Correlation between copy number variations of arm-level result and molecular subtypes
Sarcoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1R210V5
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/C1R210V5
Overview
Introduction

This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and molecular subtypes.

Summary

Testing the association between copy number variation 82 arm-level events and 10 molecular subtypes across 257 patients, 376 significant findings detected with P value < 0.05 and Q value < 0.25.

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

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

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

  • 2q gain cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

  • 4q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

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

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

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

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

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

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

  • 8p gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 8q gain cnv correlated to 'CN_CNMF',  'RPPA_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 9p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

  • 10p gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

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

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

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

  • 14q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL', and 'MRNASEQ_CHIERARCHICAL'.

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

  • 16p gain cnv correlated to 'CN_CNMF'.

  • 16q gain cnv correlated to 'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • 18p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 18q gain cnv correlated to 'CN_CNMF'.

  • 19p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL', and 'MRNASEQ_CHIERARCHICAL'.

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

  • 20p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

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

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

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

  • xp gain cnv correlated to 'CN_CNMF'.

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

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

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

  • 2q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

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

  • 4p loss cnv correlated to 'CN_CNMF'.

  • 4q loss cnv correlated to 'CN_CNMF'.

  • 5p loss cnv correlated to 'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

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

  • 6p loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 6q loss cnv correlated to 'CN_CNMF'.

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

  • 7q loss cnv correlated to 'CN_CNMF'.

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

  • 8q loss cnv correlated to 'CN_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 9p loss cnv correlated to 'CN_CNMF'.

  • 9q loss cnv correlated to 'CN_CNMF'.

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

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

  • 11p loss cnv correlated to 'CN_CNMF' and 'RPPA_CHIERARCHICAL'.

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

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

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

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

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

  • 15q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 16p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'RPPA_CHIERARCHICAL'.

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

  • 17q loss cnv correlated to 'CN_CNMF'.

  • 18p loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

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

  • 19p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL', and 'MRNASEQ_CHIERARCHICAL'.

  • 19q loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

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

  • 20q loss cnv correlated to 'CN_CNMF'.

  • 21q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 22q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

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

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 82 arm-level events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 376 significant findings detected.

