Correlation between copy number variations of arm-level result and molecular subtypes
Colon Adenocarcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1XD1128
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1XD1128
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 81 arm-level events and 12 molecular subtypes across 451 patients, 390 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 1p gain cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 1q gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.

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

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

  • 3p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • 3q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 4p gain cnv correlated to 'CN_CNMF'.

  • 4q gain cnv correlated to 'CN_CNMF'.

  • 5p gain cnv correlated to 'CN_CNMF'.

  • 5q gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • 6p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 6q gain cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF', and 'MIRSEQ_CNMF'.

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

  • 7q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 8p gain cnv correlated to 'CN_CNMF'.

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

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

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

  • 10p gain cnv correlated to 'CN_CNMF'.

  • 10q gain cnv correlated to 'CN_CNMF'.

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

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

  • 12p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

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

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

  • 14q gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 15q gain cnv correlated to 'RPPA_CNMF' and 'RPPA_CHIERARCHICAL'.

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

  • 16q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

  • 18p gain cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 18q gain cnv correlated to 'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 19p gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 19q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • 21q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 22q gain cnv correlated to 'CN_CNMF'.

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

  • xq gain cnv correlated to 'MRNA_CNMF',  'CN_CNMF', and 'RPPA_CNMF'.

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

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

  • 2p loss cnv correlated to 'CN_CNMF'.

  • 3p loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • 3q loss cnv correlated to 'CN_CNMF'.

  • 4p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 4q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

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

  • 6q loss cnv correlated to 'MIRSEQ_MATURE_CNMF'.

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

  • 8p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

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

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

  • 9q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

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

  • 10q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

  • 11q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 12p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 12q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 13q loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

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

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

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

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

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

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

  • 19p loss cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 19q loss cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

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

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

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

  • xp loss cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'RPPA_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 81 arm-level events and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 390 significant findings detected.

