact test), Q value = 0.002

Table S150.  Gene #32: '18p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
18P GAIN MUTATED 51 69 16
18P GAIN WILD-TYPE 112 259 110

Figure S150.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'18p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00037

Table S151.  Gene #32: '18p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
18P GAIN MUTATED 42 30 25 29 10
18P GAIN WILD-TYPE 85 113 139 65 79

Figure S151.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00073 (Fisher's exact test), Q value = 0.0025

Table S152.  Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
18P GAIN MUTATED 42 54 22
18P GAIN WILD-TYPE 103 151 147

Figure S152.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'18p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00078 (Fisher's exact test), Q value = 0.0027

Table S153.  Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
18P GAIN MUTATED 56 23 11 28
18P GAIN WILD-TYPE 142 107 88 64

Figure S153.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q gain' versus 'CN_CNMF'

P value = 0.00225 (Fisher's exact test), Q value = 0.0068

Table S154.  Gene #33: '18q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
18Q GAIN MUTATED 30 33 19
18Q GAIN WILD-TYPE 136 177 230

Figure S154.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #1: 'CN_CNMF'

'18q gain' versus 'METHLYATION_CNMF'

P value = 0.00448 (Fisher's exact test), Q value = 0.012

Table S155.  Gene #33: '18q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
18Q GAIN MUTATED 26 33 17
18Q GAIN WILD-TYPE 222 124 155

Figure S155.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18q gain' versus 'MIRSEQ_CNMF'

P value = 0.0276 (Fisher's exact test), Q value = 0.058

Table S156.  Gene #33: '18q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
18Q GAIN MUTATED 29 44 9
18Q GAIN WILD-TYPE 134 284 117

Figure S156.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'18q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0474 (Fisher's exact test), Q value = 0.092

Table S157.  Gene #33: '18q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
18Q GAIN MUTATED 25 21 14 14 8
18Q GAIN WILD-TYPE 102 122 150 80 81

Figure S157.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19p gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9.8e-05

Table S158.  Gene #34: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
19P GAIN MUTATED 25 42 16
19P GAIN WILD-TYPE 141 168 233

Figure S158.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

'19q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S159.  Gene #35: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
19Q GAIN MUTATED 41 55 21
19Q GAIN WILD-TYPE 125 155 228

Figure S159.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

'19q gain' versus 'RPPA_CNMF'

P value = 0.00641 (Fisher's exact test), Q value = 0.016

Table S160.  Gene #35: '19q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 137 136 64
19Q GAIN MUTATED 39 18 17 11
19Q GAIN WILD-TYPE 106 119 119 53

Figure S160.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'19q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0164 (Fisher's exact test), Q value = 0.038

Table S161.  Gene #35: '19q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 110 99
19Q GAIN MUTATED 60 14 11
19Q GAIN WILD-TYPE 213 96 88

Figure S161.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00037 (Fisher's exact test), Q value = 0.0014

Table S162.  Gene #35: '19q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
19Q GAIN MUTATED 41 28 23 15 9
19Q GAIN WILD-TYPE 86 115 141 79 80

Figure S162.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0178 (Fisher's exact test), Q value = 0.04

Table S163.  Gene #35: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
19Q GAIN MUTATED 50 22 11 14
19Q GAIN WILD-TYPE 148 108 88 78

Figure S163.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S164.  Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
20P GAIN MUTATED 131 124 94
20P GAIN WILD-TYPE 35 86 155

Figure S164.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 0.00678 (Fisher's exact test), Q value = 0.017

Table S165.  Gene #36: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
20P GAIN MUTATED 138 102 82
20P GAIN WILD-TYPE 110 55 90

Figure S165.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20p gain' versus 'MIRSEQ_CNMF'

P value = 0.0154 (Fisher's exact test), Q value = 0.035

Table S166.  Gene #36: '20p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
20P GAIN MUTATED 104 182 59
20P GAIN WILD-TYPE 59 146 67

Figure S166.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S167.  Gene #36: '20p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
20P GAIN MUTATED 95 85 75 50 40
20P GAIN WILD-TYPE 32 58 89 44 49

Figure S167.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0294 (Fisher's exact test), Q value = 0.062

Table S168.  Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
20P GAIN MUTATED 93 110 84
20P GAIN WILD-TYPE 52 95 85

Figure S168.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'20p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0105 (Fisher's exact test), Q value = 0.025

Table S169.  Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
20P GAIN MUTATED 127 61 49 50
20P GAIN WILD-TYPE 71 69 50 42

Figure S169.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S170.  Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
20Q GAIN MUTATED 147 144 104
20Q GAIN WILD-TYPE 19 66 145

Figure S170.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 0.00828 (Fisher's exact test), Q value = 0.021

Table S171.  Gene #37: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
20Q GAIN MUTATED 62 37 12 5
20Q GAIN WILD-TYPE 19 32 10 6

Figure S171.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0038 (Fisher's exact test), Q value = 0.011

Table S172.  Gene #37: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
20Q GAIN MUTATED 51 15 50
20Q GAIN WILD-TYPE 16 5 46

Figure S172.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S173.  Gene #37: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
20Q GAIN MUTATED 114 97 86 48 44
20Q GAIN WILD-TYPE 13 46 78 46 45

Figure S173.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 9.8e-05

Table S174.  Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
20Q GAIN MUTATED 150 69 61 48
20Q GAIN WILD-TYPE 48 61 38 44

Figure S174.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S175.  Gene #38: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
21Q GAIN MUTATED 18 17 1
21Q GAIN WILD-TYPE 148 193 248

Figure S175.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

'21q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S176.  Gene #38: '21q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
21Q GAIN MUTATED 9 25 1
21Q GAIN WILD-TYPE 239 132 171

Figure S176.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'21q gain' versus 'MIRSEQ_CNMF'

P value = 0.0215 (Fisher's exact test), Q value = 0.048

Table S177.  Gene #38: '21q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
21Q GAIN MUTATED 16 16 3
21Q GAIN WILD-TYPE 147 312 123

Figure S177.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'21q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.0012

Table S178.  Gene #38: '21q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
21Q GAIN MUTATED 14 6 5 10 0
21Q GAIN WILD-TYPE 113 137 159 84 89

Figure S178.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'21q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0241 (Fisher's exact test), Q value = 0.052

Table S179.  Gene #38: '21q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
21Q GAIN MUTATED 13 15 4
21Q GAIN WILD-TYPE 132 190 165

Figure S179.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'21q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0376 (Fisher's exact test), Q value = 0.076

Table S180.  Gene #38: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
21Q GAIN MUTATED 15 5 2 10
21Q GAIN WILD-TYPE 183 125 97 82

Figure S180.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S181.  Gene #39: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
22Q GAIN MUTATED 15 41 8
22Q GAIN WILD-TYPE 151 169 241

Figure S181.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

'22q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S182.  Gene #39: '22q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
22Q GAIN MUTATED 15 38 9
22Q GAIN WILD-TYPE 233 119 163

