Correlation between copy number variations of arm-level result and molecular subtypes
Colorectal Adenocarcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C13T9GK3
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/C13T9GK3
Overview
Introduction

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

Summary

Testing the association between copy number variation 82 arm-level events and 12 molecular subtypes across 616 patients, 349 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 1p gain cnv correlated to 'RPPA_CNMF'.

  • 1q gain cnv correlated to 'CN_CNMF'.

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

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

  • 3p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

  • 4p gain cnv correlated to 'RPPA_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • 4q gain cnv correlated to 'CN_CNMF'.

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

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

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

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

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

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

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

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

  • 9p gain cnv correlated to 'CN_CNMF'.

  • 9q gain cnv correlated to 'CN_CNMF'.

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

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

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

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

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

  • 12q gain cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

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

  • 14q gain cnv correlated to 'CN_CNMF'.

  • 15q gain cnv correlated to 'MRNA_CHIERARCHICAL'.

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

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

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

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

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

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

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

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

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

  • 21q gain cnv correlated to 'CN_CNMF'.

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

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

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

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

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

  • 2p loss cnv correlated to 'CN_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 2q loss cnv correlated to 'RPPA_CHIERARCHICAL',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 3p loss cnv correlated to 'CN_CNMF'.

  • 3q loss cnv correlated to 'CN_CNMF'.

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

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

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

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

  • 6p loss cnv correlated to 'MRNA_CHIERARCHICAL' and 'MRNASEQ_CHIERARCHICAL'.

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

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

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

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

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

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

  • 11p loss cnv correlated to 'CN_CNMF'.

  • 11q loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

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

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

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

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

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

  • 16p loss cnv correlated to 'CN_CNMF'.

  • 16q loss cnv correlated to 'MRNA_CNMF' and 'CN_CNMF'.

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

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

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

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

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

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

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

  • 20q loss cnv correlated to 'RPPA_CNMF'.

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

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

  • xp loss cnv correlated to 'RPPA_CNMF',  'RPPA_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 82 arm-level events and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 349 significant findings detected.