Clinical
Features 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
6q gain 49 (19%) 208 3e-05
(0.000482) 		0.00669
(0.0274) 		0.00525
(0.0235) 		0.0265
(0.0707) 		0.00158
(0.00946) 		0.00045
(0.00351) 		0.0103
(0.0354) 		0.00944
(0.0335) 		0.0174
(0.0519) 		0.0207
(0.0586)
10q loss 131 (51%) 126 1e-05
(0.000216) 		1e-05
(0.000216) 		4e-05
(0.000575) 		1e-05
(0.000216) 		1e-05
(0.000216) 		1e-05
(0.000216) 		4e-05
(0.000575) 		1e-05
(0.000216) 		0.00035
(0.00284) 		2e-05
(0.000364)
16q loss 124 (48%) 133 1e-05
(0.000216) 		1e-05
(0.000216) 		0.00541
(0.0239) 		0.0366
(0.0892) 		0.00092
(0.00615) 		0.00019
(0.00188) 		0.0172
(0.0517) 		0.00024
(0.00226) 		0.0005
(0.00373) 		7e-05
(0.000911)
3p gain 38 (15%) 219 0.00025
(0.00233) 		0.00032
(0.00282) 		0.00983
(0.0342) 		0.0147
(0.0468) 		0.0167
(0.0512) 		8e-05
(0.000994) 		0.158
(0.254) 		0.0253
(0.0681) 		0.00014
(0.00151) 		0.00764
(0.0289)
3q gain 35 (14%) 222 0.00118
(0.00733) 		0.00601
(0.0255) 		0.00116
(0.00732) 		0.01
(0.0346) 		0.0196
(0.0565) 		0.00268
(0.0139) 		0.179
(0.278) 		0.0132
(0.043) 		0.00063
(0.00442) 		0.00255
(0.0136)
6p gain 52 (20%) 205 1e-05
(0.000216) 		0.00021
(0.00203) 		0.00035
(0.00284) 		5e-05
(0.000672) 		0.00034
(0.00282) 		5e-05
(0.000672) 		0.0272
(0.072) 		0.0388
(0.0928) 		0.0515
(0.111) 		0.00783
(0.0292)
9q gain 71 (28%) 186 1e-05
(0.000216) 		1e-05
(0.000216) 		0.00842
(0.031) 		0.00016
(0.00164) 		0.00015
(0.0016) 		1e-05
(0.000216) 		0.0127
(0.042) 		0.00195
(0.011) 		0.0769
(0.149) 		0.00093
(0.00615)
2p loss 92 (36%) 165 1e-05
(0.000216) 		8e-05
(0.000994) 		0.071
(0.14) 		0.00304
(0.0153) 		3e-05
(0.000482) 		0.00016
(0.00164) 		0.00172
(0.0101) 		2e-05
(0.000364) 		0.00049
(0.00369) 		7e-05
(0.000911)
3p loss 56 (22%) 201 0.0881
(0.165) 		0.00032
(0.00282) 		0.00628
(0.0265) 		0.0026
(0.0136) 		0.00013
(0.00144) 		0.00024
(0.00226) 		9e-05
(0.0011) 		0.00767
(0.0289) 		1e-05
(0.000216) 		0.00109
(0.00693)
3q loss 51 (20%) 206 0.0214
(0.0597) 		0.00336
(0.0164) 		0.00743
(0.0287) 		0.0831
(0.158) 		0.00359
(0.0173) 		0.032
(0.0821) 		0.00572
(0.0247) 		0.0338
(0.0863) 		0.00818
(0.0302) 		0.0133
(0.0434)
xq loss 102 (40%) 155 1e-05
(0.000216) 		2e-05
(0.000364) 		0.00049
(0.00369) 		0.0403
(0.0953) 		4e-05
(0.000575) 		0.00033
(0.00282) 		0.00047
(0.0036) 		0.00072
(0.00492) 		0.0169
(0.0513) 		0.0924
(0.171)
2p gain 22 (9%) 235 0.017
(0.0513) 		0.00768
(0.0289) 		0.186
(0.286) 		0.0277
(0.0724) 		0.00103
(0.0067) 		0.00094
(0.00617) 		0.0971
(0.177) 		0.027
(0.0718) 		0.0486
(0.106) 		0.00383
(0.0182)
7p gain 82 (32%) 175 1e-05
(0.000216) 		0.00042
(0.00331) 		0.0437
(0.0994) 		0.00196
(0.011) 		0.00406
(0.0189) 		0.0201
(0.0575) 		0.072
(0.141) 		0.309
(0.416) 		0.00394
(0.0186) 		0.00213
(0.0118)
7q gain 67 (26%) 190 0.00067
(0.00466) 		0.0004
(0.00318) 		0.161
(0.259) 		0.00665
(0.0274) 		0.00164
(0.00974) 		0.0415
(0.0962) 		0.00874
(0.0319) 		0.311
(0.417) 		0.00105
(0.00678) 		0.00896
(0.0324)
9p gain 53 (21%) 204 1e-05
(0.000216) 		0.00055
(0.00403) 		0.0434
(0.0994) 		0.00061
(0.00435) 		0.0068
(0.0276) 		0.00057
(0.00414) 		0.0435
(0.0994) 		0.0115
(0.0387) 		0.156
(0.252) 		0.0885
(0.165)
12p gain 41 (16%) 216 0.00011
(0.00125) 		0.0201
(0.0575) 		0.0065
(0.0271) 		0.0524
(0.112) 		0.00034
(0.00282) 		0.00087
(0.0059) 		0.0462
(0.102) 		0.0607
(0.125) 		0.0047
(0.0214) 		0.0194
(0.0562)
20q gain 83 (32%) 174 1e-05
(0.000216) 		1e-05
(0.000216) 		0.00755
(0.0289) 		0.00427
(0.0197) 		0.0524
(0.112) 		0.0194
(0.0562) 		0.233
(0.337) 		0.00561
(0.0245) 		0.00441
(0.0202) 		0.0074
(0.0287)
22q gain 58 (23%) 199 0.00013
(0.00144) 		0.00014
(0.00151) 		0.00727
(0.0286) 		0.00039
(0.00314) 		0.0415
(0.0962) 		0.00714
(0.0286) 		0.591
(0.676) 		0.113
(0.199) 		0.0138
(0.0444) 		0.0408
(0.0957)
18q loss 69 (27%) 188 0.00303
(0.0153) 		0.0002
(0.00195) 		0.00365
(0.0175) 		0.00018
(0.0018) 		0.0479
(0.105) 		0.0274
(0.0721) 		0.0364
(0.0888) 		0.172
(0.271) 		0.0163
(0.0506) 		0.0735
(0.144)
4p gain 69 (27%) 188 1e-05
(0.000216) 		1e-05
(0.000216) 		0.0178
(0.0527) 		0.00034
(0.00282) 		0.048
(0.105) 		0.00701
(0.0282) 		0.0439
(0.0995) 		0.0536
(0.113) 		0.113
(0.199) 		0.124
(0.213)
12q gain 31 (12%) 226 0.00972
(0.0341) 		0.0589
(0.123) 		0.00257
(0.0136) 		0.265
(0.376) 		0.0112
(0.0379) 		0.0378
(0.0918) 		0.0104
(0.0356) 		0.0716
(0.141) 		0.0156
(0.049) 		0.0167
(0.0512)
17p gain 61 (24%) 196 1e-05
(0.000216) 		4e-05
(0.000575) 		0.0167
(0.0512) 		0.0654
(0.132) 		0.0233
(0.0638) 		0.0181
(0.0533) 		0.0968
(0.177) 		0.00896
(0.0324) 		0.228
(0.331) 		0.0213
(0.0596)
19q gain 64 (25%) 193 1e-05
(0.000216) 		3e-05
(0.000482) 		0.0179
(0.0527) 		0.00011
(0.00125) 		0.00311
(0.0155) 		0.00011
(0.00125) 		0.742
(0.808) 		0.169
(0.269) 		0.309
(0.416) 		0.0109
(0.0371)
1q gain 51 (20%) 206 2e-05
(0.000364) 		0.00158
(0.00946) 		0.205
(0.308) 		0.0281
(0.0732) 		0.00472
(0.0214) 		0.144
(0.239) 		0.0713
(0.141) 		0.0899
(0.167) 		0.0443
(0.0999) 		0.0137
(0.0441)
5p gain 98 (38%) 159 1e-05
(0.000216) 		2e-05
(0.000364) 		0.183
(0.282) 		0.0192
(0.0561) 		0.0427
(0.0985) 		4e-05
(0.000575) 		0.757
(0.818) 		0.00184
(0.0106) 		0.89
(0.922) 		0.147
(0.242)
17q gain 56 (22%) 201 1e-05
(0.000216) 		0.0003
(0.00273) 		0.0809
(0.154) 		0.00694
(0.028) 		0.0808
(0.154) 		0.00292
(0.015) 		0.066
(0.133) 		0.0347
(0.0872) 		0.173
(0.271) 		0.0107
(0.0364)
1q loss 40 (16%) 217 0.00679
(0.0276) 		0.0192
(0.0561) 		0.29
(0.397) 		0.0949
(0.175) 		0.0777
(0.15) 		0.226
(0.331) 		0.0459
(0.102) 		0.0172
(0.0518) 		0.0234
(0.0641) 		0.00329
(0.0162)
5p loss 23 (9%) 234 0.451
(0.544) 		0.00728
(0.0286) 		0.0388
(0.0928) 		0.0454
(0.102) 		0.0437
(0.0994) 		0.0097
(0.0341) 		0.171
(0.271) 		0.601
(0.682) 		0.0163
(0.0506) 		0.064
(0.13)
2q gain 22 (9%) 235 0.0551
(0.116) 		0.035
(0.0872) 		0.288
(0.397) 		0.141
(0.235) 		0.00572
(0.0247) 		0.0098
(0.0342) 		0.209
(0.312) 		0.0465
(0.103) 		0.125
(0.214) 		0.0351
(0.0872)
16q gain 19 (7%) 238 0.0502
(0.109) 		0.0173
(0.0518) 		0.0243
(0.0661) 		0.00032
(0.00282) 		0.013
(0.0426) 		0.115
(0.202) 		1
(1.00) 		0.982
(0.985) 		0.0535
(0.113) 		0.0006
(0.00432)
5q loss 34 (13%) 223 0.0018
(0.0105) 		0.00051
(0.00377) 		0.0302
(0.078) 		0.00345
(0.0167) 		0.0763
(0.148) 		0.0352
(0.0872) 		0.78
(0.833) 		0.064
(0.13) 		0.063
(0.129) 		0.137
(0.231)
7p loss 32 (12%) 225 0.00783
(0.0292) 		0.00669
(0.0274) 		0.0149
(0.0472) 		0.117
(0.204) 		0.00903
(0.0325) 		0.0361
(0.0887) 		0.25
(0.357) 		0.356
(0.46) 		0.327
(0.43) 		0.433
(0.527)
8q loss 45 (18%) 212 0.00016
(0.00164) 		0.125
(0.213) 		0.432
(0.527) 		0.00033
(0.00282) 		0.0382
(0.0923) 		0.0357
(0.0879) 		0.269
(0.38) 		0.00588
(0.0252) 		0.218
(0.324) 		0.108
(0.191)
12p loss 67 (26%) 190 1e-05
(0.000216) 		0.00137
(0.00838) 		0.763
(0.823) 		0.46
(0.553) 		0.0302
(0.078) 		0.0027
(0.0139) 		0.792
(0.843) 		0.78
(0.833) 		0.0389
(0.0928) 		0.581
(0.672)
14q loss 62 (24%) 195 0.021
(0.0592) 		0.723
(0.791) 		0.931
(0.948) 		0.73
(0.798) 		0.41
(0.51) 		0.00026
(0.0024) 		0.187
(0.287) 		0.0452
(0.102) 		0.00233
(0.0125) 		0.015
(0.0472)
15q loss 46 (18%) 211 0.0128
(0.0422) 		0.035
(0.0872) 		0.202
(0.305) 		0.0646
(0.131) 		0.0802
(0.154) 		0.1
(0.181) 		0.0803
(0.154) 		0.00219
(0.012) 		0.0273
(0.072) 		0.0148
(0.0472)
20p loss 55 (21%) 202 0.00768
(0.0289) 		0.00787
(0.0292) 		0.966
(0.973) 		0.114
(0.2) 		0.0341
(0.0863) 		0.0754
(0.147) 		0.362
(0.466) 		0.00408
(0.0189) 		0.703
(0.772) 		0.00913
(0.0327)
xp loss 63 (25%) 194 0.00178
(0.0104) 		0.00329
(0.0162) 		0.0199
(0.0572) 		0.139
(0.233) 		0.00093
(0.00615) 		0.0249
(0.0671) 		0.0634
(0.129) 		0.0888
(0.165) 		0.721
(0.79) 		0.394
(0.494)
10q gain 11 (4%) 246 0.101
(0.183) 		0.0688
(0.137) 		0.0441
(0.0996) 		0.444
(0.537) 		0.0215
(0.0597) 		0.0405
(0.0955) 		0.339
(0.443) 		0.201
(0.304) 		0.0308
(0.0792) 		0.052
(0.111)
14q gain 56 (22%) 201 1e-05
(0.000216) 		0.00214
(0.0118) 		0.097
(0.177) 		3e-05
(0.000482) 		0.322
(0.428) 		0.00189
(0.0108) 		0.694
(0.766) 		0.689
(0.762) 		0.0571
(0.12) 		0.526
(0.618)
19p gain 88 (34%) 169 1e-05
(0.000216) 		0.0238
(0.0647) 		0.341
(0.445) 		0.0136
(0.044) 		0.118
(0.205) 		0.00294
(0.015) 		0.748
(0.811) 		0.308
(0.416) 		0.664
(0.74) 		0.372
(0.472)
20p gain 62 (24%) 195 1e-05
(0.000216) 		0.00232
(0.0125) 		0.365
(0.467) 		0.168
(0.267) 		0.464
(0.555) 		0.0415
(0.0962) 		0.751
(0.813) 		0.107
(0.191) 		0.0339
(0.0863) 		0.347
(0.451)
8p loss 62 (24%) 195 0.00017
(0.00172) 		0.0262
(0.0703) 		0.145
(0.24) 		0.00188
(0.0108) 		0.119
(0.206) 		0.0402
(0.0953) 		0.398
(0.499) 		0.0844
(0.16) 		0.405
(0.506) 		0.113
(0.199)
10p loss 121 (47%) 136 1e-05
(0.000216) 		0.0123
(0.0409) 		0.0458
(0.102) 		0.0686
(0.137) 		0.0941
(0.174) 		0.0161
(0.0502) 		0.138
(0.231) 		0.0618
(0.127) 		0.159
(0.256) 		0.509
(0.601)
13q loss 132 (51%) 125 1e-05
(0.000216) 		3e-05
(0.000482) 		0.0515
(0.111) 		0.0388
(0.0928) 		0.155
(0.251) 		0.00069
(0.00475) 		0.392
(0.493) 		0.143
(0.238) 		0.0789
(0.152) 		0.435
(0.528)
19p loss 24 (9%) 233 0.0202
(0.0575) 		0.00259
(0.0136) 		0.663
(0.74) 		0.0211
(0.0592) 		0.585
(0.673) 		0.0248
(0.0671) 		0.66
(0.738) 		0.869
(0.904) 		0.0658
(0.133) 		0.454
(0.547)
21q loss 50 (19%) 207 0.0021
(0.0117) 		0.0142
(0.0454) 		0.432
(0.527) 		0.00746
(0.0287) 		0.185
(0.285) 		0.326
(0.43) 		0.0433
(0.0994) 		0.421
(0.519) 		0.327
(0.43) 		0.222
(0.327)
5q gain 72 (28%) 185 0.00034
(0.00282) 		0.00641
(0.0268) 		0.51
(0.602) 		0.3
(0.408) 		0.616
(0.696) 		0.0123
(0.0409) 		0.369
(0.47) 		0.189
(0.29) 		0.596
(0.68) 		0.541
(0.631)
8q gain 66 (26%) 191 0.00139
(0.00844) 		0.162
(0.259) 		0.109
(0.194) 		0.00601
(0.0255) 		0.9
(0.927) 		0.0784
(0.151) 		0.351
(0.454) 		0.291
(0.398) 		0.0219
(0.0607) 		0.0697
(0.138)
11p gain 23 (9%) 234 0.00998
(0.0345) 		0.0352
(0.0872) 		0.95
(0.961) 		0.434
(0.528) 		0.12
(0.207) 		0.00725
(0.0286) 		0.365
(0.467) 		0.144
(0.239) 		0.137
(0.231) 		0.201
(0.304)
11q gain 21 (8%) 236 0.0207
(0.0586) 		0.0494
(0.108) 		1
(1.00) 		0.787
(0.839) 		0.438
(0.53) 		0.00952
(0.0336) 		0.765
(0.823) 		0.362
(0.466) 		0.406
(0.507) 		0.623
(0.7)
15q gain 62 (24%) 195 4e-05
(0.000575) 		0.0286
(0.0742) 		0.866
(0.903) 		0.716
(0.785) 		0.131
(0.223) 		0.0276
(0.0722) 		0.182
(0.282) 		0.169
(0.269) 		0.0597
(0.124) 		0.068
(0.136)
21q gain 59 (23%) 198 1e-05
(0.000216) 		0.00384
(0.0182) 		0.225
(0.331) 		0.016
(0.05) 		0.753
(0.814) 		0.63
(0.708) 		0.837
(0.883) 		0.772
(0.827) 		0.0514
(0.111) 		0.306
(0.414)
2q loss 75 (29%) 182 1e-05
(0.000216) 		0.00109
(0.00693) 		0.061
(0.126) 		0.363
(0.466) 		0.15
(0.245) 		0.109
(0.193) 		0.779
(0.833) 		0.00729
(0.0286) 		0.499
(0.591) 		0.203
(0.305)
11q loss 93 (36%) 164 1e-05
(0.000216) 		0.28
(0.39) 		0.247
(0.354) 		0.00557
(0.0244) 		0.518
(0.61) 		0.0229
(0.063) 		0.291
(0.398) 		0.8
(0.848) 		0.212
(0.316) 		0.291
(0.398)
12q loss 59 (23%) 198 5e-05
(0.000672) 		0.00745
(0.0287) 		0.829
(0.876) 		0.467
(0.558) 		0.123
(0.211) 		0.0176
(0.0522) 		0.59
(0.676) 		0.68
(0.755) 		0.0864
(0.162) 		0.447
(0.54)
16p loss 75 (29%) 182 3e-05
(0.000482) 		0.00328
(0.0162) 		0.29
(0.397) 		0.0455
(0.102) 		0.879
(0.913) 		0.0679
(0.136) 		0.298
(0.405) 		0.27
(0.38) 		0.403
(0.503) 		0.413
(0.511)
22q loss 67 (26%) 190 5e-05
(0.000672) 		0.0353
(0.0872) 		0.385
(0.487) 		0.0556
(0.117) 		0.285
(0.395) 		0.00856
(0.0313) 		0.366
(0.467) 		0.489
(0.582) 		0.324
(0.43) 		0.201
(0.304)
1p gain 59 (23%) 198 1e-05
(0.000216) 		0.0001
(0.00119) 		0.235
(0.339) 		0.15
(0.245) 		0.316
(0.423) 		0.0505
(0.11) 		0.53
(0.62) 		0.323
(0.429) 		0.23
(0.333) 		0.0759
(0.148)
4q gain 48 (19%) 209 0.00401
(0.0188) 		0.00129
(0.00795) 		0.0527
(0.112) 		0.311
(0.417) 		0.339
(0.443) 		0.176
(0.275) 		0.384
(0.487) 		0.0595
(0.124) 		0.151
(0.246) 		0.228
(0.331)
8p gain 52 (20%) 205 0.0403
(0.0953) 		0.227
(0.331) 		0.347
(0.451) 		0.587
(0.675) 		0.647
(0.726) 		0.137
(0.231) 		0.759
(0.818) 		0.325
(0.43) 		0.175
(0.274) 		0.034
(0.0863)
10p gain 22 (9%) 235 0.00543
(0.0239) 		0.119
(0.206) 		0.26
(0.37) 		0.341
(0.445) 		0.0856
(0.161) 		0.137
(0.231) 		0.289
(0.397) 		0.367
(0.468) 		0.151
(0.246) 		0.0384
(0.0925)
13q gain 15 (6%) 242 0.00223
(0.0121) 		0.0415
(0.0962) 		0.278
(0.388) 		0.303
(0.411) 		0.0877
(0.164) 		0.134
(0.226) 		0.366
(0.467) 		0.771
(0.827) 		0.322
(0.428) 		0.651
(0.729)
18p gain 52 (20%) 205 0.0001
(0.00119) 		0.00924
(0.0329) 		0.411
(0.51) 		0.232
(0.336) 		0.105
(0.189) 		0.418
(0.516) 		0.281
(0.39) 		0.207
(0.31) 		0.463
(0.555) 		0.271
(0.381)
xq gain 34 (13%) 223 0.0272
(0.072) 		0.226
(0.331) 		0.198
(0.301) 		0.528
(0.619) 		0.196
(0.298) 		0.0812
(0.155) 		0.0437
(0.0994) 		0.425
(0.523) 		0.244
(0.35) 		0.281
(0.39)
6p loss 60 (23%) 197 8e-05
(0.000994) 		0.0406
(0.0955) 		0.147
(0.241) 		0.697
(0.767) 		0.122
(0.211) 		0.0956
(0.176) 		0.217
(0.324) 		0.596
(0.68) 		0.287
(0.397) 		0.173
(0.271)
11p loss 96 (37%) 161 2e-05
(0.000364) 		0.159
(0.256) 		0.903
(0.929) 		0.0345
(0.0871) 		0.931
(0.948) 		0.168
(0.267) 		0.671
(0.746) 		0.62
(0.698) 		0.12
(0.207) 		0.968
(0.974)
18p loss 61 (24%) 196 0.0113
(0.038) 		0.00637
(0.0268) 		0.106
(0.19) 		0.0622
(0.127) 		0.744
(0.809) 		0.386
(0.487) 		0.889
(0.922) 		0.112
(0.198) 		0.277
(0.388) 		0.7
(0.769)
19q loss 41 (16%) 216 0.00117
(0.00732) 		0.00062
(0.00438) 		0.53
(0.62) 		0.0509
(0.11) 		0.8
(0.848) 		0.261
(0.371) 		0.925
(0.946) 		0.588
(0.675) 		0.357
(0.461) 		0.927
(0.946)
16p gain 40 (16%) 217 1e-05
(0.000216) 		0.272
(0.381) 		0.219
(0.324) 		0.165
(0.263) 		0.131
(0.222) 		0.223
(0.329) 		0.949
(0.961) 		0.267
(0.377) 		0.539
(0.63) 		0.795
(0.846)
18q gain 37 (14%) 220 0.00542
(0.0239) 		0.39
(0.491) 		0.192
(0.293) 		0.129
(0.219) 		0.601
(0.682) 		0.247
(0.354) 		0.591
(0.676) 		0.177
(0.275) 		0.414
(0.512) 		0.859
(0.899)
xp gain 74 (29%) 183 0.00046
(0.00356) 		0.14
(0.233) 		0.431
(0.527) 		0.583
(0.673) 		0.865
(0.903) 		0.175
(0.274) 		0.266
(0.376) 		0.856
(0.898) 		0.455
(0.547) 		0.289
(0.397)
4p loss 41 (16%) 216 0.0364
(0.0888) 		0.688
(0.762) 		0.67
(0.746) 		0.911
(0.935) 		0.801
(0.848) 		0.955
(0.965) 		0.541
(0.631) 		0.859
(0.899) 		0.854
(0.897) 		0.294
(0.4)
4q loss 50 (19%) 207 0.0169
(0.0513) 		0.493
(0.586) 		0.905
(0.93) 		0.547
(0.636) 		0.899
(0.927) 		0.694
(0.766) 		0.601
(0.682) 		0.846
(0.891) 		0.556
(0.644) 		0.961
(0.971)
6q loss 52 (20%) 205 2e-05
(0.000364) 		0.105
(0.189) 		0.142
(0.236) 		0.101
(0.182) 		0.606
(0.685) 		0.0602
(0.125) 		0.485
(0.579) 		0.58
(0.671) 		0.0845
(0.16) 		0.963
(0.971)
7q loss 36 (14%) 221 0.0228
(0.063) 		0.343
(0.446) 		0.932
(0.948) 		0.734
(0.8) 		0.148
(0.243) 		0.108
(0.191) 		0.566
(0.656) 		0.327
(0.43) 		0.62
(0.698) 		0.869
(0.904)
9p loss 82 (32%) 175 1e-05
(0.000216) 		0.307
(0.415) 		0.184
(0.283) 		0.489
(0.582) 		0.393
(0.494) 		0.0869
(0.163) 		0.227
(0.331) 		0.666
(0.742) 		0.505
(0.598) 		0.218
(0.324)
9q loss 50 (19%) 207 1e-05
(0.000216) 		0.336
(0.441) 		0.602
(0.682) 		0.838
(0.883) 		0.22
(0.324) 		0.208
(0.311) 		0.598
(0.681) 		0.919
(0.941) 		0.173
(0.271) 		0.327
(0.43)
17q loss 49 (19%) 208 0.00507
(0.0228) 		0.411
(0.51) 		0.152
(0.248) 		0.18
(0.28) 		0.938
(0.953) 		0.419
(0.516) 		0.695
(0.767) 		0.431
(0.527) 		0.898
(0.927) 		0.362
(0.466)
20q loss 25 (10%) 232 0.0476
(0.105) 		0.892
(0.922) 		0.432
(0.527) 		0.177
(0.276) 		0.202
(0.304) 		0.747
(0.811) 		0.0997
(0.181) 		0.238
(0.343) 		0.389
(0.491) 		0.0558
(0.117)
1p loss 32 (12%) 225 0.0991
(0.181) 		0.234
(0.338) 		0.548
(0.636) 		0.914
(0.937) 		1
(1.00) 		0.495
(0.587) 		0.969
(0.974) 		0.526
(0.618) 		0.946
(0.96) 		0.435
(0.528)
17p loss 57 (22%) 200 0.069
(0.137) 		0.77
(0.827) 		0.823
(0.871) 		0.0997
(0.181) 		0.89
(0.922) 		0.257
(0.366) 		0.275
(0.385) 		0.27
(0.38) 		0.849
(0.893) 		0.319
(0.426)
'1p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
1P GAIN MUTATED 22 3 6 28
1P GAIN WILD-TYPE 73 57 33 35

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

'1p gain' versus 'METHLYATION_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.0012

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 56 72 75
1P GAIN MUTATED 7 5 16 31
1P GAIN WILD-TYPE 47 51 56 44

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

'1q gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00036

Table S3.  Gene #2: '1q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
1Q GAIN MUTATED 17 3 6 25
1Q GAIN WILD-TYPE 78 57 33 38

Figure S3.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #1: 'CN_CNMF'

'1q gain' versus 'METHLYATION_CNMF'

P value = 0.00158 (Fisher's exact test), Q value = 0.0095

Table S4.  Gene #2: '1q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 56 72 75
1Q GAIN MUTATED 3 8 22 18
1Q GAIN WILD-TYPE 51 48 50 57

Figure S4.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0281 (Fisher's exact test), Q value = 0.073

Table S5.  Gene #2: '1q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 35 49 68 22 22
1Q GAIN MUTATED 4 4 12 19 0 3
1Q GAIN WILD-TYPE 20 31 37 49 22 19

Figure S5.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'1q gain' versus 'MRNASEQ_CNMF'

P value = 0.00472 (Fisher's exact test), Q value = 0.021

Table S6.  Gene #2: '1q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 77 64
1Q GAIN MUTATED 21 24 6
1Q GAIN WILD-TYPE 93 53 58

Figure S6.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'1q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0443 (Fisher's exact test), Q value = 0.1

Table S7.  Gene #2: '1q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 27 47 23 39
1Q GAIN MUTATED 6 4 15 6 11
1Q GAIN WILD-TYPE 52 23 32 17 28