Figure S182.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S183.  Gene #39: '22q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
22Q GAIN MUTATED 2 23 4 3
22Q GAIN WILD-TYPE 79 46 18 8

Figure S183.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'22q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S184.  Gene #39: '22q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
22Q GAIN MUTATED 3 0 29
22Q GAIN WILD-TYPE 64 20 67

Figure S184.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S185.  Gene #39: '22q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
22Q GAIN MUTATED 37 19 8
22Q GAIN WILD-TYPE 126 309 118

Figure S185.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'22q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S186.  Gene #39: '22q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
22Q GAIN MUTATED 11 10 10 29 4
22Q GAIN WILD-TYPE 116 133 154 65 85

Figure S186.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S187.  Gene #39: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
22Q GAIN MUTATED 33 13 13
22Q GAIN WILD-TYPE 112 192 156

Figure S187.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'22q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S188.  Gene #39: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
22Q GAIN MUTATED 15 11 4 29
22Q GAIN WILD-TYPE 183 119 95 63

Figure S188.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xp gain' versus 'CN_CNMF'

P value = 0.0033 (Fisher's exact test), Q value = 0.0094

Table S189.  Gene #40: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
XP GAIN MUTATED 29 25 17
XP GAIN WILD-TYPE 137 185 232

Figure S189.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'

'xp gain' versus 'METHLYATION_CNMF'

P value = 0.0101 (Fisher's exact test), Q value = 0.024

Table S190.  Gene #40: 'xp gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
XP GAIN MUTATED 30 25 10
XP GAIN WILD-TYPE 218 132 162

Figure S190.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xp gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00944 (Fisher's exact test), Q value = 0.023

Table S191.  Gene #40: 'xp gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
XP GAIN MUTATED 17 23 8 13 7
XP GAIN WILD-TYPE 110 120 156 81 82

Figure S191.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'xq gain' versus 'CN_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.00081

Table S192.  Gene #41: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
XQ GAIN MUTATED 36 35 20
XQ GAIN WILD-TYPE 130 175 229

Figure S192.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

'xq gain' versus 'METHLYATION_CNMF'

P value = 0.0016 (Fisher's exact test), Q value = 0.005

Table S193.  Gene #41: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
XQ GAIN MUTATED 37 35 14
XQ GAIN WILD-TYPE 211 122 158

Figure S193.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq gain' versus 'MIRSEQ_CNMF'

P value = 0.00054 (Fisher's exact test), Q value = 0.0019

Table S194.  Gene #41: 'xq gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
XQ GAIN MUTATED 35 46 7
XQ GAIN WILD-TYPE 128 282 119

Figure S194.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'xq gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00131 (Fisher's exact test), Q value = 0.0042

Table S195.  Gene #41: 'xq gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
XQ GAIN MUTATED 19 24 12 24 9
XQ GAIN WILD-TYPE 108 119 152 70 80

Figure S195.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'xq gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00236 (Fisher's exact test), Q value = 0.007

Table S196.  Gene #41: 'xq gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
XQ GAIN MUTATED 30 9 13 23
XQ GAIN WILD-TYPE 168 121 86 69

Figure S196.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S197.  Gene #42: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
1P LOSS MUTATED 47 44 4
1P LOSS WILD-TYPE 119 166 245

Figure S197.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.0017

Table S198.  Gene #42: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
1P LOSS MUTATED 43 35 13
1P LOSS WILD-TYPE 205 122 159

Figure S198.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 0.0375 (Fisher's exact test), Q value = 0.076

Table S199.  Gene #42: '1p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
1P LOSS MUTATED 23 9 4 0
1P LOSS WILD-TYPE 58 60 18 11

Figure S199.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'1p loss' versus 'MIRSEQ_CNMF'

P value = 0.0131 (Fisher's exact test), Q value = 0.031

Table S200.  Gene #42: '1p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
1P LOSS MUTATED 29 55 9
1P LOSS WILD-TYPE 134 273 117

Figure S200.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'1p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7e-04 (Fisher's exact test), Q value = 0.0024

Table S201.  Gene #42: '1p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
1P LOSS MUTATED 30 29 14 13 7
1P LOSS WILD-TYPE 97 114 150 81 82

Figure S201.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'1q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S202.  Gene #43: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
1Q LOSS MUTATED 21 25 1
1Q LOSS WILD-TYPE 145 185 248

Figure S202.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

'1q loss' versus 'METHLYATION_CNMF'

P value = 0.0216 (Fisher's exact test), Q value = 0.048

Table S203.  Gene #43: '1q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
1Q LOSS MUTATED 23 17 6
1Q LOSS WILD-TYPE 225 140 166

Figure S203.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0385 (Fisher's exact test), Q value = 0.078

Table S204.  Gene #43: '1q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
1Q LOSS MUTATED 7 5 6
1Q LOSS WILD-TYPE 60 15 90

Figure S204.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2p loss' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00014

Table S205.  Gene #44: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
2P LOSS MUTATED 16 19 3
2P LOSS WILD-TYPE 150 191 246

Figure S205.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

'2p loss' versus 'RPPA_CNMF'

P value = 0.023 (Fisher's exact test), Q value = 0.05

Table S206.  Gene #44: '2p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 137 136 64
2P LOSS MUTATED 11 15 3 3
2P LOSS WILD-TYPE 134 122 133 61

Figure S206.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'2p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00766 (Fisher's exact test), Q value = 0.019

Table S207.  Gene #44: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
2P LOSS MUTATED 14 8 3 9 4
2P LOSS WILD-TYPE 113 135 161 85 85

Figure S207.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2q loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9.8e-05

Table S208.  Gene #45: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
2Q LOSS MUTATED 20 26 5
2Q LOSS WILD-TYPE 146 184 244

Figure S208.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

'2q loss' versus 'METHLYATION_CNMF'

P value = 0.012 (Fisher's exact test), Q value = 0.028

Table S209.  Gene #45: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
2Q LOSS MUTATED 17 22 9
2Q LOSS WILD-TYPE 231 135 163

Figure S209.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0333 (Fisher's exact test), Q value = 0.069

Table S210.  Gene #45: '2q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
2Q LOSS MUTATED 2 2 14
2Q LOSS WILD-TYPE 65 18 82

Figure S210.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_CNMF'

P value = 0.0379 (Fisher's exact test), Q value = 0.077

Table S211.  Gene #45: '2q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
2Q LOSS MUTATED 20 26 5
2Q LOSS WILD-TYPE 143 302 121

Figure S211.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'2q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00474 (Fisher's exact test), Q value = 0.013

Table S212.  Gene #45: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
2Q LOSS MUTATED 16 11 6 14 4
2Q LOSS WILD-TYPE 111 132 158 80 85

Figure S212.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0222 (Fisher's exact test), Q value = 0.049

Table S213.  Gene #45: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
2Q LOSS MUTATED 19 14 8
2Q LOSS WILD-TYPE 126 191 161

Figure S213.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'2q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0221 (Fisher's exact test), Q value = 0.049

Table S214.  Gene #45: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
2Q LOSS MUTATED 15 9 3 14
2Q LOSS WILD-TYPE 183 121 96 78