Clinical
Features 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
14q loss 207 (34%) 409 0.00024
(0.00169) 		3e-05
(0.000278) 		1e-05
(0.000102) 		1e-05
(0.000102) 		0.0961
(0.228) 		0.0313
(0.0957) 		1e-05
(0.000102) 		1e-05
(0.000102) 		0.00183
(0.00995) 		1e-05
(0.000102) 		0.0175
(0.0621) 		0.0183
(0.0629)
7q gain 312 (51%) 304 0.00021
(0.00151) 		1e-05
(0.000102) 		1e-05
(0.000102) 		0.00988
(0.0389) 		0.0544
(0.149) 		0.00263
(0.0134) 		0.00014
(0.00104) 		1e-05
(0.000102) 		0.00444
(0.0207) 		1e-05
(0.000102) 		0.0482
(0.137) 		0.635
(0.801)
20q gain 463 (75%) 153 1e-05
(0.000102) 		1e-05
(0.000102) 		1e-05
(0.000102) 		1e-05
(0.000102) 		0.0127
(0.0481) 		0.58
(0.764) 		1e-05
(0.000102) 		1e-05
(0.000102) 		1e-05
(0.000102) 		1e-05
(0.000102) 		9e-05
(0.000708) 		0.126
(0.281)
18p loss 381 (62%) 235 1e-05
(0.000102) 		1e-05
(0.000102) 		1e-05
(0.000102) 		1e-05
(0.000102) 		0.151
(0.325) 		0.555
(0.747) 		1e-05
(0.000102) 		1e-05
(0.000102) 		1e-05
(0.000102) 		1e-05
(0.000102) 		0.00019
(0.00137) 		8e-05
(0.000645)
18q loss 408 (66%) 208 1e-05
(0.000102) 		1e-05
(0.000102) 		1e-05
(0.000102) 		1e-05
(0.000102) 		0.146
(0.317) 		0.374
(0.585) 		1e-05
(0.000102) 		1e-05
(0.000102) 		1e-05
(0.000102) 		1e-05
(0.000102) 		0.00224
(0.0117) 		0.00025
(0.00174)
7p gain 349 (57%) 267 0.00047
(0.0031) 		1e-05
(0.000102) 		1e-05
(0.000102) 		0.00019
(0.00137) 		0.0908
(0.219) 		0.00572
(0.0251) 		2e-05
(0.000193) 		1e-05
(0.000102) 		0.00137
(0.00798) 		1e-05
(0.000102) 		0.0509
(0.143) 		0.264
(0.464)
13q gain 372 (60%) 244 1e-05
(0.000102) 		1e-05
(0.000102) 		1e-05
(0.000102) 		1e-05
(0.000102) 		0.453
(0.662) 		0.118
(0.269) 		0.00013
(0.000976) 		1e-05
(0.000102) 		1e-05
(0.000102) 		1e-05
(0.000102) 		0.00236
(0.0122) 		0.264
(0.464)
8q gain 316 (51%) 300 0.146
(0.317) 		0.0385
(0.113) 		1e-05
(0.000102) 		0.00119
(0.00714) 		0.238
(0.435) 		0.0326
(0.0995) 		0.00167
(0.00928) 		0.0168
(0.0606) 		0.306
(0.507) 		0.0127
(0.0481) 		0.00266
(0.0135) 		0.662
(0.824)
17q gain 113 (18%) 503 0.0047
(0.0214) 		0.0036
(0.0173) 		1e-05
(0.000102) 		0.00957
(0.0381) 		0.264
(0.464) 		0.00746
(0.0308) 		1e-05
(0.000102) 		1e-05
(0.000102) 		0.181
(0.366) 		0.00852
(0.0342) 		0.177
(0.362) 		0.862
(0.951)
20p gain 353 (57%) 263 0.00031
(0.00213) 		1e-05
(0.000102) 		1e-05
(0.000102) 		0.00724
(0.0302) 		0.063
(0.167) 		0.292
(0.497) 		0.025
(0.0807) 		1e-05
(0.000102) 		0.0621
(0.166) 		1e-05
(0.000102) 		0.0463
(0.132) 		0.451
(0.66)
15q loss 230 (37%) 386 0.0001
(0.000769) 		3e-05
(0.000278) 		1e-05
(0.000102) 		0.0001
(0.000769) 		0.225
(0.423) 		0.548
(0.745) 		1e-05
(0.000102) 		1e-05
(0.000102) 		0.00155
(0.00872) 		0.00022
(0.00157) 		0.166
(0.346) 		0.259
(0.46)
17p loss 340 (55%) 276 3e-05
(0.000278) 		2e-05
(0.000193) 		1e-05
(0.000102) 		1e-05
(0.000102) 		0.596
(0.77) 		0.948
(1.00) 		1e-05
(0.000102) 		1e-05
(0.000102) 		0.00065
(0.00418) 		1e-05
(0.000102) 		0.0714
(0.184) 		0.0817
(0.204)
2q gain 122 (20%) 494 0.045
(0.129) 		0.00104
(0.0064) 		1e-05
(0.000102) 		0.00595
(0.0259) 		0.742
(0.868) 		0.481
(0.682) 		5e-05
(0.000432) 		1e-05
(0.000102) 		0.0896
(0.218) 		0.0243
(0.0787) 		0.426
(0.639) 		0.824
(0.918)
3q gain 98 (16%) 518 0.0221
(0.0735) 		0.0027
(0.0136) 		1e-05
(0.000102) 		0.0243
(0.0787) 		0.438
(0.647) 		0.591
(0.769) 		0.0841
(0.208) 		0.00333
(0.0161) 		0.0237
(0.0777) 		0.107
(0.249) 		0.0199
(0.0675) 		0.563
(0.747)
11p gain 85 (14%) 531 0.0065
(0.0278) 		0.00185
(0.01) 		1e-05
(0.000102) 		0.00013
(0.000976) 		0.432
(0.644) 		0.257
(0.457) 		0.00096
(0.00598) 		0.0001
(0.000769) 		0.197
(0.387) 		0.00204
(0.0108) 		0.507
(0.708) 		0.933
(0.997)
11q gain 78 (13%) 538 0.00697
(0.0292) 		0.00046
(0.00306) 		1e-05
(0.000102) 		2e-05
(0.000193) 		0.314
(0.516) 		0.255
(0.456) 		7e-05
(0.000574) 		1e-05
(0.000102) 		0.773
(0.885) 		0.00142
(0.00817) 		0.0515
(0.144) 		0.462
(0.668)
19q gain 113 (18%) 503 0.0228
(0.0757) 		0.00299
(0.0148) 		5e-05
(0.000432) 		0.706
(0.85) 		0.0486
(0.138) 		0.51
(0.708) 		0.293
(0.497) 		0.00107
(0.0065) 		0.0417
(0.12) 		0.0123
(0.0475) 		0.055
(0.15) 		0.672
(0.828)
1p loss 139 (23%) 477 0.155
(0.331) 		0.00686
(0.029) 		1e-05
(0.000102) 		0.0174
(0.0621) 		0.9
(0.975) 		0.978
(1.00) 		9e-05
(0.000708) 		5e-05
(0.000432) 		0.0372
(0.109) 		0.00113
(0.00682) 		0.386
(0.599) 		0.458
(0.666)
4p loss 197 (32%) 419 0.0409
(0.118) 		0.00194
(0.0103) 		1e-05
(0.000102) 		0.0112
(0.0435) 		0.555
(0.747) 		0.463
(0.668) 		0.00148
(0.00847) 		8e-05
(0.000645) 		0.204
(0.398) 		0.00464
(0.0213) 		0.673
(0.828) 		0.593
(0.769)
4q loss 191 (31%) 425 0.018
(0.0624) 		0.0158
(0.0577) 		1e-05
(0.000102) 		0.0205
(0.0692) 		0.901
(0.975) 		0.534
(0.733) 		0.00476
(0.0216) 		1e-05
(0.000102) 		0.179
(0.364) 		0.00727
(0.0302) 		0.467
(0.671) 		0.786
(0.895)
5q loss 120 (19%) 496 0.00435
(0.0205) 		0.00459
(0.0212) 		1e-05
(0.000102) 		0.0163
(0.0593) 		0.407
(0.618) 		0.9
(0.975) 		0.0209
(0.0703) 		0.00155
(0.00872) 		0.243
(0.439) 		0.00235
(0.0122) 		0.924
(0.992) 		0.608
(0.779)
8p loss 217 (35%) 399 0.0047
(0.0214) 		0.00107
(0.0065) 		1e-05
(0.000102) 		0.0007
(0.00442) 		0.404
(0.616) 		0.974
(1.00) 		0.00353
(0.017) 		6e-05
(0.000505) 		0.181
(0.366) 		0.0299
(0.0921) 		0.0847
(0.208) 		0.673
(0.828)
2p gain 123 (20%) 493 0.0822
(0.205) 		0.00321
(0.0156) 		1e-05
(0.000102) 		0.00278
(0.0139) 		0.571
(0.755) 		0.763
(0.883) 		1e-05
(0.000102) 		1e-05
(0.000102) 		0.076
(0.194) 		0.00435
(0.0205) 		0.697
(0.847) 		0.991
(1.00)
3p gain 75 (12%) 541 0.0243
(0.0787) 		0.0253
(0.0814) 		1e-05
(0.000102) 		0.0581
(0.157) 		0.124
(0.277) 		0.676
(0.83) 		0.589
(0.769) 		0.0124
(0.0475) 		0.0185
(0.0632) 		0.022
(0.0735) 		0.0777
(0.197) 		0.586
(0.769)
16p gain 148 (24%) 468 0.0344
(0.103) 		0.00188
(0.0101) 		1e-05
(0.000102) 		0.0847
(0.208) 		0.0531
(0.146) 		0.289
(0.496) 		0.00068
(0.00434) 		4e-05
(0.000355) 		0.703
(0.847) 		0.0015
(0.00853) 		0.161
(0.34) 		0.236
(0.433)
16q gain 145 (24%) 471 0.0295
(0.0915) 		0.00046
(0.00306) 		1e-05
(0.000102) 		0.154
(0.328) 		0.12
(0.271) 		0.726
(0.86) 		0.00178
(0.00978) 		4e-05
(0.000355) 		0.444
(0.654) 		0.00183
(0.00995) 		0.171
(0.351) 		0.17
(0.351)
9q loss 78 (13%) 538 0.124
(0.277) 		0.0238
(0.0777) 		1e-05
(0.000102) 		0.00014
(0.00104) 		0.756
(0.881) 		0.249
(0.448) 		7e-05
(0.000574) 		0.00124
(0.00739) 		0.364
(0.573) 		0.0179
(0.0624) 		0.123
(0.277) 		0.318
(0.521)
20p loss 65 (11%) 551 0.103
(0.24) 		0.00963
(0.0381) 		1e-05
(0.000102) 		0.00082
(0.00514) 		0.965
(1.00) 		0.561
(0.747) 		0.101
(0.236) 		0.00035
(0.00236) 		0.235
(0.431) 		0.0656
(0.172) 		0.0288
(0.0908) 		0.0405
(0.118)
21q loss 193 (31%) 423 0.0111
(0.0434) 		0.00253
(0.013) 		1e-05
(0.000102) 		0.105
(0.244) 		0.423
(0.637) 		0.195
(0.385) 		6e-05
(0.000505) 		0.00218
(0.0114) 		0.0844
(0.208) 		0.00798
(0.0326) 		0.167
(0.347) 		0.119
(0.269)
22q loss 203 (33%) 413 0.00689
(0.029) 		2e-05
(0.000193) 		1e-05
(0.000102) 		0.232
(0.43) 		0.243
(0.439) 		0.58
(0.764) 		0.0489
(0.138) 		1e-05
(0.000102) 		0.178
(0.362) 		0.00139
(0.00805) 		0.454
(0.663) 		0.256
(0.456)
12q gain 114 (19%) 502 0.0434
(0.124) 		0.168
(0.348) 		0.00837
(0.0338) 		0.0174
(0.0621) 		0.891
(0.97) 		0.397
(0.611) 		0.36
(0.57) 		0.00818
(0.0332) 		0.0183
(0.0629) 		0.379
(0.59) 		0.89
(0.97) 		0.687
(0.837)
19p gain 105 (17%) 511 0.377
(0.588) 		0.00821
(0.0332) 		4e-05
(0.000355) 		0.242
(0.439) 		0.0934
(0.223) 		0.14
(0.305) 		0.309
(0.509) 		3e-05
(0.000278) 		0.0172
(0.0616) 		0.00633
(0.0274) 		0.0777
(0.197) 		0.447
(0.657)
10q loss 111 (18%) 505 0.00897
(0.0359) 		0.278
(0.483) 		1e-05
(0.000102) 		0.0149
(0.0546) 		0.672
(0.828) 		0.432
(0.645) 		0.00318
(0.0156) 		2e-05
(0.000193) 		0.308
(0.509) 		0.299
(0.503) 		0.0895
(0.218) 		0.332
(0.536)
12p loss 71 (12%) 545 0.0298
(0.092) 		0.00292
(0.0145) 		1e-05
(0.000102) 		0.079
(0.198) 		0.787
(0.896) 		0.398
(0.612) 		0.0283
(0.0898) 		9e-05
(0.000708) 		0.136
(0.3) 		0.514
(0.71) 		0.942
(1.00) 		0.121
(0.272)
12q loss 71 (12%) 545 0.0582
(0.157) 		0.0076
(0.0313) 		1e-05
(0.000102) 		0.241
(0.439) 		0.396
(0.61) 		0.115
(0.264) 		0.0128
(0.0482) 		4e-05
(0.000355) 		0.037
(0.109) 		0.289
(0.496) 		1
(1.00) 		0.305
(0.507)
6p gain 122 (20%) 494 0.0155
(0.0567) 		0.00064
(0.00414) 		1e-05
(0.000102) 		0.449
(0.659) 		0.0764
(0.195) 		0.774
(0.885) 		0.706
(0.85) 		0.0363
(0.108) 		0.56
(0.747) 		0.29
(0.496) 		0.654
(0.818) 		0.434
(0.645)
18q gain 19 (3%) 597 0.217
(0.414) 		0.456
(0.665) 		0.00404
(0.0192) 		0.0136
(0.0508) 		0.274
(0.48) 		0.816
(0.913) 		0.0519
(0.145) 		0.00192
(0.0103) 		0.767
(0.885) 		0.00643
(0.0276) 		1
(1.00) 		0.798
(0.904)
xp gain 100 (16%) 516 0.0167
(0.0605) 		0.0772
(0.196) 		0.00018
(0.00132) 		0.0389
(0.113) 		0.0278
(0.089) 		0.227
(0.424) 		0.114
(0.262) 		0.212
(0.409) 		0.301
(0.504) 		0.753
(0.88) 		0.513
(0.71) 		0.678
(0.83)
1q loss 82 (13%) 534 0.22
(0.417) 		0.0849
(0.208) 		1e-05
(0.000102) 		0.0111
(0.0434) 		0.953
(1.00) 		0.59
(0.769) 		4e-05
(0.000355) 		0.00101
(0.00625) 		0.411
(0.625) 		0.0624
(0.166) 		0.231
(0.429) 		0.127
(0.282)
2p loss 17 (3%) 599 0.914
(0.985) 		0.807
(0.908) 		0.029
(0.0909) 		0.0783
(0.198) 		0.421
(0.634) 		0.0125
(0.0478) 		0.0529
(0.146) 		0.00781
(0.032) 		0.0178
(0.0624) 		0.798
(0.904)
9p loss 76 (12%) 540 0.48
(0.682) 		0.193
(0.383) 		1e-05
(0.000102) 		0.00134
(0.00785) 		0.951
(1.00) 		0.355
(0.564) 		0.00035
(0.00236) 		0.0177
(0.0622) 		0.324
(0.524) 		0.0556
(0.151) 		0.808
(0.908) 		0.351
(0.559)
10p loss 102 (17%) 514 0.00445
(0.0207) 		0.172
(0.352) 		1e-05
(0.000102) 		0.0525
(0.146) 		0.754
(0.88) 		0.731
(0.861) 		0.0031
(0.0153) 		0.00035
(0.00236) 		0.298
(0.503) 		0.317
(0.521) 		0.163
(0.343) 		0.338
(0.543)
19p loss 62 (10%) 554 0.589
(0.769) 		0.185
(0.371) 		2e-05
(0.000193) 		0.142
(0.31) 		0.727
(0.86) 		0.597
(0.77) 		0.0136
(0.0508) 		0.0215
(0.072) 		0.168
(0.347) 		0.0341
(0.103) 		0.342
(0.548) 		0.148
(0.32)
4p gain 20 (3%) 596 0.819
(0.915) 		0.293
(0.497) 		0.0523
(0.145) 		0.227
(0.424) 		0.0096
(0.0381) 		0.29
(0.496) 		0.0186
(0.0632) 		0.157
(0.333) 		0.128
(0.284) 		0.463
(0.668) 		0.0048
(0.0217) 		0.0552
(0.151)
5q gain 67 (11%) 549 0.614
(0.783) 		0.5
(0.703) 		6e-05
(0.000505) 		0.801
(0.905) 		0.663
(0.824) 		0.868
(0.954) 		0.334
(0.537) 		0.0344
(0.103) 		0.316
(0.52) 		0.00575
(0.0251) 		0.571
(0.755) 		0.978
(1.00)
18p gain 31 (5%) 585 0.355
(0.564) 		0.222
(0.42) 		0.00133
(0.00784) 		0.00364
(0.0174) 		0.462
(0.668) 		0.726
(0.86) 		0.0705
(0.182) 		0.00211
(0.0111) 		0.701
(0.847) 		0.0664
(0.172) 		0.613
(0.783) 		0.495
(0.697)
2q loss 14 (2%) 602 0.299
(0.503) 		0.67
(0.828) 		0.261
(0.461) 		0.0626
(0.166) 		0.136
(0.3) 		0.0127
(0.0481) 		0.0963
(0.228) 		0.00554
(0.0244) 		0.0176
(0.0622) 		0.437
(0.647)
5p loss 84 (14%) 532 0.293
(0.497) 		0.505
(0.707) 		1e-05
(0.000102) 		0.0237
(0.0777) 		0.415
(0.628) 		0.23
(0.429) 		0.683
(0.832) 		0.00668
(0.0285) 		0.728
(0.86) 		0.109
(0.252) 		0.301
(0.504) 		0.635
(0.801)
8q loss 36 (6%) 580 0.774
(0.885) 		0.831
(0.923) 		1e-05
(0.000102) 		0.514
(0.71) 		0.225
(0.423) 		0.19
(0.379) 		0.598
(0.77) 		0.664
(0.824) 		0.307
(0.509) 		0.0337
(0.102) 		0.0236
(0.0777) 		0.0908
(0.219)
xp loss 91 (15%) 525 0.964
(1.00) 		0.722
(0.86) 		0.112
(0.257) 		0.734
(0.861) 		0.0134
(0.0502) 		0.0146
(0.0537) 		0.708
(0.85) 		0.957
(1.00) 		0.231
(0.429) 		0.0757
(0.194) 		0.334
(0.537) 		0.0292
(0.0911)
xq loss 79 (13%) 537 0.941
(1.00) 		0.773
(0.885) 		0.0924
(0.222) 		0.553
(0.747) 		0.0657
(0.172) 		0.0334
(0.101) 		0.419
(0.632) 		0.436
(0.646) 		0.199
(0.389) 		0.0487
(0.138) 		0.208
(0.402) 		0.00529
(0.0236)
5p gain 108 (18%) 508 0.509
(0.708) 		0.0644
(0.169) 		1e-05
(0.000102) 		1
(1.00) 		0.066
(0.172) 		0.395
(0.61) 		0.0289
(0.0908) 		0.079
(0.198) 		0.652
(0.818) 		0.592
(0.769) 		0.509
(0.708) 		0.956
(1.00)
6q gain 111 (18%) 505 0.138
(0.303) 		0.00132
(0.00782) 		1e-05
(0.000102) 		0.473
(0.677) 		0.215
(0.412) 		0.987
(1.00) 		0.562
(0.747) 		0.198
(0.388) 		0.19
(0.379) 		0.562
(0.747) 		0.727
(0.86) 		0.417
(0.631)
8p gain 169 (27%) 447 0.414
(0.627) 		0.627
(0.794) 		0.00166
(0.00928) 		0.643
(0.809) 		0.45
(0.66) 		0.579
(0.764) 		0.00679
(0.0288) 		0.163
(0.343) 		0.656
(0.819) 		0.314
(0.516) 		0.0757
(0.194) 		0.398
(0.611)
10p gain 49 (8%) 567 0.137
(0.302) 		0.18
(0.365) 		0.00052
(0.00339) 		0.82
(0.915) 		0.682
(0.832) 		0.037
(0.109) 		0.559
(0.747) 		0.809
(0.908) 		0.559
(0.747) 		0.575
(0.759) 		0.283
(0.491) 		0.774
(0.885)
10q gain 29 (5%) 587 0.872
(0.955) 		0.3
(0.503) 		0.00538
(0.0238) 		0.159
(0.337) 		0.304
(0.507) 		0.458
(0.666) 		0.66
(0.824) 		0.604
(0.776) 		0.597
(0.77) 		0.623
(0.792) 		0.0282
(0.0898) 		0.76
(0.882)
12p gain 128 (21%) 488 0.051
(0.143) 		0.332
(0.536) 		0.0298
(0.092) 		0.0975
(0.23) 		0.935
(0.997) 		0.536
(0.734) 		0.597
(0.77) 		0.0181
(0.0629) 		0.0933
(0.223) 		0.32
(0.521) 		0.869
(0.955) 		0.559
(0.747)
22q gain 23 (4%) 593 0.11
(0.254) 		0.0937
(0.223) 		0.0143
(0.0528) 		0.489
(0.691) 		0.0855
(0.209) 		0.51
(0.708) 		0.184
(0.37) 		0.277
(0.482) 		0.00446
(0.0207) 		0.603
(0.775) 		0.757
(0.882) 		1
(1.00)
xq gain 109 (18%) 507 0.0931
(0.223) 		0.34
(0.546) 		0.00272
(0.0137) 		0.0594
(0.16) 		0.0185
(0.0632) 		0.194
(0.384) 		0.702
(0.847) 		0.318
(0.521) 		0.487
(0.69) 		0.896
(0.975) 		0.535
(0.734) 		0.762
(0.883)
6p loss 47 (8%) 569 0.504
(0.707) 		0.0112
(0.0434) 		0.146
(0.317) 		1
(1.00) 		0.772
(0.885) 		0.734
(0.861) 		0.555
(0.747) 		0.0289
(0.0908) 		0.276
(0.482) 		0.319
(0.521) 		0.234
(0.431) 		0.205
(0.398)
11q loss 92 (15%) 524 0.865
(0.953) 		0.475
(0.677) 		0.00531
(0.0236) 		0.258
(0.458) 		0.404
(0.616) 		0.97
(1.00) 		0.924
(0.992) 		0.164
(0.343) 		0.164
(0.343) 		0.0425
(0.122) 		0.478
(0.679) 		0.62
(0.789)
13q loss 18 (3%) 598 0.217
(0.414) 		0.00508
(0.0228) 		0.00026
(0.0018) 		0.596
(0.77) 		0.771
(0.885) 		0.866
(0.953) 		0.758
(0.882) 		0.171
(0.351) 		1
(1.00) 		0.971
(1.00) 		0.76
(0.882) 		0.349
(0.557)
16q loss 44 (7%) 572 0.0341
(0.103) 		0.404
(0.616) 		0.00069
(0.00438) 		0.363
(0.572) 		0.403
(0.616) 		0.731
(0.861) 		0.726
(0.86) 		0.553
(0.747) 		0.161
(0.34) 		0.203
(0.397) 		0.969
(1.00) 		0.734
(0.861)
17q loss 93 (15%) 523 0.926
(0.992) 		0.784
(0.894) 		1e-05
(0.000102) 		0.952
(1.00) 		0.426
(0.639) 		0.541
(0.738) 		0.891
(0.97) 		0.0293
(0.0914) 		0.122
(0.274) 		0.605
(0.777) 		0.807
(0.908) 		0.654
(0.818)
19q loss 56 (9%) 560 0.724
(0.86) 		0.0839
(0.208) 		7e-05
(0.000574) 		0.171
(0.351) 		0.283
(0.491) 		0.85
(0.939) 		0.152
(0.327) 		0.0596
(0.16) 		0.215
(0.412) 		0.0262
(0.0841) 		0.518
(0.713) 		0.162
(0.342)
1p gain 50 (8%) 566 0.247
(0.444) 		0.265
(0.465) 		0.0835
(0.207) 		0.32
(0.521) 		0.0361
(0.107) 		0.217
(0.414) 		0.991
(1.00) 		0.613
(0.783) 		0.518
(0.713) 		0.558
(0.747) 		0.251
(0.45) 		0.289
(0.496)
1q gain 113 (18%) 503 0.918
(0.987) 		0.737
(0.863) 		0.0138
(0.0512) 		1
(1.00) 		0.0544
(0.149) 		0.225
(0.423) 		0.936
(0.997) 		0.425
(0.638) 		0.218
(0.415) 		0.431
(0.644) 		0.0599
(0.161) 		0.324
(0.524)
4q gain 21 (3%) 595 0.196
(0.386) 		0.0609
(0.163) 		0.00173
(0.00956) 		0.637
(0.803) 		0.241
(0.439) 		0.446
(0.657) 		0.358
(0.567) 		0.288
(0.496) 		0.0905
(0.219) 		0.361
(0.571) 		0.559
(0.747) 		0.835
(0.926)
9p gain 124 (20%) 492 0.588
(0.769) 		0.156
(0.332) 		0.00011
(0.000839) 		0.372
(0.583) 		0.464
(0.668) 		0.244
(0.44) 		0.902
(0.975) 		0.388
(0.6) 		0.664
(0.824) 		0.903
(0.975) 		0.109
(0.252) 		0.7
(0.847)
9q gain 103 (17%) 513 0.721
(0.86) 		0.33
(0.534) 		0.00051
(0.00335) 		0.505
(0.707) 		0.47
(0.674) 		0.0672
(0.174) 		0.915
(0.985) 		0.843
(0.933) 		0.967
(1.00) 		0.791
(0.898) 		0.402
(0.616) 		0.767
(0.885)
14q gain 43 (7%) 573 0.825
(0.918) 		0.434
(0.645) 		1e-05
(0.000102) 		0.364
(0.573) 		0.734
(0.861) 		0.877
(0.958) 		0.79
(0.897) 		0.612
(0.783) 		0.907
(0.979) 		0.474
(0.677) 		0.217
(0.414) 		0.26
(0.46)
15q gain 15 (2%) 601 0.365
(0.573) 		0.0354
(0.106) 		0.0797
(0.2) 		0.435
(0.646) 		0.651
(0.817) 		1
(1.00) 		0.954
(1.00) 		0.929
(0.994) 		0.939
(1) 		0.717
(0.86)
21q gain 34 (6%) 582 0.209
(0.404) 		0.206
(0.4) 		0.00024
(0.00169) 		0.195
(0.385) 		0.816
(0.913) 		0.183
(0.369) 		0.806
(0.908) 		0.104
(0.242) 		0.474
(0.677) 		0.725
(0.86) 		0.509
(0.708) 		0.702
(0.847)
3p loss 68 (11%) 548 0.512
(0.709) 		0.846
(0.935) 		0.0207
(0.0698) 		0.556
(0.747) 		0.0955
(0.227) 		0.586
(0.769) 		0.673
(0.828) 		0.717
(0.86) 		0.673
(0.828) 		0.675
(0.829) 		0.541
(0.738) 		0.727
(0.86)
3q loss 45 (7%) 571 0.295
(0.498) 		0.116
(0.266) 		0.0409
(0.118) 		0.384
(0.596) 		0.167
(0.347) 		0.771
(0.885) 		0.678
(0.83) 		0.234
(0.431) 		0.461
(0.668) 		0.774
(0.885) 		0.699
(0.847) 		0.635
(0.801)
11p loss 75 (12%) 541 0.955
(1.00) 		0.934
(0.997) 		0.00639
(0.0276) 		0.475
(0.677) 		0.376
(0.588) 		0.963
(1.00) 		0.803
(0.906) 		0.133
(0.295) 		0.252
(0.45) 		0.0984
(0.231) 		0.557
(0.747) 		0.902
(0.975)
16p loss 40 (6%) 576 0.12
(0.271) 		0.293
(0.497) 		0.0177
(0.0622) 		0.243
(0.439) 		0.235
(0.431) 		0.494
(0.697) 		0.54
(0.738) 		0.189
(0.378) 		0.226
(0.423) 		0.303
(0.506) 		1
(1.00) 		0.947
(1.00)
20q loss 8 (1%) 608 1
(1.00) 		0.779
(0.889) 		0.0304
(0.0931) 		0.681
(0.832) 		0.646
(0.812) 		0.886
(0.967) 		0.94
(1.00) 		1
(1.00)
17p gain 39 (6%) 577 0.498
(0.701) 		0.24
(0.438) 		0.348
(0.556) 		0.626
(0.794) 		0.59
(0.769) 		0.223
(0.421) 		0.294
(0.497) 		0.0664
(0.172) 		0.837
(0.928) 		0.151
(0.326) 		0.464
(0.668) 		0.872
(0.955)
6q loss 69 (11%) 547 0.568
(0.753) 		0.235
(0.431) 		0.3
(0.503) 		0.799
(0.904) 		0.184
(0.37) 		0.378
(0.588) 		0.136
(0.3) 		0.0642
(0.169) 		0.192
(0.383) 		0.728
(0.86) 		0.0975
(0.23) 		0.286
(0.494)
7p loss 3 (0%) 613 0.818
(0.915) 		0.626
(0.794) 		0.153
(0.327)
7q loss 5 (1%) 611 0.873
(0.956) 		0.211
(0.408) 		0.276
(0.482) 		0.523
(0.718) 		0.826
(0.918) 		0.702
(0.847) 		1
(1.00) 		0.543
(0.739)
'1p gain' versus 'RPPA_CNMF'