Figure S7.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'1q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0137 (Fisher's exact test), Q value = 0.044

Table S8.  Gene #2: '1q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 49 21 42 24
1Q GAIN MUTATED 7 16 8 9 2
1Q GAIN WILD-TYPE 51 33 13 33 22

Figure S8.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2p gain' versus 'CN_CNMF'

P value = 0.017 (Fisher's exact test), Q value = 0.051

Table S9.  Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
2P GAIN MUTATED 15 2 3 2
2P GAIN WILD-TYPE 80 58 36 61

Figure S9.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

'2p gain' versus 'METHLYATION_CNMF'

P value = 0.00768 (Fisher's exact test), Q value = 0.029

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 56 72 75
2P GAIN MUTATED 3 6 1 12
2P GAIN WILD-TYPE 51 50 71 63

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

'2p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0277 (Fisher's exact test), Q value = 0.072

Table S11.  Gene #3: '2p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 35 49 68 22 22
2P GAIN MUTATED 2 3 7 2 2 6
2P GAIN WILD-TYPE 22 32 42 66 20 16

Figure S11.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'2p gain' versus 'MRNASEQ_CNMF'

P value = 0.00103 (Fisher's exact test), Q value = 0.0067

Table S12.  Gene #3: '2p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 77 64
2P GAIN MUTATED 9 1 12
2P GAIN WILD-TYPE 105 76 52

Figure S12.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00094 (Fisher's exact test), Q value = 0.0062

Table S13.  Gene #3: '2p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 21 49 46 30 29 33
2P GAIN MUTATED 3 0 1 10 6 0 2
2P GAIN WILD-TYPE 44 21 48 36 24 29 31

Figure S13.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.027 (Fisher's exact test), Q value = 0.072

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 82 37 114 22
2P GAIN MUTATED 10 6 4 2
2P GAIN WILD-TYPE 72 31 110 20

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

'2p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0486 (Fisher's exact test), Q value = 0.11

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 27 47 23 39
2P GAIN MUTATED 8 3 0 2 5
2P GAIN WILD-TYPE 50 24 47 21 34

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

'2p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00383 (Fisher's exact test), Q value = 0.018

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 49 21 42 24
2P GAIN MUTATED 5 0 1 6 6
2P GAIN WILD-TYPE 53 49 20 36 18

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

'2q gain' versus 'METHLYATION_CNMF'

P value = 0.035 (Fisher's exact test), Q value = 0.087

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 56 72 75
2Q GAIN MUTATED 5 7 1 9
2Q GAIN WILD-TYPE 49 49 71 66

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

'2q gain' versus 'MRNASEQ_CNMF'

P value = 0.00572 (Fisher's exact test), Q value = 0.025

Table S18.  Gene #4: '2q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 77 64
2Q GAIN MUTATED 11 1 10
2Q GAIN WILD-TYPE 103 76 54

Figure S18.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0098 (Fisher's exact test), Q value = 0.034

Table S19.  Gene #4: '2q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 21 49 46 30 29 33
2Q GAIN MUTATED 4 2 1 8 6 0 1
2Q GAIN WILD-TYPE 43 19 48 38 24 29 32

Figure S19.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0465 (Fisher's exact test), Q value = 0.1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 82 37 114 22
2Q GAIN MUTATED 8 7 5 2
2Q GAIN WILD-TYPE 74 30 109 20

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

'2q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0351 (Fisher's exact test), Q value = 0.087

Table S21.  Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 49 21 42 24
2Q GAIN MUTATED 4 1 2 7 5
2Q GAIN WILD-TYPE 54 48 19 35 19

Figure S21.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3p gain' versus 'CN_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.0023

Table S22.  Gene #5: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
3P GAIN MUTATED 16 1 4 17
3P GAIN WILD-TYPE 79 59 35 46

Figure S22.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'

'3p gain' versus 'METHLYATION_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.0028

Table S23.  Gene #5: '3p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 56 72 75
3P GAIN MUTATED 9 0 12 17
3P GAIN WILD-TYPE 45 56 60 58

Figure S23.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p gain' versus 'RPPA_CNMF'

P value = 0.00983 (Fisher's exact test), Q value = 0.034

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 45 61 56
3P GAIN MUTATED 3 5 7 15
3P GAIN WILD-TYPE 55 40 54 41

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

'3p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0147 (Fisher's exact test), Q value = 0.047

Table S25.  Gene #5: '3p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 35 49 68 22 22
3P GAIN MUTATED 2 4 15 7 1 1
3P GAIN WILD-TYPE 22 31 34 61 21 21

Figure S25.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'3p gain' versus 'MRNASEQ_CNMF'

P value = 0.0167 (Fisher's exact test), Q value = 0.051

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 77 64
3P GAIN MUTATED 22 13 3
3P GAIN WILD-TYPE 92 64 61

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

'3p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00099

Table S27.  Gene #5: '3p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 21 49 46 30 29 33
3P GAIN MUTATED 3 4 9 0 11 3 8
3P GAIN WILD-TYPE 44 17 40 46 19 26 25

Figure S27.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0253 (Fisher's exact test), Q value = 0.068

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 82 37 114 22
3P GAIN MUTATED 14 2 22 0
3P GAIN WILD-TYPE 68 35 92 22

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

'3p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.0015

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 27 47 23 39
3P GAIN MUTATED 5 1 9 4 17
3P GAIN WILD-TYPE 53 26 38 19 22

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

'3p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00764 (Fisher's exact test), Q value = 0.029

Table S30.  Gene #5: '3p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 49 21 42 24
3P GAIN MUTATED 8 10 8 10 0
3P GAIN WILD-TYPE 50 39 13 32 24

Figure S30.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q gain' versus 'CN_CNMF'

P value = 0.00118 (Fisher's exact test), Q value = 0.0073

Table S31.  Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
3Q GAIN MUTATED 15 1 4 15
3Q GAIN WILD-TYPE 80 59 35 48

Figure S31.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

'3q gain' versus 'METHLYATION_CNMF'

P value = 0.00601 (Fisher's exact test), Q value = 0.026

Table S32.  Gene #6: '3q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 56 72 75
3Q GAIN MUTATED 10 1 9 15
3Q GAIN WILD-TYPE 44 55 63 60

Figure S32.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3q gain' versus 'RPPA_CNMF'

P value = 0.00116 (Fisher's exact test), Q value = 0.0073

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 45 61 56
3Q GAIN MUTATED 2 5 6 16
3Q GAIN WILD-TYPE 56 40 55 40

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

'3q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.01 (Fisher's exact test), Q value = 0.035

Table S34.  Gene #6: '3q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 35 49 68 22 22
3Q GAIN MUTATED 2 4 15 5 1 2
3Q GAIN WILD-TYPE 22 31 34 63 21 20

Figure S34.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'3q gain' versus 'MRNASEQ_CNMF'

P value = 0.0196 (Fisher's exact test), Q value = 0.057

Table S35.  Gene #6: '3q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 77 64
3Q GAIN MUTATED 22 10 3
3Q GAIN WILD-TYPE 92 67 61

Figure S35.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00268 (Fisher's exact test), Q value = 0.014

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 21 49 46 30 29 33
3Q GAIN MUTATED 4 4 7 1 10 2 7
3Q GAIN WILD-TYPE 43 17 42 45 20 27 26

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

'3q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0132 (Fisher's exact test), Q value = 0.043

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 82 37 114 22
3Q GAIN MUTATED 13 1 21 0
3Q GAIN WILD-TYPE 69 36 93 22

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

'3q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00063 (Fisher's exact test), Q value = 0.0044

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 27 47 23 39
3Q GAIN MUTATED 4 2 7 4 16
3Q GAIN WILD-TYPE 54 25 40 19 23

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

'3q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00255 (Fisher's exact test), Q value = 0.014

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 49 21 42 24
3Q GAIN MUTATED 7 8 9 9 0
3Q GAIN WILD-TYPE 51 41 12 33 24

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

'4p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S40.  Gene #7: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
4P GAIN MUTATED 34 3 8 24
4P GAIN WILD-TYPE 61 57 31 39

Figure S40.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

'4p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S41.  Gene #7: '4p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 56 72 75
4P GAIN MUTATED 9 9 14 37
4P GAIN WILD-TYPE 45 47 58 38

Figure S41.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4p gain' versus 'RPPA_CNMF'

P value = 0.0178 (Fisher's exact test), Q value = 0.053

Table S42.  Gene #7: '4p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 45 61 56
4P GAIN MUTATED 15 20 10 16
4P GAIN WILD-TYPE 43 25 51 40

Figure S42.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'4p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00034 (Fisher's exact test), Q value = 0.0028

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 35 49 68 22 22
4P GAIN MUTATED 8 9 26 11 3 4
4P GAIN WILD-TYPE 16 26 23 57 19 18

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

'4p gain' versus 'MRNASEQ_CNMF'

P value = 0.048 (Fisher's exact test), Q value = 0.11

Table S44.  Gene #7: '4p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 77 64
4P GAIN MUTATED 39 14 16
4P GAIN WILD-TYPE 75 63 48

Figure S44.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00701 (Fisher's exact test), Q value = 0.028

Table S45.  Gene #7: '4p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 21 49 46 30 29 33
4P GAIN MUTATED 14 3 8 9 15 6 14
4P GAIN WILD-TYPE 33 18 41 37 15 23 19

Figure S45.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4p gain' versus 'MIRSEQ_CNMF'

P value = 0.0439 (Fisher's exact test), Q value = 0.099

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 50 100
4P GAIN MUTATED 32 17 18
4P GAIN WILD-TYPE 73 33 82

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

'4q gain' versus 'CN_CNMF'

P value = 0.00401 (Fisher's exact test), Q value = 0.019

Table S47.  Gene #8: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
4Q GAIN MUTATED 20 3 7 18
4Q GAIN WILD-TYPE 75 57 32 45

Figure S47.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

'4q gain' versus 'METHLYATION_CNMF'

P value = 0.00129 (Fisher's exact test), Q value = 0.008

Table S48.  Gene #8: '4q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 56 72 75
4Q GAIN MUTATED 8 4 11 25
4Q GAIN WILD-TYPE 46 52 61 50

Figure S48.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S49.  Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
5P GAIN MUTATED 52 6 11 29
5P GAIN WILD-TYPE 43 54 28 34

Figure S49.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00036

Table S50.  Gene #9: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 56 72 75
5P GAIN MUTATED 15 11 26 46
5P GAIN WILD-TYPE 39 45 46 29

Figure S50.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0192 (Fisher's exact test), Q value = 0.056

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 35 49 68 22 22
5P GAIN MUTATED 11 13 29 21 7 5
5P GAIN WILD-TYPE 13 22 20 47 15 17

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

'5p gain' versus 'MRNASEQ_CNMF'

P value = 0.0427 (Fisher's exact test), Q value = 0.099

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 77 64
5P GAIN MUTATED 53 27 18
5P GAIN WILD-TYPE 61 50 46

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

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00058

Table S53.  Gene #9: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 21 49 46 30 29 33
5P GAIN MUTATED 26 4 22 10 18 4 14
5P GAIN WILD-TYPE 21 17 27 36 12 25 19

Figure S53.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00184 (Fisher's exact test), Q value = 0.011

Table S54.  Gene #9: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 82 37 114 22
5P GAIN MUTATED 40 10 46 2
5P GAIN WILD-TYPE 42 27 68 20

Figure S54.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5q gain' versus 'CN_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.0028

Table S55.  Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
5Q GAIN MUTATED 35 5 10 22
5Q GAIN WILD-TYPE 60 55 29 41

Figure S55.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

'5q gain' versus 'METHLYATION_CNMF'

P value = 0.00641 (Fisher's exact test), Q value = 0.027

Table S56.  Gene #10: '5q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 56 72 75
5Q GAIN MUTATED 13 8 20 31
5Q GAIN WILD-TYPE 41 48 52 44

Figure S56.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0123 (Fisher's exact test), Q value = 0.041

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 21 49 46 30 29 33
5Q GAIN MUTATED 19 3 17 8 12 3 9
5Q GAIN WILD-TYPE 28 18 32 38 18 26 24

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

'6p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S58.  Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
6P GAIN MUTATED 30 2 1 19
6P GAIN WILD-TYPE 65 58 38 44

Figure S58.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

'6p gain' versus 'METHLYATION_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.002

Table S59.  Gene #11: '6p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 56 72 75
6P GAIN MUTATED 9 9 6 28
6P GAIN WILD-TYPE 45 47 66 47

Figure S59.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p gain' versus 'RPPA_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.0028

Table S60.  Gene #11: '6p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 45 61 56
6P GAIN MUTATED 17 15 3 11
6P GAIN WILD-TYPE 41 30 58 45

Figure S60.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'6p gain' versus 'RPPA_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00067

Table S61.  Gene #11: '6p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 35 49 68 22 22
6P GAIN MUTATED 13 5 15 5 3 5
6P GAIN WILD-TYPE 11 30 34 63 19 17

Figure S61.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'6p gain' versus 'MRNASEQ_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.0028

Table S62.  Gene #11: '6p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 77 64
6P GAIN MUTATED 35 6 11
6P GAIN WILD-TYPE 79 71 53

Figure S62.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'6p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00067

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 21 49 46 30 29 33
6P GAIN MUTATED 22 3 3 6 7 3 8
6P GAIN WILD-TYPE 25 18 46 40 23 26 25

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

'6p gain' versus 'MIRSEQ_CNMF'

P value = 0.0272 (Fisher's exact test), Q value = 0.072

Table S64.  Gene #11: '6p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 50 100
6P GAIN MUTATED 25 14 12
6P GAIN WILD-TYPE 80 36 88

Figure S64.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'6p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0388 (Fisher's exact test), Q value = 0.093

Table S65.  Gene #11: '6p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 82 37 114 22
6P GAIN MUTATED 24 7 19 1
6P GAIN WILD-TYPE 58 30 95 21

Figure S65.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00783 (Fisher's exact test), Q value = 0.029

Table S66.  Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 49 21 42 24
6P GAIN MUTATED 17 5 9 9 2
6P GAIN WILD-TYPE 41 44 12 33 22

Figure S66.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q gain' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00048

Table S67.  Gene #12: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
6Q GAIN MUTATED 28 4 1 16
6Q GAIN WILD-TYPE 67 56 38 47

Figure S67.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

'6q gain' versus 'METHLYATION_CNMF'

P value = 0.00669 (Fisher's exact test), Q value = 0.027

Table S68.  Gene #12: '6q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 56 72 75
6Q GAIN MUTATED 9 9 7 24
6Q GAIN WILD-TYPE 45 47 65 51

Figure S68.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q gain' versus 'RPPA_CNMF'

P value = 0.00525 (Fisher's exact test), Q value = 0.024

Table S69.  Gene #12: '6q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 45 61 56
6Q GAIN MUTATED 18 12 5 8
6Q GAIN WILD-TYPE 40 33 56 48

Figure S69.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'6q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0265 (Fisher's exact test), Q value = 0.071

Table S70.  Gene #12: '6q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 35 49 68 22 22
6Q GAIN MUTATED 10 8 12 7 3 3
6Q GAIN WILD-TYPE 14 27 37 61 19 19