Figure S214.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S215.  Gene #46: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
3P LOSS MUTATED 69 96 22
3P LOSS WILD-TYPE 97 114 227

Figure S215.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S216.  Gene #46: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
3P LOSS MUTATED 69 81 30
3P LOSS WILD-TYPE 179 76 142

Figure S216.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00043

Table S217.  Gene #46: '3p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
3P LOSS MUTATED 28 50 9 6
3P LOSS WILD-TYPE 53 19 13 5

Figure S217.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S218.  Gene #46: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
3P LOSS MUTATED 19 9 65
3P LOSS WILD-TYPE 48 11 31

Figure S218.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S219.  Gene #46: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
3P LOSS MUTATED 80 82 23
3P LOSS WILD-TYPE 83 246 103

Figure S219.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S220.  Gene #46: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
3P LOSS MUTATED 40 50 17 66 12
3P LOSS WILD-TYPE 87 93 147 28 77

Figure S220.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S221.  Gene #46: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
3P LOSS MUTATED 72 48 42
3P LOSS WILD-TYPE 73 157 127

Figure S221.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'3p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S222.  Gene #46: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
3P LOSS MUTATED 53 28 16 65
3P LOSS WILD-TYPE 145 102 83 27

Figure S222.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S223.  Gene #47: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
3Q LOSS MUTATED 49 31 10
3Q LOSS WILD-TYPE 117 179 239

Figure S223.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

'3q loss' versus 'METHLYATION_CNMF'

P value = 0.0017 (Fisher's exact test), Q value = 0.0053

Table S224.  Gene #47: '3q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
3Q LOSS MUTATED 40 33 13
3Q LOSS WILD-TYPE 208 124 159

Figure S224.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3q loss' versus 'RPPA_CNMF'

P value = 0.0329 (Fisher's exact test), Q value = 0.068

Table S225.  Gene #47: '3q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 137 136 64
3Q LOSS MUTATED 28 11 19 12
3Q LOSS WILD-TYPE 117 126 117 52

Figure S225.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'3q loss' versus 'MIRSEQ_CNMF'

P value = 0.0137 (Fisher's exact test), Q value = 0.032

Table S226.  Gene #47: '3q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
3Q LOSS MUTATED 31 48 9
3Q LOSS WILD-TYPE 132 280 117

Figure S226.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S227.  Gene #47: '3q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
3Q LOSS MUTATED 26 30 6 19 7
3Q LOSS WILD-TYPE 101 113 158 75 82

Figure S227.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S228.  Gene #48: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
4P LOSS MUTATED 100 131 40
4P LOSS WILD-TYPE 66 79 209

Figure S228.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S229.  Gene #48: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
4P LOSS MUTATED 95 102 55
4P LOSS WILD-TYPE 153 55 117

Figure S229.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S230.  Gene #48: '4p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
4P LOSS MUTATED 101 133 36
4P LOSS WILD-TYPE 62 195 90

Figure S230.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'4p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S231.  Gene #48: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
4P LOSS MUTATED 80 65 40 57 28
4P LOSS WILD-TYPE 47 78 124 37 61

Figure S231.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S232.  Gene #48: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
4P LOSS MUTATED 96 76 60
4P LOSS WILD-TYPE 49 129 109

Figure S232.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S233.  Gene #48: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
4P LOSS MUTATED 105 35 35 57
4P LOSS WILD-TYPE 93 95 64 35

Figure S233.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S234.  Gene #49: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
4Q LOSS MUTATED 97 115 39
4Q LOSS WILD-TYPE 69 95 210

Figure S234.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 4e-04

Table S235.  Gene #49: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
4Q LOSS MUTATED 98 85 52
4Q LOSS WILD-TYPE 150 72 120

Figure S235.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4q loss' versus 'MIRSEQ_CNMF'

P value = 0.00507 (Fisher's exact test), Q value = 0.014

Table S236.  Gene #49: '4q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
4Q LOSS MUTATED 80 131 38
4Q LOSS WILD-TYPE 83 197 88

Figure S236.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'4q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S237.  Gene #49: '4q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
4Q LOSS MUTATED 79 63 41 39 27
4Q LOSS WILD-TYPE 48 80 123 55 62

Figure S237.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00073 (Fisher's exact test), Q value = 0.0025

Table S238.  Gene #49: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
4Q LOSS MUTATED 80 75 61
4Q LOSS WILD-TYPE 65 130 108

Figure S238.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'4q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00289 (Fisher's exact test), Q value = 0.0084

Table S239.  Gene #49: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
4Q LOSS MUTATED 100 39 38 39
4Q LOSS WILD-TYPE 98 91 61 53

Figure S239.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S240.  Gene #50: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
5P LOSS MUTATED 53 41 18
5P LOSS WILD-TYPE 113 169 231

Figure S240.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'

'5p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S241.  Gene #50: '5p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
5P LOSS MUTATED 58 36 13
5P LOSS WILD-TYPE 190 121 159

Figure S241.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p loss' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00043

Table S242.  Gene #50: '5p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
5P LOSS MUTATED 32 13 0 1
5P LOSS WILD-TYPE 49 56 22 10

Figure S242.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.00047

Table S243.  Gene #50: '5p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
5P LOSS MUTATED 22 11 13
5P LOSS WILD-TYPE 45 9 83

Figure S243.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.0012

Table S244.  Gene #50: '5p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
5P LOSS MUTATED 35 66 8
5P LOSS WILD-TYPE 128 262 118

Figure S244.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'5p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S245.  Gene #50: '5p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
5P LOSS MUTATED 42 39 12 11 5
5P LOSS WILD-TYPE 85 104 152 83 84

Figure S245.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0462 (Fisher's exact test), Q value = 0.091

Table S246.  Gene #50: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
5P LOSS MUTATED 34 41 22
5P LOSS WILD-TYPE 111 164 147

Figure S246.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'5p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.00055

Table S247.  Gene #50: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
5P LOSS MUTATED 57 18 11 11
5P LOSS WILD-TYPE 141 112 88 81

Figure S247.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S248.  Gene #51: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
5Q LOSS MUTATED 84 89 22
5Q LOSS WILD-TYPE 82 121 227

Figure S248.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S249.  Gene #51: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
5Q LOSS MUTATED 80 80 27
5Q LOSS WILD-TYPE 168 77 145

Figure S249.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q loss' versus 'RPPA_CNMF'

P value = 0.0298 (Fisher's exact test), Q value = 0.063

Table S250.  Gene #51: '5q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 137 136 64
5Q LOSS MUTATED 50 41 29 25
5Q LOSS WILD-TYPE 95 96 107 39

Figure S250.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'5q loss' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9.8e-05

Table S251.  Gene #51: '5q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
5Q LOSS MUTATED 71 102 20
5Q LOSS WILD-TYPE 92 226 106

Figure S251.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S252.  Gene #51: '5q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
5Q LOSS MUTATED 69 52 25 37 10
5Q LOSS WILD-TYPE 58 91 139 57 79