Clinical
Features 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
20q gain 321 (71%) 130 1e-05
(9.17e-05) 		1e-05
(9.17e-05) 		1e-05
(9.17e-05) 		1e-05
(9.17e-05) 		0.00821
(0.0293) 		3e-05
(0.000245) 		1e-05
(9.17e-05) 		1e-05
(9.17e-05) 		1e-05
(9.17e-05) 		1e-05
(9.17e-05) 		1e-05
(9.17e-05) 		0.0485
(0.122)
7p gain 246 (55%) 205 6e-05
(0.000449) 		1e-05
(9.17e-05) 		1e-05
(9.17e-05) 		2e-05
(0.000168) 		0.0297
(0.0858) 		0.0022
(0.0102) 		0.00011
(0.000742) 		1e-05
(9.17e-05) 		0.00028
(0.00165) 		2e-05
(0.000168) 		0.0582
(0.139) 		0.0369
(0.101)
7q gain 223 (49%) 228 0.00032
(0.00186) 		1e-05
(9.17e-05) 		1e-05
(9.17e-05) 		0.00058
(0.0032) 		0.0568
(0.137) 		0.00471
(0.0185) 		0.00541
(0.0209) 		1e-05
(9.17e-05) 		0.00538
(0.0208) 		0.00018
(0.00115) 		0.00145
(0.00701) 		0.0258
(0.0766)
18p loss 252 (56%) 199 1e-05
(9.17e-05) 		1e-05
(9.17e-05) 		1e-05
(9.17e-05) 		1e-05
(9.17e-05) 		0.31
(0.483) 		0.00384
(0.0158) 		1e-05
(9.17e-05) 		1e-05
(9.17e-05) 		1e-05
(9.17e-05) 		1e-05
(9.17e-05) 		0.00027
(0.00161) 		0.00109
(0.00546)
18q loss 268 (59%) 183 1e-05
(9.17e-05) 		1e-05
(9.17e-05) 		1e-05
(9.17e-05) 		1e-05
(9.17e-05) 		0.409
(0.583) 		0.0128
(0.0428) 		1e-05
(9.17e-05) 		1e-05
(9.17e-05) 		1e-05
(9.17e-05) 		1e-05
(9.17e-05) 		0.00019
(0.00121) 		0.013
(0.0436)
4p loss 139 (31%) 312 2e-05
(0.000168) 		0.00182
(0.00863) 		1e-05
(9.17e-05) 		0.00802
(0.0289) 		0.919
(0.983) 		0.0357
(0.0986) 		1e-05
(9.17e-05) 		1e-05
(9.17e-05) 		0.00015
(0.000999) 		0.0221
(0.0676) 		0.0139
(0.0457) 		0.0865
(0.187)
8p loss 138 (31%) 313 0.00244
(0.011) 		0.00441
(0.0178) 		1e-05
(9.17e-05) 		0.0182
(0.0576) 		0.575
(0.734) 		0.0149
(0.0484) 		0.00112
(0.00558) 		1e-05
(9.17e-05) 		0.00033
(0.00191) 		0.0446
(0.114) 		0.0103
(0.036) 		0.159
(0.302)
17p loss 236 (52%) 215 1e-05
(9.17e-05) 		1e-05
(9.17e-05) 		1e-05
(9.17e-05) 		1e-05
(9.17e-05) 		0.179
(0.325) 		0.00612
(0.0231) 		1e-05
(9.17e-05) 		1e-05
(9.17e-05) 		1e-05
(9.17e-05) 		1e-05
(9.17e-05) 		0.0035
(0.0147) 		0.053
(0.13)
16p gain 106 (24%) 345 1e-05
(9.17e-05) 		1e-05
(9.17e-05) 		1e-05
(9.17e-05) 		0.0488
(0.122) 		0.0393
(0.104) 		0.107
(0.221) 		0.0041
(0.0168) 		1e-05
(9.17e-05) 		0.0175
(0.0556) 		0.00094
(0.00483) 		0.0858
(0.186) 		0.31
(0.483)
16q gain 104 (23%) 347 1e-05
(9.17e-05) 		1e-05
(9.17e-05) 		1e-05
(9.17e-05) 		0.0349
(0.0969) 		0.0452
(0.115) 		0.112
(0.229) 		0.00279
(0.0124) 		1e-05
(9.17e-05) 		0.00964
(0.0339) 		0.00281
(0.0124) 		0.0572
(0.138) 		0.367
(0.54)
20p gain 244 (54%) 207 1e-05
(9.17e-05) 		1e-05
(9.17e-05) 		1e-05
(9.17e-05) 		0.00275
(0.0123) 		0.045
(0.115) 		0.435
(0.608) 		0.00026
(0.00158) 		1e-05
(9.17e-05) 		0.00077
(0.00409) 		1e-05
(9.17e-05) 		0.144
(0.281) 		0.377
(0.548)
14q loss 139 (31%) 312 1e-05
(9.17e-05) 		1e-05
(9.17e-05) 		1e-05
(9.17e-05) 		4e-05
(0.000311) 		0.0775
(0.172) 		0.0647
(0.149) 		1e-05
(9.17e-05) 		1e-05
(9.17e-05) 		1e-05
(9.17e-05) 		1e-05
(9.17e-05) 		0.00375
(0.0156) 		0.16
(0.302)
15q loss 158 (35%) 293 2e-05
(0.000168) 		0.00128
(0.00632) 		1e-05
(9.17e-05) 		0.00034
(0.00194) 		0.128
(0.255) 		0.321
(0.492) 		1e-05
(9.17e-05) 		1e-05
(9.17e-05) 		1e-05
(9.17e-05) 		0.00141
(0.00689) 		0.0422
(0.11) 		0.104
(0.218)
8q gain 227 (50%) 224 0.0223
(0.0676) 		0.0401
(0.106) 		1e-05
(9.17e-05) 		0.0381
(0.103) 		0.31
(0.483) 		0.103
(0.215) 		0.00089
(0.00465) 		0.00027
(0.00161) 		0.236
(0.396) 		0.00462
(0.0183) 		0.0119
(0.0408) 		0.0842
(0.184)
11p gain 54 (12%) 397 4e-05
(0.000311) 		0.00068
(0.00369) 		1e-05
(9.17e-05) 		0.00022
(0.00138) 		0.406
(0.582) 		0.137
(0.27) 		0.00278
(0.0124) 		2e-05
(0.000168) 		0.0363
(0.0997) 		0.00227
(0.0104) 		0.41
(0.584) 		0.6
(0.751)
13q gain 255 (57%) 196 1e-05
(9.17e-05) 		1e-05
(9.17e-05) 		1e-05
(9.17e-05) 		1e-05
(9.17e-05) 		0.357
(0.533) 		0.243
(0.404) 		1e-05
(9.17e-05) 		1e-05
(9.17e-05) 		1e-05
(9.17e-05) 		0.00031
(0.00182) 		0.0974
(0.205) 		0.333
(0.505)
19q gain 84 (19%) 367 0.0452
(0.115) 		0.0264
(0.0779) 		0.00588
(0.0223) 		0.878
(0.96) 		0.0126
(0.0427) 		0.107
(0.222) 		0.339
(0.513) 		0.00016
(0.00104) 		0.00381
(0.0158) 		0.156
(0.296) 		0.0194
(0.061) 		0.00472
(0.0185)
4q loss 127 (28%) 324 0.00014
(0.000938) 		0.00699
(0.0257) 		1e-05
(9.17e-05) 		0.027
(0.0792) 		0.673
(0.816) 		0.368
(0.54) 		1e-05
(9.17e-05) 		1e-05
(9.17e-05) 		0.00028
(0.00165) 		0.0351
(0.0972) 		0.0754
(0.169) 		0.723
(0.849)
9q loss 54 (12%) 397 0.002
(0.00935) 		0.0487
(0.122) 		1e-05
(9.17e-05) 		0.00325
(0.014) 		0.818
(0.918) 		0.19
(0.341) 		7e-05
(5e-04) 		0.00097
(0.00494) 		0.00699
(0.0257) 		0.239
(0.4) 		0.041
(0.108) 		0.307
(0.482)
22q loss 146 (32%) 305 0.00011
(0.000742) 		4e-05
(0.000311) 		1e-05
(9.17e-05) 		0.166
(0.309) 		0.207
(0.363) 		0.0064
(0.0239) 		7e-05
(5e-04) 		1e-05
(9.17e-05) 		0.00023
(0.00142) 		0.00416
(0.0169) 		0.405
(0.582) 		0.885
(0.961)
2p gain 82 (18%) 369 0.00636
(0.0239) 		0.0375
(0.101) 		1e-05
(9.17e-05) 		0.0153
(0.0494) 		0.32
(0.492) 		0.74
(0.861) 		3e-05
(0.000245) 		0.0033
(0.0142) 		0.0948
(0.2) 		7e-05
(5e-04) 		0.926
(0.983) 		0.847
(0.943)
2q gain 79 (18%) 372 0.0138
(0.0454) 		0.0392
(0.104) 		1e-05
(9.17e-05) 		0.0372
(0.101) 		0.323
(0.495) 		0.806
(0.911) 		0.00011
(0.000742) 		0.00066
(0.0036) 		0.194
(0.346) 		0.00074
(0.00395) 		0.804
(0.909) 		0.31
(0.483)
11q gain 51 (11%) 400 2e-05
(0.000168) 		1e-05
(9.17e-05) 		1e-05
(9.17e-05) 		0.00332
(0.0142) 		0.383
(0.555) 		0.0761
(0.169) 		0.00026
(0.00158) 		1e-05
(9.17e-05) 		0.0621
(0.146) 		0.00289
(0.0127) 		0.236
(0.396) 		0.245
(0.406)
17q gain 84 (19%) 367 0.085
(0.185) 		0.0331
(0.0932) 		1e-05
(9.17e-05) 		0.00191
(0.00901) 		0.592
(0.743) 		0.148
(0.286) 		1e-05
(9.17e-05) 		7e-05
(5e-04) 		0.0478
(0.121) 		0.0234
(0.0703) 		0.24
(0.4) 		0.438
(0.61)
1p loss 92 (20%) 359 0.0289
(0.0835) 		0.166
(0.309) 		1e-05
(9.17e-05) 		0.00701
(0.0257) 		0.851
(0.944) 		0.0672
(0.154) 		3e-05
(0.000245) 		6e-05
(0.000449) 		0.00157
(0.00752) 		0.00302
(0.0132) 		0.115
(0.233) 		0.574
(0.734)
9p loss 54 (12%) 397 0.0313
(0.0893) 		0.012
(0.0409) 		1e-05
(9.17e-05) 		0.0131
(0.0436) 		1
(1.00) 		0.218
(0.376) 		7e-05
(5e-04) 		0.00044
(0.00249) 		0.00461
(0.0183) 		0.209
(0.364) 		0.184
(0.333) 		0.341
(0.515)
12p loss 48 (11%) 403 0.00062
(0.0034) 		0.0156
(0.0502) 		1e-05
(9.17e-05) 		0.00379
(0.0157) 		0.332
(0.505) 		0.895
(0.967) 		0.00333
(0.0142) 		4e-05
(0.000311) 		0.015
(0.0486) 		0.643
(0.794) 		0.175
(0.32) 		0.414
(0.588)
12q loss 50 (11%) 401 0.00074
(0.00395) 		0.0212
(0.0653) 		1e-05
(9.17e-05) 		0.0142
(0.0462) 		0.418
(0.593) 		0.734
(0.857) 		0.00105
(0.00532) 		0.00011
(0.000742) 		0.00443
(0.0178) 		0.347
(0.52) 		0.577
(0.734) 		0.413
(0.588)
5q loss 80 (18%) 371 0.0173
(0.055) 		0.203
(0.358) 		1e-05
(9.17e-05) 		0.028
(0.0814) 		0.833
(0.931) 		0.538
(0.707) 		0.00016
(0.00104) 		0.00022
(0.00138) 		0.00414
(0.0169) 		0.11
(0.227) 		0.292
(0.465) 		0.688
(0.831)
10p loss 68 (15%) 383 0.00086
(0.00452) 		0.0522
(0.128) 		1e-05
(9.17e-05) 		0.00179
(0.00853) 		0.711
(0.847) 		0.442
(0.612) 		0.00016
(0.00104) 		0.0001
(0.000699) 		0.268
(0.435) 		0.171
(0.316) 		0.225
(0.386) 		0.0275
(0.0804)
10q loss 73 (16%) 378 0.00039
(0.00222) 		0.022
(0.0675) 		1e-05
(9.17e-05) 		0.00197
(0.00925) 		0.419
(0.593) 		0.201
(0.355) 		7e-05
(5e-04) 		2e-05
(0.000168) 		0.0514
(0.127) 		0.264
(0.431) 		0.223
(0.383) 		0.109
(0.224)
21q loss 124 (27%) 327 4e-05
(0.000311) 		0.0219
(0.0675) 		1e-05
(9.17e-05) 		0.0713
(0.162) 		0.976
(1.00) 		0.341
(0.515) 		2e-05
(0.000168) 		0.0084
(0.0299) 		0.0477
(0.121) 		0.0749
(0.169) 		0.295
(0.47) 		0.815
(0.918)
3p gain 47 (10%) 404 0.0307
(0.0879) 		0.0383
(0.103) 		2e-05
(0.000168) 		0.0326
(0.0924) 		0.262
(0.429) 		0.0623
(0.146) 		0.754
(0.872) 		0.289
(0.462) 		0.106
(0.221) 		0.274
(0.442) 		0.0228
(0.0687) 		0.415
(0.588)
3q gain 64 (14%) 387 0.00255
(0.0115) 		0.00126
(0.00625) 		1e-05
(9.17e-05) 		0.0643
(0.149) 		0.562
(0.723) 		0.327
(0.499) 		0.547
(0.714) 		0.0326
(0.0924) 		0.0675
(0.154) 		0.303
(0.477) 		0.00437
(0.0177) 		0.287
(0.46)
6p gain 84 (19%) 367 0.0329
(0.0928) 		0.00018
(0.00115) 		1e-05
(9.17e-05) 		0.19
(0.341) 		0.149
(0.288) 		0.466
(0.634) 		0.226
(0.386) 		0.00909
(0.0321) 		0.00456
(0.0182) 		0.0806
(0.177) 		0.228
(0.388) 		0.258
(0.425)
19p gain 73 (16%) 378 0.0674
(0.154) 		0.0891
(0.191) 		6e-05
(0.000449) 		0.389
(0.564) 		0.107
(0.222) 		0.154
(0.296) 		0.276
(0.445) 		0.00011
(0.000742) 		4e-05
(0.000311) 		0.0335
(0.0937) 		0.217
(0.375) 		0.00797
(0.0288)
11q loss 63 (14%) 388 0.00522
(0.0203) 		0.00055
(0.00305) 		8e-05
(0.000568) 		0.124
(0.25) 		0.528
(0.697) 		0.889
(0.964) 		0.358
(0.534) 		0.00201
(0.00935) 		0.00023
(0.00142) 		0.204
(0.359) 		0.16
(0.302) 		0.905
(0.976)
19p loss 40 (9%) 411 0.00349
(0.0147) 		0.57
(0.731) 		0.0072
(0.0262) 		0.717
(0.847) 		0.35
(0.524) 		0.669
(0.812) 		0.00649
(0.0241) 		0.0222
(0.0676) 		0.929
(0.985) 		0.0171
(0.0544) 		0.465
(0.633) 		0.195
(0.346)
19q loss 33 (7%) 418 0.00471
(0.0185) 		0.625
(0.775) 		0.00109
(0.00546) 		0.639
(0.791) 		0.261
(0.428) 		0.138
(0.271) 		0.0135
(0.0447) 		0.0081
(0.0291) 		0.977
(1.00) 		0.207
(0.363) 		0.0417
(0.109) 		0.0639
(0.149)
xp loss 64 (14%) 387 0.303
(0.477) 		0.0441
(0.113) 		0.00045
(0.00253) 		0.363
(0.538) 		0.0206
(0.0641) 		0.269
(0.437) 		0.645
(0.796) 		0.533
(0.703) 		0.15
(0.29) 		0.005
(0.0195) 		0.374
(0.546) 		0.0122
(0.0413)
xq loss 51 (11%) 400 0.131
(0.26) 		0.056
(0.136) 		0.00025
(0.00154) 		0.0925
(0.196) 		0.0871
(0.187) 		0.0196
(0.0613) 		0.309
(0.483) 		0.344
(0.518) 		0.00342
(0.0145) 		0.00708
(0.0259) 		0.24
(0.4) 		0.00145
(0.00701)
1p gain 40 (9%) 411 0.135
(0.265) 		0.264
(0.431) 		0.0085
(0.0302) 		0.0781
(0.173) 		0.0489
(0.122) 		0.547
(0.714) 		0.615
(0.766) 		0.0303
(0.087) 		0.333
(0.505) 		0.0365
(0.0997) 		0.216
(0.375) 		0.229
(0.389)
18p gain 23 (5%) 428 0.165
(0.309) 		0.579
(0.734) 		0.053
(0.13) 		0.028
(0.0814) 		0.467
(0.634) 		0.855
(0.946) 		0.039
(0.104) 		6e-05
(0.000449) 		0.0663
(0.152) 		0.0135
(0.0447) 		0.462
(0.631) 		0.773
(0.885)
xp gain 68 (15%) 383 0.00228
(0.0104) 		0.274
(0.442) 		0.00096
(0.00491) 		0.0755
(0.169) 		0.00345
(0.0146) 		0.114
(0.233) 		0.443
(0.612) 		0.0361
(0.0995) 		0.884
(0.961) 		0.912
(0.98) 		0.691
(0.833) 		0.0621
(0.146)
1q loss 54 (12%) 397 0.88
(0.961) 		0.608
(0.76) 		1e-05
(9.17e-05) 		0.15
(0.288) 		0.91
(0.98) 		0.35
(0.524) 		0.00309
(0.0134) 		0.0102
(0.0357) 		0.0752
(0.169) 		0.0162
(0.0518) 		0.0514
(0.127) 		0.125
(0.251)
5p loss 60 (13%) 391 0.562
(0.723) 		0.655
(0.804) 		1e-05
(9.17e-05) 		0.0024
(0.0109) 		0.891
(0.964) 		0.796
(0.904) 		0.0898
(0.191) 		0.00054
(0.00302) 		0.0434
(0.113) 		0.505
(0.676) 		0.464
(0.633) 		0.724
(0.849)
11p loss 51 (11%) 400 0.0862
(0.187) 		0.0271
(0.0793) 		0.00645
(0.024) 		0.501
(0.671) 		0.753
(0.872) 		0.953
(1.00) 		0.133
(0.264) 		0.0436
(0.113) 		0.00093
(0.00481) 		0.133
(0.264) 		0.436
(0.608) 		0.96
(1.00)
20p loss 43 (10%) 408 0.36
(0.536) 		0.0103
(0.036) 		1e-05
(9.17e-05) 		0.0123
(0.0417) 		0.519
(0.688) 		0.318
(0.49) 		0.0892
(0.191) 		0.0206
(0.0641) 		0.111
(0.228) 		0.439
(0.611) 		0.499
(0.671) 		0.174
(0.32)
6q gain 76 (17%) 375 0.0978
(0.206) 		0.00027
(0.00161) 		1e-05
(9.17e-05) 		0.223
(0.383) 		0.421
(0.595) 		0.0643
(0.149) 		0.598
(0.75) 		0.103
(0.215) 		0.00785
(0.0285) 		0.197
(0.349) 		0.527
(0.697) 		0.319
(0.49)
18q gain 14 (3%) 437 0.194
(0.346) 		0.796
(0.904) 		0.0645
(0.149) 		0.177
(0.323) 		0.423
(0.597) 		0.871
(0.958) 		0.0114
(0.0392) 		5e-05
(0.000386) 		0.269
(0.436) 		0.0193
(0.0606) 		0.433
(0.608) 		0.853
(0.945)
xq gain 79 (18%) 372 0.0109
(0.0377) 		0.238
(0.399) 		0.00093
(0.00481) 		0.156
(0.298) 		0.00141
(0.00689) 		0.257
(0.424) 		0.935
(0.989) 		0.374
(0.546) 		0.997
(1.00) 		0.714
(0.847) 		0.757
(0.875) 		0.312
(0.483)
3p loss 54 (12%) 397 0.208
(0.364) 		0.572
(0.732) 		0.00017
(0.0011) 		0.465
(0.633) 		0.217
(0.376) 		0.993
(1.00) 		0.0393
(0.104) 		0.0604
(0.143) 		0.719
(0.848) 		0.661
(0.807) 		0.0303
(0.087) 		0.71
(0.847)
8q loss 26 (6%) 425 0.346
(0.519) 		0.364
(0.538) 		0.0001
(0.000699) 		0.587
(0.74) 		0.589
(0.74) 		0.277
(0.446) 		0.734
(0.857) 		0.624
(0.775) 		0.473
(0.64) 		0.587
(0.74) 		0.00289
(0.0127) 		0.00601
(0.0227)
17q loss 64 (14%) 387 0.0347
(0.0966) 		0.227
(0.388) 		1e-05
(9.17e-05) 		0.914
(0.981) 		0.896
(0.967) 		0.312
(0.483) 		0.577
(0.734) 		0.137
(0.269) 		0.0127
(0.0427) 		0.236
(0.396) 		0.169
(0.313) 		0.163
(0.306)
1q gain 81 (18%) 370 0.0588
(0.141) 		0.403
(0.58) 		0.00082
(0.00433) 		0.0604
(0.143) 		0.0788
(0.174) 		0.555
(0.721) 		0.428
(0.603) 		0.172
(0.316) 		0.0578
(0.139) 		0.111
(0.228) 		0.00561
(0.0216) 		0.658
(0.807)
5q gain 42 (9%) 409 0.477
(0.645) 		0.767
(0.882) 		0.00034
(0.00194) 		0.715
(0.847) 		0.543
(0.711) 		0.794
(0.904) 		0.3
(0.474) 		0.123
(0.249) 		0.0759
(0.169) 		0.0403
(0.106) 		0.682
(0.825) 		0.883
(0.961)
9p gain 81 (18%) 370 0.034
(0.0949) 		0.0642
(0.149) 		0.0138
(0.0454) 		0.768
(0.882) 		0.0797
(0.175) 		0.661
(0.807) 		0.925
(0.983) 		0.648
(0.799) 		0.177
(0.322) 		0.981
(1.00) 		0.26
(0.426) 		0.44
(0.611)
9q gain 71 (16%) 380 0.0223
(0.0676) 		0.0902
(0.192) 		0.0418
(0.109) 		0.615
(0.766) 		0.0551
(0.134) 		0.612
(0.764) 		0.876
(0.96) 		0.927
(0.984) 		0.145
(0.282) 		0.859
(0.949) 		0.814
(0.918) 		0.772
(0.885)
12p gain 93 (21%) 358 0.0613
(0.145) 		0.875
(0.96) 		0.0268
(0.0789) 		0.0421
(0.11) 		0.693
(0.835) 		0.436
(0.608) 		0.79
(0.901) 		0.434
(0.608) 		0.127
(0.255) 		0.751
(0.871) 		0.585
(0.74) 		0.989
(1.00)
12q gain 88 (20%) 363 0.0729
(0.165) 		0.558
(0.723) 		0.0241
(0.0721) 		0.0119
(0.0408) 		0.584
(0.739) 		0.379
(0.551) 		0.556
(0.721) 		0.374
(0.546) 		0.175
(0.32) 		0.664
(0.808) 		0.742
(0.863) 		0.832
(0.931)
14q gain 35 (8%) 416 0.155
(0.296) 		0.699
(0.838) 		0.00151
(0.00727) 		0.407
(0.582) 		0.859
(0.949) 		0.664
(0.808) 		0.566
(0.727) 		0.577
(0.734) 		0.332
(0.505) 		0.399
(0.576) 		0.141
(0.275) 		0.0335
(0.0937)
15q gain 11 (2%) 440 0.723
(0.849) 		0.796
(0.904) 		0.172
(0.316) 		1
(1.00) 		0.0387
(0.104) 		0.0144
(0.0468) 		0.818
(0.918) 		0.848
(0.943) 		0.724
(0.849) 		0.889
(0.964)
21q gain 24 (5%) 427 0.245
(0.406) 		0.117
(0.237) 		0.0441
(0.113) 		0.0441
(0.113) 		0.344
(0.518) 		0.567
(0.729) 		0.447
(0.615) 		0.0931
(0.197) 		0.271
(0.438) 		0.868
(0.955)
7q loss 4 (1%) 447 0.0375
(0.101) 		0.0211
(0.0653) 		0.846
(0.943) 		0.726
(0.85) 		0.369
(0.542) 		1
(1.00)
13q loss 12 (3%) 439 0.518
(0.688) 		0.449
(0.616) 		0.0109
(0.0377) 		0.0261
(0.0774) 		0.231
(0.393) 		0.0543
(0.133) 		0.54
(0.708) 		0.933
(0.988) 		0.212
(0.369) 		0.923
(0.983) 		0.142
(0.277) 		0.209
(0.364)
4p gain 12 (3%) 439 0.00574
(0.022) 		0.134
(0.265) 		0.0599
(0.143) 		0.441
(0.612) 		0.161
(0.303) 		0.653
(0.803) 		0.56
(0.723) 		0.266
(0.434)
4q gain 17 (4%) 434 0.297
(0.472) 		0.167
(0.311) 		0.00579
(0.0221) 		0.538
(0.707) 		0.365
(0.539) 		0.433
(0.608) 		0.39
(0.564) 		0.362
(0.537) 		0.662
(0.807) 		0.0626
(0.147)
5p gain 70 (16%) 381 0.0566
(0.137) 		0.105
(0.22) 		2e-05
(0.000168) 		0.763
(0.879) 		0.183
(0.331) 		0.816
(0.918) 		0.312
(0.483) 		0.0807
(0.177) 		0.249
(0.411) 		0.848
(0.943) 		0.172
(0.316) 		0.667
(0.811)
8p gain 134 (30%) 317 0.298
(0.472) 		0.937
(0.99) 		1e-05
(9.17e-05) 		0.963
(1.00) 		0.444
(0.612) 		0.715
(0.847) 		0.0735
(0.166) 		0.0876
(0.188) 		0.518
(0.688) 		0.233
(0.393) 		0.451
(0.617) 		0.2
(0.354)
10p gain 38 (8%) 413 0.408
(0.583) 		0.0519
(0.128) 		0.0228
(0.0687) 		0.544
(0.712) 		1
(1.00) 		0.595
(0.746) 		0.66
(0.807) 		0.397
(0.573) 		0.133
(0.264) 		0.982
(1.00) 		0.0744
(0.168) 		0.851
(0.944)
10q gain 23 (5%) 428 0.292
(0.465) 		0.376
(0.547) 		0.00221
(0.0102) 		0.0759
(0.169) 		0.191
(0.343) 		0.884
(0.961) 		0.621
(0.772) 		0.579
(0.734) 		0.451
(0.617) 		0.838
(0.936) 		0.153
(0.294) 		0.878
(0.96)
22q gain 12 (3%) 439 0.919
(0.983) 		1
(1.00) 		0.0364
(0.0997) 		0.223
(0.383) 		0.315
(0.486) 		0.588
(0.74) 		0.159
(0.302) 		0.235
(0.396) 		0.72
(0.848) 		0.763
(0.879) 		0.764
(0.879) 		1
(1.00)
2p loss 6 (1%) 445 0.479
(0.646) 		0.694
(0.835) 		0.049
(0.122) 		1
(1.00) 		1
(1.00) 		0.142
(0.276) 		0.124
(0.249) 		0.195
(0.346) 		0.632
(0.782)
3q loss 35 (8%) 416 0.534
(0.703) 		0.917
(0.982) 		0.00069
(0.00373) 		0.702
(0.84) 		0.552
(0.718) 		0.908
(0.979) 		0.0508
(0.126) 		0.187
(0.337) 		0.406
(0.582) 		0.8
(0.906) 		0.361
(0.536) 		0.472
(0.64)
6q loss 46 (10%) 405 0.881
(0.961) 		0.654
(0.804) 		0.164
(0.308) 		0.365
(0.539) 		0.33
(0.504) 		0.521
(0.69) 		0.435
(0.608) 		0.716
(0.847) 		0.862
(0.951) 		0.713
(0.847) 		0.0254
(0.0756) 		0.11
(0.226)
17p gain 29 (6%) 422 0.0669
(0.153) 		0.732
(0.857) 		0.797
(0.904) 		0.924
(0.983) 		0.578
(0.734) 		0.923
(0.983) 		0.285
(0.457) 		0.114
(0.232) 		0.298
(0.472) 		0.736
(0.858) 		0.0869
(0.187) 		0.124
(0.249)
2q loss 7 (2%) 444 0.717
(0.847) 		0.444
(0.612) 		0.155
(0.296) 		0.559
(0.723) 		0.772
(0.885) 		0.373
(0.546) 		0.0634
(0.148) 		0.172
(0.316) 		0.31
(0.483)
6p loss 34 (8%) 417 0.511
(0.681) 		0.313
(0.484) 		0.193
(0.346) 		0.512
(0.681) 		0.446
(0.614) 		0.818
(0.918) 		0.481
(0.648) 		0.967
(1.00) 		0.557
(0.722) 		0.697
(0.838) 		0.081
(0.177) 		0.185
(0.334)
16p loss 31 (7%) 420 1
(1.00) 		0.786
(0.897) 		0.233
(0.393) 		0.716
(0.847) 		0.745
(0.865) 		0.478
(0.646) 		0.237
(0.398) 		0.193
(0.346) 		0.868
(0.955) 		0.827
(0.927) 		0.509
(0.68) 		0.975
(1.00)
16q loss 29 (6%) 422 1
(1.00) 		0.785
(0.897) 		0.168
(0.312) 		0.923
(0.983) 		0.916
(0.982) 		0.491
(0.66) 		0.22
(0.379) 		0.302
(0.476) 		0.702
(0.84) 		0.984
(1.00) 		0.51
(0.68) 		0.974
(1.00)
20q loss 4 (1%) 447 1
(1.00) 		0.0554
(0.135) 		0.699
(0.838) 		0.258
(0.425) 		0.551
(0.717) 		0.873
(0.958) 		0.681
(0.824)
'1p gain' versus 'CN_CNMF'