Figure S70.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'6q gain' versus 'MRNASEQ_CNMF'

P value = 0.00158 (Fisher's exact test), Q value = 0.0095

Table S71.  Gene #12: '6q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 77 64
6Q GAIN MUTATED 33 7 9
6Q GAIN WILD-TYPE 81 70 55

Figure S71.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'6q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00045 (Fisher's exact test), Q value = 0.0035

Table S72.  Gene #12: '6q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 21 49 46 30 29 33
6Q GAIN MUTATED 21 4 4 6 4 3 7
6Q GAIN WILD-TYPE 26 17 45 40 26 26 26

Figure S72.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6q gain' versus 'MIRSEQ_CNMF'

P value = 0.0103 (Fisher's exact test), Q value = 0.035

Table S73.  Gene #12: '6q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 50 100
6Q GAIN MUTATED 25 13 10
6Q GAIN WILD-TYPE 80 37 90

Figure S73.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'6q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00944 (Fisher's exact test), Q value = 0.034

Table S74.  Gene #12: '6q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 82 37 114 22
6Q GAIN MUTATED 25 5 17 1
6Q GAIN WILD-TYPE 57 32 97 21

Figure S74.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0174 (Fisher's exact test), Q value = 0.052

Table S75.  Gene #12: '6q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 27 47 23 39
6Q GAIN MUTATED 10 12 5 6 9
6Q GAIN WILD-TYPE 48 15 42 17 30

Figure S75.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'6q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0207 (Fisher's exact test), Q value = 0.059

Table S76.  Gene #12: '6q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 49 21 42 24
6Q GAIN MUTATED 18 5 7 10 2
6Q GAIN WILD-TYPE 40 44 14 32 22

Figure S76.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S77.  Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
7P GAIN MUTATED 44 4 8 26
7P GAIN WILD-TYPE 51 56 31 37

Figure S77.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 0.00042 (Fisher's exact test), Q value = 0.0033

Table S78.  Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 56 72 75
7P GAIN MUTATED 16 13 15 38
7P GAIN WILD-TYPE 38 43 57 37

Figure S78.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p gain' versus 'RPPA_CNMF'

P value = 0.0437 (Fisher's exact test), Q value = 0.099

Table S79.  Gene #13: '7p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 45 61 56
7P GAIN MUTATED 21 18 13 25
7P GAIN WILD-TYPE 37 27 48 31

Figure S79.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'7p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00196 (Fisher's exact test), Q value = 0.011

Table S80.  Gene #13: '7p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 35 49 68 22 22
7P GAIN MUTATED 13 8 24 14 11 7
7P GAIN WILD-TYPE 11 27 25 54 11 15

Figure S80.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 0.00406 (Fisher's exact test), Q value = 0.019

Table S81.  Gene #13: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 77 64
7P GAIN MUTATED 48 15 19
7P GAIN WILD-TYPE 66 62 45

Figure S81.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0201 (Fisher's exact test), Q value = 0.058

Table S82.  Gene #13: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 21 49 46 30 29 33
7P GAIN MUTATED 21 5 9 12 15 7 13
7P GAIN WILD-TYPE 26 16 40 34 15 22 20

Figure S82.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00394 (Fisher's exact test), Q value = 0.019

Table S83.  Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 27 47 23 39
7P GAIN MUTATED 16 11 8 11 20
7P GAIN WILD-TYPE 42 16 39 12 19

Figure S83.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'7p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00213 (Fisher's exact test), Q value = 0.012

Table S84.  Gene #13: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 49 21 42 24
7P GAIN MUTATED 17 9 13 20 7
7P GAIN WILD-TYPE 41 40 8 22 17

Figure S84.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 0.00067 (Fisher's exact test), Q value = 0.0047

Table S85.  Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
7Q GAIN MUTATED 37 6 9 15
7Q GAIN WILD-TYPE 58 54 30 48

Figure S85.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.0032

Table S86.  Gene #14: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 56 72 75
7Q GAIN MUTATED 17 8 11 31
7Q GAIN WILD-TYPE 37 48 61 44

Figure S86.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00665 (Fisher's exact test), Q value = 0.027

Table S87.  Gene #14: '7q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 35 49 68 22 22
7Q GAIN MUTATED 10 9 20 10 8 3
7Q GAIN WILD-TYPE 14 26 29 58 14 19

Figure S87.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 0.00164 (Fisher's exact test), Q value = 0.0097

Table S88.  Gene #14: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 77 64
7Q GAIN MUTATED 42 11 14
7Q GAIN WILD-TYPE 72 66 50

Figure S88.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0415 (Fisher's exact test), Q value = 0.096

Table S89.  Gene #14: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 21 49 46 30 29 33
7Q GAIN MUTATED 18 5 8 9 10 4 13
7Q GAIN WILD-TYPE 29 16 41 37 20 25 20

Figure S89.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_CNMF'

P value = 0.00874 (Fisher's exact test), Q value = 0.032

Table S90.  Gene #14: '7q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 50 100
7Q GAIN MUTATED 28 21 18
7Q GAIN WILD-TYPE 77 29 82

Figure S90.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'7q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00105 (Fisher's exact test), Q value = 0.0068

Table S91.  Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 27 47 23 39
7Q GAIN MUTATED 13 7 6 9 20
7Q GAIN WILD-TYPE 45 20 41 14 19

Figure S91.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'7q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00896 (Fisher's exact test), Q value = 0.032

Table S92.  Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 49 21 42 24
7Q GAIN MUTATED 17 7 10 17 4
7Q GAIN WILD-TYPE 41 42 11 25 20

Figure S92.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

P value = 0.0403 (Fisher's exact test), Q value = 0.095

Table S93.  Gene #15: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
8P GAIN MUTATED 24 5 10 13
8P GAIN WILD-TYPE 71 55 29 50

Figure S93.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

'8p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.034 (Fisher's exact test), Q value = 0.086

Table S94.  Gene #15: '8p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 49 21 42 24
8P GAIN MUTATED 11 9 11 9 4
8P GAIN WILD-TYPE 47 40 10 33 20

Figure S94.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q gain' versus 'CN_CNMF'

P value = 0.00139 (Fisher's exact test), Q value = 0.0084

Table S95.  Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
8Q GAIN MUTATED 33 5 11 17
8Q GAIN WILD-TYPE 62 55 28 46

Figure S95.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

'8q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00601 (Fisher's exact test), Q value = 0.026

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 35 49 68 22 22
8Q GAIN MUTATED 3 5 21 15 3 9
8Q GAIN WILD-TYPE 21 30 28 53 19 13

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

'8q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0219 (Fisher's exact test), Q value = 0.061

Table S97.  Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 27 47 23 39
8Q GAIN MUTATED 12 4 11 10 17
8Q GAIN WILD-TYPE 46 23 36 13 22

Figure S97.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'9p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S98.  Gene #17: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
9P GAIN MUTATED 21 5 2 25
9P GAIN WILD-TYPE 74 55 37 38

Figure S98.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

'9p gain' versus 'METHLYATION_CNMF'

P value = 0.00055 (Fisher's exact test), Q value = 0.004

Table S99.  Gene #17: '9p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 56 72 75
9P GAIN MUTATED 12 6 8 27
9P GAIN WILD-TYPE 42 50 64 48

Figure S99.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p gain' versus 'RPPA_CNMF'

P value = 0.0434 (Fisher's exact test), Q value = 0.099

Table S100.  Gene #17: '9p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 45 61 56
9P GAIN MUTATED 15 13 6 14
9P GAIN WILD-TYPE 43 32 55 42

Figure S100.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'9p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00061 (Fisher's exact test), Q value = 0.0043

Table S101.  Gene #17: '9p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 35 49 68 22 22
9P GAIN MUTATED 10 4 18 6 5 5
9P GAIN WILD-TYPE 14 31 31 62 17 17

Figure S101.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'9p gain' versus 'MRNASEQ_CNMF'

P value = 0.0068 (Fisher's exact test), Q value = 0.028

Table S102.  Gene #17: '9p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 77 64
9P GAIN MUTATED 33 8 12
9P GAIN WILD-TYPE 81 69 52

Figure S102.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00057 (Fisher's exact test), Q value = 0.0041

Table S103.  Gene #17: '9p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 21 49 46 30 29 33
9P GAIN MUTATED 17 7 5 3 10 3 8
9P GAIN WILD-TYPE 30 14 44 43 20 26 25

Figure S103.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9p gain' versus 'MIRSEQ_CNMF'

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

Table S104.  Gene #17: '9p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 50 100
9P GAIN MUTATED 28 12 13
9P GAIN WILD-TYPE 77 38 87

Figure S104.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'9p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0115 (Fisher's exact test), Q value = 0.039

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 82 37 114 22
9P GAIN MUTATED 26 9 16 2
9P GAIN WILD-TYPE 56 28 98 20

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

'9q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S106.  Gene #18: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
9Q GAIN MUTATED 37 5 3 26
9Q GAIN WILD-TYPE 58 55 36 37

Figure S106.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

'9q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S107.  Gene #18: '9q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 56 72 75
9Q GAIN MUTATED 17 7 11 36
9Q GAIN WILD-TYPE 37 49 61 39

Figure S107.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9q gain' versus 'RPPA_CNMF'

P value = 0.00842 (Fisher's exact test), Q value = 0.031

Table S108.  Gene #18: '9q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 45 61 56
9Q GAIN MUTATED 19 16 8 21
9Q GAIN WILD-TYPE 39 29 53 35

Figure S108.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'9q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.0016

Table S109.  Gene #18: '9q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 35 49 68 22 22
9Q GAIN MUTATED 12 7 23 9 8 5
9Q GAIN WILD-TYPE 12 28 26 59 14 17

Figure S109.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'9q gain' versus 'MRNASEQ_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.0016

Table S110.  Gene #18: '9q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 77 64
9Q GAIN MUTATED 46 11 14
9Q GAIN WILD-TYPE 68 66 50

Figure S110.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S111.  Gene #18: '9q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 21 49 46 30 29 33
9Q GAIN MUTATED 22 9 10 5 15 1 9
9Q GAIN WILD-TYPE 25 12 39 41 15 28 24

Figure S111.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9q gain' versus 'MIRSEQ_CNMF'

P value = 0.0127 (Fisher's exact test), Q value = 0.042

Table S112.  Gene #18: '9q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 50 100
9Q GAIN MUTATED 34 19 18
9Q GAIN WILD-TYPE 71 31 82

Figure S112.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'9q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00195 (Fisher's exact test), Q value = 0.011

Table S113.  Gene #18: '9q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 82 37 114 22
9Q GAIN MUTATED 32 13 25 1
9Q GAIN WILD-TYPE 50 24 89 21

Figure S113.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'9q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00093 (Fisher's exact test), Q value = 0.0061

Table S114.  Gene #18: '9q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 49 21 42 24
9Q GAIN MUTATED 21 10 11 20 2
9Q GAIN WILD-TYPE 37 39 10 22 22

Figure S114.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p gain' versus 'CN_CNMF'

P value = 0.00543 (Fisher's exact test), Q value = 0.024

Table S115.  Gene #19: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
10P GAIN MUTATED 9 2 0 11
10P GAIN WILD-TYPE 86 58 39 52

Figure S115.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

'10p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0384 (Fisher's exact test), Q value = 0.093

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 49 21 42 24
10P GAIN MUTATED 2 3 5 6 1
10P GAIN WILD-TYPE 56 46 16 36 23

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

'10q gain' versus 'RPPA_CNMF'

P value = 0.0441 (Fisher's exact test), Q value = 0.1

Table S117.  Gene #20: '10q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 45 61 56
10Q GAIN MUTATED 3 2 0 6
10Q GAIN WILD-TYPE 55 43 61 50

Figure S117.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'10q gain' versus 'MRNASEQ_CNMF'

P value = 0.0215 (Fisher's exact test), Q value = 0.06

Table S118.  Gene #20: '10q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 77 64
10Q GAIN MUTATED 9 0 2
10Q GAIN WILD-TYPE 105 77 62

Figure S118.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0405 (Fisher's exact test), Q value = 0.095

Table S119.  Gene #20: '10q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 21 49 46 30 29 33
10Q GAIN MUTATED 3 1 0 3 4 0 0
10Q GAIN WILD-TYPE 44 20 49 43 26 29 33

Figure S119.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0308 (Fisher's exact test), Q value = 0.079

Table S120.  Gene #20: '10q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 27 47 23 39
10Q GAIN MUTATED 3 3 0 0 5
10Q GAIN WILD-TYPE 55 24 47 23 34

Figure S120.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'11p gain' versus 'CN_CNMF'

P value = 0.00998 (Fisher's exact test), Q value = 0.035

Table S121.  Gene #21: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
11P GAIN MUTATED 12 0 3 8
11P GAIN WILD-TYPE 83 60 36 55

Figure S121.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

'11p gain' versus 'METHLYATION_CNMF'

P value = 0.0352 (Fisher's exact test), Q value = 0.087

Table S122.  Gene #21: '11p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 56 72 75
11P GAIN MUTATED 6 2 3 12
11P GAIN WILD-TYPE 48 54 69 63

Figure S122.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00725 (Fisher's exact test), Q value = 0.029

Table S123.  Gene #21: '11p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 21 49 46 30 29 33
11P GAIN MUTATED 6 0 1 2 8 2 3
11P GAIN WILD-TYPE 41 21 48 44 22 27 30

Figure S123.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11q gain' versus 'CN_CNMF'

P value = 0.0207 (Fisher's exact test), Q value = 0.059

Table S124.  Gene #22: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
11Q GAIN MUTATED 11 0 4 6
11Q GAIN WILD-TYPE 84 60 35 57

Figure S124.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

'11q gain' versus 'METHLYATION_CNMF'

P value = 0.0494 (Fisher's exact test), Q value = 0.11

Table S125.  Gene #22: '11q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 56 72 75
11Q GAIN MUTATED 5 1 4 11
11Q GAIN WILD-TYPE 49 55 68 64

Figure S125.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00952 (Fisher's exact test), Q value = 0.034

Table S126.  Gene #22: '11q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 21 49 46 30 29 33
11Q GAIN MUTATED 4 0 1 2 8 3 3
11Q GAIN WILD-TYPE 43 21 48 44 22 26 30

Figure S126.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'CN_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.0013

Table S127.  Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
12P GAIN MUTATED 28 3 5 5
12P GAIN WILD-TYPE 67 57 34 58

Figure S127.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 0.0201 (Fisher's exact test), Q value = 0.058

Table S128.  Gene #23: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 56 72 75
12P GAIN MUTATED 10 10 4 17
12P GAIN WILD-TYPE 44 46 68 58

Figure S128.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p gain' versus 'RPPA_CNMF'

P value = 0.0065 (Fisher's exact test), Q value = 0.027

Table S129.  Gene #23: '12p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 45 61 56
12P GAIN MUTATED 12 11 3 14
12P GAIN WILD-TYPE 46 34 58 42

Figure S129.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.0028

Table S130.  Gene #23: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 77 64
12P GAIN MUTATED 18 4 19
12P GAIN WILD-TYPE 96 73 45

Figure S130.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00087 (Fisher's exact test), Q value = 0.0059