Figure S252.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00055

Table S253.  Gene #51: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
5Q LOSS MUTATED 68 67 40
5Q LOSS WILD-TYPE 77 138 129

Figure S253.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'5q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 9.8e-05

Table S254.  Gene #51: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
5Q LOSS MUTATED 87 32 19 37
5Q LOSS WILD-TYPE 111 98 80 55

Figure S254.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S255.  Gene #52: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
6P LOSS MUTATED 28 57 8
6P LOSS WILD-TYPE 138 153 241

Figure S255.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

'6p loss' versus 'METHLYATION_CNMF'

P value = 0.00469 (Fisher's exact test), Q value = 0.013

Table S256.  Gene #52: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
6P LOSS MUTATED 36 36 17
6P LOSS WILD-TYPE 212 121 155

Figure S256.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p loss' versus 'MIRSEQ_CNMF'

P value = 0.00638 (Fisher's exact test), Q value = 0.016

Table S257.  Gene #52: '6p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
6P LOSS MUTATED 33 50 9
6P LOSS WILD-TYPE 130 278 117

Figure S257.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'6p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.00077

Table S258.  Gene #52: '6p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
6P LOSS MUTATED 22 26 16 24 4
6P LOSS WILD-TYPE 105 117 148 70 85

Figure S258.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0121 (Fisher's exact test), Q value = 0.029

Table S259.  Gene #52: '6p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
6P LOSS MUTATED 32 30 17
6P LOSS WILD-TYPE 113 175 152

Figure S259.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'6p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00271 (Fisher's exact test), Q value = 0.008

Table S260.  Gene #52: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
6P LOSS MUTATED 33 14 8 24
6P LOSS WILD-TYPE 165 116 91 68

Figure S260.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S261.  Gene #53: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
6Q LOSS MUTATED 34 63 13
6Q LOSS WILD-TYPE 132 147 236

Figure S261.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

'7p loss' versus 'CN_CNMF'

P value = 0.00117 (Fisher's exact test), Q value = 0.0038

Table S262.  Gene #54: '7p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
7P LOSS MUTATED 15 14 4
7P LOSS WILD-TYPE 151 196 245

Figure S262.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #1: 'CN_CNMF'

'7p loss' versus 'METHLYATION_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.0014

Table S263.  Gene #54: '7p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
7P LOSS MUTATED 8 18 4
7P LOSS WILD-TYPE 240 139 168

Figure S263.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p loss' versus 'MIRSEQ_CNMF'

P value = 0.0486 (Fisher's exact test), Q value = 0.094

Table S264.  Gene #54: '7p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
7P LOSS MUTATED 15 14 4
7P LOSS WILD-TYPE 148 314 122

Figure S264.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'7p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0441 (Fisher's exact test), Q value = 0.087

Table S265.  Gene #54: '7p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
7P LOSS MUTATED 12 5 4 8 4
7P LOSS WILD-TYPE 115 138 160 86 85

Figure S265.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7q loss' versus 'CN_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 4e-04

Table S266.  Gene #55: '7q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
7Q LOSS MUTATED 21 23 7
7Q LOSS WILD-TYPE 145 187 242

Figure S266.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #1: 'CN_CNMF'

'7q loss' versus 'METHLYATION_CNMF'

P value = 0.00838 (Fisher's exact test), Q value = 0.021

Table S267.  Gene #55: '7q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
7Q LOSS MUTATED 18 22 8
7Q LOSS WILD-TYPE 230 135 164

Figure S267.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q loss' versus 'MIRSEQ_CNMF'

P value = 0.00981 (Fisher's exact test), Q value = 0.024

Table S268.  Gene #55: '7q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
7Q LOSS MUTATED 22 23 5
7Q LOSS WILD-TYPE 141 305 121

Figure S268.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'8p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S269.  Gene #56: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
8P LOSS MUTATED 54 81 18
8P LOSS WILD-TYPE 112 129 231

Figure S269.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 0.00559 (Fisher's exact test), Q value = 0.015

Table S270.  Gene #56: '8p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
8P LOSS MUTATED 58 54 33
8P LOSS WILD-TYPE 190 103 139

Figure S270.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0345 (Fisher's exact test), Q value = 0.071

Table S271.  Gene #56: '8p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 110 99
8P LOSS MUTATED 79 21 18
8P LOSS WILD-TYPE 194 89 81

Figure S271.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00019

Table S272.  Gene #56: '8p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
8P LOSS MUTATED 56 80 15
8P LOSS WILD-TYPE 107 248 111

Figure S272.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'8p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S273.  Gene #56: '8p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
8P LOSS MUTATED 40 40 25 37 9
8P LOSS WILD-TYPE 87 103 139 57 80

Figure S273.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00055 (Fisher's exact test), Q value = 0.002

Table S274.  Gene #56: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
8P LOSS MUTATED 54 48 31
8P LOSS WILD-TYPE 91 157 138

Figure S274.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'8p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S275.  Gene #56: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
8P LOSS MUTATED 57 29 10 37
8P LOSS WILD-TYPE 141 101 89 55

Figure S275.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S276.  Gene #57: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
8Q LOSS MUTATED 23 28 6
8Q LOSS WILD-TYPE 143 182 243

Figure S276.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

'8q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00768 (Fisher's exact test), Q value = 0.019

Table S277.  Gene #57: '8q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
8Q LOSS MUTATED 25 11 2 12
8Q LOSS WILD-TYPE 173 119 97 80

Figure S277.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S278.  Gene #58: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
9P LOSS MUTATED 98 115 37
9P LOSS WILD-TYPE 68 95 212

Figure S278.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 7e-04

Table S279.  Gene #58: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
9P LOSS MUTATED 93 86 58
9P LOSS WILD-TYPE 155 71 114

Figure S279.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p loss' versus 'MIRSEQ_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.00088

Table S280.  Gene #58: '9p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
9P LOSS MUTATED 85 125 37
9P LOSS WILD-TYPE 78 203 89

Figure S280.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'9p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S281.  Gene #58: '9p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
9P LOSS MUTATED 74 63 37 51 22
9P LOSS WILD-TYPE 53 80 127 43 67

Figure S281.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00608 (Fisher's exact test), Q value = 0.016

Table S282.  Gene #58: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
9P LOSS MUTATED 78 78 65
9P LOSS WILD-TYPE 67 127 104

Figure S282.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'9p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00036 (Fisher's exact test), Q value = 0.0014

Table S283.  Gene #58: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
9P LOSS MUTATED 95 39 36 51
9P LOSS WILD-TYPE 103 91 63 41

Figure S283.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S284.  Gene #59: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
9Q LOSS MUTATED 65 85 25
9Q LOSS WILD-TYPE 101 125 224

Figure S284.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 4e-04

Table S285.  Gene #59: '9q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
9Q LOSS MUTATED 57 66 43
9Q LOSS WILD-TYPE 191 91 129

Figure S285.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9q loss' versus 'MIRSEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 4e-04

Table S286.  Gene #59: '9q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
9Q LOSS MUTATED 67 79 27
9Q LOSS WILD-TYPE 96 249 99