P value = 0.0085 (Fisher's exact test), Q value = 0.03

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
1P GAIN MUTATED 9 23 8
1P GAIN WILD-TYPE 44 198 169

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

'1p gain' versus 'RPPA_CNMF'

P value = 0.0489 (Fisher's exact test), Q value = 0.12

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 145 125
1P GAIN MUTATED 10 16 5
1P GAIN WILD-TYPE 75 129 120

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

'1p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0303 (Fisher's exact test), Q value = 0.087

Table S3.  Gene #1: '1p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
1P GAIN MUTATED 6 15 3 15 1
1P GAIN WILD-TYPE 73 93 93 114 36

Figure S3.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0365 (Fisher's exact test), Q value = 0.1

Table S4.  Gene #1: '1p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 79 55 46 17 55 20 26 42 58
1P GAIN MUTATED 8 4 1 0 1 3 4 4 10
1P GAIN WILD-TYPE 71 51 45 17 54 17 22 38 48

Figure S4.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1q gain' versus 'CN_CNMF'

P value = 0.00082 (Fisher's exact test), Q value = 0.0043

Table S5.  Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
1Q GAIN MUTATED 17 45 19
1Q GAIN WILD-TYPE 36 176 158

Figure S5.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

'1q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00561 (Fisher's exact test), Q value = 0.022

Table S6.  Gene #2: '1q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 20 16 11 11 9
1Q GAIN MUTATED 2 4 1 6 0 0
1Q GAIN WILD-TYPE 16 16 15 5 11 9

Figure S6.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'2p gain' versus 'MRNA_CNMF'

P value = 0.00636 (Fisher's exact test), Q value = 0.024

Table S7.  Gene #3: '2p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
2P GAIN MUTATED 1 5 7 1 7
2P GAIN WILD-TYPE 30 12 42 26 16

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

'2p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0375 (Fisher's exact test), Q value = 0.1

Table S8.  Gene #3: '2p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
2P GAIN MUTATED 2 10 9
2P GAIN WILD-TYPE 40 58 28

Figure S8.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'2p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S9.  Gene #3: '2p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
2P GAIN MUTATED 16 53 13
2P GAIN WILD-TYPE 37 168 164

Figure S9.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #3: 'CN_CNMF'

'2p gain' versus 'METHLYATION_CNMF'

P value = 0.0153 (Fisher's exact test), Q value = 0.049

Table S10.  Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
2P GAIN MUTATED 16 30 14
2P GAIN WILD-TYPE 69 73 92

Figure S10.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2p gain' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00025

Table S11.  Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
2P GAIN MUTATED 41 8 17 16
2P GAIN WILD-TYPE 86 86 80 115

Figure S11.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0033 (Fisher's exact test), Q value = 0.014

Table S12.  Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
2P GAIN MUTATED 16 30 12 23 1
2P GAIN WILD-TYPE 63 78 84 106 36

Figure S12.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 5e-04

Table S13.  Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 79 55 46 17 55 20 26 42 58
2P GAIN MUTATED 12 11 17 2 13 0 5 0 9
2P GAIN WILD-TYPE 67 44 29 15 42 20 21 42 49

Figure S13.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2q gain' versus 'MRNA_CNMF'

P value = 0.0138 (Fisher's exact test), Q value = 0.045

Table S14.  Gene #4: '2q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
2Q GAIN MUTATED 1 5 6 2 7
2Q GAIN WILD-TYPE 30 12 43 25 16

Figure S14.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'2q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0392 (Fisher's exact test), Q value = 0.1

Table S15.  Gene #4: '2q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
2Q GAIN MUTATED 2 10 9
2Q GAIN WILD-TYPE 40 58 28

Figure S15.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'2q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S16.  Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
2Q GAIN MUTATED 17 51 11
2Q GAIN WILD-TYPE 36 170 166

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

'2q gain' versus 'METHLYATION_CNMF'

P value = 0.0372 (Fisher's exact test), Q value = 0.1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
2Q GAIN MUTATED 15 28 14
2Q GAIN WILD-TYPE 70 75 92

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

'2q gain' versus 'MRNASEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00074

Table S18.  Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
2Q GAIN MUTATED 39 9 15 16
2Q GAIN WILD-TYPE 88 85 82 115

Figure S18.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00066 (Fisher's exact test), Q value = 0.0036

Table S19.  Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
2Q GAIN MUTATED 16 30 9 23 1
2Q GAIN WILD-TYPE 63 78 87 106 36

Figure S19.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00074 (Fisher's exact test), Q value = 0.004

Table S20.  Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 79 55 46 17 55 20 26 42 58
2Q GAIN MUTATED 13 10 14 2 14 0 4 0 9
2Q GAIN WILD-TYPE 66 45 32 15 41 20 22 42 49

Figure S20.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3p gain' versus 'MRNA_CNMF'

P value = 0.0307 (Fisher's exact test), Q value = 0.088

Table S21.  Gene #5: '3p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
3P GAIN MUTATED 1 3 6 0 5
3P GAIN WILD-TYPE 30 14 43 27 18

Figure S21.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'3p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0383 (Fisher's exact test), Q value = 0.1

Table S22.  Gene #5: '3p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
3P GAIN MUTATED 2 5 8
3P GAIN WILD-TYPE 40 63 29

Figure S22.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'3p gain' versus 'CN_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
3P GAIN MUTATED 7 35 5
3P GAIN WILD-TYPE 46 186 172

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

'3p gain' versus 'METHLYATION_CNMF'

P value = 0.0326 (Fisher's exact test), Q value = 0.092

Table S24.  Gene #5: '3p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
3P GAIN MUTATED 4 17 11
3P GAIN WILD-TYPE 81 86 95

Figure S24.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0228 (Fisher's exact test), Q value = 0.069

Table S25.  Gene #5: '3p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 20 16 11 11 9
3P GAIN MUTATED 4 2 0 2 0 4
3P GAIN WILD-TYPE 14 18 16 9 11 5

Figure S25.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'3q gain' versus 'MRNA_CNMF'

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

Table S26.  Gene #6: '3q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
3Q GAIN MUTATED 1 4 8 0 7
3Q GAIN WILD-TYPE 30 13 41 27 16

Figure S26.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'3q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00126 (Fisher's exact test), Q value = 0.0062

Table S27.  Gene #6: '3q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
3Q GAIN MUTATED 2 6 12
3Q GAIN WILD-TYPE 40 62 25

Figure S27.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'3q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
3Q GAIN MUTATED 8 50 6
3Q GAIN WILD-TYPE 45 171 171

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

'3q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0326 (Fisher's exact test), Q value = 0.092

Table S29.  Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
3Q GAIN MUTATED 15 19 8 21 1
3Q GAIN WILD-TYPE 64 89 88 108 36

Figure S29.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00437 (Fisher's exact test), Q value = 0.018

Table S30.  Gene #6: '3q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 20 16 11 11 9
3Q GAIN MUTATED 5 3 0 3 0 5
3Q GAIN WILD-TYPE 13 17 16 8 11 4

Figure S30.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4p gain' versus 'CN_CNMF'

P value = 0.00574 (Fisher's exact test), Q value = 0.022

Table S31.  Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
4P GAIN MUTATED 2 10 0
4P GAIN WILD-TYPE 51 211 177

Figure S31.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

'4q gain' versus 'CN_CNMF'

P value = 0.00579 (Fisher's exact test), Q value = 0.022

Table S32.  Gene #8: '4q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
4Q GAIN MUTATED 3 13 1
4Q GAIN WILD-TYPE 50 208 176

Figure S32.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #3: 'CN_CNMF'

'5p gain' versus 'CN_CNMF'

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

Table S33.  Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
5P GAIN MUTATED 17 41 12
5P GAIN WILD-TYPE 36 180 165

Figure S33.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

'5q gain' versus 'CN_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.0019

Table S34.  Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
5Q GAIN MUTATED 10 26 6
5Q GAIN WILD-TYPE 43 195 171

Figure S34.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'

'5q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0403 (Fisher's exact test), Q value = 0.11

Table S35.  Gene #10: '5q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 79 55 46 17 55 20 26 42 58
5Q GAIN MUTATED 7 6 2 1 0 2 5 4 9
5Q GAIN WILD-TYPE 72 49 44 16 55 18 21 38 49

Figure S35.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6p gain' versus 'MRNA_CNMF'

P value = 0.0329 (Fisher's exact test), Q value = 0.093

Table S36.  Gene #11: '6p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
6P GAIN MUTATED 4 5 10 1 8
6P GAIN WILD-TYPE 27 12 39 26 15

Figure S36.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'6p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.0012

Table S37.  Gene #11: '6p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
6P GAIN MUTATED 4 8 16
6P GAIN WILD-TYPE 38 60 21

Figure S37.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S38.  Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
6P GAIN MUTATED 15 58 11
6P GAIN WILD-TYPE 38 163 166

Figure S38.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

'6p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00909 (Fisher's exact test), Q value = 0.032

Table S39.  Gene #11: '6p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
6P GAIN MUTATED 20 21 9 31 3
6P GAIN WILD-TYPE 59 87 87 98 34

Figure S39.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_CNMF'

P value = 0.00456 (Fisher's exact test), Q value = 0.018

Table S40.  Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
6P GAIN MUTATED 17 13 11 22 11
6P GAIN WILD-TYPE 43 75 60 53 93

Figure S40.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 0.0016

Table S41.  Gene #12: '6q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
6Q GAIN MUTATED 4 5 14
6Q GAIN WILD-TYPE 38 63 23

Figure S41.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S42.  Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
6Q GAIN MUTATED 9 55 12
6Q GAIN WILD-TYPE 44 166 165

Figure S42.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

'6q gain' versus 'MIRSEQ_CNMF'

P value = 0.00785 (Fisher's exact test), Q value = 0.028

Table S43.  Gene #12: '6q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
6Q GAIN MUTATED 16 12 10 20 10
6Q GAIN WILD-TYPE 44 76 61 55 94

Figure S43.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7p gain' versus 'MRNA_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00045

Table S44.  Gene #13: '7p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
7P GAIN MUTATED 4 11 31 10 13
7P GAIN WILD-TYPE 27 6 18 17 10

Figure S44.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'7p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S45.  Gene #13: '7p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
7P GAIN MUTATED 9 33 27
7P GAIN WILD-TYPE 33 35 10

Figure S45.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S46.  Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
7P GAIN MUTATED 40 157 49
7P GAIN WILD-TYPE 13 64 128

Figure S46.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

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

Table S47.  Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
7P GAIN MUTATED 45 79 48
7P GAIN WILD-TYPE 40 24 58

Figure S47.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p gain' versus 'RPPA_CNMF'

P value = 0.0297 (Fisher's exact test), Q value = 0.086

Table S48.  Gene #13: '7p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 145 125
7P GAIN MUTATED 55 74 58
7P GAIN WILD-TYPE 30 71 67

Figure S48.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'7p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0022 (Fisher's exact test), Q value = 0.01

Table S49.  Gene #13: '7p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 51 33 35 39 43 86 22 20 26
7P GAIN MUTATED 37 11 20 16 27 38 9 11 18
7P GAIN WILD-TYPE 14 22 15 23 16 48 13 9 8

Figure S49.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00074

Table S50.  Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
7P GAIN MUTATED 89 38 52 66
7P GAIN WILD-TYPE 38 56 45 65

Figure S50.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S51.  Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
7P GAIN MUTATED 58 71 33 75 8
7P GAIN WILD-TYPE 21 37 63 54 29

Figure S51.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.0016

Table S52.  Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
7P GAIN MUTATED 43 37 45 48 47
7P GAIN WILD-TYPE 17 51 26 27 57

Figure S52.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7p gain' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S53.  Gene #13: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 79 55 46 17 55 20 26 42 58
7P GAIN MUTATED 51 30 24 3 38 11 15 10 38
7P GAIN WILD-TYPE 28 25 22 14 17 9 11 32 20

Figure S53.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0369 (Fisher's exact test), Q value = 0.1

Table S54.  Gene #13: '7p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 12 9 8 12 9 7 13 9 6
7P GAIN MUTATED 12 4 7 7 5 5 5 6 4
7P GAIN WILD-TYPE 0 5 1 5 4 2 8 3 2

Figure S54.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q gain' versus 'MRNA_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.0019

Table S55.  Gene #14: '7q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
7Q GAIN MUTATED 3 8 27 9 12
7Q GAIN WILD-TYPE 28 9 22 18 11

Figure S55.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'7q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S56.  Gene #14: '7q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
7Q GAIN MUTATED 7 28 24
7Q GAIN WILD-TYPE 35 40 13

Figure S56.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S57.  Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
7Q GAIN MUTATED 36 141 46
7Q GAIN WILD-TYPE 17 80 131

Figure S57.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 0.00058 (Fisher's exact test), Q value = 0.0032

Table S58.  Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
7Q GAIN MUTATED 44 70 44
7Q GAIN WILD-TYPE 41 33 62