P value = 0.0361 (Fisher's exact test), Q value = 0.11

Table S1.  Gene #1: '1p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 197 177
1P GAIN MUTATED 10 21 7
1P GAIN WILD-TYPE 98 176 170

Figure S1.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'1q gain' versus 'CN_CNMF'

P value = 0.0138 (Fisher's exact test), Q value = 0.051

Table S2.  Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
1Q GAIN MUTATED 26 50 33 4
1Q GAIN WILD-TYPE 189 197 99 18

Figure S2.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

'2p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00321 (Fisher's exact test), Q value = 0.016

Table S3.  Gene #3: '2p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
2P GAIN MUTATED 3 22 7
2P GAIN WILD-TYPE 47 67 70

Figure S3.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'2p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S4.  Gene #3: '2p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
2P GAIN MUTATED 20 63 29 11
2P GAIN WILD-TYPE 195 184 103 11

Figure S4.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #3: 'CN_CNMF'

'2p gain' versus 'METHLYATION_CNMF'

P value = 0.00278 (Fisher's exact test), Q value = 0.014

Table S5.  Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
2P GAIN MUTATED 22 43 24
2P GAIN WILD-TYPE 95 86 120

Figure S5.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S6.  Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
2P GAIN MUTATED 56 14 25 27
2P GAIN WILD-TYPE 100 114 106 171

Figure S6.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S7.  Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
2P GAIN MUTATED 25 14 8 12 28 30 5
2P GAIN WILD-TYPE 55 72 56 45 62 108 93

Figure S7.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00435 (Fisher's exact test), Q value = 0.02

Table S8.  Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
2P GAIN MUTATED 7 16 4 20 5 20 12 6 13
2P GAIN WILD-TYPE 42 58 25 66 72 34 45 26 68

Figure S8.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2q gain' versus 'MRNA_CNMF'

P value = 0.045 (Fisher's exact test), Q value = 0.13

Table S9.  Gene #4: '2q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
2Q GAIN MUTATED 5 14 13 2
2Q GAIN WILD-TYPE 40 49 52 41

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

'2q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00104 (Fisher's exact test), Q value = 0.0064

Table S10.  Gene #4: '2q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
2Q GAIN MUTATED 3 24 7
2Q GAIN WILD-TYPE 47 65 70

Figure S10.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'2q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S11.  Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
2Q GAIN MUTATED 19 64 28 11
2Q GAIN WILD-TYPE 196 183 104 11

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

'2q gain' versus 'METHLYATION_CNMF'

P value = 0.00595 (Fisher's exact test), Q value = 0.026

Table S12.  Gene #4: '2q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
2Q GAIN MUTATED 20 41 25
2Q GAIN WILD-TYPE 97 88 119

Figure S12.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2q gain' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00043

Table S13.  Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
2Q GAIN MUTATED 51 15 25 30
2Q GAIN WILD-TYPE 105 113 106 168

Figure S13.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S14.  Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
2Q GAIN MUTATED 23 15 5 12 29 31 6
2Q GAIN WILD-TYPE 57 71 59 45 61 107 92

Figure S14.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0243 (Fisher's exact test), Q value = 0.079

Table S15.  Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
2Q GAIN MUTATED 7 15 4 21 5 17 12 5 15
2Q GAIN WILD-TYPE 42 59 25 65 72 37 45 27 66

Figure S15.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3p gain' versus 'MRNA_CNMF'

P value = 0.0243 (Fisher's exact test), Q value = 0.079

Table S16.  Gene #5: '3p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
3P GAIN MUTATED 2 10 11 1
3P GAIN WILD-TYPE 43 53 54 42

Figure S16.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'3p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0253 (Fisher's exact test), Q value = 0.081

Table S17.  Gene #5: '3p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
3P GAIN MUTATED 2 16 6
3P GAIN WILD-TYPE 48 73 71

Figure S17.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'3p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S18.  Gene #5: '3p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
3P GAIN MUTATED 8 47 15 5
3P GAIN WILD-TYPE 207 200 117 17

Figure S18.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #3: 'CN_CNMF'

'3p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0124 (Fisher's exact test), Q value = 0.048

Table S19.  Gene #5: '3p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
3P GAIN MUTATED 7 14 3 6 19 20 6
3P GAIN WILD-TYPE 73 72 61 51 71 118 92

Figure S19.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3p gain' versus 'MIRSEQ_CNMF'

P value = 0.0185 (Fisher's exact test), Q value = 0.063

Table S20.  Gene #5: '3p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 95 86 205
3P GAIN MUTATED 17 15 18 17
3P GAIN WILD-TYPE 136 80 68 188

Figure S20.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.022 (Fisher's exact test), Q value = 0.073

Table S21.  Gene #5: '3p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
3P GAIN MUTATED 5 12 2 8 3 7 15 5 10
3P GAIN WILD-TYPE 44 62 27 78 74 47 42 27 71

Figure S21.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3q gain' versus 'MRNA_CNMF'

P value = 0.0221 (Fisher's exact test), Q value = 0.074

Table S22.  Gene #6: '3q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
3Q GAIN MUTATED 3 12 14 2
3Q GAIN WILD-TYPE 42 51 51 41

Figure S22.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'3q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0027 (Fisher's exact test), Q value = 0.014

Table S23.  Gene #6: '3q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
3Q GAIN MUTATED 2 21 8
3Q GAIN WILD-TYPE 48 68 69

Figure S23.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'3q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
3Q GAIN MUTATED 9 60 24 5
3Q GAIN WILD-TYPE 206 187 108 17

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

'3q gain' versus 'METHLYATION_CNMF'

P value = 0.0243 (Fisher's exact test), Q value = 0.079

Table S25.  Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
3Q GAIN MUTATED 15 32 20
3Q GAIN WILD-TYPE 102 97 124

Figure S25.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00333 (Fisher's exact test), Q value = 0.016

Table S26.  Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
3Q GAIN MUTATED 10 17 4 9 24 26 8
3Q GAIN WILD-TYPE 70 69 60 48 66 112 90

Figure S26.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_CNMF'

P value = 0.0237 (Fisher's exact test), Q value = 0.078

Table S27.  Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 95 86 205
3Q GAIN MUTATED 23 19 22 24
3Q GAIN WILD-TYPE 130 76 64 181

Figure S27.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0199 (Fisher's exact test), Q value = 0.067

Table S28.  Gene #6: '3q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 40 38 22
3Q GAIN MUTATED 8 12 9 0
3Q GAIN WILD-TYPE 27 28 29 22

Figure S28.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4p gain' versus 'RPPA_CNMF'

P value = 0.0096 (Fisher's exact test), Q value = 0.038

Table S29.  Gene #7: '4p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 197 177
4P GAIN MUTATED 8 2 7
4P GAIN WILD-TYPE 100 195 170

Figure S29.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'4p gain' versus 'MRNASEQ_CNMF'

P value = 0.0186 (Fisher's exact test), Q value = 0.063

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
4P GAIN MUTATED 11 2 1 6
4P GAIN WILD-TYPE 145 126 130 192

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

'4p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0048 (Fisher's exact test), Q value = 0.022

Table S31.  Gene #7: '4p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 40 38 22
4P GAIN MUTATED 0 0 5 0
4P GAIN WILD-TYPE 35 40 33 22

Figure S31.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4q gain' versus 'CN_CNMF'

P value = 0.00173 (Fisher's exact test), Q value = 0.0096

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
4Q GAIN MUTATED 1 9 9 2
4Q GAIN WILD-TYPE 214 238 123 20

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

'5p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
5P GAIN MUTATED 19 59 22 8
5P GAIN WILD-TYPE 196 188 110 14

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

'5p gain' versus 'MRNASEQ_CNMF'

P value = 0.0289 (Fisher's exact test), Q value = 0.091

Table S34.  Gene #9: '5p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
5P GAIN MUTATED 33 12 27 36
5P GAIN WILD-TYPE 123 116 104 162

Figure S34.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5q gain' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 5e-04

Table S35.  Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
5Q GAIN MUTATED 16 42 5 4
5Q GAIN WILD-TYPE 199 205 127 18

Figure S35.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'

'5q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0344 (Fisher's exact test), Q value = 0.1

Table S36.  Gene #10: '5q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
5Q GAIN MUTATED 9 11 1 3 13 21 9
5Q GAIN WILD-TYPE 71 75 63 54 77 117 89