Figure S286.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'9q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S287.  Gene #59: '9q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
9Q LOSS MUTATED 58 33 31 38 13
9Q LOSS WILD-TYPE 69 110 133 56 76

Figure S287.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.0014

Table S288.  Gene #59: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
9Q LOSS MUTATED 61 47 44
9Q LOSS WILD-TYPE 84 158 125

Figure S288.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'9q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0023 (Fisher's exact test), Q value = 0.0069

Table S289.  Gene #59: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
9Q LOSS MUTATED 64 25 25 38
9Q LOSS WILD-TYPE 134 105 74 54

Figure S289.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S290.  Gene #60: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
10P LOSS MUTATED 35 69 13
10P LOSS WILD-TYPE 131 141 236

Figure S290.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S291.  Gene #60: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
10P LOSS MUTATED 32 52 26
10P LOSS WILD-TYPE 216 105 146

Figure S291.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 0.0225 (Fisher's exact test), Q value = 0.049

Table S292.  Gene #60: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
10P LOSS MUTATED 14 26 8 2
10P LOSS WILD-TYPE 67 43 14 9

Figure S292.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.015 (Fisher's exact test), Q value = 0.035

Table S293.  Gene #60: '10p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
10P LOSS MUTATED 12 3 35
10P LOSS WILD-TYPE 55 17 61

Figure S293.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_CNMF'

P value = 0.00206 (Fisher's exact test), Q value = 0.0063

Table S294.  Gene #60: '10p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
10P LOSS MUTATED 46 53 17
10P LOSS WILD-TYPE 117 275 109

Figure S294.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'10p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S295.  Gene #60: '10p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
10P LOSS MUTATED 31 23 22 36 4
10P LOSS WILD-TYPE 96 120 142 58 85

Figure S295.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.0014

Table S296.  Gene #60: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
10P LOSS MUTATED 44 32 23
10P LOSS WILD-TYPE 101 173 146

Figure S296.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'10p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S297.  Gene #60: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
10P LOSS MUTATED 36 16 11 36
10P LOSS WILD-TYPE 162 114 88 56

Figure S297.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S298.  Gene #61: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
10Q LOSS MUTATED 42 65 10
10Q LOSS WILD-TYPE 124 145 239

Figure S298.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S299.  Gene #61: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
10Q LOSS MUTATED 31 56 21
10Q LOSS WILD-TYPE 217 101 151

Figure S299.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 0.00859 (Fisher's exact test), Q value = 0.021

Table S300.  Gene #61: '10q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
10Q LOSS MUTATED 12 25 8 4
10Q LOSS WILD-TYPE 69 44 14 7

Figure S300.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00226 (Fisher's exact test), Q value = 0.0068

Table S301.  Gene #61: '10q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
10Q LOSS MUTATED 11 2 36
10Q LOSS WILD-TYPE 56 18 60

Figure S301.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_CNMF'

P value = 0.00078 (Fisher's exact test), Q value = 0.0027

Table S302.  Gene #61: '10q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
10Q LOSS MUTATED 45 58 13
10Q LOSS WILD-TYPE 118 270 113

Figure S302.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S303.  Gene #61: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
10Q LOSS MUTATED 33 25 18 36 4
10Q LOSS WILD-TYPE 94 118 146 58 85

Figure S303.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00109 (Fisher's exact test), Q value = 0.0036

Table S304.  Gene #61: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
10Q LOSS MUTATED 42 31 23
10Q LOSS WILD-TYPE 103 174 146

Figure S304.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'10q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S305.  Gene #61: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
10Q LOSS MUTATED 35 14 11 36
10Q LOSS WILD-TYPE 163 116 88 56

Figure S305.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S306.  Gene #62: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
11P LOSS MUTATED 39 66 13
11P LOSS WILD-TYPE 127 144 236

Figure S306.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S307.  Gene #62: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
11P LOSS MUTATED 43 49 18
11P LOSS WILD-TYPE 205 108 154

Figure S307.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11p loss' versus 'MIRSEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 4e-04

Table S308.  Gene #62: '11p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
11P LOSS MUTATED 49 54 14
11P LOSS WILD-TYPE 114 274 112

Figure S308.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'11p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00014

Table S309.  Gene #62: '11p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
11P LOSS MUTATED 31 32 20 28 6
11P LOSS WILD-TYPE 96 111 144 66 83

Figure S309.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.0014

Table S310.  Gene #62: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
11P LOSS MUTATED 44 33 22
11P LOSS WILD-TYPE 101 172 147

Figure S310.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'11p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00853 (Fisher's exact test), Q value = 0.021

Table S311.  Gene #62: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
11P LOSS MUTATED 41 20 11 27
11P LOSS WILD-TYPE 157 110 88 65

Figure S311.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S312.  Gene #63: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
11Q LOSS MUTATED 37 70 13
11Q LOSS WILD-TYPE 129 140 236

Figure S312.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S313.  Gene #63: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
11Q LOSS MUTATED 37 57 20
11Q LOSS WILD-TYPE 211 100 152

Figure S313.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11q loss' versus 'MRNASEQ_CNMF'

P value = 0.0306 (Fisher's exact test), Q value = 0.064

Table S314.  Gene #63: '11q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
11Q LOSS MUTATED 19 31 6 2
11Q LOSS WILD-TYPE 62 38 16 9

Figure S314.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'11q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0365 (Fisher's exact test), Q value = 0.075

Table S315.  Gene #63: '11q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
11Q LOSS MUTATED 14 6 38
11Q LOSS WILD-TYPE 53 14 58

Figure S315.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S316.  Gene #63: '11q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
11Q LOSS MUTATED 58 48 12
11Q LOSS WILD-TYPE 105 280 114

Figure S316.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'11q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S317.  Gene #63: '11q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
11Q LOSS MUTATED 28 27 18 37 8
11Q LOSS WILD-TYPE 99 116 146 57 81

Figure S317.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S318.  Gene #63: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
11Q LOSS MUTATED 53 23 25
11Q LOSS WILD-TYPE 92 182 144

Figure S318.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'11q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00014

Table S319.  Gene #63: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
11Q LOSS MUTATED 37 18 10 36
11Q LOSS WILD-TYPE 161 112 89 56

Figure S319.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S320.  Gene #64: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
12P LOSS MUTATED 56 32 7
12P LOSS WILD-TYPE 110 178 242

Figure S320.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

'12p loss' versus 'METHLYATION_CNMF'

P value = 0.00621 (Fisher's exact test), Q value = 0.016

Table S321.  Gene #64: '12p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
12P LOSS MUTATED 37 33 15
12P LOSS WILD-TYPE 211 124 157

Figure S321.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p loss' versus 'MRNASEQ_CNMF'

P value = 0.00061 (Fisher's exact test), Q value = 0.0022

Table S322.  Gene #64: '12p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
12P LOSS MUTATED 24 8 0 0
12P LOSS WILD-TYPE 57 61 22 11

Figure S322.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00145 (Fisher's exact test), Q value = 0.0046