Figure S58.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00471 (Fisher's exact test), Q value = 0.018

Table S59.  Gene #14: '7q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 51 33 35 39 43 86 22 20 26
7Q GAIN MUTATED 34 8 17 17 21 35 9 10 18
7Q GAIN WILD-TYPE 17 25 18 22 22 51 13 10 8

Figure S59.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 0.00541 (Fisher's exact test), Q value = 0.021

Table S60.  Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
7Q GAIN MUTATED 78 36 48 60
7Q GAIN WILD-TYPE 49 58 49 71

Figure S60.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S61.  Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
7Q GAIN MUTATED 54 64 32 67 5
7Q GAIN WILD-TYPE 25 44 64 62 32

Figure S61.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_CNMF'

P value = 0.00538 (Fisher's exact test), Q value = 0.021

Table S62.  Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
7Q GAIN MUTATED 38 35 43 40 43
7Q GAIN WILD-TYPE 22 53 28 35 61

Figure S62.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.0012

Table S63.  Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 79 55 46 17 55 20 26 42 58
7Q GAIN MUTATED 49 28 22 3 31 9 13 9 35
7Q GAIN WILD-TYPE 30 27 24 14 24 11 13 33 23

Figure S63.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00145 (Fisher's exact test), Q value = 0.007

Table S64.  Gene #14: '7q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 20 16 11 11 9
7Q GAIN MUTATED 9 14 8 9 2 9
7Q GAIN WILD-TYPE 9 6 8 2 9 0

Figure S64.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0258 (Fisher's exact test), Q value = 0.077

Table S65.  Gene #14: '7q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 12 9 8 12 9 7 13 9 6
7Q GAIN MUTATED 12 4 5 6 5 5 5 7 2
7Q GAIN WILD-TYPE 0 5 3 6 4 2 8 2 4

Figure S65.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S66.  Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
8P GAIN MUTATED 32 59 43
8P GAIN WILD-TYPE 21 162 134

Figure S66.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'MRNA_CNMF'

P value = 0.0223 (Fisher's exact test), Q value = 0.068

Table S67.  Gene #16: '8q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
8Q GAIN MUTATED 7 11 22 12 14
8Q GAIN WILD-TYPE 24 6 27 15 9

Figure S67.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'8q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0401 (Fisher's exact test), Q value = 0.11

Table S68.  Gene #16: '8q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
8Q GAIN MUTATED 13 31 22
8Q GAIN WILD-TYPE 29 37 15

Figure S68.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'8q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S69.  Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
8Q GAIN MUTATED 38 132 57
8Q GAIN WILD-TYPE 15 89 120

Figure S69.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 0.0381 (Fisher's exact test), Q value = 0.1

Table S70.  Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
8Q GAIN MUTATED 43 66 50
8Q GAIN WILD-TYPE 42 37 56

Figure S70.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 0.00089 (Fisher's exact test), Q value = 0.0047

Table S71.  Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
8Q GAIN MUTATED 76 33 56 60
8Q GAIN WILD-TYPE 51 61 41 71

Figure S71.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 0.0016

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
8Q GAIN MUTATED 48 62 39 68 8
8Q GAIN WILD-TYPE 31 46 57 61 29

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

'8q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00462 (Fisher's exact test), Q value = 0.018

Table S73.  Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 79 55 46 17 55 20 26 42 58
8Q GAIN MUTATED 29 34 27 8 36 10 12 13 31
8Q GAIN WILD-TYPE 50 21 19 9 19 10 14 29 27

Figure S73.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0119 (Fisher's exact test), Q value = 0.041

Table S74.  Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 20 16 11 11 9
8Q GAIN MUTATED 12 14 5 9 3 3
8Q GAIN WILD-TYPE 6 6 11 2 8 6

Figure S74.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9p gain' versus 'MRNA_CNMF'

P value = 0.034 (Fisher's exact test), Q value = 0.095

Table S75.  Gene #17: '9p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
9P GAIN MUTATED 0 2 10 6 4
9P GAIN WILD-TYPE 31 15 39 21 19

Figure S75.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'9p gain' versus 'CN_CNMF'

P value = 0.0138 (Fisher's exact test), Q value = 0.045

Table S76.  Gene #17: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
9P GAIN MUTATED 14 46 21
9P GAIN WILD-TYPE 39 175 156

Figure S76.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'

'9q gain' versus 'MRNA_CNMF'

P value = 0.0223 (Fisher's exact test), Q value = 0.068

Table S77.  Gene #18: '9q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
9Q GAIN MUTATED 0 1 10 6 4
9Q GAIN WILD-TYPE 31 16 39 21 19

Figure S77.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'9q gain' versus 'CN_CNMF'

P value = 0.0418 (Fisher's exact test), Q value = 0.11

Table S78.  Gene #18: '9q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
9Q GAIN MUTATED 14 36 21
9Q GAIN WILD-TYPE 39 185 156

Figure S78.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #3: 'CN_CNMF'

'10p gain' versus 'CN_CNMF'

P value = 0.0228 (Fisher's exact test), Q value = 0.069

Table S79.  Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
10P GAIN MUTATED 8 22 8
10P GAIN WILD-TYPE 45 199 169

Figure S79.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

'10q gain' versus 'CN_CNMF'

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

Table S80.  Gene #20: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
10Q GAIN MUTATED 8 11 4
10Q GAIN WILD-TYPE 45 210 173

Figure S80.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

'11p gain' versus 'MRNA_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
11P GAIN MUTATED 0 2 6 0 9
11P GAIN WILD-TYPE 31 15 43 27 14

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

'11p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00068 (Fisher's exact test), Q value = 0.0037

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
11P GAIN MUTATED 1 5 11
11P GAIN WILD-TYPE 41 63 26

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

'11p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S83.  Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
11P GAIN MUTATED 7 47 0
11P GAIN WILD-TYPE 46 174 177

Figure S83.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

'11p gain' versus 'METHLYATION_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.0014

Table S84.  Gene #21: '11p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
11P GAIN MUTATED 10 23 4
11P GAIN WILD-TYPE 75 80 102

Figure S84.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p gain' versus 'MRNASEQ_CNMF'

P value = 0.00278 (Fisher's exact test), Q value = 0.012

Table S85.  Gene #21: '11p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
11P GAIN MUTATED 24 3 10 17
11P GAIN WILD-TYPE 103 91 87 114

Figure S85.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11p gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S86.  Gene #21: '11p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
11P GAIN MUTATED 14 17 1 22 0
11P GAIN WILD-TYPE 65 91 95 107 37

Figure S86.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11p gain' versus 'MIRSEQ_CNMF'

P value = 0.0363 (Fisher's exact test), Q value = 0.1

Table S87.  Gene #21: '11p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
11P GAIN MUTATED 8 6 10 16 8
11P GAIN WILD-TYPE 52 82 61 59 96

Figure S87.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11p gain' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S88.  Gene #21: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 79 55 46 17 55 20 26 42 58
11P GAIN MUTATED 7 8 8 0 10 0 2 0 13
11P GAIN WILD-TYPE 72 47 38 17 45 20 24 42 45

Figure S88.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11q gain' versus 'MRNA_CNMF'

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

Table S89.  Gene #22: '11q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
11Q GAIN MUTATED 0 2 5 0 11
11Q GAIN WILD-TYPE 31 15 44 27 12

Figure S89.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'11q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S90.  Gene #22: '11q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
11Q GAIN MUTATED 1 4 13
11Q GAIN WILD-TYPE 41 64 24

Figure S90.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'11q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S91.  Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
11Q GAIN MUTATED 8 43 0
11Q GAIN WILD-TYPE 45 178 177

Figure S91.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

'11q gain' versus 'METHLYATION_CNMF'

P value = 0.00332 (Fisher's exact test), Q value = 0.014

Table S92.  Gene #22: '11q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
11Q GAIN MUTATED 8 20 5
11Q GAIN WILD-TYPE 77 83 101

Figure S92.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11q gain' versus 'MRNASEQ_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.0016

Table S93.  Gene #22: '11q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
11Q GAIN MUTATED 25 2 8 16
11Q GAIN WILD-TYPE 102 92 89 115

Figure S93.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S94.  Gene #22: '11q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
11Q GAIN MUTATED 13 18 0 20 0
11Q GAIN WILD-TYPE 66 90 96 109 37

Figure S94.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00289 (Fisher's exact test), Q value = 0.013

Table S95.  Gene #22: '11q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 79 55 46 17 55 20 26 42 58
11Q GAIN MUTATED 5 7 7 0 11 0 1 1 13
11Q GAIN WILD-TYPE 74 48 39 17 44 20 25 41 45

Figure S95.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12p gain' versus 'CN_CNMF'

P value = 0.0268 (Fisher's exact test), Q value = 0.079

Table S96.  Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
12P GAIN MUTATED 16 35 42
12P GAIN WILD-TYPE 37 186 135

Figure S96.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 0.0421 (Fisher's exact test), Q value = 0.11

Table S97.  Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
12P GAIN MUTATED 17 13 28
12P GAIN WILD-TYPE 68 90 78

Figure S97.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12q gain' versus 'CN_CNMF'

P value = 0.0241 (Fisher's exact test), Q value = 0.072

Table S98.  Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
12Q GAIN MUTATED 14 32 42
12Q GAIN WILD-TYPE 39 189 135

Figure S98.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

'12q gain' versus 'METHLYATION_CNMF'

P value = 0.0119 (Fisher's exact test), Q value = 0.041

Table S99.  Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
12Q GAIN MUTATED 14 11 28
12Q GAIN WILD-TYPE 71 92 78

Figure S99.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S100.  Gene #25: '13q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
13Q GAIN MUTATED 7 13 38 10 17
13Q GAIN WILD-TYPE 24 4 11 17 6

Figure S100.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'13q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S101.  Gene #25: '13q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
13Q GAIN MUTATED 11 45 29
13Q GAIN WILD-TYPE 31 23 8

Figure S101.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'13q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S102.  Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
13Q GAIN MUTATED 37 181 37
13Q GAIN WILD-TYPE 16 40 140

Figure S102.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

'13q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S103.  Gene #25: '13q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
13Q GAIN MUTATED 39 79 49
13Q GAIN WILD-TYPE 46 24 57

Figure S103.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S104.  Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
13Q GAIN MUTATED 89 33 54 77
13Q GAIN WILD-TYPE 38 61 43 54

Figure S104.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S105.  Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
13Q GAIN MUTATED 61 71 26 87 8
13Q GAIN WILD-TYPE 18 37 70 42 29

Figure S105.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S106.  Gene #25: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
13Q GAIN MUTATED 48 36 42 53 49
13Q GAIN WILD-TYPE 12 52 29 22 55

Figure S106.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'13q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.0018

Table S107.  Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 79 55 46 17 55 20 26 42 58
13Q GAIN MUTATED 48 31 24 5 36 11 16 13 44
13Q GAIN WILD-TYPE 31 24 22 12 19 9 10 29 14

Figure S107.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q gain' versus 'CN_CNMF'

P value = 0.00151 (Fisher's exact test), Q value = 0.0073

Table S108.  Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
14Q GAIN MUTATED 11 16 8
14Q GAIN WILD-TYPE 42 205 169

Figure S108.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

'14q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0335 (Fisher's exact test), Q value = 0.094

Table S109.  Gene #26: '14q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 12 9 8 12 9 7 13 9 6
14Q GAIN MUTATED 0 1 2 0 0 3 2 0 1
14Q GAIN WILD-TYPE 12 8 6 12 9 4 11 9 5

Figure S109.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q gain' versus 'RPPA_CNMF'

P value = 0.0387 (Fisher's exact test), Q value = 0.1

Table S110.  Gene #27: '15q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 145 125
15Q GAIN MUTATED 4 5 0
15Q GAIN WILD-TYPE 81 140 125

Figure S110.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'15q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0144 (Fisher's exact test), Q value = 0.047

Table S111.  Gene #27: '15q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 51 33 35 39 43 86 22 20 26
15Q GAIN MUTATED 2 0 0 2 0 0 2 2 1
15Q GAIN WILD-TYPE 49 33 35 37 43 86 20 18 25

Figure S111.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'16p gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S112.  Gene #28: '16p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
16P GAIN MUTATED 0 8 17 2 14
16P GAIN WILD-TYPE 31 9 32 25 9

Figure S112.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'16p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S113.  Gene #28: '16p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
16P GAIN MUTATED 3 17 21
16P GAIN WILD-TYPE 39 51 16

Figure S113.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'16p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S114.  Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
16P GAIN MUTATED 15 85 6
16P GAIN WILD-TYPE 38 136 171

Figure S114.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

'16p gain' versus 'METHLYATION_CNMF'

P value = 0.0488 (Fisher's exact test), Q value = 0.12

Table S115.  Gene #28: '16p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
16P GAIN MUTATED 21 28 15
16P GAIN WILD-TYPE 64 75 91

Figure S115.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16p gain' versus 'RPPA_CNMF'

P value = 0.0393 (Fisher's exact test), Q value = 0.1

Table S116.  Gene #28: '16p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 145 125
16P GAIN MUTATED 27 25 26
16P GAIN WILD-TYPE 58 120 99

Figure S116.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 0.0041 (Fisher's exact test), Q value = 0.017

Table S117.  Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
16P GAIN MUTATED 35 12 18 41
16P GAIN WILD-TYPE 92 82 79 90

Figure S117.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S118.  Gene #28: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
16P GAIN MUTATED 25 22 9 50 0
16P GAIN WILD-TYPE 54 86 87 79 37

Figure S118.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_CNMF'

P value = 0.0175 (Fisher's exact test), Q value = 0.056

Table S119.  Gene #28: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
16P GAIN MUTATED 18 14 21 26 19
16P GAIN WILD-TYPE 42 74 50 49 85

Figure S119.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00094 (Fisher's exact test), Q value = 0.0048

Table S120.  Gene #28: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 79 55 46 17 55 20 26 42 58
16P GAIN MUTATED 18 14 10 0 14 3 10 4 25
16P GAIN WILD-TYPE 61 41 36 17 41 17 16 38 33

Figure S120.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16q gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S121.  Gene #29: '16q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
16Q GAIN MUTATED 0 6 17 2 13
16Q GAIN WILD-TYPE 31 11 32 25 10

Figure S121.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'16q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S122.  Gene #29: '16q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
16Q GAIN MUTATED 2 16 20
16Q GAIN WILD-TYPE 40 52 17

Figure S122.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'16q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S123.  Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
16Q GAIN MUTATED 14 85 5
16Q GAIN WILD-TYPE 39 136 172

Figure S123.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

'16q gain' versus 'METHLYATION_CNMF'

P value = 0.0349 (Fisher's exact test), Q value = 0.097

Table S124.  Gene #29: '16q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
16Q GAIN MUTATED 21 29 15
16Q GAIN WILD-TYPE 64 74 91

Figure S124.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16q gain' versus 'RPPA_CNMF'

P value = 0.0452 (Fisher's exact test), Q value = 0.11

Table S125.  Gene #29: '16q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 145 125
16Q GAIN MUTATED 27 26 25
16Q GAIN WILD-TYPE 58 119 100