Figure S36.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00575 (Fisher's exact test), Q value = 0.025

Table S37.  Gene #10: '5q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
5Q GAIN MUTATED 4 10 1 2 5 4 9 5 16
5Q GAIN WILD-TYPE 45 64 28 84 72 50 48 27 65

Figure S37.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6p gain' versus 'MRNA_CNMF'

P value = 0.0155 (Fisher's exact test), Q value = 0.057

Table S38.  Gene #11: '6p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
6P GAIN MUTATED 10 11 18 2
6P GAIN WILD-TYPE 35 52 47 41

Figure S38.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'6p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00064 (Fisher's exact test), Q value = 0.0041

Table S39.  Gene #11: '6p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
6P GAIN MUTATED 5 28 8
6P GAIN WILD-TYPE 45 61 69

Figure S39.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S40.  Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
6P GAIN MUTATED 10 75 27 10
6P GAIN WILD-TYPE 205 172 105 12

Figure S40.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

'6p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0363 (Fisher's exact test), Q value = 0.11

Table S41.  Gene #11: '6p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
6P GAIN MUTATED 14 15 6 16 23 34 14
6P GAIN WILD-TYPE 66 71 58 41 67 104 84

Figure S41.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00132 (Fisher's exact test), Q value = 0.0078

Table S42.  Gene #12: '6q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
6Q GAIN MUTATED 5 23 5
6Q GAIN WILD-TYPE 45 66 72

Figure S42.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S43.  Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
6Q GAIN MUTATED 9 66 27 9
6Q GAIN WILD-TYPE 206 181 105 13

Figure S43.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'MRNA_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.0031

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
7P GAIN MUTATED 15 42 35 14
7P GAIN WILD-TYPE 30 21 30 29

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

'7p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
7P GAIN MUTATED 12 64 30
7P GAIN WILD-TYPE 38 25 47

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

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
7P GAIN MUTATED 57 185 86 21
7P GAIN WILD-TYPE 158 62 46 1

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

'7p gain' versus 'METHLYATION_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.0014

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
7P GAIN MUTATED 65 97 76
7P GAIN WILD-TYPE 52 32 68

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

'7p gain' versus 'RPPA_CHIERARCHICAL'

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

Table S48.  Gene #13: '7p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 168 86
7P GAIN MUTATED 135 78 56
7P GAIN WILD-TYPE 93 90 30

Figure S48.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00019

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
7P GAIN MUTATED 113 59 76 99
7P GAIN WILD-TYPE 43 69 55 99

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

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S50.  Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
7P GAIN MUTATED 50 50 14 41 72 90 30
7P GAIN WILD-TYPE 30 36 50 16 18 48 68

Figure S50.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_CNMF'

P value = 0.00137 (Fisher's exact test), Q value = 0.008

Table S51.  Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 95 86 205
7P GAIN MUTATED 92 61 59 96
7P GAIN WILD-TYPE 61 34 27 109

Figure S51.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S52.  Gene #13: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
7P GAIN MUTATED 32 47 16 57 20 25 39 16 56
7P GAIN WILD-TYPE 17 27 13 29 57 29 18 16 25

Figure S52.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7q gain' versus 'MRNA_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.0015

Table S53.  Gene #14: '7q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
7Q GAIN MUTATED 10 37 33 13
7Q GAIN WILD-TYPE 35 26 32 30

Figure S53.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'7q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S54.  Gene #14: '7q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
7Q GAIN MUTATED 9 57 27
7Q GAIN WILD-TYPE 41 32 50

Figure S54.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S55.  Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
7Q GAIN MUTATED 54 161 77 20
7Q GAIN WILD-TYPE 161 86 55 2

Figure S55.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 0.00988 (Fisher's exact test), Q value = 0.039

Table S56.  Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
7Q GAIN MUTATED 59 84 69
7Q GAIN WILD-TYPE 58 45 75

Figure S56.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00263 (Fisher's exact test), Q value = 0.013

Table S57.  Gene #14: '7q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 168 86
7Q GAIN MUTATED 126 65 47
7Q GAIN WILD-TYPE 102 103 39

Figure S57.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.001

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
7Q GAIN MUTATED 103 54 64 89
7Q GAIN WILD-TYPE 53 74 67 109

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

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S59.  Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
7Q GAIN MUTATED 46 46 13 36 63 80 26
7Q GAIN WILD-TYPE 34 40 51 21 27 58 72

Figure S59.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_CNMF'

P value = 0.00444 (Fisher's exact test), Q value = 0.021

Table S60.  Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 95 86 205
7Q GAIN MUTATED 85 54 52 85
7Q GAIN WILD-TYPE 68 41 34 120

Figure S60.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S61.  Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
7Q GAIN MUTATED 32 41 15 47 18 23 34 14 52
7Q GAIN WILD-TYPE 17 33 14 39 59 31 23 18 29

Figure S61.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0482 (Fisher's exact test), Q value = 0.14

Table S62.  Gene #14: '7q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 40 38 22
7Q GAIN MUTATED 24 28 21 8
7Q GAIN WILD-TYPE 11 12 17 14

Figure S62.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8p gain' versus 'CN_CNMF'

P value = 0.00166 (Fisher's exact test), Q value = 0.0093

Table S63.  Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
8P GAIN MUTATED 43 67 50 9
8P GAIN WILD-TYPE 172 180 82 13

Figure S63.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

'8p gain' versus 'MRNASEQ_CNMF'

P value = 0.00679 (Fisher's exact test), Q value = 0.029

Table S64.  Gene #15: '8p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
8P GAIN MUTATED 57 32 38 40
8P GAIN WILD-TYPE 99 96 93 158

Figure S64.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0385 (Fisher's exact test), Q value = 0.11

Table S65.  Gene #16: '8q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
8Q GAIN MUTATED 17 50 35
8Q GAIN WILD-TYPE 33 39 42

Figure S65.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'8q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S66.  Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
8Q GAIN MUTATED 59 130 114 13
8Q GAIN WILD-TYPE 156 117 18 9

Figure S66.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 0.00119 (Fisher's exact test), Q value = 0.0071

Table S67.  Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
8Q GAIN MUTATED 59 87 67
8Q GAIN WILD-TYPE 58 42 77

Figure S67.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0326 (Fisher's exact test), Q value = 0.099

Table S68.  Gene #16: '8q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 168 86
8Q GAIN MUTATED 129 73 42
8Q GAIN WILD-TYPE 99 95 44

Figure S68.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 0.00167 (Fisher's exact test), Q value = 0.0093

Table S69.  Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
8Q GAIN MUTATED 94 50 74 95
8Q GAIN WILD-TYPE 62 78 57 103

Figure S69.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0168 (Fisher's exact test), Q value = 0.061

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
8Q GAIN MUTATED 46 39 28 30 58 73 39
8Q GAIN WILD-TYPE 34 47 36 27 32 65 59

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

'8q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0127 (Fisher's exact test), Q value = 0.048

Table S71.  Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
8Q GAIN MUTATED 18 43 15 58 30 28 29 17 40
8Q GAIN WILD-TYPE 31 31 14 28 47 26 28 15 41

Figure S71.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00266 (Fisher's exact test), Q value = 0.013

Table S72.  Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 40 38 22
8Q GAIN MUTATED 13 30 27 11
8Q GAIN WILD-TYPE 22 10 11 11

Figure S72.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9p gain' versus 'CN_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00084

Table S73.  Gene #17: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
9P GAIN MUTATED 26 56 31 11
9P GAIN WILD-TYPE 189 191 101 11

Figure S73.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'

'9q gain' versus 'CN_CNMF'

P value = 0.00051 (Fisher's exact test), Q value = 0.0033

Table S74.  Gene #18: '9q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
9Q GAIN MUTATED 23 46 24 10
9Q GAIN WILD-TYPE 192 201 108 12

Figure S74.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #3: 'CN_CNMF'

'10p gain' versus 'CN_CNMF'

P value = 0.00052 (Fisher's exact test), Q value = 0.0034

Table S75.  Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
10P GAIN MUTATED 5 27 14 3
10P GAIN WILD-TYPE 210 220 118 19

Figure S75.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

'10p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.037 (Fisher's exact test), Q value = 0.11

Table S76.  Gene #19: '10p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 168 86
10P GAIN MUTATED 25 14 2
10P GAIN WILD-TYPE 203 154 84

Figure S76.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'10q gain' versus 'CN_CNMF'

P value = 0.00538 (Fisher's exact test), Q value = 0.024

Table S77.  Gene #20: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
10Q GAIN MUTATED 3 14 9 3
10Q GAIN WILD-TYPE 212 233 123 19

Figure S77.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

'10q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0282 (Fisher's exact test), Q value = 0.09

Table S78.  Gene #20: '10q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 40 38 22
10Q GAIN MUTATED 5 1 0 2
10Q GAIN WILD-TYPE 30 39 38 20

Figure S78.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11p gain' versus 'MRNA_CNMF'

P value = 0.0065 (Fisher's exact test), Q value = 0.028

Table S79.  Gene #21: '11p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
11P GAIN MUTATED 2 11 13 1
11P GAIN WILD-TYPE 43 52 52 42

Figure S79.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'11p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00185 (Fisher's exact test), Q value = 0.01

Table S80.  Gene #21: '11p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
11P GAIN MUTATED 1 19 7
11P GAIN WILD-TYPE 49 70 70

Figure S80.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'11p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S81.  Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
11P GAIN MUTATED 6 49 24 6
11P GAIN WILD-TYPE 209 198 108 16

Figure S81.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

'11p gain' versus 'METHLYATION_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00098

Table S82.  Gene #21: '11p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
11P GAIN MUTATED 17 32 9
11P GAIN WILD-TYPE 100 97 135

Figure S82.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p gain' versus 'MRNASEQ_CNMF'

P value = 0.00096 (Fisher's exact test), Q value = 0.006

Table S83.  Gene #21: '11p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
11P GAIN MUTATED 34 7 18 26
11P GAIN WILD-TYPE 122 121 113 172

Figure S83.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00077

Table S84.  Gene #21: '11p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
11P GAIN MUTATED 17 8 1 9 18 26 6
11P GAIN WILD-TYPE 63 78 63 48 72 112 92

Figure S84.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00204 (Fisher's exact test), Q value = 0.011

Table S85.  Gene #21: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
11P GAIN MUTATED 4 12 1 16 2 8 12 2 17
11P GAIN WILD-TYPE 45 62 28 70 75 46 45 30 64

Figure S85.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11q gain' versus 'MRNA_CNMF'

P value = 0.00697 (Fisher's exact test), Q value = 0.029

Table S86.  Gene #22: '11q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
11Q GAIN MUTATED 3 8 15 1
11Q GAIN WILD-TYPE 42 55 50 42

Figure S86.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'11q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00046 (Fisher's exact test), Q value = 0.0031

Table S87.  Gene #22: '11q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
11Q GAIN MUTATED 1 20 6
11Q GAIN WILD-TYPE 49 69 71

Figure S87.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'11q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S88.  Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
11Q GAIN MUTATED 3 45 26 4
11Q GAIN WILD-TYPE 212 202 106 18

Figure S88.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

'11q gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00019

Table S89.  Gene #22: '11q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
11Q GAIN MUTATED 13 31 7
11Q GAIN WILD-TYPE 104 98 137

Figure S89.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11q gain' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00057

Table S90.  Gene #22: '11q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
11Q GAIN MUTATED 35 5 14 24
11Q GAIN WILD-TYPE 121 123 117 174

Figure S90.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S91.  Gene #22: '11q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
11Q GAIN MUTATED 17 6 0 7 19 24 5
11Q GAIN WILD-TYPE 63 80 64 50 71 114 93

Figure S91.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00142 (Fisher's exact test), Q value = 0.0082

Table S92.  Gene #22: '11q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
11Q GAIN MUTATED 2 11 2 18 2 7 8 1 16
11Q GAIN WILD-TYPE 47 63 27 68 75 47 49 31 65

Figure S92.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12p gain' versus 'CN_CNMF'

P value = 0.0298 (Fisher's exact test), Q value = 0.092

Table S93.  Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
12P GAIN MUTATED 54 37 32 5
12P GAIN WILD-TYPE 161 210 100 17

Figure S93.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0181 (Fisher's exact test), Q value = 0.063

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
12P GAIN MUTATED 13 24 15 7 15 23 31
12P GAIN WILD-TYPE 67 62 49 50 75 115 67

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

'12q gain' versus 'MRNA_CNMF'

P value = 0.0434 (Fisher's exact test), Q value = 0.12

Table S95.  Gene #24: '12q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
12Q GAIN MUTATED 14 10 8 12
12Q GAIN WILD-TYPE 31 53 57 31

Figure S95.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'12q gain' versus 'CN_CNMF'

P value = 0.00837 (Fisher's exact test), Q value = 0.034

Table S96.  Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
12Q GAIN MUTATED 54 33 25 2
12Q GAIN WILD-TYPE 161 214 107 20

Figure S96.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

'12q gain' versus 'METHLYATION_CNMF'

P value = 0.0174 (Fisher's exact test), Q value = 0.062

Table S97.  Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
12Q GAIN MUTATED 18 14 34
12Q GAIN WILD-TYPE 99 115 110

Figure S97.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00818 (Fisher's exact test), Q value = 0.033

Table S98.  Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
12Q GAIN MUTATED 13 23 13 5 11 21 28
12Q GAIN WILD-TYPE 67 63 51 52 79 117 70

Figure S98.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_CNMF'