Table S323.  Gene #64: '12p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
12P LOSS MUTATED 17 7 8
12P LOSS WILD-TYPE 50 13 88

Figure S323.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S324.  Gene #64: '12p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
12P LOSS MUTATED 43 20 16 8 6
12P LOSS WILD-TYPE 84 123 148 86 83

Figure S324.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0468 (Fisher's exact test), Q value = 0.092

Table S325.  Gene #64: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
12P LOSS MUTATED 26 38 17
12P LOSS WILD-TYPE 119 167 152

Figure S325.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'12p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00982 (Fisher's exact test), Q value = 0.024

Table S326.  Gene #64: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
12P LOSS MUTATED 44 18 11 8
12P LOSS WILD-TYPE 154 112 88 84

Figure S326.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S327.  Gene #65: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
12Q LOSS MUTATED 44 32 6
12Q LOSS WILD-TYPE 122 178 243

Figure S327.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'

'12q loss' versus 'MRNASEQ_CNMF'

P value = 0.00916 (Fisher's exact test), Q value = 0.022

Table S328.  Gene #65: '12q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
12Q LOSS MUTATED 22 5 3 1
12Q LOSS WILD-TYPE 59 64 19 10

Figure S328.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00575 (Fisher's exact test), Q value = 0.015

Table S329.  Gene #65: '12q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
12Q LOSS MUTATED 15 7 9
12Q LOSS WILD-TYPE 52 13 87

Figure S329.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00023

Table S330.  Gene #65: '12q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
12Q LOSS MUTATED 32 22 13 8 5
12Q LOSS WILD-TYPE 95 121 151 86 84

Figure S330.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0372 (Fisher's exact test), Q value = 0.076

Table S331.  Gene #65: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
12Q LOSS MUTATED 39 16 9 9
12Q LOSS WILD-TYPE 159 114 90 83

Figure S331.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S332.  Gene #66: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
13Q LOSS MUTATED 11 77 14
13Q LOSS WILD-TYPE 155 133 235

Figure S332.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S333.  Gene #66: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
13Q LOSS MUTATED 32 46 17
13Q LOSS WILD-TYPE 216 111 155

Figure S333.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0432 (Fisher's exact test), Q value = 0.086

Table S334.  Gene #66: '13q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
13Q LOSS MUTATED 21 3 41
13Q LOSS WILD-TYPE 46 17 55

Figure S334.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S335.  Gene #66: '13q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
13Q LOSS MUTATED 54 34 14
13Q LOSS WILD-TYPE 109 294 112

Figure S335.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'13q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S336.  Gene #66: '13q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
13Q LOSS MUTATED 21 15 17 42 7
13Q LOSS WILD-TYPE 106 128 147 52 82

Figure S336.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S337.  Gene #66: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
13Q LOSS MUTATED 45 20 24
13Q LOSS WILD-TYPE 100 185 145

Figure S337.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'13q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S338.  Gene #66: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
13Q LOSS MUTATED 26 12 10 41
13Q LOSS WILD-TYPE 172 118 89 51

Figure S338.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S339.  Gene #67: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
14Q LOSS MUTATED 68 62 28
14Q LOSS WILD-TYPE 98 148 221

Figure S339.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 0.0129 (Fisher's exact test), Q value = 0.03

Table S340.  Gene #67: '14q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
14Q LOSS MUTATED 66 50 31
14Q LOSS WILD-TYPE 182 107 141

Figure S340.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 0.0056 (Fisher's exact test), Q value = 0.015

Table S341.  Gene #67: '14q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
14Q LOSS MUTATED 30 14 1 2
14Q LOSS WILD-TYPE 51 55 21 9

Figure S341.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0173 (Fisher's exact test), Q value = 0.039

Table S342.  Gene #67: '14q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
14Q LOSS MUTATED 25 5 17
14Q LOSS WILD-TYPE 42 15 79

Figure S342.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S343.  Gene #67: '14q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
14Q LOSS MUTATED 59 37 27 16 16
14Q LOSS WILD-TYPE 68 106 137 78 73

Figure S343.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00227 (Fisher's exact test), Q value = 0.0068

Table S344.  Gene #67: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
14Q LOSS MUTATED 68 27 19 16
14Q LOSS WILD-TYPE 130 103 80 76

Figure S344.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S345.  Gene #68: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
15Q LOSS MUTATED 61 64 24
15Q LOSS WILD-TYPE 105 146 225

Figure S345.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00047 (Fisher's exact test), Q value = 0.0017

Table S346.  Gene #68: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
15Q LOSS MUTATED 45 40 26 23 13
15Q LOSS WILD-TYPE 82 103 138 71 76

Figure S346.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S347.  Gene #69: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
16P LOSS MUTATED 74 61 21
16P LOSS WILD-TYPE 92 149 228

Figure S347.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

'16p loss' versus 'METHLYATION_CNMF'

P value = 0.00308 (Fisher's exact test), Q value = 0.0088

Table S348.  Gene #69: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
16P LOSS MUTATED 63 53 30
16P LOSS WILD-TYPE 185 104 142

Figure S348.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p loss' versus 'MRNASEQ_CNMF'

P value = 0.00048 (Fisher's exact test), Q value = 0.0017

Table S349.  Gene #69: '16p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
16P LOSS MUTATED 36 11 6 1
16P LOSS WILD-TYPE 45 58 16 10

Figure S349.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 4e-04

Table S350.  Gene #69: '16p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
16P LOSS MUTATED 27 11 16
16P LOSS WILD-TYPE 40 9 80

Figure S350.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_CNMF'

P value = 0.0152 (Fisher's exact test), Q value = 0.035

Table S351.  Gene #69: '16p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
16P LOSS MUTATED 49 85 20
16P LOSS WILD-TYPE 114 243 106

Figure S351.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S352.  Gene #69: '16p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
16P LOSS MUTATED 54 54 18 15 13
16P LOSS WILD-TYPE 73 89 146 79 76

Figure S352.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00793 (Fisher's exact test), Q value = 0.02

Table S353.  Gene #69: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
16P LOSS MUTATED 45 58 29
16P LOSS WILD-TYPE 100 147 140

Figure S353.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S354.  Gene #69: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
16P LOSS MUTATED 78 22 17 15
16P LOSS WILD-TYPE 120 108 82 77

Figure S354.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S355.  Gene #70: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
16Q LOSS MUTATED 79 64 25
16Q LOSS WILD-TYPE 87 146 224

Figure S355.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 0.0455 (Fisher's exact test), Q value = 0.09

Table S356.  Gene #70: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
16Q LOSS MUTATED 63 54 39
16Q LOSS WILD-TYPE 185 103 133

Figure S356.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S357.  Gene #70: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
16Q LOSS MUTATED 38 8 7 0
16Q LOSS WILD-TYPE 43 61 15 11

Figure S357.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S358.  Gene #70: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
16Q LOSS MUTATED 31 9 13
16Q LOSS WILD-TYPE 36 11 83