Table S131.  Gene #23: '12p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 21 49 46 30 29 33
12P GAIN MUTATED 7 1 4 13 10 0 6
12P GAIN WILD-TYPE 40 20 45 33 20 29 27

Figure S131.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_CNMF'

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

Table S132.  Gene #23: '12p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 50 100
12P GAIN MUTATED 20 11 9
12P GAIN WILD-TYPE 85 39 91

Figure S132.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'12p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0047 (Fisher's exact test), Q value = 0.021

Table S133.  Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 27 47 23 39
12P GAIN MUTATED 14 2 2 6 11
12P GAIN WILD-TYPE 44 25 45 17 28

Figure S133.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'12p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0194 (Fisher's exact test), Q value = 0.056

Table S134.  Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 49 21 42 24
12P GAIN MUTATED 11 2 5 11 6
12P GAIN WILD-TYPE 47 47 16 31 18

Figure S134.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q gain' versus 'CN_CNMF'

P value = 0.00972 (Fisher's exact test), Q value = 0.034

Table S135.  Gene #24: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
12Q GAIN MUTATED 20 3 4 4
12Q GAIN WILD-TYPE 75 57 35 59

Figure S135.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

'12q gain' versus 'RPPA_CNMF'

P value = 0.00257 (Fisher's exact test), Q value = 0.014

Table S136.  Gene #24: '12q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 45 61 56
12Q GAIN MUTATED 9 10 1 10
12Q GAIN WILD-TYPE 49 35 60 46

Figure S136.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'12q gain' versus 'MRNASEQ_CNMF'

P value = 0.0112 (Fisher's exact test), Q value = 0.038

Table S137.  Gene #24: '12q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 77 64
12Q GAIN MUTATED 16 3 12
12Q GAIN WILD-TYPE 98 74 52

Figure S137.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0378 (Fisher's exact test), Q value = 0.092

Table S138.  Gene #24: '12q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 21 49 46 30 29 33
12Q GAIN MUTATED 9 1 2 8 7 1 3
12Q GAIN WILD-TYPE 38 20 47 38 23 28 30

Figure S138.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_CNMF'

P value = 0.0104 (Fisher's exact test), Q value = 0.036

Table S139.  Gene #24: '12q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 50 100
12Q GAIN MUTATED 15 10 5
12Q GAIN WILD-TYPE 90 40 95

Figure S139.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'12q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0156 (Fisher's exact test), Q value = 0.049

Table S140.  Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 27 47 23 39
12Q GAIN MUTATED 11 1 2 3 10
12Q GAIN WILD-TYPE 47 26 45 20 29

Figure S140.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'12q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0167 (Fisher's exact test), Q value = 0.051

Table S141.  Gene #24: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 49 21 42 24
12Q GAIN MUTATED 8 1 4 10 4
12Q GAIN WILD-TYPE 50 48 17 32 20

Figure S141.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q gain' versus 'CN_CNMF'

P value = 0.00223 (Fisher's exact test), Q value = 0.012

Table S142.  Gene #25: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
13Q GAIN MUTATED 2 1 2 10
13Q GAIN WILD-TYPE 93 59 37 53

Figure S142.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

'13q gain' versus 'METHLYATION_CNMF'

P value = 0.0415 (Fisher's exact test), Q value = 0.096

Table S143.  Gene #25: '13q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 56 72 75
13Q GAIN MUTATED 0 2 8 5
13Q GAIN WILD-TYPE 54 54 64 70

Figure S143.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'14q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S144.  Gene #26: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
14Q GAIN MUTATED 27 1 6 22
14Q GAIN WILD-TYPE 68 59 33 41

Figure S144.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

'14q gain' versus 'METHLYATION_CNMF'

P value = 0.00214 (Fisher's exact test), Q value = 0.012

Table S145.  Gene #26: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 56 72 75
14Q GAIN MUTATED 5 9 15 27
14Q GAIN WILD-TYPE 49 47 57 48

Figure S145.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'14q gain' versus 'RPPA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00048

Table S146.  Gene #26: '14q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 35 49 68 22 22
14Q GAIN MUTATED 9 4 24 10 1 3
14Q GAIN WILD-TYPE 15 31 25 58 21 19

Figure S146.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00189 (Fisher's exact test), Q value = 0.011

Table S147.  Gene #26: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 21 49 46 30 29 33
14Q GAIN MUTATED 10 2 12 6 16 3 7
14Q GAIN WILD-TYPE 37 19 37 40 14 26 26

Figure S147.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'15q gain' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00058

Table S148.  Gene #27: '15q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
15Q GAIN MUTATED 29 2 11 20
15Q GAIN WILD-TYPE 66 58 28 43

Figure S148.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #1: 'CN_CNMF'

'15q gain' versus 'METHLYATION_CNMF'

P value = 0.0286 (Fisher's exact test), Q value = 0.074

Table S149.  Gene #27: '15q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 56 72 75
15Q GAIN MUTATED 10 7 24 21
15Q GAIN WILD-TYPE 44 49 48 54

Figure S149.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'15q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0276 (Fisher's exact test), Q value = 0.072

Table S150.  Gene #27: '15q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 21 49 46 30 29 33
15Q GAIN MUTATED 12 2 19 9 11 5 4
15Q GAIN WILD-TYPE 35 19 30 37 19 24 29

Figure S150.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S151.  Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
16P GAIN MUTATED 22 1 1 16
16P GAIN WILD-TYPE 73 59 38 47

Figure S151.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

'16q gain' versus 'METHLYATION_CNMF'

P value = 0.0173 (Fisher's exact test), Q value = 0.052

Table S152.  Gene #29: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 56 72 75
16Q GAIN MUTATED 4 3 1 11
16Q GAIN WILD-TYPE 50 53 71 64

Figure S152.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q gain' versus 'RPPA_CNMF'

P value = 0.0243 (Fisher's exact test), Q value = 0.066

Table S153.  Gene #29: '16q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 45 61 56
16Q GAIN MUTATED 5 5 0 6
16Q GAIN WILD-TYPE 53 40 61 50

Figure S153.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'16q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00032 (Fisher's exact test), Q value = 0.0028

Table S154.  Gene #29: '16q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 35 49 68 22 22
16Q GAIN MUTATED 4 1 9 0 0 2
16Q GAIN WILD-TYPE 20 34 40 68 22 20

Figure S154.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'16q gain' versus 'MRNASEQ_CNMF'

P value = 0.013 (Fisher's exact test), Q value = 0.043

Table S155.  Gene #29: '16q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 77 64
16Q GAIN MUTATED 14 1 4
16Q GAIN WILD-TYPE 100 76 60

Figure S155.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6e-04 (Fisher's exact test), Q value = 0.0043

Table S156.  Gene #29: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 49 21 42 24
16Q GAIN MUTATED 6 0 6 1 3
16Q GAIN WILD-TYPE 52 49 15 41 21

Figure S156.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S157.  Gene #30: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
17P GAIN MUTATED 34 2 4 21
17P GAIN WILD-TYPE 61 58 35 42

Figure S157.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

'17p gain' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00058

Table S158.  Gene #30: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 56 72 75
17P GAIN MUTATED 9 8 10 34
17P GAIN WILD-TYPE 45 48 62 41

Figure S158.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p gain' versus 'RPPA_CNMF'

P value = 0.0167 (Fisher's exact test), Q value = 0.051

Table S159.  Gene #30: '17p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 45 61 56
17P GAIN MUTATED 11 14 8 20
17P GAIN WILD-TYPE 47 31 53 36

Figure S159.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'17p gain' versus 'MRNASEQ_CNMF'

P value = 0.0233 (Fisher's exact test), Q value = 0.064

Table S160.  Gene #30: '17p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 77 64
17P GAIN MUTATED 36 12 12
17P GAIN WILD-TYPE 78 65 52

Figure S160.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0181 (Fisher's exact test), Q value = 0.053

Table S161.  Gene #30: '17p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 21 49 46 30 29 33
17P GAIN MUTATED 19 3 6 8 11 6 7
17P GAIN WILD-TYPE 28 18 43 38 19 23 26

Figure S161.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00896 (Fisher's exact test), Q value = 0.032

Table S162.  Gene #30: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 82 37 114 22
17P GAIN MUTATED 24 14 22 1
17P GAIN WILD-TYPE 58 23 92 21

Figure S162.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0213 (Fisher's exact test), Q value = 0.06

Table S163.  Gene #30: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 49 21 42 24
17P GAIN MUTATED 15 7 7 16 2
17P GAIN WILD-TYPE 43 42 14 26 22

Figure S163.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S164.  Gene #31: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
17Q GAIN MUTATED 25 1 7 23
17Q GAIN WILD-TYPE 70 59 32 40

Figure S164.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.0027

Table S165.  Gene #31: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 56 72 75
17Q GAIN MUTATED 9 7 10 30
17Q GAIN WILD-TYPE 45 49 62 45

Figure S165.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00694 (Fisher's exact test), Q value = 0.028

Table S166.  Gene #31: '17q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 35 49 68 22 22
17Q GAIN MUTATED 11 6 15 7 5 4
17Q GAIN WILD-TYPE 13 29 34 61 17 18

Figure S166.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00292 (Fisher's exact test), Q value = 0.015

Table S167.  Gene #31: '17q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 21 49 46 30 29 33
17Q GAIN MUTATED 17 2 4 6 11 8 7
17Q GAIN WILD-TYPE 30 19 45 40 19 21 26

Figure S167.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0347 (Fisher's exact test), Q value = 0.087

Table S168.  Gene #31: '17q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 82 37 114 22
17Q GAIN MUTATED 22 12 21 1
17Q GAIN WILD-TYPE 60 25 93 21

Figure S168.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0107 (Fisher's exact test), Q value = 0.036

Table S169.  Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 49 21 42 24
17Q GAIN MUTATED 12 9 7 18 2
17Q GAIN WILD-TYPE 46 40 14 24 22

Figure S169.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p gain' versus 'CN_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.0012

Table S170.  Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
18P GAIN MUTATED 24 2 6 20
18P GAIN WILD-TYPE 71 58 33 43

Figure S170.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 0.00924 (Fisher's exact test), Q value = 0.033

Table S171.  Gene #32: '18p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 56 72 75
18P GAIN MUTATED 9 6 12 25
18P GAIN WILD-TYPE 45 50 60 50

Figure S171.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18q gain' versus 'CN_CNMF'

P value = 0.00542 (Fisher's exact test), Q value = 0.024

Table S172.  Gene #33: '18q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
18Q GAIN MUTATED 16 2 4 15
18Q GAIN WILD-TYPE 79 58 35 48

Figure S172.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #1: 'CN_CNMF'

'19p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S173.  Gene #34: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
19P GAIN MUTATED 57 3 6 22
19P GAIN WILD-TYPE 38 57 33 41

Figure S173.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

'19p gain' versus 'METHLYATION_CNMF'

P value = 0.0238 (Fisher's exact test), Q value = 0.065

Table S174.  Gene #34: '19p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 56 72 75
19P GAIN MUTATED 18 14 20 36
19P GAIN WILD-TYPE 36 42 52 39

Figure S174.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0136 (Fisher's exact test), Q value = 0.044

Table S175.  Gene #34: '19p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 35 49 68 22 22
19P GAIN MUTATED 15 11 22 19 9 4
19P GAIN WILD-TYPE 9 24 27 49 13 18

Figure S175.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00294 (Fisher's exact test), Q value = 0.015

Table S176.  Gene #34: '19p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 21 49 46 30 29 33
19P GAIN MUTATED 28 6 13 13 13 9 6
19P GAIN WILD-TYPE 19 15 36 33 17 20 27

Figure S176.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S177.  Gene #35: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
19Q GAIN MUTATED 39 2 3 20
19Q GAIN WILD-TYPE 56 58 36 43

Figure S177.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

'19q gain' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00048

Table S178.  Gene #35: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 56 72 75
19Q GAIN MUTATED 14 6 11 33
19Q GAIN WILD-TYPE 40 50 61 42

Figure S178.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19q gain' versus 'RPPA_CNMF'

P value = 0.0179 (Fisher's exact test), Q value = 0.053

Table S179.  Gene #35: '19q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 45 61 56
19Q GAIN MUTATED 22 13 8 14
19Q GAIN WILD-TYPE 36 32 53 42

Figure S179.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'19q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.0013

Table S180.  Gene #35: '19q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 35 49 68 22 22
19Q GAIN MUTATED 14 9 18 8 6 2
19Q GAIN WILD-TYPE 10 26 31 60 16 20

Figure S180.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 0.00311 (Fisher's exact test), Q value = 0.016

Table S181.  Gene #35: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 77 64
19Q GAIN MUTATED 40 11 13
19Q GAIN WILD-TYPE 74 66 51

Figure S181.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.0013

Table S182.  Gene #35: '19q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 21 49 46 30 29 33
19Q GAIN MUTATED 24 4 7 6 12 4 7
19Q GAIN WILD-TYPE 23 17 42 40 18 25 26

Figure S182.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0109 (Fisher's exact test), Q value = 0.037

Table S183.  Gene #35: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 49 21 42 24
19Q GAIN MUTATED 20 10 9 11 1
19Q GAIN WILD-TYPE 38 39 12 31 23

Figure S183.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S184.  Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
20P GAIN MUTATED 38 1 9 14
20P GAIN WILD-TYPE 57 59 30 49

Figure S184.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 0.00232 (Fisher's exact test), Q value = 0.012

Table S185.  Gene #36: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 56 72 75
20P GAIN MUTATED 8 9 15 30
20P GAIN WILD-TYPE 46 47 57 45

Figure S185.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0415 (Fisher's exact test), Q value = 0.096

Table S186.  Gene #36: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 21 49 46 30 29 33
20P GAIN MUTATED 18 1 11 8 10 5 9
20P GAIN WILD-TYPE 29 20 38 38 20 24 24

Figure S186.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0339 (Fisher's exact test), Q value = 0.086

Table S187.  Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 27 47 23 39
20P GAIN MUTATED 9 10 9 9 14
20P GAIN WILD-TYPE 49 17 38 14 25

Figure S187.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S188.  Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
20Q GAIN MUTATED 53 2 9 19
20Q GAIN WILD-TYPE 42 58 30 44

Figure S188.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S189.  Gene #37: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 56 72 75
20Q GAIN MUTATED 11 12 15 45
20Q GAIN WILD-TYPE 43 44 57 30

Figure S189.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20q gain' versus 'RPPA_CNMF'

P value = 0.00755 (Fisher's exact test), Q value = 0.029

Table S190.  Gene #37: '20q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 45 61 56
20Q GAIN MUTATED 16 23 14 24
20Q GAIN WILD-TYPE 42 22 47 32

Figure S190.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'20q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00427 (Fisher's exact test), Q value = 0.02

Table S191.  Gene #37: '20q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 35 49 68 22 22
20Q GAIN MUTATED 9 11 28 14 7 8
20Q GAIN WILD-TYPE 15 24 21 54 15 14

Figure S191.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0194 (Fisher's exact test), Q value = 0.056

Table S192.  Gene #37: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 21 49 46 30 29 33
20Q GAIN MUTATED 20 5 12 14 16 4 12
20Q GAIN WILD-TYPE 27 16 37 32 14 25 21