P value = 0.0183 (Fisher's exact test), Q value = 0.063

Table S99.  Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 95 86 205
12Q GAIN MUTATED 30 11 11 51
12Q GAIN WILD-TYPE 123 84 75 154

Figure S99.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'13q gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
13Q GAIN MUTATED 17 47 49 17
13Q GAIN WILD-TYPE 28 16 16 26

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

'13q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
13Q GAIN MUTATED 13 70 47
13Q GAIN WILD-TYPE 37 19 30

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

'13q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
13Q GAIN MUTATED 64 221 74 13
13Q GAIN WILD-TYPE 151 26 58 9

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

'13q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
13Q GAIN MUTATED 65 103 72
13Q GAIN WILD-TYPE 52 26 72

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

'13q gain' versus 'MRNASEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00098

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
13Q GAIN MUTATED 115 61 73 120
13Q GAIN WILD-TYPE 41 67 58 78

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

'13q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
13Q GAIN MUTATED 56 48 14 44 67 105 35
13Q GAIN WILD-TYPE 24 38 50 13 23 33 63

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

'13q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 95 86 205
13Q GAIN MUTATED 92 60 72 107
13Q GAIN WILD-TYPE 61 35 14 98

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

'13q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
13Q GAIN MUTATED 30 45 17 58 27 29 45 19 61
13Q GAIN WILD-TYPE 19 29 12 28 50 25 12 13 20

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

'13q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00236 (Fisher's exact test), Q value = 0.012

Table S108.  Gene #25: '13q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 40 38 22
13Q GAIN MUTATED 23 30 34 10
13Q GAIN WILD-TYPE 12 10 4 12

Figure S108.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'14q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S109.  Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
14Q GAIN MUTATED 6 12 21 4
14Q GAIN WILD-TYPE 209 235 111 18

Figure S109.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

'15q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0354 (Fisher's exact test), Q value = 0.11

Table S110.  Gene #27: '15q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
15Q GAIN MUTATED 3 0 1
15Q GAIN WILD-TYPE 47 89 76

Figure S110.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'16p gain' versus 'MRNA_CNMF'

P value = 0.0344 (Fisher's exact test), Q value = 0.1

Table S111.  Gene #28: '16p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
16P GAIN MUTATED 8 21 22 6
16P GAIN WILD-TYPE 37 42 43 37

Figure S111.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'16p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00188 (Fisher's exact test), Q value = 0.01

Table S112.  Gene #28: '16p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
16P GAIN MUTATED 6 34 17
16P GAIN WILD-TYPE 44 55 60

Figure S112.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'16p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S113.  Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
16P GAIN MUTATED 8 103 28 9
16P GAIN WILD-TYPE 207 144 104 13

Figure S113.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 0.00068 (Fisher's exact test), Q value = 0.0043

Table S114.  Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
16P GAIN MUTATED 49 17 25 56
16P GAIN WILD-TYPE 107 111 106 142

Figure S114.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00035

Table S115.  Gene #28: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
16P GAIN MUTATED 15 19 4 14 30 49 16
16P GAIN WILD-TYPE 65 67 60 43 60 89 82

Figure S115.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0015 (Fisher's exact test), Q value = 0.0085

Table S116.  Gene #28: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
16P GAIN MUTATED 11 21 4 22 7 10 16 12 30
16P GAIN WILD-TYPE 38 53 25 64 70 44 41 20 51

Figure S116.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16q gain' versus 'MRNA_CNMF'

P value = 0.0295 (Fisher's exact test), Q value = 0.091

Table S117.  Gene #29: '16q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
16Q GAIN MUTATED 6 19 21 6
16Q GAIN WILD-TYPE 39 44 44 37

Figure S117.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'16q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00046 (Fisher's exact test), Q value = 0.0031

Table S118.  Gene #29: '16q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
16Q GAIN MUTATED 4 32 16
16Q GAIN WILD-TYPE 46 57 61

Figure S118.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'16q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S119.  Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
16Q GAIN MUTATED 7 103 26 9
16Q GAIN WILD-TYPE 208 144 106 13

Figure S119.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

'16q gain' versus 'MRNASEQ_CNMF'

P value = 0.00178 (Fisher's exact test), Q value = 0.0098

Table S120.  Gene #29: '16q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
16Q GAIN MUTATED 49 17 26 52
16Q GAIN WILD-TYPE 107 111 105 146

Figure S120.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00035

Table S121.  Gene #29: '16q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
16Q GAIN MUTATED 16 19 4 13 32 46 14
16Q GAIN WILD-TYPE 64 67 60 44 58 92 84

Figure S121.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00183 (Fisher's exact test), Q value = 0.0099

Table S122.  Gene #29: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
16Q GAIN MUTATED 11 23 3 20 7 11 15 11 29
16Q GAIN WILD-TYPE 38 51 26 66 70 43 42 21 52

Figure S122.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17q gain' versus 'MRNA_CNMF'

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

Table S123.  Gene #31: '17q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
17Q GAIN MUTATED 3 18 13 3
17Q GAIN WILD-TYPE 42 45 52 40

Figure S123.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'17q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0036 (Fisher's exact test), Q value = 0.017

Table S124.  Gene #31: '17q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
17Q GAIN MUTATED 3 24 10
17Q GAIN WILD-TYPE 47 65 67

Figure S124.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S125.  Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
17Q GAIN MUTATED 15 61 34 3
17Q GAIN WILD-TYPE 200 186 98 19

Figure S125.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 0.00957 (Fisher's exact test), Q value = 0.038

Table S126.  Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
17Q GAIN MUTATED 18 37 22
17Q GAIN WILD-TYPE 99 92 122

Figure S126.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00746 (Fisher's exact test), Q value = 0.031

Table S127.  Gene #31: '17q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 168 86
17Q GAIN MUTATED 42 20 24
17Q GAIN WILD-TYPE 186 148 62

Figure S127.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S128.  Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
17Q GAIN MUTATED 53 15 14 31
17Q GAIN WILD-TYPE 103 113 117 167

Figure S128.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S129.  Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
17Q GAIN MUTATED 27 17 3 7 18 35 6
17Q GAIN WILD-TYPE 53 69 61 50 72 103 92

Figure S129.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00852 (Fisher's exact test), Q value = 0.034

Table S130.  Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
17Q GAIN MUTATED 12 11 3 25 4 10 12 5 15
17Q GAIN WILD-TYPE 37 63 26 61 73 44 45 27 66

Figure S130.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p gain' versus 'CN_CNMF'

P value = 0.00133 (Fisher's exact test), Q value = 0.0078

Table S131.  Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
18P GAIN MUTATED 12 4 12 3
18P GAIN WILD-TYPE 203 243 120 19

Figure S131.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 0.00364 (Fisher's exact test), Q value = 0.017

Table S132.  Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
18P GAIN MUTATED 8 1 13
18P GAIN WILD-TYPE 109 128 131

Figure S132.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00211 (Fisher's exact test), Q value = 0.011

Table S133.  Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
18P GAIN MUTATED 1 3 10 3 5 2 7
18P GAIN WILD-TYPE 79 83 54 54 85 136 91

Figure S133.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q gain' versus 'CN_CNMF'

P value = 0.00404 (Fisher's exact test), Q value = 0.019

Table S134.  Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
18Q GAIN MUTATED 9 2 5 3
18Q GAIN WILD-TYPE 206 245 127 19

Figure S134.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

'18q gain' versus 'METHLYATION_CNMF'

P value = 0.0136 (Fisher's exact test), Q value = 0.051

Table S135.  Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
18Q GAIN MUTATED 6 0 7
18Q GAIN WILD-TYPE 111 129 137

Figure S135.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00192 (Fisher's exact test), Q value = 0.01

Table S136.  Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
18Q GAIN MUTATED 0 1 7 1 4 1 5
18Q GAIN WILD-TYPE 80 85 57 56 86 137 93

Figure S136.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00643 (Fisher's exact test), Q value = 0.028

Table S137.  Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
18Q GAIN MUTATED 1 6 1 0 8 1 1 0 1
18Q GAIN WILD-TYPE 48 68 28 86 69 53 56 32 80

Figure S137.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00821 (Fisher's exact test), Q value = 0.033

Table S138.  Gene #34: '19p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
19P GAIN MUTATED 2 20 9
19P GAIN WILD-TYPE 48 69 68

Figure S138.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'19p gain' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00035

Table S139.  Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
19P GAIN MUTATED 16 60 24 5
19P GAIN WILD-TYPE 199 187 108 17

Figure S139.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00028

Table S140.  Gene #34: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
19P GAIN MUTATED 11 20 3 13 23 29 5
19P GAIN WILD-TYPE 69 66 61 44 67 109 93

Figure S140.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_CNMF'

P value = 0.0172 (Fisher's exact test), Q value = 0.062

Table S141.  Gene #34: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 95 86 205
19P GAIN MUTATED 28 24 12 23
19P GAIN WILD-TYPE 125 71 74 182

Figure S141.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00633 (Fisher's exact test), Q value = 0.027

Table S142.  Gene #34: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
19P GAIN MUTATED 11 14 6 13 3 8 7 11 14
19P GAIN WILD-TYPE 38 60 23 73 74 46 50 21 67

Figure S142.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q gain' versus 'MRNA_CNMF'

P value = 0.0228 (Fisher's exact test), Q value = 0.076

Table S143.  Gene #35: '19q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
19Q GAIN MUTATED 3 16 6 8
19Q GAIN WILD-TYPE 42 47 59 35

Figure S143.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'19q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00299 (Fisher's exact test), Q value = 0.015

Table S144.  Gene #35: '19q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
19Q GAIN MUTATED 1 19 13
19Q GAIN WILD-TYPE 49 70 64

Figure S144.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'19q gain' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00043

Table S145.  Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
19Q GAIN MUTATED 22 63 21 7
19Q GAIN WILD-TYPE 193 184 111 15

Figure S145.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

'19q gain' versus 'RPPA_CNMF'

P value = 0.0486 (Fisher's exact test), Q value = 0.14

Table S146.  Gene #35: '19q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 197 177
19Q GAIN MUTATED 26 42 24
19Q GAIN WILD-TYPE 82 155 153

Figure S146.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'19q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00107 (Fisher's exact test), Q value = 0.0065

Table S147.  Gene #35: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
19Q GAIN MUTATED 14 21 4 12 23 30 8
19Q GAIN WILD-TYPE 66 65 60 45 67 108 90

Figure S147.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_CNMF'

P value = 0.0417 (Fisher's exact test), Q value = 0.12

Table S148.  Gene #35: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 95 86 205
19Q GAIN MUTATED 29 25 10 30
19Q GAIN WILD-TYPE 124 70 76 175

Figure S148.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0123 (Fisher's exact test), Q value = 0.048

Table S149.  Gene #35: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
19Q GAIN MUTATED 14 13 5 16 5 9 6 11 15
19Q GAIN WILD-TYPE 35 61 24 70 72 45 51 21 66

Figure S149.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MRNA_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.0021

Table S150.  Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
20P GAIN MUTATED 16 41 48 21
20P GAIN WILD-TYPE 29 22 17 22

Figure S150.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S151.  Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
20P GAIN MUTATED 13 60 53
20P GAIN WILD-TYPE 37 29 24

Figure S151.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S152.  Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
20P GAIN MUTATED 82 174 76 21
20P GAIN WILD-TYPE 133 73 56 1

Figure S152.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 0.00724 (Fisher's exact test), Q value = 0.03

Table S153.  Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
20P GAIN MUTATED 68 86 69
20P GAIN WILD-TYPE 49 43 75

Figure S153.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 0.025 (Fisher's exact test), Q value = 0.081

Table S154.  Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
20P GAIN MUTATED 102 61 72 115
20P GAIN WILD-TYPE 54 67 59 83

Figure S154.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S155.  Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
20P GAIN MUTATED 52 46 16 45 56 97 38
20P GAIN WILD-TYPE 28 40 48 12 34 41 60

Figure S155.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S156.  Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
20P GAIN MUTATED 26 41 16 52 19 37 41 17 61
20P GAIN WILD-TYPE 23 33 13 34 58 17 16 15 20

Figure S156.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0463 (Fisher's exact test), Q value = 0.13

Table S157.  Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 40 38 22
20P GAIN MUTATED 25 29 21 9
20P GAIN WILD-TYPE 10 11 17 13

Figure S157.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S158.  Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
20Q GAIN MUTATED 19 61 59 24
20Q GAIN WILD-TYPE 26 2 6 19

Figure S158.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S159.  Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
20Q GAIN MUTATED 15 86 62
20Q GAIN WILD-TYPE 35 3 15

Figure S159.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S160.  Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
20Q GAIN MUTATED 91 241 109 22
20Q GAIN WILD-TYPE 124 6 23 0

Figure S160.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S161.  Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
20Q GAIN MUTATED 82 126 86
20Q GAIN WILD-TYPE 35 3 58

Figure S161.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q gain' versus 'RPPA_CNMF'

P value = 0.0127 (Fisher's exact test), Q value = 0.048

Table S162.  Gene #37: '20q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 197 177
20Q GAIN MUTATED 86 155 118
20Q GAIN WILD-TYPE 22 42 59

Figure S162.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S163.  Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
20Q GAIN MUTATED 150 73 91 146
20Q GAIN WILD-TYPE 6 55 40 52

Figure S163.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S164.  Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
20Q GAIN MUTATED 71 62 18 50 83 131 45
20Q GAIN WILD-TYPE 9 24 46 7 7 7 53

Figure S164.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S165.  Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 95 86 205
20Q GAIN MUTATED 110 78 82 135
20Q GAIN WILD-TYPE 43 17 4 70