Figure S358.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S359.  Gene #70: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
16Q LOSS MUTATED 63 49 25 12 16
16Q LOSS WILD-TYPE 64 94 139 82 73

Figure S359.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0103 (Fisher's exact test), Q value = 0.025

Table S360.  Gene #70: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
16Q LOSS MUTATED 47 62 32
16Q LOSS WILD-TYPE 98 143 137

Figure S360.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S361.  Gene #70: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
16Q LOSS MUTATED 83 24 22 12
16Q LOSS WILD-TYPE 115 106 77 80

Figure S361.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S362.  Gene #71: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
17P LOSS MUTATED 105 88 43
17P LOSS WILD-TYPE 61 122 206

Figure S362.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 0.00051 (Fisher's exact test), Q value = 0.0018

Table S363.  Gene #71: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
17P LOSS MUTATED 107 68 45
17P LOSS WILD-TYPE 141 89 127

Figure S363.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 0.00189 (Fisher's exact test), Q value = 0.0059

Table S364.  Gene #71: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
17P LOSS MUTATED 44 18 6 3
17P LOSS WILD-TYPE 37 51 16 8

Figure S364.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00083 (Fisher's exact test), Q value = 0.0028

Table S365.  Gene #71: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
17P LOSS MUTATED 36 10 25
17P LOSS WILD-TYPE 31 10 71

Figure S365.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CNMF'

P value = 0.00662 (Fisher's exact test), Q value = 0.017

Table S366.  Gene #71: '17p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
17P LOSS MUTATED 60 138 33
17P LOSS WILD-TYPE 103 190 93

Figure S366.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S367.  Gene #71: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
17P LOSS MUTATED 76 65 49 24 17
17P LOSS WILD-TYPE 51 78 115 70 72

Figure S367.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00014

Table S368.  Gene #71: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
17P LOSS MUTATED 100 45 28 23
17P LOSS WILD-TYPE 98 85 71 69

Figure S368.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S369.  Gene #72: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
17Q LOSS MUTATED 50 31 18
17Q LOSS WILD-TYPE 116 179 231

Figure S369.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

'17q loss' versus 'METHLYATION_CNMF'

P value = 0.0206 (Fisher's exact test), Q value = 0.046

Table S370.  Gene #72: '17q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
17Q LOSS MUTATED 30 35 24
17Q LOSS WILD-TYPE 218 122 148

Figure S370.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q loss' versus 'MIRSEQ_CNMF'

P value = 0.0288 (Fisher's exact test), Q value = 0.061

Table S371.  Gene #72: '17q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
17Q LOSS MUTATED 25 61 11
17Q LOSS WILD-TYPE 138 267 115

Figure S371.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.00059

Table S372.  Gene #72: '17q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
17Q LOSS MUTATED 36 26 17 11 7
17Q LOSS WILD-TYPE 91 117 147 83 82

Figure S372.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S373.  Gene #73: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
18P LOSS MUTATED 71 72 44
18P LOSS WILD-TYPE 95 138 205

Figure S373.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

'18p loss' versus 'RPPA_CNMF'

P value = 0.0425 (Fisher's exact test), Q value = 0.085

Table S374.  Gene #73: '18p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 137 136 64
18P LOSS MUTATED 44 34 54 16
18P LOSS WILD-TYPE 101 103 82 48

Figure S374.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'18p loss' versus 'MRNASEQ_CNMF'

P value = 0.00121 (Fisher's exact test), Q value = 0.0039

Table S375.  Gene #73: '18p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
18P LOSS MUTATED 41 18 3 4
18P LOSS WILD-TYPE 40 51 19 7

Figure S375.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'18p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00326 (Fisher's exact test), Q value = 0.0093

Table S376.  Gene #73: '18p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
18P LOSS MUTATED 34 8 24
18P LOSS WILD-TYPE 33 12 72

Figure S376.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S377.  Gene #74: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
18Q LOSS MUTATED 90 116 50
18Q LOSS WILD-TYPE 76 94 199

Figure S377.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 0.025 (Fisher's exact test), Q value = 0.053

Table S378.  Gene #74: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
18Q LOSS MUTATED 104 76 58
18Q LOSS WILD-TYPE 144 81 114

Figure S378.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 0.00514 (Fisher's exact test), Q value = 0.014

Table S379.  Gene #74: '18q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
18Q LOSS MUTATED 54 33 6 6
18Q LOSS WILD-TYPE 27 36 16 5

Figure S379.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0263 (Fisher's exact test), Q value = 0.056

Table S380.  Gene #74: '18q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
18Q LOSS MUTATED 44 12 43
18Q LOSS WILD-TYPE 23 8 53

Figure S380.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_CNMF'

P value = 0.0232 (Fisher's exact test), Q value = 0.05

Table S381.  Gene #74: '18q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
18Q LOSS MUTATED 79 133 41
18Q LOSS WILD-TYPE 84 195 85

Figure S381.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'18q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00073 (Fisher's exact test), Q value = 0.0025

Table S382.  Gene #74: '18q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
18Q LOSS MUTATED 67 59 56 46 25
18Q LOSS WILD-TYPE 60 84 108 48 64

Figure S382.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.039 (Fisher's exact test), Q value = 0.079

Table S383.  Gene #74: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
18Q LOSS MUTATED 72 78 62
18Q LOSS WILD-TYPE 73 127 107

Figure S383.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'19p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S384.  Gene #75: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
19P LOSS MUTATED 85 79 13
19P LOSS WILD-TYPE 81 131 236

Figure S384.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S385.  Gene #75: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
19P LOSS MUTATED 55 83 29
19P LOSS WILD-TYPE 193 74 143

Figure S385.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S386.  Gene #75: '19p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
19P LOSS MUTATED 71 89 15
19P LOSS WILD-TYPE 92 239 111

Figure S386.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'19p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S387.  Gene #75: '19p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
19P LOSS MUTATED 71 39 23 34 8
19P LOSS WILD-TYPE 56 104 141 60 81

Figure S387.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S388.  Gene #75: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
19P LOSS MUTATED 68 54 29
19P LOSS WILD-TYPE 77 151 140

Figure S388.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'19p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00063 (Fisher's exact test), Q value = 0.0022

Table S389.  Gene #75: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
19P LOSS MUTATED 72 29 17 33
19P LOSS WILD-TYPE 126 101 82 59

Figure S389.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S390.  Gene #76: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
19Q LOSS MUTATED 66 58 12
19Q LOSS WILD-TYPE 100 152 237

Figure S390.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S391.  Gene #76: '19q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
19Q LOSS MUTATED 36 71 19
19Q LOSS WILD-TYPE 212 86 153

Figure S391.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00428 (Fisher's exact test), Q value = 0.012

Table S392.  Gene #76: '19q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
19Q LOSS MUTATED 18 0 31
19Q LOSS WILD-TYPE 49 20 65

Figure S392.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S393.  Gene #76: '19q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
19Q LOSS MUTATED 60 65 10
19Q LOSS WILD-TYPE 103 263 116