Figure S125.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'16q gain' versus 'MRNASEQ_CNMF'

P value = 0.00279 (Fisher's exact test), Q value = 0.012

Table S126.  Gene #29: '16q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
16Q GAIN MUTATED 37 12 16 39
16Q GAIN WILD-TYPE 90 82 81 92

Figure S126.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S127.  Gene #29: '16q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
16Q GAIN MUTATED 25 23 9 47 0
16Q GAIN WILD-TYPE 54 85 87 82 37

Figure S127.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_CNMF'

P value = 0.00964 (Fisher's exact test), Q value = 0.034

Table S128.  Gene #29: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
16Q GAIN MUTATED 18 14 22 25 17
16Q GAIN WILD-TYPE 42 74 49 50 87

Figure S128.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00281 (Fisher's exact test), Q value = 0.012

Table S129.  Gene #29: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 79 55 46 17 55 20 26 42 58
16Q GAIN MUTATED 17 14 11 0 14 3 9 4 24
16Q GAIN WILD-TYPE 62 41 35 17 41 17 17 38 34

Figure S129.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0331 (Fisher's exact test), Q value = 0.093

Table S130.  Gene #31: '17q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
17Q GAIN MUTATED 3 11 11
17Q GAIN WILD-TYPE 39 57 26

Figure S130.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S131.  Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
17Q GAIN MUTATED 10 60 14
17Q GAIN WILD-TYPE 43 161 163

Figure S131.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 0.00191 (Fisher's exact test), Q value = 0.009

Table S132.  Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
17Q GAIN MUTATED 12 33 15
17Q GAIN WILD-TYPE 73 70 91

Figure S132.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S133.  Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
17Q GAIN MUTATED 46 9 11 18
17Q GAIN WILD-TYPE 81 85 86 113

Figure S133.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 5e-04

Table S134.  Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
17Q GAIN MUTATED 17 32 6 26 3
17Q GAIN WILD-TYPE 62 76 90 103 34

Figure S134.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_CNMF'

P value = 0.0478 (Fisher's exact test), Q value = 0.12

Table S135.  Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
17Q GAIN MUTATED 16 14 13 20 12
17Q GAIN WILD-TYPE 44 74 58 55 92

Figure S135.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0234 (Fisher's exact test), Q value = 0.07

Table S136.  Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 79 55 46 17 55 20 26 42 58
17Q GAIN MUTATED 18 10 11 0 16 2 6 2 10
17Q GAIN WILD-TYPE 61 45 35 17 39 18 20 40 48

Figure S136.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p gain' versus 'METHLYATION_CNMF'

P value = 0.028 (Fisher's exact test), Q value = 0.081

Table S137.  Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
18P GAIN MUTATED 4 2 11
18P GAIN WILD-TYPE 81 101 95

Figure S137.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p gain' versus 'MRNASEQ_CNMF'

P value = 0.039 (Fisher's exact test), Q value = 0.1

Table S138.  Gene #32: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
18P GAIN MUTATED 2 8 8 5
18P GAIN WILD-TYPE 125 86 89 126

Figure S138.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00045

Table S139.  Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
18P GAIN MUTATED 3 2 13 1 4
18P GAIN WILD-TYPE 76 106 83 128 33

Figure S139.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0135 (Fisher's exact test), Q value = 0.045

Table S140.  Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 79 55 46 17 55 20 26 42 58
18P GAIN MUTATED 5 6 0 3 3 1 0 4 0
18P GAIN WILD-TYPE 74 49 46 14 52 19 26 38 58

Figure S140.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18q gain' versus 'MRNASEQ_CNMF'

P value = 0.0114 (Fisher's exact test), Q value = 0.039

Table S141.  Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
18Q GAIN MUTATED 0 3 7 4
18Q GAIN WILD-TYPE 127 91 90 127

Figure S141.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00039

Table S142.  Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
18Q GAIN MUTATED 2 0 8 0 4
18Q GAIN WILD-TYPE 77 108 88 129 33

Figure S142.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0193 (Fisher's exact test), Q value = 0.061

Table S143.  Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 79 55 46 17 55 20 26 42 58
18Q GAIN MUTATED 1 5 0 2 2 1 0 3 0
18Q GAIN WILD-TYPE 78 50 46 15 53 19 26 39 58

Figure S143.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p gain' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00045

Table S144.  Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
19P GAIN MUTATED 13 48 12
19P GAIN WILD-TYPE 40 173 165

Figure S144.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.00074

Table S145.  Gene #34: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
19P GAIN MUTATED 26 18 9 19 1
19P GAIN WILD-TYPE 53 90 87 110 36

Figure S145.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_CNMF'

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

Table S146.  Gene #34: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
19P GAIN MUTATED 19 11 17 10 5
19P GAIN WILD-TYPE 41 77 54 65 99

Figure S146.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0335 (Fisher's exact test), Q value = 0.094

Table S147.  Gene #34: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 79 55 46 17 55 20 26 42 58
19P GAIN MUTATED 12 14 6 0 8 4 8 2 8
19P GAIN WILD-TYPE 67 41 40 17 47 16 18 40 50

Figure S147.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00797 (Fisher's exact test), Q value = 0.029

Table S148.  Gene #34: '19p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 12 9 8 12 9 7 13 9 6
19P GAIN MUTATED 3 4 5 1 1 0 0 1 1
19P GAIN WILD-TYPE 9 5 3 11 8 7 13 8 5

Figure S148.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q gain' versus 'MRNA_CNMF'

P value = 0.0452 (Fisher's exact test), Q value = 0.11

Table S149.  Gene #35: '19q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
19Q GAIN MUTATED 0 4 7 5 2
19Q GAIN WILD-TYPE 31 13 42 22 21

Figure S149.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'19q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0264 (Fisher's exact test), Q value = 0.078

Table S150.  Gene #35: '19q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
19Q GAIN MUTATED 1 13 4
19Q GAIN WILD-TYPE 41 55 33

Figure S150.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'19q gain' versus 'CN_CNMF'

P value = 0.00588 (Fisher's exact test), Q value = 0.022

Table S151.  Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
19Q GAIN MUTATED 15 48 21
19Q GAIN WILD-TYPE 38 173 156

Figure S151.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

'19q gain' versus 'RPPA_CNMF'

P value = 0.0126 (Fisher's exact test), Q value = 0.043

Table S152.  Gene #35: '19q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 145 125
19Q GAIN MUTATED 23 33 15
19Q GAIN WILD-TYPE 62 112 110

Figure S152.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'19q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.001

Table S153.  Gene #35: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
19Q GAIN MUTATED 28 20 12 23 1
19Q GAIN WILD-TYPE 51 88 84 106 36

Figure S153.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_CNMF'

P value = 0.00381 (Fisher's exact test), Q value = 0.016

Table S154.  Gene #35: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
19Q GAIN MUTATED 17 13 21 9 12
19Q GAIN WILD-TYPE 43 75 50 66 92

Figure S154.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0194 (Fisher's exact test), Q value = 0.061

Table S155.  Gene #35: '19q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 20 16 11 11 9
19Q GAIN MUTATED 4 7 0 4 0 2
19Q GAIN WILD-TYPE 14 13 16 7 11 7

Figure S155.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00472 (Fisher's exact test), Q value = 0.018

Table S156.  Gene #35: '19q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 12 9 8 12 9 7 13 9 6
19Q GAIN MUTATED 4 4 5 1 0 1 0 1 1
19Q GAIN WILD-TYPE 8 5 3 11 9 6 13 8 5

Figure S156.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S157.  Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
20P GAIN MUTATED 4 11 34 15 19
20P GAIN WILD-TYPE 27 6 15 12 4

Figure S157.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S158.  Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
20P GAIN MUTATED 9 51 23
20P GAIN WILD-TYPE 33 17 14

Figure S158.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S159.  Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
20P GAIN MUTATED 52 144 48
20P GAIN WILD-TYPE 1 77 129

Figure S159.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 0.00275 (Fisher's exact test), Q value = 0.012

Table S160.  Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
20P GAIN MUTATED 42 69 47
20P GAIN WILD-TYPE 43 34 59

Figure S160.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p gain' versus 'RPPA_CNMF'

P value = 0.045 (Fisher's exact test), Q value = 0.11

Table S161.  Gene #36: '20p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 145 125
20P GAIN MUTATED 51 78 54
20P GAIN WILD-TYPE 34 67 71

Figure S161.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.0016

Table S162.  Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
20P GAIN MUTATED 85 36 48 73
20P GAIN WILD-TYPE 42 58 49 58

Figure S162.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S163.  Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
20P GAIN MUTATED 48 71 30 88 5
20P GAIN WILD-TYPE 31 37 66 41 32

Figure S163.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_CNMF'

P value = 0.00077 (Fisher's exact test), Q value = 0.0041

Table S164.  Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
20P GAIN MUTATED 36 35 44 52 49
20P GAIN WILD-TYPE 24 53 27 23 55

Figure S164.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S165.  Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 79 55 46 17 55 20 26 42 58
20P GAIN MUTATED 42 29 31 4 35 11 13 7 44
20P GAIN WILD-TYPE 37 26 15 13 20 9 13 35 14

Figure S165.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S166.  Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
20Q GAIN MUTATED 5 14 48 16 21
20Q GAIN WILD-TYPE 26 3 1 11 2

Figure S166.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S167.  Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
20Q GAIN MUTATED 11 58 35
20Q GAIN WILD-TYPE 31 10 2

Figure S167.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S168.  Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
20Q GAIN MUTATED 53 210 58
20Q GAIN WILD-TYPE 0 11 119

Figure S168.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S169.  Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
20Q GAIN MUTATED 52 100 59
20Q GAIN WILD-TYPE 33 3 47

Figure S169.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q gain' versus 'RPPA_CNMF'

P value = 0.00821 (Fisher's exact test), Q value = 0.029

Table S170.  Gene #37: '20q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 145 125
20Q GAIN MUTATED 67 106 75
20Q GAIN WILD-TYPE 18 39 50

Figure S170.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'20q gain' versus 'RPPA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00025

Table S171.  Gene #37: '20q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 51 33 35 39 43 86 22 20 26
20Q GAIN MUTATED 46 20 29 25 31 47 11 16 23
20Q GAIN WILD-TYPE 5 13 6 14 12 39 11 4 3

Figure S171.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S172.  Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
20Q GAIN MUTATED 122 41 67 89
20Q GAIN WILD-TYPE 5 53 30 42

Figure S172.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
20Q GAIN MUTATED 73 95 34 111 6
20Q GAIN WILD-TYPE 6 13 62 18 31

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

'20q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S174.  Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
20Q GAIN MUTATED 54 45 57 69 58
20Q GAIN WILD-TYPE 6 43 14 6 46

Figure S174.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S175.  Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 79 55 46 17 55 20 26 42 58
20Q GAIN MUTATED 59 40 42 4 44 13 16 12 53
20Q GAIN WILD-TYPE 20 15 4 13 11 7 10 30 5

Figure S175.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S176.  Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 20 16 11 11 9
20Q GAIN MUTATED 17 18 9 11 3 9
20Q GAIN WILD-TYPE 1 2 7 0 8 0

Figure S176.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0485 (Fisher's exact test), Q value = 0.12

Table S177.  Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 12 9 8 12 9 7 13 9 6
20Q GAIN MUTATED 12 7 8 8 6 5 7 8 6
20Q GAIN WILD-TYPE 0 2 0 4 3 2 6 1 0

Figure S177.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q gain' versus 'CN_CNMF'

P value = 0.0441 (Fisher's exact test), Q value = 0.11

Table S178.  Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
21Q GAIN MUTATED 3 17 4
21Q GAIN WILD-TYPE 50 204 173

Figure S178.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

'21q gain' versus 'METHLYATION_CNMF'

P value = 0.0441 (Fisher's exact test), Q value = 0.11

Table S179.  Gene #38: '21q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
21Q GAIN MUTATED 1 9 9
21Q GAIN WILD-TYPE 84 94 97

Figure S179.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q gain' versus 'CN_CNMF'

P value = 0.0364 (Fisher's exact test), Q value = 0.1

Table S180.  Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
22Q GAIN MUTATED 1 10 1
22Q GAIN WILD-TYPE 52 211 176

Figure S180.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

'xp gain' versus 'MRNA_CNMF'

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

Table S181.  Gene #40: 'xp gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
XP GAIN MUTATED 1 2 9 9 0
XP GAIN WILD-TYPE 30 15 40 18 23

Figure S181.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'xp gain' versus 'CN_CNMF'

P value = 0.00096 (Fisher's exact test), Q value = 0.0049

Table S182.  Gene #40: 'xp gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
XP GAIN MUTATED 13 41 14
XP GAIN WILD-TYPE 40 180 163

Figure S182.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #3: 'CN_CNMF'

'xp gain' versus 'RPPA_CNMF'

P value = 0.00345 (Fisher's exact test), Q value = 0.015

Table S183.  Gene #40: 'xp gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 145 125
XP GAIN MUTATED 14 35 11
XP GAIN WILD-TYPE 71 110 114

Figure S183.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'xp gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0361 (Fisher's exact test), Q value = 0.1

Table S184.  Gene #40: 'xp gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
XP GAIN MUTATED 11 25 7 19 5
XP GAIN WILD-TYPE 68 83 89 110 32

Figure S184.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xq gain' versus 'MRNA_CNMF'

P value = 0.0109 (Fisher's exact test), Q value = 0.038

Table S185.  Gene #41: 'xq gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
XQ GAIN MUTATED 1 2 9 9 1
XQ GAIN WILD-TYPE 30 15 40 18 22

Figure S185.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'xq gain' versus 'CN_CNMF'

P value = 0.00093 (Fisher's exact test), Q value = 0.0048

Table S186.  Gene #41: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
XQ GAIN MUTATED 16 45 18
XQ GAIN WILD-TYPE 37 176 159

Figure S186.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

'xq gain' versus 'RPPA_CNMF'

P value = 0.00141 (Fisher's exact test), Q value = 0.0069

Table S187.  Gene #41: 'xq gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 145 125
XQ GAIN MUTATED 18 38 12
XQ GAIN WILD-TYPE 67 107 113

Figure S187.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'1p loss' versus 'MRNA_CNMF'

P value = 0.0289 (Fisher's exact test), Q value = 0.084

Table S188.  Gene #42: '1p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
1P LOSS MUTATED 2 6 12 2 6
1P LOSS WILD-TYPE 29 11 37 25 17

Figure S188.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'1p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S189.  Gene #42: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
1P LOSS MUTATED 16 70 6
1P LOSS WILD-TYPE 37 151 171

Figure S189.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 0.00701 (Fisher's exact test), Q value = 0.026

Table S190.  Gene #42: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
1P LOSS MUTATED 14 32 15
1P LOSS WILD-TYPE 71 71 91

Figure S190.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00025

Table S191.  Gene #42: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
1P LOSS MUTATED 38 6 23 24
1P LOSS WILD-TYPE 89 88 74 107

Figure S191.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00045

Table S192.  Gene #42: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
1P LOSS MUTATED 29 23 8 28 3
1P LOSS WILD-TYPE 50 85 88 101 34