Figure S165.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S166.  Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
20Q GAIN MUTATED 36 56 20 72 28 47 50 20 76
20Q GAIN WILD-TYPE 13 18 9 14 49 7 7 12 5

Figure S166.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00071

Table S167.  Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 40 38 22
20Q GAIN MUTATED 29 37 36 11
20Q GAIN WILD-TYPE 6 3 2 11

Figure S167.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'21q gain' versus 'CN_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.0017

Table S168.  Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
21Q GAIN MUTATED 2 17 13 2
21Q GAIN WILD-TYPE 213 230 119 20

Figure S168.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

'22q gain' versus 'CN_CNMF'

P value = 0.0143 (Fisher's exact test), Q value = 0.053

Table S169.  Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
22Q GAIN MUTATED 2 12 9 0
22Q GAIN WILD-TYPE 213 235 123 22

Figure S169.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

'22q gain' versus 'MIRSEQ_CNMF'

P value = 0.00446 (Fisher's exact test), Q value = 0.021

Table S170.  Gene #39: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 95 86 205
22Q GAIN MUTATED 1 5 8 6
22Q GAIN WILD-TYPE 152 90 78 199

Figure S170.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xp gain' versus 'MRNA_CNMF'

P value = 0.0167 (Fisher's exact test), Q value = 0.06

Table S171.  Gene #40: 'xp gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
XP GAIN MUTATED 3 16 6 9
XP GAIN WILD-TYPE 42 47 59 34

Figure S171.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'xp gain' versus 'CN_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.0013

Table S172.  Gene #40: 'xp gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
XP GAIN MUTATED 18 57 22 3
XP GAIN WILD-TYPE 197 190 110 19

Figure S172.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #3: 'CN_CNMF'

'xp gain' versus 'METHLYATION_CNMF'

P value = 0.0389 (Fisher's exact test), Q value = 0.11

Table S173.  Gene #40: 'xp gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
XP GAIN MUTATED 11 27 25
XP GAIN WILD-TYPE 106 102 119

Figure S173.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xp gain' versus 'RPPA_CNMF'

P value = 0.0278 (Fisher's exact test), Q value = 0.089

Table S174.  Gene #40: 'xp gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 197 177
XP GAIN MUTATED 19 44 21
XP GAIN WILD-TYPE 89 153 156

Figure S174.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'xq gain' versus 'CN_CNMF'

P value = 0.00272 (Fisher's exact test), Q value = 0.014

Table S175.  Gene #41: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
XQ GAIN MUTATED 22 55 28 4
XQ GAIN WILD-TYPE 193 192 104 18

Figure S175.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

'xq gain' versus 'RPPA_CNMF'

P value = 0.0185 (Fisher's exact test), Q value = 0.063

Table S176.  Gene #41: 'xq gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 197 177
XQ GAIN MUTATED 22 46 22
XQ GAIN WILD-TYPE 86 151 155

Figure S176.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'1p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00686 (Fisher's exact test), Q value = 0.029

Table S177.  Gene #42: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
1P LOSS MUTATED 6 28 11
1P LOSS WILD-TYPE 44 61 66

Figure S177.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S178.  Gene #42: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
1P LOSS MUTATED 14 78 33 14
1P LOSS WILD-TYPE 201 169 99 8

Figure S178.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 0.0174 (Fisher's exact test), Q value = 0.062

Table S179.  Gene #42: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
1P LOSS MUTATED 29 39 23
1P LOSS WILD-TYPE 88 90 121

Figure S179.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00071

Table S180.  Gene #42: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
1P LOSS MUTATED 51 14 33 40
1P LOSS WILD-TYPE 105 114 98 158

Figure S180.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00043

Table S181.  Gene #42: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
1P LOSS MUTATED 24 14 5 15 30 39 11
1P LOSS WILD-TYPE 56 72 59 42 60 99 87

Figure S181.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_CNMF'

P value = 0.0372 (Fisher's exact test), Q value = 0.11

Table S182.  Gene #42: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 95 86 205
1P LOSS MUTATED 33 27 26 35
1P LOSS WILD-TYPE 120 68 60 170

Figure S182.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00113 (Fisher's exact test), Q value = 0.0068

Table S183.  Gene #42: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
1P LOSS MUTATED 13 14 4 22 5 20 15 5 23
1P LOSS WILD-TYPE 36 60 25 64 72 34 42 27 58

Figure S183.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S184.  Gene #43: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
1Q LOSS MUTATED 7 42 22 11
1Q LOSS WILD-TYPE 208 205 110 11

Figure S184.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

'1q loss' versus 'METHLYATION_CNMF'

P value = 0.0111 (Fisher's exact test), Q value = 0.043

Table S185.  Gene #43: '1q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
1Q LOSS MUTATED 15 27 12
1Q LOSS WILD-TYPE 102 102 132

Figure S185.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1q loss' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00035

Table S186.  Gene #43: '1q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
1Q LOSS MUTATED 34 4 18 25
1Q LOSS WILD-TYPE 122 124 113 173

Figure S186.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00101 (Fisher's exact test), Q value = 0.0063

Table S187.  Gene #43: '1q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
1Q LOSS MUTATED 16 6 3 7 19 24 6
1Q LOSS WILD-TYPE 64 80 61 50 71 114 92

Figure S187.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p loss' versus 'CN_CNMF'

P value = 0.029 (Fisher's exact test), Q value = 0.091

Table S188.  Gene #44: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
2P LOSS MUTATED 1 10 6 0
2P LOSS WILD-TYPE 214 237 126 22

Figure S188.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

'2p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0125 (Fisher's exact test), Q value = 0.048

Table S189.  Gene #44: '2p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 168 86
2P LOSS MUTATED 5 1 6
2P LOSS WILD-TYPE 223 167 80

Figure S189.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'2p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00781 (Fisher's exact test), Q value = 0.032

Table S190.  Gene #44: '2p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
2P LOSS MUTATED 0 0 0 2 3 4 8
2P LOSS WILD-TYPE 80 86 64 55 87 134 90

Figure S190.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_CNMF'

P value = 0.0178 (Fisher's exact test), Q value = 0.062

Table S191.  Gene #44: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 95 86 205
2P LOSS MUTATED 2 0 6 8
2P LOSS WILD-TYPE 151 95 80 197

Figure S191.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0127 (Fisher's exact test), Q value = 0.048

Table S192.  Gene #45: '2q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 168 86
2Q LOSS MUTATED 5 0 4
2Q LOSS WILD-TYPE 223 168 82

Figure S192.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'2q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00554 (Fisher's exact test), Q value = 0.024

Table S193.  Gene #45: '2q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
2Q LOSS MUTATED 0 0 0 1 2 3 8
2Q LOSS WILD-TYPE 80 86 64 56 88 135 90

Figure S193.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_CNMF'

P value = 0.0176 (Fisher's exact test), Q value = 0.062

Table S194.  Gene #45: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 95 86 205
2Q LOSS MUTATED 1 0 5 7
2Q LOSS WILD-TYPE 152 95 81 198

Figure S194.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3p loss' versus 'CN_CNMF'

P value = 0.0207 (Fisher's exact test), Q value = 0.07

Table S195.  Gene #46: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
3P LOSS MUTATED 15 35 13 5
3P LOSS WILD-TYPE 200 212 119 17

Figure S195.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

'3q loss' versus 'CN_CNMF'

P value = 0.0409 (Fisher's exact test), Q value = 0.12

Table S196.  Gene #47: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
3Q LOSS MUTATED 11 20 9 5
3Q LOSS WILD-TYPE 204 227 123 17

Figure S196.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'MRNA_CNMF'

P value = 0.0409 (Fisher's exact test), Q value = 0.12

Table S197.  Gene #48: '4p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
4P LOSS MUTATED 13 24 26 7
4P LOSS WILD-TYPE 32 39 39 36

Figure S197.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'4p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00194 (Fisher's exact test), Q value = 0.01

Table S198.  Gene #48: '4p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
4P LOSS MUTATED 11 41 18
4P LOSS WILD-TYPE 39 48 59

Figure S198.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S199.  Gene #48: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
4P LOSS MUTATED 20 108 53 16
4P LOSS WILD-TYPE 195 139 79 6

Figure S199.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 0.0112 (Fisher's exact test), Q value = 0.044

Table S200.  Gene #48: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
4P LOSS MUTATED 33 54 37
4P LOSS WILD-TYPE 84 75 107

Figure S200.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 0.00148 (Fisher's exact test), Q value = 0.0085

Table S201.  Gene #48: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
4P LOSS MUTATED 64 25 43 64
4P LOSS WILD-TYPE 92 103 88 134

Figure S201.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00065

Table S202.  Gene #48: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
4P LOSS MUTATED 33 22 7 19 37 54 24
4P LOSS WILD-TYPE 47 64 57 38 53 84 74

Figure S202.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00464 (Fisher's exact test), Q value = 0.021

Table S203.  Gene #48: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
4P LOSS MUTATED 16 17 10 33 12 15 22 10 36
4P LOSS WILD-TYPE 33 57 19 53 65 39 35 22 45

Figure S203.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4q loss' versus 'MRNA_CNMF'

P value = 0.018 (Fisher's exact test), Q value = 0.062

Table S204.  Gene #49: '4q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
4Q LOSS MUTATED 12 23 26 6
4Q LOSS WILD-TYPE 33 40 39 37

Figure S204.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'4q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0158 (Fisher's exact test), Q value = 0.058

Table S205.  Gene #49: '4q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
4Q LOSS MUTATED 10 37 20
4Q LOSS WILD-TYPE 40 52 57

Figure S205.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S206.  Gene #49: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
4Q LOSS MUTATED 18 110 48 15
4Q LOSS WILD-TYPE 197 137 84 7

Figure S206.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 0.0205 (Fisher's exact test), Q value = 0.069

Table S207.  Gene #49: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
4Q LOSS MUTATED 39 49 33
4Q LOSS WILD-TYPE 78 80 111

Figure S207.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 0.00476 (Fisher's exact test), Q value = 0.022

Table S208.  Gene #49: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
4Q LOSS MUTATED 61 25 41 63
4Q LOSS WILD-TYPE 95 103 90 135

Figure S208.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S209.  Gene #49: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
4Q LOSS MUTATED 32 21 5 21 36 51 24
4Q LOSS WILD-TYPE 48 65 59 36 54 87 74

Figure S209.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00727 (Fisher's exact test), Q value = 0.03

Table S210.  Gene #49: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
4Q LOSS MUTATED 17 17 8 34 12 17 19 7 34
4Q LOSS WILD-TYPE 32 57 21 52 65 37 38 25 47

Figure S210.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S211.  Gene #50: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
5P LOSS MUTATED 6 38 33 7
5P LOSS WILD-TYPE 209 209 99 15

Figure S211.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

'5p loss' versus 'METHLYATION_CNMF'

P value = 0.0237 (Fisher's exact test), Q value = 0.078

Table S212.  Gene #50: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
5P LOSS MUTATED 14 28 15
5P LOSS WILD-TYPE 103 101 129

Figure S212.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00668 (Fisher's exact test), Q value = 0.028

Table S213.  Gene #50: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
5P LOSS MUTATED 14 13 1 14 10 20 12
5P LOSS WILD-TYPE 66 73 63 43 80 118 86

Figure S213.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MRNA_CNMF'

P value = 0.00435 (Fisher's exact test), Q value = 0.02

Table S214.  Gene #51: '5q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
5Q LOSS MUTATED 7 14 17 1
5Q LOSS WILD-TYPE 38 49 48 42

Figure S214.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'5q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00459 (Fisher's exact test), Q value = 0.021

Table S215.  Gene #51: '5q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
5Q LOSS MUTATED 7 25 7
5Q LOSS WILD-TYPE 43 64 70

Figure S215.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'5q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S216.  Gene #51: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
5Q LOSS MUTATED 6 50 54 10
5Q LOSS WILD-TYPE 209 197 78 12

Figure S216.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 0.0163 (Fisher's exact test), Q value = 0.059

Table S217.  Gene #51: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
5Q LOSS MUTATED 24 37 21
5Q LOSS WILD-TYPE 93 92 123

Figure S217.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 0.0209 (Fisher's exact test), Q value = 0.07

Table S218.  Gene #51: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
5Q LOSS MUTATED 40 15 29 36
5Q LOSS WILD-TYPE 116 113 102 162

Figure S218.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00155 (Fisher's exact test), Q value = 0.0087

Table S219.  Gene #51: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
5Q LOSS MUTATED 19 12 4 18 22 32 13
5Q LOSS WILD-TYPE 61 74 60 39 68 106 85

Figure S219.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00235 (Fisher's exact test), Q value = 0.012

Table S220.  Gene #51: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
5Q LOSS MUTATED 9 12 9 26 6 4 12 7 19
5Q LOSS WILD-TYPE 40 62 20 60 71 50 45 25 62

Figure S220.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0112 (Fisher's exact test), Q value = 0.043

Table S221.  Gene #52: '6p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
6P LOSS MUTATED 5 2 11
6P LOSS WILD-TYPE 45 87 66

Figure S221.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0289 (Fisher's exact test), Q value = 0.091

Table S222.  Gene #52: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
6P LOSS MUTATED 8 3 4 1 12 7 12
6P LOSS WILD-TYPE 72 83 60 56 78 131 86

Figure S222.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'MRNA_CNMF'

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

Table S223.  Gene #56: '8p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
8P LOSS MUTATED 12 30 31 9
8P LOSS WILD-TYPE 33 33 34 34