Figure S393.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'19q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S394.  Gene #76: '19q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
19Q LOSS MUTATED 53 31 13 31 7
19Q LOSS WILD-TYPE 74 112 151 63 82

Figure S394.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S395.  Gene #76: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
19Q LOSS MUTATED 54 41 19
19Q LOSS WILD-TYPE 91 164 150

Figure S395.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'19q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.00047

Table S396.  Gene #76: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
19Q LOSS MUTATED 53 19 11 31
19Q LOSS WILD-TYPE 145 111 88 61

Figure S396.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p loss' versus 'CN_CNMF'

P value = 0.0019 (Fisher's exact test), Q value = 0.0059

Table S397.  Gene #77: '20p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
20P LOSS MUTATED 11 23 7
20P LOSS WILD-TYPE 155 187 242

Figure S397.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #1: 'CN_CNMF'

'20q loss' versus 'MIRSEQ_CNMF'

P value = 0.00574 (Fisher's exact test), Q value = 0.015

Table S398.  Gene #78: '20q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
20Q LOSS MUTATED 6 1 1
20Q LOSS WILD-TYPE 157 327 125

Figure S398.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S399.  Gene #79: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
21Q LOSS MUTATED 96 131 62
21Q LOSS WILD-TYPE 70 79 187

Figure S399.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

'21q loss' versus 'MRNASEQ_CNMF'

P value = 0.0423 (Fisher's exact test), Q value = 0.085

Table S400.  Gene #79: '21q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
21Q LOSS MUTATED 55 37 12 3
21Q LOSS WILD-TYPE 26 32 10 8

Figure S400.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'21q loss' versus 'MIRSEQ_CNMF'

P value = 0.00299 (Fisher's exact test), Q value = 0.0087

Table S401.  Gene #79: '21q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
21Q LOSS MUTATED 88 155 43
21Q LOSS WILD-TYPE 75 173 83

Figure S401.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'21q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 9.8e-05

Table S402.  Gene #79: '21q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
21Q LOSS MUTATED 74 78 56 50 28
21Q LOSS WILD-TYPE 53 65 108 44 61

Figure S402.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.003 (Fisher's exact test), Q value = 0.0087

Table S403.  Gene #79: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
21Q LOSS MUTATED 85 95 67
21Q LOSS WILD-TYPE 60 110 102

Figure S403.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'21q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0258 (Fisher's exact test), Q value = 0.055

Table S404.  Gene #79: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
21Q LOSS MUTATED 106 54 38 49
21Q LOSS WILD-TYPE 92 76 61 43

Figure S404.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S405.  Gene #80: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
22Q LOSS MUTATED 92 97 29
22Q LOSS WILD-TYPE 74 113 220

Figure S405.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 0.00056 (Fisher's exact test), Q value = 0.002

Table S406.  Gene #80: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
22Q LOSS MUTATED 46 19 5 3
22Q LOSS WILD-TYPE 35 50 17 8

Figure S406.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00032

Table S407.  Gene #80: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
22Q LOSS MUTATED 39 9 25
22Q LOSS WILD-TYPE 28 11 71

Figure S407.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CNMF'

P value = 0.00282 (Fisher's exact test), Q value = 0.0083

Table S408.  Gene #80: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
22Q LOSS MUTATED 59 128 28
22Q LOSS WILD-TYPE 104 200 98

Figure S408.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S409.  Gene #80: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
22Q LOSS MUTATED 73 65 33 24 20
22Q LOSS WILD-TYPE 54 78 131 70 69

Figure S409.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.001

Table S410.  Gene #80: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
22Q LOSS MUTATED 94 40 29 23
22Q LOSS WILD-TYPE 104 90 70 69

Figure S410.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xp loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S411.  Gene #81: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
XP LOSS MUTATED 40 70 12
XP LOSS WILD-TYPE 126 140 237

Figure S411.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'

'xp loss' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00023

Table S412.  Gene #81: 'xp loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
XP LOSS MUTATED 53 45 16
XP LOSS WILD-TYPE 195 112 156

Figure S412.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xp loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0166 (Fisher's exact test), Q value = 0.038

Table S413.  Gene #81: 'xp loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 110 99
XP LOSS MUTATED 65 19 11
XP LOSS WILD-TYPE 208 91 88

Figure S413.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S414.  Gene #81: 'xp loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
XP LOSS MUTATED 50 63 8
XP LOSS WILD-TYPE 113 265 118

Figure S414.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'xp loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S415.  Gene #81: 'xp loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
XP LOSS MUTATED 30 35 17 31 8
XP LOSS WILD-TYPE 97 108 147 63 81

Figure S415.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0131 (Fisher's exact test), Q value = 0.031

Table S416.  Gene #81: 'xp loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
XP LOSS MUTATED 42 41 26
XP LOSS WILD-TYPE 103 164 143

Figure S416.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xp loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.00067

Table S417.  Gene #81: 'xp loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
XP LOSS MUTATED 49 17 12 31
XP LOSS WILD-TYPE 149 113 87 61

Figure S417.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S418.  Gene #82: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
XQ LOSS MUTATED 32 54 10
XQ LOSS WILD-TYPE 134 156 239

Figure S418.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 0.00656 (Fisher's exact test), Q value = 0.017

Table S419.  Gene #82: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
XQ LOSS MUTATED 43 30 14
XQ LOSS WILD-TYPE 205 127 158

Figure S419.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq loss' versus 'RPPA_CNMF'

P value = 0.0354 (Fisher's exact test), Q value = 0.073

Table S420.  Gene #82: 'xq loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 137 136 64
XQ LOSS MUTATED 33 17 15 9
XQ LOSS WILD-TYPE 112 120 121 55

Figure S420.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'xq loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0223 (Fisher's exact test), Q value = 0.049

Table S421.  Gene #82: 'xq loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 110 99
XQ LOSS MUTATED 52 14 8
XQ LOSS WILD-TYPE 221 96 91

Figure S421.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.0014

Table S422.  Gene #82: 'xq loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
XQ LOSS MUTATED 35 53 7
XQ LOSS WILD-TYPE 128 275 119

Figure S422.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'xq loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.0012

Table S423.  Gene #82: 'xq loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
XQ LOSS MUTATED 26 33 15 16 5
XQ LOSS WILD-TYPE 101 110 149 78 84

Figure S423.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.015 (Fisher's exact test), Q value = 0.035

Table S424.  Gene #82: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
XQ LOSS MUTATED 32 32 17
XQ LOSS WILD-TYPE 113 173 152

Figure S424.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xq loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00192 (Fisher's exact test), Q value = 0.0059

Table S425.  Gene #82: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
XQ LOSS MUTATED 44 14 7 16
XQ LOSS WILD-TYPE 154 116 92 76

Figure S425.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data
Input

  • Copy number data file = broad_values_by_arm.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/STES-TP/19785966/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/STES-TP/20144037/STES-TP.transferedmergedcluster.txt

  • Number of patients = 625

  • Number of significantly arm-level cnvs = 82

  • Number of molecular subtypes = 10

  • Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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