Figure S192.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_CNMF'

P value = 0.00157 (Fisher's exact test), Q value = 0.0075

Table S193.  Gene #42: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
1P LOSS MUTATED 20 12 18 19 11
1P LOSS WILD-TYPE 40 76 53 56 93

Figure S193.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00302 (Fisher's exact test), Q value = 0.013

Table S194.  Gene #42: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 79 55 46 17 55 20 26 42 58
1P LOSS MUTATED 19 11 18 0 14 2 2 4 10
1P LOSS WILD-TYPE 60 44 28 17 41 18 24 38 48

Figure S194.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S195.  Gene #43: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
1Q LOSS MUTATED 8 42 4
1Q LOSS WILD-TYPE 45 179 173

Figure S195.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

'1q loss' versus 'MRNASEQ_CNMF'

P value = 0.00309 (Fisher's exact test), Q value = 0.013

Table S196.  Gene #43: '1q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
1Q LOSS MUTATED 23 3 14 13
1Q LOSS WILD-TYPE 104 91 83 118

Figure S196.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0102 (Fisher's exact test), Q value = 0.036

Table S197.  Gene #43: '1q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
1Q LOSS MUTATED 16 15 4 16 2
1Q LOSS WILD-TYPE 63 93 92 113 35

Figure S197.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0162 (Fisher's exact test), Q value = 0.052

Table S198.  Gene #43: '1q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 79 55 46 17 55 20 26 42 58
1Q LOSS MUTATED 11 8 11 0 10 0 1 3 3
1Q LOSS WILD-TYPE 68 47 35 17 45 20 25 39 55

Figure S198.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2p loss' versus 'CN_CNMF'

P value = 0.049 (Fisher's exact test), Q value = 0.12

Table S199.  Gene #44: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
2P LOSS MUTATED 2 4 0
2P LOSS WILD-TYPE 51 217 177

Figure S199.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

'3p loss' versus 'CN_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.0011

Table S200.  Gene #46: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
3P LOSS MUTATED 10 36 8
3P LOSS WILD-TYPE 43 185 169

Figure S200.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 0.0393 (Fisher's exact test), Q value = 0.1

Table S201.  Gene #46: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
3P LOSS MUTATED 20 4 13 17
3P LOSS WILD-TYPE 107 90 84 114

Figure S201.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0303 (Fisher's exact test), Q value = 0.087

Table S202.  Gene #46: '3p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 20 16 11 11 9
3P LOSS MUTATED 2 4 1 5 0 0
3P LOSS WILD-TYPE 16 16 15 6 11 9

Figure S202.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'3q loss' versus 'CN_CNMF'

P value = 0.00069 (Fisher's exact test), Q value = 0.0037

Table S203.  Gene #47: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
3Q LOSS MUTATED 9 21 5
3Q LOSS WILD-TYPE 44 200 172

Figure S203.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'MRNA_CNMF'

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

Table S204.  Gene #48: '4p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
4P LOSS MUTATED 3 8 21 2 13
4P LOSS WILD-TYPE 28 9 28 25 10

Figure S204.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'4p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00182 (Fisher's exact test), Q value = 0.0086

Table S205.  Gene #48: '4p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
4P LOSS MUTATED 6 22 19
4P LOSS WILD-TYPE 36 46 18

Figure S205.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S206.  Gene #48: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
4P LOSS MUTATED 30 99 10
4P LOSS WILD-TYPE 23 122 167

Figure S206.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 0.00802 (Fisher's exact test), Q value = 0.029

Table S207.  Gene #48: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
4P LOSS MUTATED 21 43 25
4P LOSS WILD-TYPE 64 60 81

Figure S207.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0357 (Fisher's exact test), Q value = 0.099

Table S208.  Gene #48: '4p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 51 33 35 39 43 86 22 20 26
4P LOSS MUTATED 16 7 13 13 17 17 7 1 10
4P LOSS WILD-TYPE 35 26 22 26 26 69 15 19 16

Figure S208.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S209.  Gene #48: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
4P LOSS MUTATED 59 11 29 39
4P LOSS WILD-TYPE 68 83 68 92

Figure S209.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S210.  Gene #48: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
4P LOSS MUTATED 35 42 8 50 3
4P LOSS WILD-TYPE 44 66 88 79 34

Figure S210.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.001

Table S211.  Gene #48: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
4P LOSS MUTATED 27 17 21 33 20
4P LOSS WILD-TYPE 33 71 50 42 84

Figure S211.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0221 (Fisher's exact test), Q value = 0.068

Table S212.  Gene #48: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 79 55 46 17 55 20 26 42 58
4P LOSS MUTATED 25 13 16 1 16 6 7 7 27
4P LOSS WILD-TYPE 54 42 30 16 39 14 19 35 31

Figure S212.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0139 (Fisher's exact test), Q value = 0.046

Table S213.  Gene #48: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 20 16 11 11 9
4P LOSS MUTATED 10 8 3 2 0 4
4P LOSS WILD-TYPE 8 12 13 9 11 5

Figure S213.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4q loss' versus 'MRNA_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00094

Table S214.  Gene #49: '4q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
4Q LOSS MUTATED 3 5 22 2 11
4Q LOSS WILD-TYPE 28 12 27 25 12

Figure S214.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'4q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00699 (Fisher's exact test), Q value = 0.026

Table S215.  Gene #49: '4q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
4Q LOSS MUTATED 5 23 15
4Q LOSS WILD-TYPE 37 45 22

Figure S215.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S216.  Gene #49: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
4Q LOSS MUTATED 25 92 10
4Q LOSS WILD-TYPE 28 129 167

Figure S216.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 0.027 (Fisher's exact test), Q value = 0.079

Table S217.  Gene #49: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
4Q LOSS MUTATED 21 38 22
4Q LOSS WILD-TYPE 64 65 84

Figure S217.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S218.  Gene #49: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
4Q LOSS MUTATED 54 9 25 38
4Q LOSS WILD-TYPE 73 85 72 93

Figure S218.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S219.  Gene #49: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
4Q LOSS MUTATED 34 38 5 46 3
4Q LOSS WILD-TYPE 45 70 91 83 34

Figure S219.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.0016

Table S220.  Gene #49: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
4Q LOSS MUTATED 25 14 19 29 19
4Q LOSS WILD-TYPE 35 74 52 46 85

Figure S220.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0351 (Fisher's exact test), Q value = 0.097

Table S221.  Gene #49: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 79 55 46 17 55 20 26 42 58
4Q LOSS MUTATED 20 13 16 1 17 4 4 7 24
4Q LOSS WILD-TYPE 59 42 30 16 38 16 22 35 34

Figure S221.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S222.  Gene #50: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
5P LOSS MUTATED 11 44 5
5P LOSS WILD-TYPE 42 177 172

Figure S222.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

'5p loss' versus 'METHLYATION_CNMF'

P value = 0.0024 (Fisher's exact test), Q value = 0.011

Table S223.  Gene #50: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
5P LOSS MUTATED 11 24 7
5P LOSS WILD-TYPE 74 79 99

Figure S223.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00054 (Fisher's exact test), Q value = 0.003

Table S224.  Gene #50: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
5P LOSS MUTATED 12 22 2 20 4
5P LOSS WILD-TYPE 67 86 94 109 33

Figure S224.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_CNMF'

P value = 0.0434 (Fisher's exact test), Q value = 0.11

Table S225.  Gene #50: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
5P LOSS MUTATED 15 7 8 9 10
5P LOSS WILD-TYPE 45 81 63 66 94

Figure S225.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5q loss' versus 'MRNA_CNMF'

P value = 0.0173 (Fisher's exact test), Q value = 0.055

Table S226.  Gene #51: '5q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
5Q LOSS MUTATED 2 6 9 1 6
5Q LOSS WILD-TYPE 29 11 40 26 17

Figure S226.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'5q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S227.  Gene #51: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
5Q LOSS MUTATED 14 59 7
5Q LOSS WILD-TYPE 39 162 170

Figure S227.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 0.028 (Fisher's exact test), Q value = 0.081

Table S228.  Gene #51: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
5Q LOSS MUTATED 18 26 12
5Q LOSS WILD-TYPE 67 77 94

Figure S228.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.001

Table S229.  Gene #51: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
5Q LOSS MUTATED 34 5 20 21
5Q LOSS WILD-TYPE 93 89 77 110

Figure S229.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.0014

Table S230.  Gene #51: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
5Q LOSS MUTATED 20 26 5 26 3
5Q LOSS WILD-TYPE 59 82 91 103 34

Figure S230.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CNMF'

P value = 0.00414 (Fisher's exact test), Q value = 0.017

Table S231.  Gene #51: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
5Q LOSS MUTATED 20 9 13 14 12
5Q LOSS WILD-TYPE 40 79 58 61 92

Figure S231.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0254 (Fisher's exact test), Q value = 0.076

Table S232.  Gene #53: '6q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 20 16 11 11 9
6Q LOSS MUTATED 2 1 0 3 0 3
6Q LOSS WILD-TYPE 16 19 16 8 11 6

Figure S232.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7q loss' versus 'CN_CNMF'

P value = 0.0375 (Fisher's exact test), Q value = 0.1

Table S233.  Gene #54: '7q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
7Q LOSS MUTATED 2 2 0
7Q LOSS WILD-TYPE 51 219 177

Figure S233.  Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #3: 'CN_CNMF'

'7q loss' versus 'METHLYATION_CNMF'

P value = 0.0211 (Fisher's exact test), Q value = 0.065

Table S234.  Gene #54: '7q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
7Q LOSS MUTATED 0 4 0
7Q LOSS WILD-TYPE 85 99 106

Figure S234.  Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p loss' versus 'MRNA_CNMF'

P value = 0.00244 (Fisher's exact test), Q value = 0.011

Table S235.  Gene #55: '8p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
8P LOSS MUTATED 2 8 20 6 9
8P LOSS WILD-TYPE 29 9 29 21 14

Figure S235.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'8p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00441 (Fisher's exact test), Q value = 0.018

Table S236.  Gene #55: '8p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
8P LOSS MUTATED 5 25 15
8P LOSS WILD-TYPE 37 43 22

Figure S236.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S237.  Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
8P LOSS MUTATED 9 117 12
8P LOSS WILD-TYPE 44 104 165

Figure S237.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 0.0182 (Fisher's exact test), Q value = 0.058

Table S238.  Gene #55: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
8P LOSS MUTATED 23 43 26
8P LOSS WILD-TYPE 62 60 80

Figure S238.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0149 (Fisher's exact test), Q value = 0.048

Table S239.  Gene #55: '8p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 51 33 35 39 43 86 22 20 26
8P LOSS MUTATED 25 6 13 12 14 16 4 6 9
8P LOSS WILD-TYPE 26 27 22 27 29 70 18 14 17

Figure S239.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 0.00112 (Fisher's exact test), Q value = 0.0056

Table S240.  Gene #55: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
8P LOSS MUTATED 51 15 29 43
8P LOSS WILD-TYPE 76 79 68 88

Figure S240.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S241.  Gene #55: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
8P LOSS MUTATED 36 34 14 51 3
8P LOSS WILD-TYPE 43 74 82 78 34

Figure S241.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.0019

Table S242.  Gene #55: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
8P LOSS MUTATED 29 13 23 26 29
8P LOSS WILD-TYPE 31 75 48 49 75

Figure S242.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0446 (Fisher's exact test), Q value = 0.11

Table S243.  Gene #55: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 79 55 46 17 55 20 26 42 58
8P LOSS MUTATED 26 16 15 1 22 4 6 7 23
8P LOSS WILD-TYPE 53 39 31 16 33 16 20 35 35

Figure S243.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0103 (Fisher's exact test), Q value = 0.036

Table S244.  Gene #55: '8p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 20 16 11 11 9
8P LOSS MUTATED 8 7 2 4 1 7
8P LOSS WILD-TYPE 10 13 14 7 10 2

Figure S244.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8q loss' versus 'CN_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 7e-04

Table S245.  Gene #56: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
8Q LOSS MUTATED 4 21 1
8Q LOSS WILD-TYPE 49 200 176

Figure S245.  Get High-res Image Gene #56: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'

'8q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00289 (Fisher's exact test), Q value = 0.013

Table S246.  Gene #56: '8q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 20 16 11 11 9
8Q LOSS MUTATED 1 3 1 0 0 5
8Q LOSS WILD-TYPE 17 17 15 11 11 4

Figure S246.  Get High-res Image Gene #56: '8q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00601 (Fisher's exact test), Q value = 0.023

Table S247.  Gene #56: '8q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 12 9 8 12 9 7 13 9 6
8Q LOSS MUTATED 6 0 0 0 1 1 1 0 1
8Q LOSS WILD-TYPE 6 9 8 12 8 6 12 9 5

Figure S247.  Get High-res Image Gene #56: '8q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p loss' versus 'MRNA_CNMF'

P value = 0.0313 (Fisher's exact test), Q value = 0.089

Table S248.  Gene #57: '9p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
9P LOSS MUTATED 0 4 7 1 3
9P LOSS WILD-TYPE 31 13 42 26 20

Figure S248.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'9p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.012 (Fisher's exact test), Q value = 0.041

Table S249.  Gene #57: '9p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
9P LOSS MUTATED 0 9 6
9P LOSS WILD-TYPE 42 59 31

Figure S249.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S250.  Gene #57: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
9P LOSS MUTATED 7 41 6
9P LOSS WILD-TYPE 46 180 171

Figure S250.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 0.0131 (Fisher's exact test), Q value = 0.044

Table S251.  Gene #57: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
9P LOSS MUTATED 11 21 7
9P LOSS WILD-TYPE 74 82 99

Figure S251.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 5e-04

Table S252.  Gene #57: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
9P LOSS MUTATED 26 2 15 11
9P LOSS WILD-TYPE 101 92 82 120

Figure S252.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00044 (Fisher's exact test), Q value = 0.0025

Table S253.  Gene #57: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
9P LOSS MUTATED 16 18 4 16 0
9P LOSS WILD-TYPE 63 90 92 113 37

Figure S253.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_CNMF'

P value = 0.00461 (Fisher's exact test), Q value = 0.018

Table S254.  Gene #57: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
9P LOSS MUTATED 9 6 10 16 5
9P LOSS WILD-TYPE 51 82 61 59 99

Figure S254.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9q loss' versus 'MRNA_CNMF'

P value = 0.002 (Fisher's exact test), Q value = 0.0093

Table S255.  Gene #58: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
9Q LOSS MUTATED 0 5 6 0 4
9Q LOSS WILD-TYPE 31 12 43 27 19

Figure S255.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'9q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0487 (Fisher's exact test), Q value = 0.12

Table S256.  Gene #58: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
9Q LOSS MUTATED 1 7 7
9Q LOSS WILD-TYPE 41 61 30

Figure S256.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S257.  Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
9Q LOSS MUTATED 7 42 5
9Q LOSS WILD-TYPE 46 179 172

Figure S257.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 0.00325 (Fisher's exact test), Q value = 0.014

Table S258.  Gene #58: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
9Q LOSS MUTATED 11 22 6
9Q LOSS WILD-TYPE 74 81 100