Figure S223.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'8p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00107 (Fisher's exact test), Q value = 0.0065

Table S224.  Gene #56: '8p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
8P LOSS MUTATED 9 44 29
8P LOSS WILD-TYPE 41 45 48

Figure S224.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S225.  Gene #56: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
8P LOSS MUTATED 17 118 74 8
8P LOSS WILD-TYPE 198 129 58 14

Figure S225.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 7e-04 (Fisher's exact test), Q value = 0.0044

Table S226.  Gene #56: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
8P LOSS MUTATED 38 61 36
8P LOSS WILD-TYPE 79 68 108

Figure S226.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 0.00353 (Fisher's exact test), Q value = 0.017

Table S227.  Gene #56: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
8P LOSS MUTATED 61 28 48 79
8P LOSS WILD-TYPE 95 100 83 119

Figure S227.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 5e-04

Table S228.  Gene #56: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
8P LOSS MUTATED 28 25 8 24 40 64 27
8P LOSS WILD-TYPE 52 61 56 33 50 74 71

Figure S228.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0299 (Fisher's exact test), Q value = 0.092

Table S229.  Gene #56: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
8P LOSS MUTATED 17 23 9 37 15 20 26 9 34
8P LOSS WILD-TYPE 32 51 20 49 62 34 31 23 47

Figure S229.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S230.  Gene #57: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
8Q LOSS MUTATED 2 18 10 6
8Q LOSS WILD-TYPE 213 229 122 16

Figure S230.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'

'8q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0337 (Fisher's exact test), Q value = 0.1

Table S231.  Gene #57: '8q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
8Q LOSS MUTATED 5 4 1 3 0 3 5 1 10
8Q LOSS WILD-TYPE 44 70 28 83 77 51 52 31 71

Figure S231.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0236 (Fisher's exact test), Q value = 0.078

Table S232.  Gene #57: '8q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 40 38 22
8Q LOSS MUTATED 8 2 3 0
8Q LOSS WILD-TYPE 27 38 35 22

Figure S232.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S233.  Gene #58: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
9P LOSS MUTATED 8 47 17 4
9P LOSS WILD-TYPE 207 200 115 18

Figure S233.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 0.00134 (Fisher's exact test), Q value = 0.0078

Table S234.  Gene #58: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
9P LOSS MUTATED 17 27 9
9P LOSS WILD-TYPE 100 102 135

Figure S234.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.0024

Table S235.  Gene #58: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
9P LOSS MUTATED 32 7 20 17
9P LOSS WILD-TYPE 124 121 111 181

Figure S235.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0177 (Fisher's exact test), Q value = 0.062

Table S236.  Gene #58: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
9P LOSS MUTATED 13 9 2 12 15 18 7
9P LOSS WILD-TYPE 67 77 62 45 75 120 91

Figure S236.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0238 (Fisher's exact test), Q value = 0.078

Table S237.  Gene #59: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
9Q LOSS MUTATED 2 17 7
9Q LOSS WILD-TYPE 48 72 70

Figure S237.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S238.  Gene #59: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
9Q LOSS MUTATED 7 50 17 4
9Q LOSS WILD-TYPE 208 197 115 18

Figure S238.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.001

Table S239.  Gene #59: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
9Q LOSS MUTATED 19 27 7
9Q LOSS WILD-TYPE 98 102 137

Figure S239.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00057

Table S240.  Gene #59: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
9Q LOSS MUTATED 33 6 21 18
9Q LOSS WILD-TYPE 123 122 110 180

Figure S240.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00124 (Fisher's exact test), Q value = 0.0074

Table S241.  Gene #59: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
9Q LOSS MUTATED 11 7 2 12 19 21 6
9Q LOSS WILD-TYPE 69 79 62 45 71 117 92

Figure S241.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0179 (Fisher's exact test), Q value = 0.062

Table S242.  Gene #59: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
9Q LOSS MUTATED 9 9 3 18 2 9 5 2 11
9Q LOSS WILD-TYPE 40 65 26 68 75 45 52 30 70

Figure S242.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10p loss' versus 'MRNA_CNMF'

P value = 0.00445 (Fisher's exact test), Q value = 0.021

Table S243.  Gene #60: '10p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
10P LOSS MUTATED 3 4 17 4
10P LOSS WILD-TYPE 42 59 48 39

Figure S243.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'10p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S244.  Gene #60: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
10P LOSS MUTATED 10 48 35 9
10P LOSS WILD-TYPE 205 199 97 13

Figure S244.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 0.0031 (Fisher's exact test), Q value = 0.015

Table S245.  Gene #60: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
10P LOSS MUTATED 40 13 21 27
10P LOSS WILD-TYPE 116 115 110 171

Figure S245.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00035 (Fisher's exact test), Q value = 0.0024

Table S246.  Gene #60: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
10P LOSS MUTATED 16 10 3 11 28 23 10
10P LOSS WILD-TYPE 64 76 61 46 62 115 88

Figure S246.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MRNA_CNMF'

P value = 0.00897 (Fisher's exact test), Q value = 0.036

Table S247.  Gene #61: '10q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
10Q LOSS MUTATED 5 6 19 4
10Q LOSS WILD-TYPE 40 57 46 39

Figure S247.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'10q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S248.  Gene #61: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
10Q LOSS MUTATED 7 55 41 8
10Q LOSS WILD-TYPE 208 192 91 14

Figure S248.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 0.0149 (Fisher's exact test), Q value = 0.055

Table S249.  Gene #61: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
10Q LOSS MUTATED 17 36 23
10Q LOSS WILD-TYPE 100 93 121

Figure S249.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 0.00318 (Fisher's exact test), Q value = 0.016

Table S250.  Gene #61: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
10Q LOSS MUTATED 42 13 22 33
10Q LOSS WILD-TYPE 114 115 109 165

Figure S250.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00019

Table S251.  Gene #61: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
10Q LOSS MUTATED 18 9 1 10 32 26 14
10Q LOSS WILD-TYPE 62 77 63 47 58 112 84

Figure S251.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 0.00639 (Fisher's exact test), Q value = 0.028

Table S252.  Gene #62: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
11P LOSS MUTATED 14 41 18 2
11P LOSS WILD-TYPE 201 206 114 20

Figure S252.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

'11q loss' versus 'CN_CNMF'

P value = 0.00531 (Fisher's exact test), Q value = 0.024

Table S253.  Gene #63: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
11Q LOSS MUTATED 19 50 19 4
11Q LOSS WILD-TYPE 196 197 113 18

Figure S253.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

'11q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0425 (Fisher's exact test), Q value = 0.12

Table S254.  Gene #63: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
11Q LOSS MUTATED 11 9 5 9 5 8 12 5 20
11Q LOSS WILD-TYPE 38 65 24 77 72 46 45 27 61

Figure S254.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12p loss' versus 'MRNA_CNMF'

P value = 0.0298 (Fisher's exact test), Q value = 0.092

Table S255.  Gene #64: '12p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
12P LOSS MUTATED 2 11 9 1
12P LOSS WILD-TYPE 43 52 56 42

Figure S255.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'12p loss' versus 'MRNA_CHIERARCHICAL'

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

Table S256.  Gene #64: '12p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
12P LOSS MUTATED 0 15 8
12P LOSS WILD-TYPE 50 74 69

Figure S256.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'12p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S257.  Gene #64: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
12P LOSS MUTATED 2 50 16 3
12P LOSS WILD-TYPE 213 197 116 19

Figure S257.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

'12p loss' versus 'MRNASEQ_CNMF'

P value = 0.0283 (Fisher's exact test), Q value = 0.09

Table S258.  Gene #64: '12p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
12P LOSS MUTATED 26 7 14 24
12P LOSS WILD-TYPE 130 121 117 174

Figure S258.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00071

Table S259.  Gene #64: '12p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
12P LOSS MUTATED 16 3 1 8 15 22 6
12P LOSS WILD-TYPE 64 83 63 49 75 116 92

Figure S259.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0076 (Fisher's exact test), Q value = 0.031

Table S260.  Gene #65: '12q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
12Q LOSS MUTATED 0 13 8
12Q LOSS WILD-TYPE 50 76 69

Figure S260.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'12q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S261.  Gene #65: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
12Q LOSS MUTATED 3 50 14 4
12Q LOSS WILD-TYPE 212 197 118 18

Figure S261.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

'12q loss' versus 'MRNASEQ_CNMF'

P value = 0.0128 (Fisher's exact test), Q value = 0.048

Table S262.  Gene #65: '12q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
12Q LOSS MUTATED 28 7 14 22
12Q LOSS WILD-TYPE 128 121 117 176

Figure S262.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00035

Table S263.  Gene #65: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
12Q LOSS MUTATED 18 2 2 8 15 21 5
12Q LOSS WILD-TYPE 62 84 62 49 75 117 93

Figure S263.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q loss' versus 'MIRSEQ_CNMF'

P value = 0.037 (Fisher's exact test), Q value = 0.11

Table S264.  Gene #65: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 95 86 205
12Q LOSS MUTATED 15 18 13 17
12Q LOSS WILD-TYPE 138 77 73 188

Figure S264.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'13q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00508 (Fisher's exact test), Q value = 0.023

Table S265.  Gene #66: '13q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
13Q LOSS MUTATED 4 0 1
13Q LOSS WILD-TYPE 46 89 76

Figure S265.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.0018

Table S266.  Gene #66: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
13Q LOSS MUTATED 3 3 8 4
13Q LOSS WILD-TYPE 212 244 124 18

Figure S266.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

'14q loss' versus 'MRNA_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.0017

Table S267.  Gene #67: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
14Q LOSS MUTATED 10 30 31 7
14Q LOSS WILD-TYPE 35 33 34 36

Figure S267.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'14q loss' versus 'MRNA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00028

Table S268.  Gene #67: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
14Q LOSS MUTATED 6 45 27
14Q LOSS WILD-TYPE 44 44 50

Figure S268.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S269.  Gene #67: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
14Q LOSS MUTATED 18 154 26 9
14Q LOSS WILD-TYPE 197 93 106 13

Figure S269.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S270.  Gene #67: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
14Q LOSS MUTATED 33 67 28
14Q LOSS WILD-TYPE 84 62 116

Figure S270.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0313 (Fisher's exact test), Q value = 0.096

Table S271.  Gene #67: '14q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 168 86
14Q LOSS MUTATED 70 55 40
14Q LOSS WILD-TYPE 158 113 46

Figure S271.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S272.  Gene #67: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
14Q LOSS MUTATED 81 23 30 72
14Q LOSS WILD-TYPE 75 105 101 126

Figure S272.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S273.  Gene #67: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
14Q LOSS MUTATED 35 26 3 21 37 65 19
14Q LOSS WILD-TYPE 45 60 61 36 53 73 79

Figure S273.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_CNMF'

P value = 0.00183 (Fisher's exact test), Q value = 0.0099

Table S274.  Gene #67: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 95 86 205
14Q LOSS MUTATED 41 34 43 60
14Q LOSS WILD-TYPE 112 61 43 145

Figure S274.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'14q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S275.  Gene #67: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
14Q LOSS MUTATED 13 20 9 27 6 29 28 12 34
14Q LOSS WILD-TYPE 36 54 20 59 71 25 29 20 47

Figure S275.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0175 (Fisher's exact test), Q value = 0.062

Table S276.  Gene #67: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 40 38 22
14Q LOSS MUTATED 14 13 23 5
14Q LOSS WILD-TYPE 21 27 15 17

Figure S276.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'14q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0183 (Fisher's exact test), Q value = 0.063

Table S277.  Gene #67: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 16 34 22
14Q LOSS MUTATED 18 6 17 14
14Q LOSS WILD-TYPE 45 10 17 8

Figure S277.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q loss' versus 'MRNA_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00077

Table S278.  Gene #68: '15q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
15Q LOSS MUTATED 11 32 35 8
15Q LOSS WILD-TYPE 34 31 30 35

Figure S278.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'15q loss' versus 'MRNA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00028

Table S279.  Gene #68: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
15Q LOSS MUTATED 11 52 23
15Q LOSS WILD-TYPE 39 37 54

Figure S279.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S280.  Gene #68: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
15Q LOSS MUTATED 17 136 61 16
15Q LOSS WILD-TYPE 198 111 71 6

Figure S280.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00077

Table S281.  Gene #68: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
15Q LOSS MUTATED 39 66 39
15Q LOSS WILD-TYPE 78 63 105

Figure S281.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S282.  Gene #68: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
15Q LOSS MUTATED 78 28 47 76
15Q LOSS WILD-TYPE 78 100 84 122

Figure S282.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S283.  Gene #68: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
15Q LOSS MUTATED 36 27 2 23 46 64 31
15Q LOSS WILD-TYPE 44 59 62 34 44 74 67

Figure S283.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_CNMF'

P value = 0.00155 (Fisher's exact test), Q value = 0.0087

Table S284.  Gene #68: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 95 86 205
15Q LOSS MUTATED 47 45 43 65
15Q LOSS WILD-TYPE 106 50 43 140

Figure S284.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.0016

Table S285.  Gene #68: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
15Q LOSS MUTATED 16 31 8 37 11 18 26 14 39
15Q LOSS WILD-TYPE 33 43 21 49 66 36 31 18 42

Figure S285.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16p loss' versus 'CN_CNMF'

P value = 0.0177 (Fisher's exact test), Q value = 0.062

Table S286.  Gene #69: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
16P LOSS MUTATED 7 16 14 3
16P LOSS WILD-TYPE 208 231 118 19

Figure S286.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

'16q loss' versus 'MRNA_CNMF'