Figure S192.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00561 (Fisher's exact test), Q value = 0.024

Table S193.  Gene #37: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 82 37 114 22
20Q GAIN MUTATED 34 13 35 1
20Q GAIN WILD-TYPE 48 24 79 21

Figure S193.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00441 (Fisher's exact test), Q value = 0.02

Table S194.  Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 27 47 23 39
20Q GAIN MUTATED 13 13 11 11 20
20Q GAIN WILD-TYPE 45 14 36 12 19

Figure S194.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0074 (Fisher's exact test), Q value = 0.029

Table S195.  Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 49 21 42 24
20Q GAIN MUTATED 22 12 10 21 3
20Q GAIN WILD-TYPE 36 37 11 21 21

Figure S195.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S196.  Gene #38: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
21Q GAIN MUTATED 26 2 5 26
21Q GAIN WILD-TYPE 69 58 34 37

Figure S196.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

'21q gain' versus 'METHLYATION_CNMF'

P value = 0.00384 (Fisher's exact test), Q value = 0.018

Table S197.  Gene #38: '21q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 56 72 75
21Q GAIN MUTATED 6 10 15 28
21Q GAIN WILD-TYPE 48 46 57 47

Figure S197.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'21q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.016 (Fisher's exact test), Q value = 0.05

Table S198.  Gene #38: '21q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 35 49 68 22 22
21Q GAIN MUTATED 10 3 16 13 3 7
21Q GAIN WILD-TYPE 14 32 33 55 19 15

Figure S198.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'22q gain' versus 'CN_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.0014

Table S199.  Gene #39: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
22Q GAIN MUTATED 31 2 10 15
22Q GAIN WILD-TYPE 64 58 29 48

Figure S199.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

'22q gain' versus 'METHLYATION_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.0015

Table S200.  Gene #39: '22q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 56 72 75
22Q GAIN MUTATED 10 4 15 29
22Q GAIN WILD-TYPE 44 52 57 46

Figure S200.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q gain' versus 'RPPA_CNMF'

P value = 0.00727 (Fisher's exact test), Q value = 0.029

Table S201.  Gene #39: '22q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 45 61 56
22Q GAIN MUTATED 8 19 12 11
22Q GAIN WILD-TYPE 50 26 49 45

Figure S201.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'22q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00039 (Fisher's exact test), Q value = 0.0031

Table S202.  Gene #39: '22q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 35 49 68 22 22
22Q GAIN MUTATED 4 3 23 13 5 2
22Q GAIN WILD-TYPE 20 32 26 55 17 20

Figure S202.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'22q gain' versus 'MRNASEQ_CNMF'

P value = 0.0415 (Fisher's exact test), Q value = 0.096

Table S203.  Gene #39: '22q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 77 64
22Q GAIN MUTATED 34 15 9
22Q GAIN WILD-TYPE 80 62 55

Figure S203.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'22q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00714 (Fisher's exact test), Q value = 0.029

Table S204.  Gene #39: '22q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 21 49 46 30 29 33
22Q GAIN MUTATED 11 3 11 4 13 4 12
22Q GAIN WILD-TYPE 36 18 38 42 17 25 21

Figure S204.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0138 (Fisher's exact test), Q value = 0.044

Table S205.  Gene #39: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 27 47 23 39
22Q GAIN MUTATED 8 4 9 10 14
22Q GAIN WILD-TYPE 50 23 38 13 25

Figure S205.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'22q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0408 (Fisher's exact test), Q value = 0.096

Table S206.  Gene #39: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 49 21 42 24
22Q GAIN MUTATED 10 11 9 13 2
22Q GAIN WILD-TYPE 48 38 12 29 22

Figure S206.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xp gain' versus 'CN_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.0036

Table S207.  Gene #40: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
XP GAIN MUTATED 36 6 9 23
XP GAIN WILD-TYPE 59 54 30 40

Figure S207.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'

'xq gain' versus 'CN_CNMF'

P value = 0.0272 (Fisher's exact test), Q value = 0.072

Table S208.  Gene #41: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
XQ GAIN MUTATED 20 4 2 8
XQ GAIN WILD-TYPE 75 56 37 55

Figure S208.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

'xq gain' versus 'MIRSEQ_CNMF'

P value = 0.0437 (Fisher's exact test), Q value = 0.099

Table S209.  Gene #41: 'xq gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 50 100
XQ GAIN MUTATED 16 10 7
XQ GAIN WILD-TYPE 89 40 93

Figure S209.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'1q loss' versus 'CN_CNMF'

P value = 0.00679 (Fisher's exact test), Q value = 0.028

Table S210.  Gene #43: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
1Q LOSS MUTATED 20 2 5 13
1Q LOSS WILD-TYPE 75 58 34 50

Figure S210.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

'1q loss' versus 'METHLYATION_CNMF'

P value = 0.0192 (Fisher's exact test), Q value = 0.056

Table S211.  Gene #43: '1q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 56 72 75
1Q LOSS MUTATED 9 7 5 19
1Q LOSS WILD-TYPE 45 49 67 56

Figure S211.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1q loss' versus 'MIRSEQ_CNMF'

P value = 0.0459 (Fisher's exact test), Q value = 0.1

Table S212.  Gene #43: '1q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 50 100
1Q LOSS MUTATED 20 11 9
1Q LOSS WILD-TYPE 85 39 91

Figure S212.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'1q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0172 (Fisher's exact test), Q value = 0.052

Table S213.  Gene #43: '1q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 82 37 114 22
1Q LOSS MUTATED 21 6 12 1
1Q LOSS WILD-TYPE 61 31 102 21

Figure S213.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'1q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0234 (Fisher's exact test), Q value = 0.064

Table S214.  Gene #43: '1q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 27 47 23 39
1Q LOSS MUTATED 12 7 4 0 8
1Q LOSS WILD-TYPE 46 20 43 23 31

Figure S214.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'1q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00329 (Fisher's exact test), Q value = 0.016

Table S215.  Gene #43: '1q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 49 21 42 24
1Q LOSS MUTATED 16 3 1 10 1
1Q LOSS WILD-TYPE 42 46 20 32 23

Figure S215.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S216.  Gene #44: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
2P LOSS MUTATED 36 2 12 42
2P LOSS WILD-TYPE 59 58 27 21

Figure S216.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

'2p loss' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00099

Table S217.  Gene #44: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 56 72 75
2P LOSS MUTATED 12 12 40 28
2P LOSS WILD-TYPE 42 44 32 47

Figure S217.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00304 (Fisher's exact test), Q value = 0.015

Table S218.  Gene #44: '2p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 35 49 68 22 22
2P LOSS MUTATED 13 8 17 32 6 2
2P LOSS WILD-TYPE 11 27 32 36 16 20

Figure S218.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'2p loss' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00048

Table S219.  Gene #44: '2p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 77 64
2P LOSS MUTATED 40 41 10
2P LOSS WILD-TYPE 74 36 54

Figure S219.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.0016

Table S220.  Gene #44: '2p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 21 49 46 30 29 33
2P LOSS MUTATED 22 6 28 6 7 12 10
2P LOSS WILD-TYPE 25 15 21 40 23 17 23

Figure S220.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_CNMF'

P value = 0.00172 (Fisher's exact test), Q value = 0.01

Table S221.  Gene #44: '2p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 50 100
2P LOSS MUTATED 25 20 47
2P LOSS WILD-TYPE 80 30 53

Figure S221.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'2p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00036

Table S222.  Gene #44: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 82 37 114 22
2P LOSS MUTATED 27 7 57 1
2P LOSS WILD-TYPE 55 30 57 21

Figure S222.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.0037

Table S223.  Gene #44: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 27 47 23 39
2P LOSS MUTATED 12 14 28 7 13
2P LOSS WILD-TYPE 46 13 19 16 26

Figure S223.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'2p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00091

Table S224.  Gene #44: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 49 21 42 24
2P LOSS MUTATED 19 29 10 15 1
2P LOSS WILD-TYPE 39 20 11 27 23

Figure S224.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S225.  Gene #45: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
2Q LOSS MUTATED 36 1 7 31
2Q LOSS WILD-TYPE 59 59 32 32

Figure S225.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

'2q loss' versus 'METHLYATION_CNMF'

P value = 0.00109 (Fisher's exact test), Q value = 0.0069

Table S226.  Gene #45: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 56 72 75
2Q LOSS MUTATED 9 9 26 31
2Q LOSS WILD-TYPE 45 47 46 44

Figure S226.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00729 (Fisher's exact test), Q value = 0.029

Table S227.  Gene #45: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 82 37 114 22
2Q LOSS MUTATED 28 4 40 3
2Q LOSS WILD-TYPE 54 33 74 19

Figure S227.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'METHLYATION_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.0028

Table S228.  Gene #46: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 56 72 75
3P LOSS MUTATED 10 17 5 24
3P LOSS WILD-TYPE 44 39 67 51

Figure S228.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p loss' versus 'RPPA_CNMF'

P value = 0.00628 (Fisher's exact test), Q value = 0.027

Table S229.  Gene #46: '3p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 45 61 56
3P LOSS MUTATED 17 16 6 11
3P LOSS WILD-TYPE 41 29 55 45

Figure S229.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'3p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0026 (Fisher's exact test), Q value = 0.014

Table S230.  Gene #46: '3p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 35 49 68 22 22
3P LOSS MUTATED 9 9 12 5 8 7
3P LOSS WILD-TYPE 15 26 37 63 14 15

Figure S230.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.0014

Table S231.  Gene #46: '3p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 77 64
3P LOSS MUTATED 31 5 20
3P LOSS WILD-TYPE 83 72 44

Figure S231.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.0023

Table S232.  Gene #46: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 21 49 46 30 29 33
3P LOSS MUTATED 19 3 3 15 8 2 6
3P LOSS WILD-TYPE 28 18 46 31 22 27 27

Figure S232.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.0011

Table S233.  Gene #46: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 50 100
3P LOSS MUTATED 31 16 8
3P LOSS WILD-TYPE 74 34 92

Figure S233.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00767 (Fisher's exact test), Q value = 0.029

Table S234.  Gene #46: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 82 37 114 22
3P LOSS MUTATED 25 7 15 8
3P LOSS WILD-TYPE 57 30 99 14

Figure S234.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S235.  Gene #46: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 27 47 23 39
3P LOSS MUTATED 14 16 2 4 9
3P LOSS WILD-TYPE 44 11 45 19 30

Figure S235.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'3p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00109 (Fisher's exact test), Q value = 0.0069

Table S236.  Gene #46: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 49 21 42 24
3P LOSS MUTATED 17 2 4 14 8
3P LOSS WILD-TYPE 41 47 17 28 16

Figure S236.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

P value = 0.0214 (Fisher's exact test), Q value = 0.06

Table S237.  Gene #47: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
3Q LOSS MUTATED 28 6 6 11
3Q LOSS WILD-TYPE 67 54 33 52

Figure S237.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

'3q loss' versus 'METHLYATION_CNMF'

P value = 0.00336 (Fisher's exact test), Q value = 0.016

Table S238.  Gene #47: '3q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 56 72 75
3Q LOSS MUTATED 7 13 7 24
3Q LOSS WILD-TYPE 47 43 65 51

Figure S238.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3q loss' versus 'RPPA_CNMF'

P value = 0.00743 (Fisher's exact test), Q value = 0.029

Table S239.  Gene #47: '3q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 45 61 56
3Q LOSS MUTATED 13 17 7 8
3Q LOSS WILD-TYPE 45 28 54 48

Figure S239.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'3q loss' versus 'MRNASEQ_CNMF'

P value = 0.00359 (Fisher's exact test), Q value = 0.017

Table S240.  Gene #47: '3q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 77 64
3Q LOSS MUTATED 24 7 20
3Q LOSS WILD-TYPE 90 70 44

Figure S240.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.032 (Fisher's exact test), Q value = 0.082

Table S241.  Gene #47: '3q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 21 49 46 30 29 33
3Q LOSS MUTATED 15 2 5 12 8 2 7
3Q LOSS WILD-TYPE 32 19 44 34 22 27 26

Figure S241.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_CNMF'

P value = 0.00572 (Fisher's exact test), Q value = 0.025

Table S242.  Gene #47: '3q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 50 100
3Q LOSS MUTATED 27 13 10
3Q LOSS WILD-TYPE 78 37 90

Figure S242.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0338 (Fisher's exact test), Q value = 0.086

Table S243.  Gene #47: '3q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 82 37 114 22
3Q LOSS MUTATED 23 7 14 6
3Q LOSS WILD-TYPE 59 30 100 16

Figure S243.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00818 (Fisher's exact test), Q value = 0.03

Table S244.  Gene #47: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 27 47 23 39
3Q LOSS MUTATED 12 12 4 3 8
3Q LOSS WILD-TYPE 46 15 43 20 31

Figure S244.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'3q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0133 (Fisher's exact test), Q value = 0.043

Table S245.  Gene #47: '3q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 49 21 42 24
3Q LOSS MUTATED 16 4 1 12 6
3Q LOSS WILD-TYPE 42 45 20 30 18

Figure S245.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

P value = 0.0364 (Fisher's exact test), Q value = 0.089

Table S246.  Gene #48: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
4P LOSS MUTATED 18 4 4 15
4P LOSS WILD-TYPE 77 56 35 48

Figure S246.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

'4q loss' versus 'CN_CNMF'

P value = 0.0169 (Fisher's exact test), Q value = 0.051

Table S247.  Gene #49: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
4Q LOSS MUTATED 23 4 7 16
4Q LOSS WILD-TYPE 72 56 32 47

Figure S247.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

'5p loss' versus 'METHLYATION_CNMF'

P value = 0.00728 (Fisher's exact test), Q value = 0.029

Table S248.  Gene #50: '5p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 56 72 75
5P LOSS MUTATED 3 4 2 14
5P LOSS WILD-TYPE 51 52 70 61

Figure S248.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p loss' versus 'RPPA_CNMF'

P value = 0.0388 (Fisher's exact test), Q value = 0.093

Table S249.  Gene #50: '5p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 45 61 56
5P LOSS MUTATED 8 5 1 8
5P LOSS WILD-TYPE 50 40 60 48

Figure S249.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'5p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0454 (Fisher's exact test), Q value = 0.1

Table S250.  Gene #50: '5p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 35 49 68 22 22
5P LOSS MUTATED 3 3 9 2 4 1
5P LOSS WILD-TYPE 21 32 40 66 18 21

Figure S250.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'5p loss' versus 'MRNASEQ_CNMF'

P value = 0.0437 (Fisher's exact test), Q value = 0.099

Table S251.  Gene #50: '5p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 77 64
5P LOSS MUTATED 14 2 7
5P LOSS WILD-TYPE 100 75 57

Figure S251.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0097 (Fisher's exact test), Q value = 0.034

Table S252.  Gene #50: '5p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 21 49 46 30 29 33
5P LOSS MUTATED 5 2 0 2 5 2 7
5P LOSS WILD-TYPE 42 19 49 44 25 27 26

Figure S252.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0163 (Fisher's exact test), Q value = 0.051

Table S253.  Gene #50: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 27 47 23 39
5P LOSS MUTATED 5 4 0 3 7
5P LOSS WILD-TYPE 53 23 47 20 32