Figure S258.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 5e-04

Table S259.  Gene #58: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
9Q LOSS MUTATED 25 2 16 11
9Q LOSS WILD-TYPE 102 92 81 120

Figure S259.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00097 (Fisher's exact test), Q value = 0.0049

Table S260.  Gene #58: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
9Q LOSS MUTATED 18 16 4 15 1
9Q LOSS WILD-TYPE 61 92 92 114 36

Figure S260.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_CNMF'

P value = 0.00699 (Fisher's exact test), Q value = 0.026

Table S261.  Gene #58: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
9Q LOSS MUTATED 8 5 12 15 6
9Q LOSS WILD-TYPE 52 83 59 60 98

Figure S261.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.041 (Fisher's exact test), Q value = 0.11

Table S262.  Gene #58: '9q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 20 16 11 11 9
9Q LOSS MUTATED 5 3 1 5 0 3
9Q LOSS WILD-TYPE 13 17 15 6 11 6

Figure S262.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10p loss' versus 'MRNA_CNMF'

P value = 0.00086 (Fisher's exact test), Q value = 0.0045

Table S263.  Gene #59: '10p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
10P LOSS MUTATED 0 3 6 0 7
10P LOSS WILD-TYPE 31 14 43 27 16

Figure S263.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'10p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S264.  Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
10P LOSS MUTATED 13 51 4
10P LOSS WILD-TYPE 40 170 173

Figure S264.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

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

Table S265.  Gene #59: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
10P LOSS MUTATED 11 29 11
10P LOSS WILD-TYPE 74 74 95

Figure S265.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.001

Table S266.  Gene #59: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
10P LOSS MUTATED 32 4 15 16
10P LOSS WILD-TYPE 95 90 82 115

Figure S266.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 7e-04

Table S267.  Gene #59: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
10P LOSS MUTATED 22 18 7 20 0
10P LOSS WILD-TYPE 57 90 89 109 37

Figure S267.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0275 (Fisher's exact test), Q value = 0.08

Table S268.  Gene #59: '10p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 12 9 8 12 9 7 13 9 6
10P LOSS MUTATED 4 1 4 0 2 1 0 2 0
10P LOSS WILD-TYPE 8 8 4 12 7 6 13 7 6

Figure S268.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q loss' versus 'MRNA_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.0022

Table S269.  Gene #60: '10q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
10Q LOSS MUTATED 0 4 8 0 7
10Q LOSS WILD-TYPE 31 13 41 27 16

Figure S269.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'10q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.022 (Fisher's exact test), Q value = 0.068

Table S270.  Gene #60: '10q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
10Q LOSS MUTATED 1 10 8
10Q LOSS WILD-TYPE 41 58 29

Figure S270.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S271.  Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
10Q LOSS MUTATED 11 58 4
10Q LOSS WILD-TYPE 42 163 173

Figure S271.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 0.00197 (Fisher's exact test), Q value = 0.0093

Table S272.  Gene #60: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
10Q LOSS MUTATED 11 30 12
10Q LOSS WILD-TYPE 74 73 94

Figure S272.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 5e-04

Table S273.  Gene #60: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
10Q LOSS MUTATED 34 4 15 19
10Q LOSS WILD-TYPE 93 90 82 112

Figure S273.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S274.  Gene #60: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
10Q LOSS MUTATED 24 19 5 24 0
10Q LOSS WILD-TYPE 55 89 91 105 37

Figure S274.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0271 (Fisher's exact test), Q value = 0.079

Table S275.  Gene #61: '11p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
11P LOSS MUTATED 1 13 4
11P LOSS WILD-TYPE 41 55 33

Figure S275.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 0.00645 (Fisher's exact test), Q value = 0.024

Table S276.  Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
11P LOSS MUTATED 9 32 10
11P LOSS WILD-TYPE 44 189 167

Figure S276.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

'11p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0436 (Fisher's exact test), Q value = 0.11

Table S277.  Gene #61: '11p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
11P LOSS MUTATED 10 16 5 19 1
11P LOSS WILD-TYPE 69 92 91 110 36

Figure S277.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_CNMF'

P value = 0.00093 (Fisher's exact test), Q value = 0.0048

Table S278.  Gene #61: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
11P LOSS MUTATED 13 6 8 14 4
11P LOSS WILD-TYPE 47 82 63 61 100

Figure S278.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11q loss' versus 'MRNA_CNMF'

P value = 0.00522 (Fisher's exact test), Q value = 0.02

Table S279.  Gene #62: '11q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
11Q LOSS MUTATED 0 4 11 1 4
11Q LOSS WILD-TYPE 31 13 38 26 19

Figure S279.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'11q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00055 (Fisher's exact test), Q value = 0.0031

Table S280.  Gene #62: '11q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
11Q LOSS MUTATED 0 16 4
11Q LOSS WILD-TYPE 42 52 33

Figure S280.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00057

Table S281.  Gene #62: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
11Q LOSS MUTATED 9 44 10
11Q LOSS WILD-TYPE 44 177 167

Figure S281.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

'11q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00201 (Fisher's exact test), Q value = 0.0093

Table S282.  Gene #62: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
11Q LOSS MUTATED 16 16 7 24 0
11Q LOSS WILD-TYPE 63 92 89 105 37

Figure S282.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.0014

Table S283.  Gene #62: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
11Q LOSS MUTATED 16 8 10 17 5
11Q LOSS WILD-TYPE 44 80 61 58 99

Figure S283.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12p loss' versus 'MRNA_CNMF'

P value = 0.00062 (Fisher's exact test), Q value = 0.0034

Table S284.  Gene #63: '12p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
12P LOSS MUTATED 0 6 6 0 3
12P LOSS WILD-TYPE 31 11 43 27 20

Figure S284.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'12p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0156 (Fisher's exact test), Q value = 0.05

Table S285.  Gene #63: '12p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
12P LOSS MUTATED 0 10 5
12P LOSS WILD-TYPE 42 58 32

Figure S285.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'12p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S286.  Gene #63: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
12P LOSS MUTATED 7 40 1
12P LOSS WILD-TYPE 46 181 176

Figure S286.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

'12p loss' versus 'METHLYATION_CNMF'

P value = 0.00379 (Fisher's exact test), Q value = 0.016

Table S287.  Gene #63: '12p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
12P LOSS MUTATED 6 21 7
12P LOSS WILD-TYPE 79 82 99

Figure S287.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p loss' versus 'MRNASEQ_CNMF'

P value = 0.00333 (Fisher's exact test), Q value = 0.014

Table S288.  Gene #63: '12p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
12P LOSS MUTATED 21 2 10 15
12P LOSS WILD-TYPE 106 92 87 116

Figure S288.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12p loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S289.  Gene #63: '12p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
12P LOSS MUTATED 15 13 1 19 0
12P LOSS WILD-TYPE 64 95 95 110 37

Figure S289.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p loss' versus 'MIRSEQ_CNMF'

P value = 0.015 (Fisher's exact test), Q value = 0.049

Table S290.  Gene #63: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
12P LOSS MUTATED 9 4 10 13 6
12P LOSS WILD-TYPE 51 84 61 62 98

Figure S290.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12q loss' versus 'MRNA_CNMF'

P value = 0.00074 (Fisher's exact test), Q value = 0.004

Table S291.  Gene #64: '12q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
12Q LOSS MUTATED 0 6 5 0 3
12Q LOSS WILD-TYPE 31 11 44 27 20

Figure S291.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'12q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0212 (Fisher's exact test), Q value = 0.065

Table S292.  Gene #64: '12q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
12Q LOSS MUTATED 0 9 5
12Q LOSS WILD-TYPE 42 59 32

Figure S292.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'12q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S293.  Gene #64: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
12Q LOSS MUTATED 8 40 2
12Q LOSS WILD-TYPE 45 181 175

Figure S293.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

'12q loss' versus 'METHLYATION_CNMF'

P value = 0.0142 (Fisher's exact test), Q value = 0.046

Table S294.  Gene #64: '12q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
12Q LOSS MUTATED 8 21 8
12Q LOSS WILD-TYPE 77 82 98

Figure S294.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12q loss' versus 'MRNASEQ_CNMF'

P value = 0.00105 (Fisher's exact test), Q value = 0.0053

Table S295.  Gene #64: '12q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
12Q LOSS MUTATED 23 2 10 15
12Q LOSS WILD-TYPE 104 92 87 116

Figure S295.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.00074

Table S296.  Gene #64: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
12Q LOSS MUTATED 15 14 2 19 0
12Q LOSS WILD-TYPE 64 94 94 110 37

Figure S296.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q loss' versus 'MIRSEQ_CNMF'

P value = 0.00443 (Fisher's exact test), Q value = 0.018

Table S297.  Gene #64: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
12Q LOSS MUTATED 11 5 11 13 5
12Q LOSS WILD-TYPE 49 83 60 62 99

Figure S297.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'13q loss' versus 'CN_CNMF'

P value = 0.0109 (Fisher's exact test), Q value = 0.038

Table S298.  Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
13Q LOSS MUTATED 5 5 2
13Q LOSS WILD-TYPE 48 216 175

Figure S298.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 0.0261 (Fisher's exact test), Q value = 0.077

Table S299.  Gene #65: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
13Q LOSS MUTATED 5 4 0
13Q LOSS WILD-TYPE 80 99 106

Figure S299.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S300.  Gene #66: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
14Q LOSS MUTATED 1 8 29 3 9
14Q LOSS WILD-TYPE 30 9 20 24 14

Figure S300.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'14q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S301.  Gene #66: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
14Q LOSS MUTATED 3 28 19
14Q LOSS WILD-TYPE 39 40 18

Figure S301.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S302.  Gene #66: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
14Q LOSS MUTATED 15 118 6
14Q LOSS WILD-TYPE 38 103 171

Figure S302.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

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

Table S303.  Gene #66: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
14Q LOSS MUTATED 18 49 20
14Q LOSS WILD-TYPE 67 54 86

Figure S303.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S304.  Gene #66: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
14Q LOSS MUTATED 64 9 23 43
14Q LOSS WILD-TYPE 63 85 74 88

Figure S304.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S305.  Gene #66: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
14Q LOSS MUTATED 33 45 4 55 2
14Q LOSS WILD-TYPE 46 63 92 74 35

Figure S305.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S306.  Gene #66: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
14Q LOSS MUTATED 25 12 24 39 19
14Q LOSS WILD-TYPE 35 76 47 36 85

Figure S306.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'14q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S307.  Gene #66: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 79 55 46 17 55 20 26 42 58
14Q LOSS MUTATED 29 11 25 0 12 5 6 3 28
14Q LOSS WILD-TYPE 50 44 21 17 43 15 20 39 30

Figure S307.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00375 (Fisher's exact test), Q value = 0.016

Table S308.  Gene #66: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 20 16 11 11 9
14Q LOSS MUTATED 9 3 5 5 0 6
14Q LOSS WILD-TYPE 9 17 11 6 11 3

Figure S308.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'15q loss' versus 'MRNA_CNMF'

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

Table S309.  Gene #67: '15q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
15Q LOSS MUTATED 2 10 23 5 13
15Q LOSS WILD-TYPE 29 7 26 22 10

Figure S309.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'15q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00128 (Fisher's exact test), Q value = 0.0063

Table S310.  Gene #67: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
15Q LOSS MUTATED 6 29 18
15Q LOSS WILD-TYPE 36 39 19

Figure S310.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S311.  Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
15Q LOSS MUTATED 28 117 13
15Q LOSS WILD-TYPE 25 104 164

Figure S311.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.0019

Table S312.  Gene #67: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
15Q LOSS MUTATED 25 52 27
15Q LOSS WILD-TYPE 60 51 79

Figure S312.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S313.  Gene #67: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
15Q LOSS MUTATED 61 14 33 49
15Q LOSS WILD-TYPE 66 80 64 82

Figure S313.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S314.  Gene #67: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
15Q LOSS MUTATED 40 45 10 58 4
15Q LOSS WILD-TYPE 39 63 86 71 33

Figure S314.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S315.  Gene #67: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
15Q LOSS MUTATED 28 15 36 33 26
15Q LOSS WILD-TYPE 32 73 35 42 78

Figure S315.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00141 (Fisher's exact test), Q value = 0.0069

Table S316.  Gene #67: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 79 55 46 17 55 20 26 42 58
15Q LOSS MUTATED 33 20 16 0 21 4 8 8 28
15Q LOSS WILD-TYPE 46 35 30 17 34 16 18 34 30

Figure S316.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0422 (Fisher's exact test), Q value = 0.11

Table S317.  Gene #67: '15q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 20 16 11 11 9
15Q LOSS MUTATED 9 9 7 7 1 7
15Q LOSS WILD-TYPE 9 11 9 4 10 2

Figure S317.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'17p loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S318.  Gene #70: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
17P LOSS MUTATED 3 11 38 10 16
17P LOSS WILD-TYPE 28 6 11 17 7

Figure S318.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17p loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S319.  Gene #70: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
17P LOSS MUTATED 7 45 26
17P LOSS WILD-TYPE 35 23 11

Figure S319.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S320.  Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
17P LOSS MUTATED 27 182 27
17P LOSS WILD-TYPE 26 39 150

Figure S320.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S321.  Gene #70: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
17P LOSS MUTATED 32 82 40
17P LOSS WILD-TYPE 53 21 66

Figure S321.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00612 (Fisher's exact test), Q value = 0.023

Table S322.  Gene #70: '17p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 51 33 35 39 43 86 22 20 26
17P LOSS MUTATED 33 12 24 21 20 34 8 10 18
17P LOSS WILD-TYPE 18 21 11 18 23 52 14 10 8

Figure S322.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S323.  Gene #70: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
17P LOSS MUTATED 94 24 48 69
17P LOSS WILD-TYPE 33 70 49 62

Figure S323.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S324.  Gene #70: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
17P LOSS MUTATED 53 73 19 86 4
17P LOSS WILD-TYPE 26 35 77 43 33

Figure S324.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S325.  Gene #70: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
17P LOSS MUTATED 46 26 38 58 42
17P LOSS WILD-TYPE 14 62 33 17 62

Figure S325.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S326.  Gene #70: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 79 55 46 17 55 20 26 42 58
17P LOSS MUTATED 45 27 31 0 34 10 10 11 42
17P LOSS WILD-TYPE 34 28 15 17 21 10 16 31 16

Figure S326.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0035 (Fisher's exact test), Q value = 0.015

Table S327.  Gene #70: '17p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 20 16 11 11 9
17P LOSS MUTATED 16 14 8 7 2 7
17P LOSS WILD-TYPE 2 6 8 4 9 2

Figure S327.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'17q loss' versus 'MRNA_CNMF'

P value = 0.0347 (Fisher's exact test), Q value = 0.097

Table S328.  Gene #71: '17q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
17Q LOSS MUTATED 1 4 11 1 3
17Q LOSS WILD-TYPE 30 13 38 26 20

Figure S328.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S329.  Gene #71: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
17Q LOSS MUTATED 13 45 6
17Q LOSS WILD-TYPE 40 176 171