P value = 0.0341 (Fisher's exact test), Q value = 0.1

Table S287.  Gene #70: '16q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
16Q LOSS MUTATED 5 7 2 0
16Q LOSS WILD-TYPE 40 56 63 43

Figure S287.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'16q loss' versus 'CN_CNMF'

P value = 0.00069 (Fisher's exact test), Q value = 0.0044

Table S288.  Gene #70: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
16Q LOSS MUTATED 7 15 19 3
16Q LOSS WILD-TYPE 208 232 113 19

Figure S288.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

'17p loss' versus 'MRNA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00028

Table S289.  Gene #71: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
17P LOSS MUTATED 16 45 44 15
17P LOSS WILD-TYPE 29 18 21 28

Figure S289.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17p loss' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00019

Table S290.  Gene #71: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
17P LOSS MUTATED 13 61 46
17P LOSS WILD-TYPE 37 28 31

Figure S290.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S291.  Gene #71: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
17P LOSS MUTATED 43 187 96 14
17P LOSS WILD-TYPE 172 60 36 8

Figure S291.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S292.  Gene #71: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
17P LOSS MUTATED 51 99 67
17P LOSS WILD-TYPE 66 30 77

Figure S292.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S293.  Gene #71: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
17P LOSS MUTATED 109 50 70 109
17P LOSS WILD-TYPE 47 78 61 89

Figure S293.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S294.  Gene #71: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
17P LOSS MUTATED 50 44 8 38 66 93 39
17P LOSS WILD-TYPE 30 42 56 19 24 45 59

Figure S294.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CNMF'

P value = 0.00065 (Fisher's exact test), Q value = 0.0042

Table S295.  Gene #71: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 95 86 205
17P LOSS MUTATED 77 54 64 103
17P LOSS WILD-TYPE 76 41 22 102

Figure S295.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S296.  Gene #71: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
17P LOSS MUTATED 23 42 16 56 20 35 38 16 52
17P LOSS WILD-TYPE 26 32 13 30 57 19 19 16 29

Figure S296.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S297.  Gene #72: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
17Q LOSS MUTATED 11 47 25 10
17Q LOSS WILD-TYPE 204 200 107 12

Figure S297.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

'17q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0293 (Fisher's exact test), Q value = 0.091

Table S298.  Gene #72: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
17Q LOSS MUTATED 13 13 2 13 18 18 16
17Q LOSS WILD-TYPE 67 73 62 44 72 120 82

Figure S298.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S299.  Gene #73: '18p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
18P LOSS MUTATED 13 53 52 13
18P LOSS WILD-TYPE 32 10 13 30

Figure S299.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'18p loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S300.  Gene #73: '18p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
18P LOSS MUTATED 10 77 44
18P LOSS WILD-TYPE 40 12 33

Figure S300.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S301.  Gene #73: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
18P LOSS MUTATED 47 223 94 17
18P LOSS WILD-TYPE 168 24 38 5

Figure S301.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S302.  Gene #73: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
18P LOSS MUTATED 61 122 65
18P LOSS WILD-TYPE 56 7 79

Figure S302.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S303.  Gene #73: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
18P LOSS MUTATED 141 48 73 117
18P LOSS WILD-TYPE 15 80 58 81

Figure S303.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S304.  Gene #73: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
18P LOSS MUTATED 67 50 7 39 72 108 36
18P LOSS WILD-TYPE 13 36 57 18 18 30 62

Figure S304.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S305.  Gene #73: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 95 86 205
18P LOSS MUTATED 86 64 75 106
18P LOSS WILD-TYPE 67 31 11 99

Figure S305.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S306.  Gene #73: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
18P LOSS MUTATED 27 43 17 59 17 41 45 17 65
18P LOSS WILD-TYPE 22 31 12 27 60 13 12 15 16

Figure S306.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.0014

Table S307.  Gene #73: '18p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 40 38 22
18P LOSS MUTATED 23 30 34 8
18P LOSS WILD-TYPE 12 10 4 14

Figure S307.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00065

Table S308.  Gene #73: '18p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 16 34 22
18P LOSS MUTATED 33 16 26 20
18P LOSS WILD-TYPE 30 0 8 2

Figure S308.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S309.  Gene #74: '18q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
18Q LOSS MUTATED 16 54 54 15
18Q LOSS WILD-TYPE 29 9 11 28

Figure S309.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'18q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S310.  Gene #74: '18q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
18Q LOSS MUTATED 13 77 49
18Q LOSS WILD-TYPE 37 12 28

Figure S310.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S311.  Gene #74: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
18Q LOSS MUTATED 52 228 111 17
18Q LOSS WILD-TYPE 163 19 21 5

Figure S311.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S312.  Gene #74: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
18Q LOSS MUTATED 67 123 76
18Q LOSS WILD-TYPE 50 6 68

Figure S312.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S313.  Gene #74: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
18Q LOSS MUTATED 140 56 82 128
18Q LOSS WILD-TYPE 16 72 49 70

Figure S313.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S314.  Gene #74: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
18Q LOSS MUTATED 66 57 10 44 76 111 42
18Q LOSS WILD-TYPE 14 29 54 13 14 27 56

Figure S314.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S315.  Gene #74: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 95 86 205
18Q LOSS MUTATED 93 65 79 118
18Q LOSS WILD-TYPE 60 30 7 87

Figure S315.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S316.  Gene #74: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
18Q LOSS MUTATED 31 46 18 64 20 42 49 19 66
18Q LOSS WILD-TYPE 18 28 11 22 57 12 8 13 15

Figure S316.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00224 (Fisher's exact test), Q value = 0.012

Table S317.  Gene #74: '18q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 40 38 22
18Q LOSS MUTATED 25 32 34 10
18Q LOSS WILD-TYPE 10 8 4 12

Figure S317.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00025 (Fisher's exact test), Q value = 0.0017

Table S318.  Gene #74: '18q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 16 34 22
18Q LOSS MUTATED 38 16 26 21
18Q LOSS WILD-TYPE 25 0 8 1

Figure S318.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00019

Table S319.  Gene #75: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
19P LOSS MUTATED 6 30 23 3
19P LOSS WILD-TYPE 209 217 109 19

Figure S319.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

'19p loss' versus 'MRNASEQ_CNMF'

P value = 0.0136 (Fisher's exact test), Q value = 0.051

Table S320.  Gene #75: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
19P LOSS MUTATED 26 7 10 19
19P LOSS WILD-TYPE 130 121 121 179

Figure S320.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0215 (Fisher's exact test), Q value = 0.072

Table S321.  Gene #75: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
19P LOSS MUTATED 16 3 3 5 11 14 10
19P LOSS WILD-TYPE 64 83 61 52 79 124 88

Figure S321.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0341 (Fisher's exact test), Q value = 0.1

Table S322.  Gene #75: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
19P LOSS MUTATED 2 4 3 18 4 4 7 3 10
19P LOSS WILD-TYPE 47 70 26 68 73 50 50 29 71

Figure S322.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00057

Table S323.  Gene #76: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
19Q LOSS MUTATED 6 25 22 3
19Q LOSS WILD-TYPE 209 222 110 19

Figure S323.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

'19q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0262 (Fisher's exact test), Q value = 0.084

Table S324.  Gene #76: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
19Q LOSS MUTATED 0 6 3 15 3 4 7 3 8
19Q LOSS WILD-TYPE 49 68 26 71 74 50 50 29 73

Figure S324.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00963 (Fisher's exact test), Q value = 0.038

Table S325.  Gene #77: '20p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
20P LOSS MUTATED 2 17 5
20P LOSS WILD-TYPE 48 72 72

Figure S325.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S326.  Gene #77: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
20P LOSS MUTATED 5 38 22 0
20P LOSS WILD-TYPE 210 209 110 22

Figure S326.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

'20p loss' versus 'METHLYATION_CNMF'

P value = 0.00082 (Fisher's exact test), Q value = 0.0051

Table S327.  Gene #77: '20p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
20P LOSS MUTATED 9 24 7
20P LOSS WILD-TYPE 108 105 137

Figure S327.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00035 (Fisher's exact test), Q value = 0.0024

Table S328.  Gene #77: '20p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
20P LOSS MUTATED 9 10 0 3 16 22 5
20P LOSS WILD-TYPE 71 76 64 54 74 116 93

Figure S328.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0288 (Fisher's exact test), Q value = 0.091

Table S329.  Gene #77: '20p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 40 38 22
20P LOSS MUTATED 0 5 7 1
20P LOSS WILD-TYPE 35 35 31 21

Figure S329.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0405 (Fisher's exact test), Q value = 0.12

Table S330.  Gene #77: '20p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 16 34 22
20P LOSS MUTATED 4 5 3 1
20P LOSS WILD-TYPE 59 11 31 21

Figure S330.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q loss' versus 'RPPA_CNMF'

P value = 0.0304 (Fisher's exact test), Q value = 0.093

Table S331.  Gene #78: '20q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 197 177
20Q LOSS MUTATED 0 1 6
20Q LOSS WILD-TYPE 108 196 171

Figure S331.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'21q loss' versus 'MRNA_CNMF'

P value = 0.0111 (Fisher's exact test), Q value = 0.043

Table S332.  Gene #79: '21q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
21Q LOSS MUTATED 10 26 22 6
21Q LOSS WILD-TYPE 35 37 43 37

Figure S332.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'21q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00253 (Fisher's exact test), Q value = 0.013

Table S333.  Gene #79: '21q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
21Q LOSS MUTATED 10 38 16
21Q LOSS WILD-TYPE 40 51 61

Figure S333.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'21q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S334.  Gene #79: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
21Q LOSS MUTATED 32 104 43 14
21Q LOSS WILD-TYPE 183 143 89 8

Figure S334.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

'21q loss' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 5e-04

Table S335.  Gene #79: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
21Q LOSS MUTATED 71 28 35 57
21Q LOSS WILD-TYPE 85 100 96 141

Figure S335.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00218 (Fisher's exact test), Q value = 0.011

Table S336.  Gene #79: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
21Q LOSS MUTATED 30 24 10 21 35 51 20
21Q LOSS WILD-TYPE 50 62 54 36 55 87 78

Figure S336.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00798 (Fisher's exact test), Q value = 0.033

Table S337.  Gene #79: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
21Q LOSS MUTATED 16 17 6 32 13 21 25 8 30
21Q LOSS WILD-TYPE 33 57 23 54 64 33 32 24 51

Figure S337.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'MRNA_CNMF'

P value = 0.00689 (Fisher's exact test), Q value = 0.029

Table S338.  Gene #80: '22q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
22Q LOSS MUTATED 12 28 27 7
22Q LOSS WILD-TYPE 33 35 38 36

Figure S338.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'22q loss' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00019

Table S339.  Gene #80: '22q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
22Q LOSS MUTATED 5 40 29
22Q LOSS WILD-TYPE 45 49 48

Figure S339.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S340.  Gene #80: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
22Q LOSS MUTATED 25 120 46 12
22Q LOSS WILD-TYPE 190 127 86 10

Figure S340.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 0.0489 (Fisher's exact test), Q value = 0.14

Table S341.  Gene #80: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
22Q LOSS MUTATED 62 31 42 67
22Q LOSS WILD-TYPE 94 97 89 131

Figure S341.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1e-04

Table S342.  Gene #80: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
22Q LOSS MUTATED 30 27 5 23 35 59 23
22Q LOSS WILD-TYPE 50 59 59 34 55 79 75

Figure S342.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00139 (Fisher's exact test), Q value = 0.008

Table S343.  Gene #80: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
22Q LOSS MUTATED 14 23 2 33 15 22 25 11 32
22Q LOSS WILD-TYPE 35 51 27 53 62 32 32 21 49

Figure S343.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'xp loss' versus 'RPPA_CNMF'

P value = 0.0134 (Fisher's exact test), Q value = 0.05

Table S344.  Gene #81: 'xp loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 197 177
XP LOSS MUTATED 12 41 19
XP LOSS WILD-TYPE 96 156 158

Figure S344.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'xp loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0146 (Fisher's exact test), Q value = 0.054

Table S345.  Gene #81: 'xp loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 168 86
XP LOSS MUTATED 23 33 16
XP LOSS WILD-TYPE 205 135 70

Figure S345.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0292 (Fisher's exact test), Q value = 0.091

Table S346.  Gene #81: 'xp loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 16 34 22
XP LOSS MUTATED 4 5 7 3
XP LOSS WILD-TYPE 59 11 27 19

Figure S346.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0334 (Fisher's exact test), Q value = 0.1

Table S347.  Gene #82: 'xq loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 168 86
XQ LOSS MUTATED 22 31 9
XQ LOSS WILD-TYPE 206 137 77

Figure S347.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0487 (Fisher's exact test), Q value = 0.14

Table S348.  Gene #82: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
XQ LOSS MUTATED 5 5 6 15 6 3 9 1 14
XQ LOSS WILD-TYPE 44 69 23 71 71 51 48 31 67

Figure S348.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00529 (Fisher's exact test), Q value = 0.024

Table S349.  Gene #82: 'xq loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 16 34 22
XQ LOSS MUTATED 3 5 8 2
XQ LOSS WILD-TYPE 60 11 26 20

Figure S349.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data
Input

  • Copy number data file = broad_values_by_arm.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/COADREAD-TP/22524545/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/COADREAD-TP/22555066/COADREAD-TP.transferedmergedcluster.txt

  • Number of patients = 616

  • Number of significantly arm-level cnvs = 82

  • Number of molecular subtypes = 12

  • Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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