Figure S253.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'5q loss' versus 'CN_CNMF'

P value = 0.0018 (Fisher's exact test), Q value = 0.01

Table S254.  Gene #51: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
5Q LOSS MUTATED 17 1 3 13
5Q LOSS WILD-TYPE 78 59 36 50

Figure S254.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 0.00051 (Fisher's exact test), Q value = 0.0038

Table S255.  Gene #51: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 56 72 75
5Q LOSS MUTATED 4 4 5 21
5Q LOSS WILD-TYPE 50 52 67 54

Figure S255.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q loss' versus 'RPPA_CNMF'

P value = 0.0302 (Fisher's exact test), Q value = 0.078

Table S256.  Gene #51: '5q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 45 61 56
5Q LOSS MUTATED 9 11 3 9
5Q LOSS WILD-TYPE 49 34 58 47

Figure S256.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'5q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00345 (Fisher's exact test), Q value = 0.017

Table S257.  Gene #51: '5q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 35 49 68 22 22
5Q LOSS MUTATED 5 3 13 3 6 2
5Q LOSS WILD-TYPE 19 32 36 65 16 20

Figure S257.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0352 (Fisher's exact test), Q value = 0.087

Table S258.  Gene #51: '5q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 21 49 46 30 29 33
5Q LOSS MUTATED 8 3 2 3 6 3 9
5Q LOSS WILD-TYPE 39 18 47 43 24 26 24

Figure S258.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6p loss' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00099

Table S259.  Gene #52: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
6P LOSS MUTATED 24 4 18 14
6P LOSS WILD-TYPE 71 56 21 49

Figure S259.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

'6p loss' versus 'METHLYATION_CNMF'

P value = 0.0406 (Fisher's exact test), Q value = 0.095

Table S260.  Gene #52: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 56 72 75
6P LOSS MUTATED 7 10 24 19
6P LOSS WILD-TYPE 47 46 48 56

Figure S260.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00036

Table S261.  Gene #53: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
6Q LOSS MUTATED 24 2 15 11
6Q LOSS WILD-TYPE 71 58 24 52

Figure S261.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

'7p loss' versus 'CN_CNMF'

P value = 0.00783 (Fisher's exact test), Q value = 0.029

Table S262.  Gene #54: '7p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
7P LOSS MUTATED 17 1 4 10
7P LOSS WILD-TYPE 78 59 35 53

Figure S262.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #1: 'CN_CNMF'

'7p loss' versus 'METHLYATION_CNMF'

P value = 0.00669 (Fisher's exact test), Q value = 0.027

Table S263.  Gene #54: '7p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 56 72 75
7P LOSS MUTATED 2 3 15 12
7P LOSS WILD-TYPE 52 53 57 63

Figure S263.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p loss' versus 'RPPA_CNMF'

P value = 0.0149 (Fisher's exact test), Q value = 0.047

Table S264.  Gene #54: '7p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 45 61 56
7P LOSS MUTATED 5 6 15 3
7P LOSS WILD-TYPE 53 39 46 53

Figure S264.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'7p loss' versus 'MRNASEQ_CNMF'

P value = 0.00903 (Fisher's exact test), Q value = 0.032

Table S265.  Gene #54: '7p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 77 64
7P LOSS MUTATED 14 15 2
7P LOSS WILD-TYPE 100 62 62

Figure S265.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0361 (Fisher's exact test), Q value = 0.089

Table S266.  Gene #54: '7p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 21 49 46 30 29 33
7P LOSS MUTATED 6 2 13 2 4 1 3
7P LOSS WILD-TYPE 41 19 36 44 26 28 30

Figure S266.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7q loss' versus 'CN_CNMF'

P value = 0.0228 (Fisher's exact test), Q value = 0.063

Table S267.  Gene #55: '7q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
7Q LOSS MUTATED 17 2 5 12
7Q LOSS WILD-TYPE 78 58 34 51

Figure S267.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #1: 'CN_CNMF'

'8p loss' versus 'CN_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.0017

Table S268.  Gene #56: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
8P LOSS MUTATED 30 4 6 22
8P LOSS WILD-TYPE 65 56 33 41

Figure S268.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 0.0262 (Fisher's exact test), Q value = 0.07

Table S269.  Gene #56: '8p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 56 72 75
8P LOSS MUTATED 9 14 12 27
8P LOSS WILD-TYPE 45 42 60 48

Figure S269.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00188 (Fisher's exact test), Q value = 0.011

Table S270.  Gene #56: '8p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 35 49 68 22 22
8P LOSS MUTATED 11 3 20 12 6 5
8P LOSS WILD-TYPE 13 32 29 56 16 17

Figure S270.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0402 (Fisher's exact test), Q value = 0.095

Table S271.  Gene #56: '8p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 21 49 46 30 29 33
8P LOSS MUTATED 17 3 6 7 10 8 10
8P LOSS WILD-TYPE 30 18 43 39 20 21 23

Figure S271.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8q loss' versus 'CN_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.0016

Table S272.  Gene #57: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
8Q LOSS MUTATED 22 3 2 18
8Q LOSS WILD-TYPE 73 57 37 45

Figure S272.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

'8q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00033 (Fisher's exact test), Q value = 0.0028

Table S273.  Gene #57: '8q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 35 49 68 22 22
8Q LOSS MUTATED 11 4 13 7 4 0
8Q LOSS WILD-TYPE 13 31 36 61 18 22

Figure S273.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'8q loss' versus 'MRNASEQ_CNMF'

P value = 0.0382 (Fisher's exact test), Q value = 0.092

Table S274.  Gene #57: '8q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 77 64
8Q LOSS MUTATED 28 10 7
8Q LOSS WILD-TYPE 86 67 57

Figure S274.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0357 (Fisher's exact test), Q value = 0.088

Table S275.  Gene #57: '8q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 21 49 46 30 29 33
8Q LOSS MUTATED 17 3 6 4 5 4 6
8Q LOSS WILD-TYPE 30 18 43 42 25 25 27

Figure S275.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00588 (Fisher's exact test), Q value = 0.025

Table S276.  Gene #57: '8q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 82 37 114 22
8Q LOSS MUTATED 23 5 17 0
8Q LOSS WILD-TYPE 59 32 97 22

Figure S276.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S277.  Gene #58: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
9P LOSS MUTATED 49 8 16 9
9P LOSS WILD-TYPE 46 52 23 54

Figure S277.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S278.  Gene #59: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
9Q LOSS MUTATED 31 2 9 8
9Q LOSS WILD-TYPE 64 58 30 55

Figure S278.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

'10p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S279.  Gene #60: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
10P LOSS MUTATED 48 6 31 36
10P LOSS WILD-TYPE 47 54 8 27

Figure S279.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 0.0123 (Fisher's exact test), Q value = 0.041

Table S280.  Gene #60: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 56 72 75
10P LOSS MUTATED 18 21 42 40
10P LOSS WILD-TYPE 36 35 30 35

Figure S280.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10p loss' versus 'RPPA_CNMF'

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

Table S281.  Gene #60: '10p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 45 61 56
10P LOSS MUTATED 19 20 35 29
10P LOSS WILD-TYPE 39 25 26 27

Figure S281.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0161 (Fisher's exact test), Q value = 0.05

Table S282.  Gene #60: '10p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 21 49 46 30 29 33
10P LOSS MUTATED 23 6 34 18 12 11 16
10P LOSS WILD-TYPE 24 15 15 28 18 18 17

Figure S282.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S283.  Gene #61: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
10Q LOSS MUTATED 47 2 33 49
10Q LOSS WILD-TYPE 48 58 6 14

Figure S283.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S284.  Gene #61: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 56 72 75
10Q LOSS MUTATED 14 12 56 49
10Q LOSS WILD-TYPE 40 44 16 26

Figure S284.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10q loss' versus 'RPPA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00058

Table S285.  Gene #61: '10q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 45 61 56
10Q LOSS MUTATED 17 20 45 28
10Q LOSS WILD-TYPE 41 25 16 28

Figure S285.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'10q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S286.  Gene #61: '10q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 35 49 68 22 22
10Q LOSS MUTATED 13 7 32 44 7 7
10Q LOSS WILD-TYPE 11 28 17 24 15 15

Figure S286.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S287.  Gene #61: '10q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 77 64
10Q LOSS MUTATED 53 59 18
10Q LOSS WILD-TYPE 61 18 46

Figure S287.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S288.  Gene #61: '10q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 21 49 46 30 29 33
10Q LOSS MUTATED 24 6 43 9 13 16 19
10Q LOSS WILD-TYPE 23 15 6 37 17 13 14

Figure S288.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00058

Table S289.  Gene #61: '10q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 50 100
10Q LOSS MUTATED 36 27 67
10Q LOSS WILD-TYPE 69 23 33

Figure S289.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S290.  Gene #61: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 82 37 114 22
10Q LOSS MUTATED 35 14 78 3
10Q LOSS WILD-TYPE 47 23 36 19

Figure S290.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.0028

Table S291.  Gene #61: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 27 47 23 39
10Q LOSS MUTATED 19 12 36 13 21
10Q LOSS WILD-TYPE 39 15 11 10 18

Figure S291.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'10q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00036

Table S292.  Gene #61: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 49 21 42 24
10Q LOSS MUTATED 23 38 11 24 5
10Q LOSS WILD-TYPE 35 11 10 18 19

Figure S292.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00036

Table S293.  Gene #62: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
11P LOSS MUTATED 47 6 11 32
11P LOSS WILD-TYPE 48 54 28 31

Figure S293.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

'11p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0345 (Fisher's exact test), Q value = 0.087

Table S294.  Gene #62: '11p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 35 49 68 22 22
11P LOSS MUTATED 16 12 14 23 11 8
11P LOSS WILD-TYPE 8 23 35 45 11 14

Figure S294.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S295.  Gene #63: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
11Q LOSS MUTATED 44 7 8 34
11Q LOSS WILD-TYPE 51 53 31 29

Figure S295.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00557 (Fisher's exact test), Q value = 0.024

Table S296.  Gene #63: '11q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 35 49 68 22 22
11Q LOSS MUTATED 15 12 15 16 12 10
11Q LOSS WILD-TYPE 9 23 34 52 10 12

Figure S296.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'11q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0229 (Fisher's exact test), Q value = 0.063

Table S297.  Gene #63: '11q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 21 49 46 30 29 33
11Q LOSS MUTATED 23 11 17 19 5 6 11
11Q LOSS WILD-TYPE 24 10 32 27 25 23 22

Figure S297.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S298.  Gene #64: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
12P LOSS MUTATED 32 2 6 27
12P LOSS WILD-TYPE 63 58 33 36

Figure S298.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

'12p loss' versus 'METHLYATION_CNMF'

P value = 0.00137 (Fisher's exact test), Q value = 0.0084

Table S299.  Gene #64: '12p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 56 72 75
12P LOSS MUTATED 6 10 22 29
12P LOSS WILD-TYPE 48 46 50 46

Figure S299.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p loss' versus 'MRNASEQ_CNMF'

P value = 0.0302 (Fisher's exact test), Q value = 0.078

Table S300.  Gene #64: '12p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 77 64
12P LOSS MUTATED 36 21 9
12P LOSS WILD-TYPE 78 56 55

Figure S300.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0027 (Fisher's exact test), Q value = 0.014

Table S301.  Gene #64: '12p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 21 49 46 30 29 33
12P LOSS MUTATED 23 4 15 5 6 6 7
12P LOSS WILD-TYPE 24 17 34 41 24 23 26

Figure S301.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0389 (Fisher's exact test), Q value = 0.093

Table S302.  Gene #64: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 27 47 23 39
12P LOSS MUTATED 11 14 11 7 10
12P LOSS WILD-TYPE 47 13 36 16 29

Figure S302.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'12q loss' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00067

Table S303.  Gene #65: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
12Q LOSS MUTATED 28 2 7 22
12Q LOSS WILD-TYPE 67 58 32 41

Figure S303.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'

'12q loss' versus 'METHLYATION_CNMF'

P value = 0.00745 (Fisher's exact test), Q value = 0.029

Table S304.  Gene #65: '12q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 56 72 75
12Q LOSS MUTATED 6 8 21 24
12Q LOSS WILD-TYPE 48 48 51 51

Figure S304.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0176 (Fisher's exact test), Q value = 0.052

Table S305.  Gene #65: '12q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 21 49 46 30 29 33
12Q LOSS MUTATED 18 4 16 4 6 5 6
12Q LOSS WILD-TYPE 29 17 33 42 24 24 27

Figure S305.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S306.  Gene #66: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
13Q LOSS MUTATED 67 6 28 31
13Q LOSS WILD-TYPE 28 54 11 32

Figure S306.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00048

Table S307.  Gene #66: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 56 72 75
13Q LOSS MUTATED 20 19 39 54
13Q LOSS WILD-TYPE 34 37 33 21

Figure S307.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0388 (Fisher's exact test), Q value = 0.093

Table S308.  Gene #66: '13q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 35 49 68 22 22
13Q LOSS MUTATED 10 17 35 33 13 8
13Q LOSS WILD-TYPE 14 18 14 35 9 14

Figure S308.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00069 (Fisher's exact test), Q value = 0.0048

Table S309.  Gene #66: '13q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 21 49 46 30 29 33
13Q LOSS MUTATED 26 7 30 14 23 11 19
13Q LOSS WILD-TYPE 21 14 19 32 7 18 14

Figure S309.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 0.021 (Fisher's exact test), Q value = 0.059

Table S310.  Gene #67: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
14Q LOSS MUTATED 28 6 10 18
14Q LOSS WILD-TYPE 67 54 29 45

Figure S310.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.0024

Table S311.  Gene #67: '14q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 21 49 46 30 29 33
14Q LOSS MUTATED 17 4 6 8 2 15 10
14Q LOSS WILD-TYPE 30 17 43 38 28 14 23

Figure S311.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0452 (Fisher's exact test), Q value = 0.1

Table S312.  Gene #67: '14q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 82 37 114 22
14Q LOSS MUTATED 18 8 35 1
14Q LOSS WILD-TYPE 64 29 79 21

Figure S312.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00233 (Fisher's exact test), Q value = 0.012

Table S313.  Gene #67: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 27 47 23 39
14Q LOSS MUTATED 8 14 9 8 7
14Q LOSS WILD-TYPE 50 13 38 15 32

Figure S313.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'14q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.015 (Fisher's exact test), Q value = 0.047

Table S314.  Gene #67: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 49 21 42 24
14Q LOSS MUTATED 15 11 10 9 1
14Q LOSS WILD-TYPE 43 38 11 33 23

Figure S314.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 0.0128 (Fisher's exact test), Q value = 0.042

Table S315.  Gene #68: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
15Q LOSS MUTATED 26 6 3 11
15Q LOSS WILD-TYPE 69 54 36 52

Figure S315.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 0.035 (Fisher's exact test), Q value = 0.087

Table S316.  Gene #68: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 56 72 75
15Q LOSS MUTATED 8 10 7 21
15Q LOSS WILD-TYPE 46 46 65 54

Figure S316.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00219 (Fisher's exact test), Q value = 0.012