Figure S329.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

'17q loss' versus 'MIRSEQ_CNMF'

P value = 0.0127 (Fisher's exact test), Q value = 0.043

Table S330.  Gene #71: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
17Q LOSS MUTATED 15 6 10 14 10
17Q LOSS WILD-TYPE 45 82 61 61 94

Figure S330.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18p loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S331.  Gene #72: '18p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
18P LOSS MUTATED 1 11 43 8 17
18P LOSS WILD-TYPE 30 6 6 19 6

Figure S331.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'18p loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S332.  Gene #72: '18p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
18P LOSS MUTATED 5 45 30
18P LOSS WILD-TYPE 37 23 7

Figure S332.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S333.  Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
18P LOSS MUTATED 37 191 24
18P LOSS WILD-TYPE 16 30 153

Figure S333.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S334.  Gene #72: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
18P LOSS MUTATED 37 96 36
18P LOSS WILD-TYPE 48 7 70

Figure S334.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00384 (Fisher's exact test), Q value = 0.016

Table S335.  Gene #72: '18p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 51 33 35 39 43 86 22 20 26
18P LOSS MUTATED 31 18 23 20 25 35 8 11 22
18P LOSS WILD-TYPE 20 15 12 19 18 51 14 9 4

Figure S335.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'18p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S336.  Gene #72: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
18P LOSS MUTATED 112 23 49 67
18P LOSS WILD-TYPE 15 71 48 64

Figure S336.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S337.  Gene #72: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
18P LOSS MUTATED 61 83 14 91 2
18P LOSS WILD-TYPE 18 25 82 38 35

Figure S337.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S338.  Gene #72: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
18P LOSS MUTATED 50 27 43 58 41
18P LOSS WILD-TYPE 10 61 28 17 63

Figure S338.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S339.  Gene #72: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 79 55 46 17 55 20 26 42 58
18P LOSS MUTATED 46 28 37 1 30 10 13 9 45
18P LOSS WILD-TYPE 33 27 9 16 25 10 13 33 13

Figure S339.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.0016

Table S340.  Gene #72: '18p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 20 16 11 11 9
18P LOSS MUTATED 16 13 6 7 1 7
18P LOSS WILD-TYPE 2 7 10 4 10 2

Figure S340.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00109 (Fisher's exact test), Q value = 0.0055

Table S341.  Gene #72: '18p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 12 9 8 12 9 7 13 9 6
18P LOSS MUTATED 10 6 6 6 2 1 5 8 6
18P LOSS WILD-TYPE 2 3 2 6 7 6 8 1 0

Figure S341.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S342.  Gene #73: '18q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
18Q LOSS MUTATED 1 14 43 9 16
18Q LOSS WILD-TYPE 30 3 6 18 7

Figure S342.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'18q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S343.  Gene #73: '18q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
18Q LOSS MUTATED 6 48 29
18Q LOSS WILD-TYPE 36 20 8

Figure S343.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S344.  Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
18Q LOSS MUTATED 38 199 31
18Q LOSS WILD-TYPE 15 22 146

Figure S344.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S345.  Gene #73: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
18Q LOSS MUTATED 41 96 44
18Q LOSS WILD-TYPE 44 7 62

Figure S345.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0128 (Fisher's exact test), Q value = 0.043

Table S346.  Gene #73: '18q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 51 33 35 39 43 86 22 20 26
18Q LOSS MUTATED 34 17 24 22 26 38 9 13 21
18Q LOSS WILD-TYPE 17 16 11 17 17 48 13 7 5

Figure S346.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S347.  Gene #73: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
18Q LOSS MUTATED 112 28 55 72
18Q LOSS WILD-TYPE 15 66 42 59

Figure S347.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S348.  Gene #73: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
18Q LOSS MUTATED 65 86 20 94 2
18Q LOSS WILD-TYPE 14 22 76 35 35

Figure S348.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S349.  Gene #73: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
18Q LOSS MUTATED 50 32 44 62 46
18Q LOSS WILD-TYPE 10 56 27 13 58

Figure S349.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S350.  Gene #73: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 79 55 46 17 55 20 26 42 58
18Q LOSS MUTATED 53 31 37 2 32 10 13 10 46
18Q LOSS WILD-TYPE 26 24 9 15 23 10 13 32 12

Figure S350.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.0012

Table S351.  Gene #73: '18q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 20 16 11 11 9
18Q LOSS MUTATED 16 14 8 8 1 8
18Q LOSS WILD-TYPE 2 6 8 3 10 1

Figure S351.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.013 (Fisher's exact test), Q value = 0.044

Table S352.  Gene #73: '18q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 12 9 8 12 9 7 13 9 6
18Q LOSS MUTATED 10 7 6 7 3 2 6 9 5
18Q LOSS WILD-TYPE 2 2 2 5 6 5 7 0 1

Figure S352.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p loss' versus 'MRNA_CNMF'

P value = 0.00349 (Fisher's exact test), Q value = 0.015

Table S353.  Gene #74: '19p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
19P LOSS MUTATED 1 7 3 3 3
19P LOSS WILD-TYPE 30 10 46 24 20

Figure S353.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'19p loss' versus 'CN_CNMF'

P value = 0.0072 (Fisher's exact test), Q value = 0.026

Table S354.  Gene #74: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
19P LOSS MUTATED 6 27 7
19P LOSS WILD-TYPE 47 194 170

Figure S354.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

'19p loss' versus 'MRNASEQ_CNMF'

P value = 0.00649 (Fisher's exact test), Q value = 0.024

Table S355.  Gene #74: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
19P LOSS MUTATED 20 3 5 12
19P LOSS WILD-TYPE 107 91 92 119

Figure S355.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0222 (Fisher's exact test), Q value = 0.068

Table S356.  Gene #74: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
19P LOSS MUTATED 4 15 3 16 2
19P LOSS WILD-TYPE 75 93 93 113 35

Figure S356.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0171 (Fisher's exact test), Q value = 0.054

Table S357.  Gene #74: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 79 55 46 17 55 20 26 42 58
19P LOSS MUTATED 6 0 4 0 10 3 1 3 8
19P LOSS WILD-TYPE 73 55 42 17 45 17 25 39 50

Figure S357.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q loss' versus 'MRNA_CNMF'

P value = 0.00471 (Fisher's exact test), Q value = 0.018

Table S358.  Gene #75: '19q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
19Q LOSS MUTATED 1 7 4 2 2
19Q LOSS WILD-TYPE 30 10 45 25 21

Figure S358.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'19q loss' versus 'CN_CNMF'

P value = 0.00109 (Fisher's exact test), Q value = 0.0055

Table S359.  Gene #75: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
19Q LOSS MUTATED 7 22 4
19Q LOSS WILD-TYPE 46 199 173

Figure S359.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

'19q loss' versus 'MRNASEQ_CNMF'

P value = 0.0135 (Fisher's exact test), Q value = 0.045

Table S360.  Gene #75: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
19Q LOSS MUTATED 16 2 4 11
19Q LOSS WILD-TYPE 111 92 93 120

Figure S360.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0081 (Fisher's exact test), Q value = 0.029

Table S361.  Gene #75: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
19Q LOSS MUTATED 1 12 3 15 2
19Q LOSS WILD-TYPE 78 96 93 114 35

Figure S361.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0417 (Fisher's exact test), Q value = 0.11

Table S362.  Gene #75: '19q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 20 16 11 11 9
19Q LOSS MUTATED 4 0 1 0 0 2
19Q LOSS WILD-TYPE 14 20 15 11 11 7

Figure S362.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0103 (Fisher's exact test), Q value = 0.036

Table S363.  Gene #76: '20p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
20P LOSS MUTATED 1 4 8
20P LOSS WILD-TYPE 41 64 29

Figure S363.  Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S364.  Gene #76: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
20P LOSS MUTATED 0 39 4
20P LOSS WILD-TYPE 53 182 173

Figure S364.  Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

'20p loss' versus 'METHLYATION_CNMF'

P value = 0.0123 (Fisher's exact test), Q value = 0.042

Table S365.  Gene #76: '20p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
20P LOSS MUTATED 6 17 5
20P LOSS WILD-TYPE 79 86 101

Figure S365.  Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0206 (Fisher's exact test), Q value = 0.064

Table S366.  Gene #76: '20p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
20P LOSS MUTATED 14 11 3 13 2
20P LOSS WILD-TYPE 65 97 93 116 35

Figure S366.  Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'21q loss' versus 'MRNA_CNMF'

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

Table S367.  Gene #78: '21q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
21Q LOSS MUTATED 2 8 23 3 3
21Q LOSS WILD-TYPE 29 9 26 24 20

Figure S367.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'21q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0219 (Fisher's exact test), Q value = 0.067

Table S368.  Gene #78: '21q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
21Q LOSS MUTATED 5 24 10
21Q LOSS WILD-TYPE 37 44 27

Figure S368.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'21q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S369.  Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
21Q LOSS MUTATED 27 79 18
21Q LOSS WILD-TYPE 26 142 159

Figure S369.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

'21q loss' versus 'MRNASEQ_CNMF'

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

Table S370.  Gene #78: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
21Q LOSS MUTATED 58 12 23 30
21Q LOSS WILD-TYPE 69 82 74 101

Figure S370.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0084 (Fisher's exact test), Q value = 0.03

Table S371.  Gene #78: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
21Q LOSS MUTATED 29 33 18 39 4
21Q LOSS WILD-TYPE 50 75 78 90 33

Figure S371.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_CNMF'

P value = 0.0477 (Fisher's exact test), Q value = 0.12

Table S372.  Gene #78: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
21Q LOSS MUTATED 22 18 22 24 20
21Q LOSS WILD-TYPE 38 70 49 51 84

Figure S372.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'22q loss' versus 'MRNA_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00074

Table S373.  Gene #79: '22q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
22Q LOSS MUTATED 3 10 25 5 9
22Q LOSS WILD-TYPE 28 7 24 22 14

Figure S373.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'22q loss' versus 'MRNA_CHIERARCHICAL'

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

Table S374.  Gene #79: '22q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
22Q LOSS MUTATED 4 34 14
22Q LOSS WILD-TYPE 38 34 23

Figure S374.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S375.  Gene #79: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
22Q LOSS MUTATED 25 107 14
22Q LOSS WILD-TYPE 28 114 163

Figure S375.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0064 (Fisher's exact test), Q value = 0.024

Table S376.  Gene #79: '22q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 51 33 35 39 43 86 22 20 26
22Q LOSS MUTATED 17 6 22 8 13 22 7 6 7
22Q LOSS WILD-TYPE 34 27 13 31 30 64 15 14 19

Figure S376.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 5e-04

Table S377.  Gene #79: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
22Q LOSS MUTATED 53 13 32 47
22Q LOSS WILD-TYPE 74 81 65 84

Figure S377.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S378.  Gene #79: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
22Q LOSS MUTATED 35 41 10 57 2
22Q LOSS WILD-TYPE 44 67 86 72 35

Figure S378.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.0014

Table S379.  Gene #79: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
22Q LOSS MUTATED 23 14 27 34 26
22Q LOSS WILD-TYPE 37 74 44 41 78

Figure S379.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00416 (Fisher's exact test), Q value = 0.017

Table S380.  Gene #79: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 79 55 46 17 55 20 26 42 58
22Q LOSS MUTATED 27 17 20 0 17 2 8 9 24
22Q LOSS WILD-TYPE 52 38 26 17 38 18 18 33 34

Figure S380.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'xp loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0441 (Fisher's exact test), Q value = 0.11

Table S381.  Gene #80: 'xp loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
XP LOSS MUTATED 2 15 5
XP LOSS WILD-TYPE 40 53 32

Figure S381.  Get High-res Image Gene #80: 'xp loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'xp loss' versus 'CN_CNMF'

P value = 0.00045 (Fisher's exact test), Q value = 0.0025

Table S382.  Gene #80: 'xp loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
XP LOSS MUTATED 7 45 12
XP LOSS WILD-TYPE 46 176 165

Figure S382.  Get High-res Image Gene #80: 'xp loss' versus Molecular Subtype #3: 'CN_CNMF'

'xp loss' versus 'RPPA_CNMF'

P value = 0.0206 (Fisher's exact test), Q value = 0.064

Table S383.  Gene #80: 'xp loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 145 125
XP LOSS MUTATED 9 29 11
XP LOSS WILD-TYPE 76 116 114

Figure S383.  Get High-res Image Gene #80: 'xp loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'xp loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.005 (Fisher's exact test), Q value = 0.02

Table S384.  Gene #80: 'xp loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 79 55 46 17 55 20 26 42 58
XP LOSS MUTATED 9 3 5 0 13 7 1 3 9
XP LOSS WILD-TYPE 70 52 41 17 42 13 25 39 49

Figure S384.  Get High-res Image Gene #80: 'xp loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0122 (Fisher's exact test), Q value = 0.041

Table S385.  Gene #80: 'xp loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 12 9 8 12 9 7 13 9 6
XP LOSS MUTATED 0 0 1 2 0 2 2 1 4
XP LOSS WILD-TYPE 12 9 7 10 9 5 11 8 2

Figure S385.  Get High-res Image Gene #80: 'xp loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq loss' versus 'CN_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.0015

Table S386.  Gene #81: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
XQ LOSS MUTATED 4 38 9
XQ LOSS WILD-TYPE 49 183 168

Figure S386.  Get High-res Image Gene #81: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'

'xq loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0196 (Fisher's exact test), Q value = 0.061

Table S387.  Gene #81: 'xq loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 51 33 35 39 43 86 22 20 26
XQ LOSS MUTATED 8 1 10 5 3 5 2 3 1
XQ LOSS WILD-TYPE 43 32 25 34 40 81 20 17 25

Figure S387.  Get High-res Image Gene #81: 'xq loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_CNMF'

P value = 0.00342 (Fisher's exact test), Q value = 0.015

Table S388.  Gene #81: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
XQ LOSS MUTATED 13 4 3 11 9
XQ LOSS WILD-TYPE 47 84 68 64 95

Figure S388.  Get High-res Image Gene #81: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xq loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00708 (Fisher's exact test), Q value = 0.026

Table S389.  Gene #81: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 79 55 46 17 55 20 26 42 58
XQ LOSS MUTATED 6 3 4 0 9 7 0 3 8
XQ LOSS WILD-TYPE 73 52 42 17 46 13 26 39 50

Figure S389.  Get High-res Image Gene #81: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00145 (Fisher's exact test), Q value = 0.007

Table S390.  Gene #81: 'xq loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 12 9 8 12 9 7 13 9 6
XQ LOSS MUTATED 0 0 2 2 0 1 0 1 4
XQ LOSS WILD-TYPE 12 9 6 10 9 6 13 8 2

Figure S390.  Get High-res Image Gene #81: 'xq loss' versus Molecular Subtype #12: '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/COAD-TP/22508740/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/COAD-TP/22541003/COAD-TP.transferedmergedcluster.txt

  • Number of patients = 451

  • Number of significantly arm-level cnvs = 81

  • Number of molecular subtypes = 12

  • Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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