Table S317.  Gene #68: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 82 37 114 22
15Q LOSS MUTATED 24 7 15 0
15Q LOSS WILD-TYPE 58 30 99 22

Figure S317.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0273 (Fisher's exact test), Q value = 0.072

Table S318.  Gene #68: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 27 47 23 39
15Q LOSS MUTATED 11 8 3 4 12
15Q LOSS WILD-TYPE 47 19 44 19 27

Figure S318.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0148 (Fisher's exact test), Q value = 0.047

Table S319.  Gene #68: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 49 21 42 24
15Q LOSS MUTATED 16 4 3 13 2
15Q LOSS WILD-TYPE 42 45 18 29 22

Figure S319.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p loss' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00048

Table S320.  Gene #69: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
16P LOSS MUTATED 36 4 12 23
16P LOSS WILD-TYPE 59 56 27 40

Figure S320.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

'16p loss' versus 'METHLYATION_CNMF'

P value = 0.00328 (Fisher's exact test), Q value = 0.016

Table S321.  Gene #69: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 56 72 75
16P LOSS MUTATED 11 11 19 34
16P LOSS WILD-TYPE 43 45 53 41

Figure S321.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0455 (Fisher's exact test), Q value = 0.1

Table S322.  Gene #69: '16p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 35 49 68 22 22
16P LOSS MUTATED 9 6 23 16 6 7
16P LOSS WILD-TYPE 15 29 26 52 16 15

Figure S322.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'16q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S323.  Gene #70: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
16Q LOSS MUTATED 50 5 28 41
16Q LOSS WILD-TYPE 45 55 11 22

Figure S323.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S324.  Gene #70: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 56 72 75
16Q LOSS MUTATED 16 16 49 43
16Q LOSS WILD-TYPE 38 40 23 32

Figure S324.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q loss' versus 'RPPA_CNMF'

P value = 0.00541 (Fisher's exact test), Q value = 0.024

Table S325.  Gene #70: '16q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 45 61 56
16Q LOSS MUTATED 19 24 39 24
16Q LOSS WILD-TYPE 39 21 22 32

Figure S325.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'16q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0366 (Fisher's exact test), Q value = 0.089

Table S326.  Gene #70: '16q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 35 49 68 22 22
16Q LOSS MUTATED 11 10 29 39 9 8
16Q LOSS WILD-TYPE 13 25 20 29 13 14

Figure S326.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 0.00092 (Fisher's exact test), Q value = 0.0061

Table S327.  Gene #70: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 77 64
16Q LOSS MUTATED 51 50 22
16Q LOSS WILD-TYPE 63 27 42

Figure S327.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.0019

Table S328.  Gene #70: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 21 49 46 30 29 33
16Q LOSS MUTATED 25 5 34 11 15 16 17
16Q LOSS WILD-TYPE 22 16 15 35 15 13 16

Figure S328.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_CNMF'

P value = 0.0172 (Fisher's exact test), Q value = 0.052

Table S329.  Gene #70: '16q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 50 100
16Q LOSS MUTATED 40 25 58
16Q LOSS WILD-TYPE 65 25 42

Figure S329.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.0023

Table S330.  Gene #70: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 82 37 114 22
16Q LOSS MUTATED 39 9 69 6
16Q LOSS WILD-TYPE 43 28 45 16

Figure S330.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-04 (Fisher's exact test), Q value = 0.0037

Table S331.  Gene #70: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 27 47 23 39
16Q LOSS MUTATED 21 11 36 13 18
16Q LOSS WILD-TYPE 37 16 11 10 21

Figure S331.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00091

Table S332.  Gene #70: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 49 21 42 24
16Q LOSS MUTATED 23 38 9 23 6
16Q LOSS WILD-TYPE 35 11 12 19 18

Figure S332.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

P value = 0.00507 (Fisher's exact test), Q value = 0.023

Table S333.  Gene #72: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
17Q LOSS MUTATED 23 3 7 16
17Q LOSS WILD-TYPE 72 57 32 47

Figure S333.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

'18p loss' versus 'CN_CNMF'

P value = 0.0113 (Fisher's exact test), Q value = 0.038

Table S334.  Gene #73: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
18P LOSS MUTATED 31 6 9 15
18P LOSS WILD-TYPE 64 54 30 48

Figure S334.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

P value = 0.00637 (Fisher's exact test), Q value = 0.027

Table S335.  Gene #73: '18p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 56 72 75
18P LOSS MUTATED 8 8 17 28
18P LOSS WILD-TYPE 46 48 55 47

Figure S335.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 0.00303 (Fisher's exact test), Q value = 0.015

Table S336.  Gene #74: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
18Q LOSS MUTATED 34 6 11 18
18Q LOSS WILD-TYPE 61 54 28 45

Figure S336.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.002

Table S337.  Gene #74: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 56 72 75
18Q LOSS MUTATED 11 10 13 35
18Q LOSS WILD-TYPE 43 46 59 40

Figure S337.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18q loss' versus 'RPPA_CNMF'

P value = 0.00365 (Fisher's exact test), Q value = 0.018

Table S338.  Gene #74: '18q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 45 61 56
18Q LOSS MUTATED 9 17 12 23
18Q LOSS WILD-TYPE 49 28 49 33

Figure S338.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'18q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.0018

Table S339.  Gene #74: '18q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 35 49 68 22 22
18Q LOSS MUTATED 4 11 25 9 4 8
18Q LOSS WILD-TYPE 20 24 24 59 18 14

Figure S339.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 0.0479 (Fisher's exact test), Q value = 0.11

Table S340.  Gene #74: '18q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 77 64
18Q LOSS MUTATED 39 14 16
18Q LOSS WILD-TYPE 75 63 48

Figure S340.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0274 (Fisher's exact test), Q value = 0.072

Table S341.  Gene #74: '18q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 21 49 46 30 29 33
18Q LOSS MUTATED 12 5 10 10 15 4 13
18Q LOSS WILD-TYPE 35 16 39 36 15 25 20

Figure S341.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_CNMF'

P value = 0.0364 (Fisher's exact test), Q value = 0.089

Table S342.  Gene #74: '18q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 50 100
18Q LOSS MUTATED 29 20 20
18Q LOSS WILD-TYPE 76 30 80

Figure S342.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'18q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0163 (Fisher's exact test), Q value = 0.051

Table S343.  Gene #74: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 27 47 23 39
18Q LOSS MUTATED 18 5 8 8 19
18Q LOSS WILD-TYPE 40 22 39 15 20

Figure S343.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'19p loss' versus 'CN_CNMF'

P value = 0.0202 (Fisher's exact test), Q value = 0.058

Table S344.  Gene #75: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
19P LOSS MUTATED 9 1 3 11
19P LOSS WILD-TYPE 86 59 36 52

Figure S344.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

P value = 0.00259 (Fisher's exact test), Q value = 0.014

Table S345.  Gene #75: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 56 72 75
19P LOSS MUTATED 1 3 5 15
19P LOSS WILD-TYPE 53 53 67 60

Figure S345.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0211 (Fisher's exact test), Q value = 0.059

Table S346.  Gene #75: '19p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 35 49 68 22 22
19P LOSS MUTATED 1 2 11 5 0 4
19P LOSS WILD-TYPE 23 33 38 63 22 18

Figure S346.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0248 (Fisher's exact test), Q value = 0.067

Table S347.  Gene #75: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 21 49 46 30 29 33
19P LOSS MUTATED 1 1 2 4 6 3 7
19P LOSS WILD-TYPE 46 20 47 42 24 26 26

Figure S347.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 0.00117 (Fisher's exact test), Q value = 0.0073

Table S348.  Gene #76: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
19Q LOSS MUTATED 20 1 8 12
19Q LOSS WILD-TYPE 75 59 31 51

Figure S348.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

P value = 0.00062 (Fisher's exact test), Q value = 0.0044

Table S349.  Gene #76: '19q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 56 72 75
19Q LOSS MUTATED 1 7 13 20
19Q LOSS WILD-TYPE 53 49 59 55

Figure S349.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20p loss' versus 'CN_CNMF'

P value = 0.00768 (Fisher's exact test), Q value = 0.029

Table S350.  Gene #77: '20p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
20P LOSS MUTATED 21 5 8 21
20P LOSS WILD-TYPE 74 55 31 42

Figure S350.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #1: 'CN_CNMF'

'20p loss' versus 'METHLYATION_CNMF'

P value = 0.00787 (Fisher's exact test), Q value = 0.029

Table S351.  Gene #77: '20p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 56 72 75
20P LOSS MUTATED 11 4 17 23
20P LOSS WILD-TYPE 43 52 55 52

Figure S351.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20p loss' versus 'MRNASEQ_CNMF'

P value = 0.0341 (Fisher's exact test), Q value = 0.086

Table S352.  Gene #77: '20p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 77 64
20P LOSS MUTATED 31 16 7
20P LOSS WILD-TYPE 83 61 57

Figure S352.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00408 (Fisher's exact test), Q value = 0.019

Table S353.  Gene #77: '20p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 82 37 114 22
20P LOSS MUTATED 24 4 26 0
20P LOSS WILD-TYPE 58 33 88 22

Figure S353.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00913 (Fisher's exact test), Q value = 0.033

Table S354.  Gene #77: '20p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 49 21 42 24
20P LOSS MUTATED 13 11 5 15 0
20P LOSS WILD-TYPE 45 38 16 27 24

Figure S354.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q loss' versus 'CN_CNMF'

P value = 0.0476 (Fisher's exact test), Q value = 0.11

Table S355.  Gene #78: '20q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
20Q LOSS MUTATED 5 5 3 12
20Q LOSS WILD-TYPE 90 55 36 51

Figure S355.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #1: 'CN_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 0.0021 (Fisher's exact test), Q value = 0.012

Table S356.  Gene #79: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
21Q LOSS MUTATED 29 4 7 10
21Q LOSS WILD-TYPE 66 56 32 53

Figure S356.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

'21q loss' versus 'METHLYATION_CNMF'

P value = 0.0142 (Fisher's exact test), Q value = 0.045

Table S357.  Gene #79: '21q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 56 72 75
21Q LOSS MUTATED 9 6 11 24
21Q LOSS WILD-TYPE 45 50 61 51

Figure S357.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'21q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00746 (Fisher's exact test), Q value = 0.029

Table S358.  Gene #79: '21q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 35 49 68 22 22
21Q LOSS MUTATED 3 8 19 8 6 2
21Q LOSS WILD-TYPE 21 27 30 60 16 20

Figure S358.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_CNMF'

P value = 0.0433 (Fisher's exact test), Q value = 0.099

Table S359.  Gene #79: '21q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 50 100
21Q LOSS MUTATED 18 16 15
21Q LOSS WILD-TYPE 87 34 85

Figure S359.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00067

Table S360.  Gene #80: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
22Q LOSS MUTATED 24 6 7 30
22Q LOSS WILD-TYPE 71 54 32 33

Figure S360.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 0.0353 (Fisher's exact test), Q value = 0.087

Table S361.  Gene #80: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 56 72 75
22Q LOSS MUTATED 7 18 17 25
22Q LOSS WILD-TYPE 47 38 55 50

Figure S361.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00856 (Fisher's exact test), Q value = 0.031

Table S362.  Gene #80: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 21 49 46 30 29 33
22Q LOSS MUTATED 18 1 9 14 4 12 8
22Q LOSS WILD-TYPE 29 20 40 32 26 17 25

Figure S362.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xp loss' versus 'CN_CNMF'

P value = 0.00178 (Fisher's exact test), Q value = 0.01

Table S363.  Gene #81: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
XP LOSS MUTATED 23 5 13 22
XP LOSS WILD-TYPE 72 55 26 41

Figure S363.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'

'xp loss' versus 'METHLYATION_CNMF'

P value = 0.00329 (Fisher's exact test), Q value = 0.016

Table S364.  Gene #81: 'xp loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 56 72 75
XP LOSS MUTATED 6 11 28 18
XP LOSS WILD-TYPE 48 45 44 57

Figure S364.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xp loss' versus 'RPPA_CNMF'

P value = 0.0199 (Fisher's exact test), Q value = 0.057

Table S365.  Gene #81: 'xp loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 45 61 56
XP LOSS MUTATED 10 10 24 10
XP LOSS WILD-TYPE 48 35 37 46

Figure S365.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'xp loss' versus 'MRNASEQ_CNMF'

P value = 0.00093 (Fisher's exact test), Q value = 0.0061

Table S366.  Gene #81: 'xp loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 77 64
XP LOSS MUTATED 24 30 8
XP LOSS WILD-TYPE 90 47 56

Figure S366.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xp loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0249 (Fisher's exact test), Q value = 0.067

Table S367.  Gene #81: 'xp loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 21 49 46 30 29 33
XP LOSS MUTATED 11 2 17 7 5 13 7
XP LOSS WILD-TYPE 36 19 32 39 25 16 26

Figure S367.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xq loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S368.  Gene #82: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 60 39 63
XQ LOSS MUTATED 39 7 21 35
XQ LOSS WILD-TYPE 56 53 18 28

Figure S368.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00036

Table S369.  Gene #82: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 56 72 75
XQ LOSS MUTATED 11 17 44 30
XQ LOSS WILD-TYPE 43 39 28 45

Figure S369.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq loss' versus 'RPPA_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.0037

Table S370.  Gene #82: 'xq loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 45 61 56
XQ LOSS MUTATED 15 19 36 16
XQ LOSS WILD-TYPE 43 26 25 40

Figure S370.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'xq loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0403 (Fisher's exact test), Q value = 0.095

Table S371.  Gene #82: 'xq loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 35 49 68 22 22
XQ LOSS MUTATED 7 10 19 37 8 5
XQ LOSS WILD-TYPE 17 25 30 31 14 17

Figure S371.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'xq loss' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00058

Table S372.  Gene #82: 'xq loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 77 64
XQ LOSS MUTATED 37 47 17
XQ LOSS WILD-TYPE 77 30 47

Figure S372.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xq loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00033 (Fisher's exact test), Q value = 0.0028

Table S373.  Gene #82: 'xq loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 21 49 46 30 29 33
XQ LOSS MUTATED 21 4 30 13 5 16 12
XQ LOSS WILD-TYPE 26 17 19 33 25 13 21

Figure S373.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.0036

Table S374.  Gene #82: 'xq loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 50 100
XQ LOSS MUTATED 29 18 54
XQ LOSS WILD-TYPE 76 32 46

Figure S374.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'xq loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00072 (Fisher's exact test), Q value = 0.0049

Table S375.  Gene #82: 'xq loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 82 37 114 22
XQ LOSS MUTATED 24 9 61 7
XQ LOSS WILD-TYPE 58 28 53 15

Figure S375.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0169 (Fisher's exact test), Q value = 0.051

Table S376.  Gene #82: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 27 47 23 39
XQ LOSS MUTATED 16 13 23 13 10
XQ LOSS WILD-TYPE 42 14 24 10 29

Figure S376.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

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/SARC-TP/22534095/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/SARC-TP/22542442/SARC-TP.transferedmergedcluster.txt

  • Number of patients = 257

  • Number of significantly arm-level cnvs = 82

  • Number of molecular subtypes = 10

  • Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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