Correlation between copy number variation genes (focal events) and molecular subtypes
Ovarian Serous Cystadenocarcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1M9084V
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 variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1M9084V
Overview
Introduction

This pipeline computes the correlation between significant copy number variation (cnv focal) genes and molecular subtypes.

Summary

Testing the association between copy number variation 73 focal events and 14 molecular subtypes across 579 patients, 312 significant findings detected with P value < 0.05 and Q value < 0.25.

  • amp_1p34.3 cnv correlated to 'MIR_CNMF',  'CN_CNMF', and 'METHLYATION_CNMF'.

  • amp_1q21.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_1q42.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_2p23.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • amp_2q31.2 cnv correlated to 'MRNA_CNMF',  'MIR_CNMF',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF', and 'RPPA_CNMF'.

  • amp_3q26.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF', and 'METHLYATION_CNMF'.

  • amp_4p16.3 cnv correlated to 'MIR_CNMF',  'CN_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_4q13.3 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • amp_5p15.33 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • amp_6p22.3 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • amp_7q36.3 cnv correlated to 'CN_CNMF'.

  • amp_8p11.21 cnv correlated to 'MIR_CNMF',  'CN_CNMF', and 'METHLYATION_CNMF'.

  • amp_8q24.21 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • amp_10p15.3 cnv correlated to 'MRNA_CNMF',  'MIR_CNMF',  'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • amp_10q22.3 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • amp_11q14.1 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • amp_12p13.33 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_12p12.1 cnv correlated to 'MRNA_CNMF',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_12q15 cnv correlated to 'MRNA_CNMF',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • amp_14q11.2 cnv correlated to 'MRNA_CNMF',  'MIR_CHIERARCHICAL',  'CN_CNMF', and 'METHLYATION_CNMF'.

  • amp_14q32.33 cnv correlated to 'MIR_CHIERARCHICAL' and 'CN_CNMF'.

  • amp_15q26.3 cnv correlated to 'CN_CNMF'.

  • amp_17q25.3 cnv correlated to 'CN_CNMF',  'RPPA_CHIERARCHICAL', and 'MRNASEQ_CNMF'.

  • amp_18q11.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • amp_19p13.12 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF', and 'RPPA_CHIERARCHICAL'.

  • amp_19q12 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'CN_CNMF',  'METHLYATION_CNMF', and 'RPPA_CNMF'.

  • amp_19q13.2 cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • amp_20p13 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_20q11.21 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_20q13.33 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_22q12.2 cnv correlated to 'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_xp11.23 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_xq28 cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.

  • del_1p36.11 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'RPPA_CNMF'.

  • del_1q41 cnv correlated to 'CN_CNMF'.

  • del_2q22.1 cnv correlated to 'MIR_CHIERARCHICAL' and 'CN_CNMF'.

  • del_2q37.3 cnv correlated to 'MRNA_CNMF',  'MIR_CHIERARCHICAL',  'CN_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_3p26.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_3q13.31 cnv correlated to 'MRNA_CNMF',  'RPPA_CHIERARCHICAL', and 'MRNASEQ_CNMF'.

  • del_4q22.1 cnv correlated to 'MRNA_CHIERARCHICAL' and 'CN_CNMF'.

  • del_4q34.3 cnv correlated to 'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_5q12.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • del_5q13.2 cnv correlated to 'CN_CNMF'.

  • del_6q27 cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • del_7p22.2 cnv correlated to 'MRNA_CNMF',  'MIR_CHIERARCHICAL', and 'CN_CNMF'.

  • del_8p23.3 cnv correlated to 'MRNA_CNMF',  'MIR_CHIERARCHICAL',  'CN_CNMF', and 'METHLYATION_CNMF'.

  • del_8p21.2 cnv correlated to 'MRNA_CNMF',  'MIR_CHIERARCHICAL',  'CN_CNMF', and 'METHLYATION_CNMF'.

  • del_9p24.3 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.

  • del_9q34.13 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL', and 'MRNASEQ_CHIERARCHICAL'.

  • del_10p15.3 cnv correlated to 'MRNA_CNMF',  'CN_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_10q23.31 cnv correlated to 'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.

  • del_10q25.1 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'RPPA_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • del_11p15.5 cnv correlated to 'CN_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_11q25 cnv correlated to 'CN_CNMF'.

  • del_12q23.1 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • del_12q24.33 cnv correlated to 'MRNA_CNMF',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_13q14.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • del_14q23.3 cnv correlated to 'CN_CNMF'.

  • del_15q11.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • del_15q15.1 cnv correlated to 'MRNA_CNMF',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_16p13.3 cnv correlated to 'MIR_CHIERARCHICAL',  'CN_CNMF', and 'RPPA_CNMF'.

  • del_16q22.1 cnv correlated to 'MIR_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • del_16q23.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_17q11.2 cnv correlated to 'CN_CNMF'.

  • del_18q23 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • del_19p13.3 cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF', and 'RPPA_CNMF'.

  • del_19q13.33 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_19q13.43 cnv correlated to 'MRNA_CNMF',  'CN_CNMF', and 'METHLYATION_CNMF'.

  • del_21q22.3 cnv correlated to 'MRNA_CHIERARCHICAL'.

  • del_22q13.32 cnv correlated to 'MRNA_CNMF',  'MIR_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • del_xp21.1 cnv correlated to 'MIRSEQ_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 73 focal events and 14 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 312 significant findings detected.

Clinical
Features 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		MIR
CNMF 		MIR
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 Fisher's exact test Fisher's exact test
del 12q23 1 198 (34%) 381 0.0101
(0.057) 		0.00413
(0.0287) 		0.0207
(0.0926) 		0.0462
(0.156) 		1e-05
(0.000165) 		0.0185
(0.0852) 		0.012
(0.0653) 		0.639
(0.804) 		0.0358
(0.134) 		0.00169
(0.0143) 		0.0987
(0.26) 		0.0409
(0.146) 		1
(1.00) 		0.473
(0.696)
amp 20p13 316 (55%) 263 0.00013
(0.00166) 		0.0047
(0.0318) 		0.0313
(0.123) 		0.0312
(0.123) 		1e-05
(0.000165) 		1e-05
(0.000165) 		0.637
(0.804) 		0.311
(0.54) 		0.0216
(0.0955) 		0.0446
(0.153) 		0.663
(0.817) 		0.00081
(0.00796) 		1
(1.00) 		0.82
(0.93)
amp 20q11 21 347 (60%) 232 1e-05
(0.000165) 		0.00322
(0.023) 		0.0392
(0.143) 		0.00299
(0.0218) 		1e-05
(0.000165) 		1e-05
(0.000165) 		0.107
(0.27) 		0.166
(0.361) 		0.00416
(0.0287) 		0.00279
(0.0207) 		0.759
(0.88) 		0.00073
(0.00761) 		1
(1.00) 		0.663
(0.817)
amp 20q13 33 401 (69%) 178 2e-05
(0.000305) 		0.00077
(0.00772) 		0.682
(0.827) 		0.00133
(0.0117) 		1e-05
(0.000165) 		1e-05
(0.000165) 		0.366
(0.606) 		0.942
(0.988) 		0.0375
(0.139) 		0.00264
(0.0201) 		0.25
(0.473) 		0.0496
(0.163) 		0.607
(0.792) 		0.031
(0.123)
del 13q14 2 364 (63%) 215 0.014
(0.0716) 		0.0166
(0.0796) 		0.214
(0.426) 		0.0427
(0.149) 		1e-05
(0.000165) 		0.0538
(0.173) 		0.00124
(0.0113) 		0.00281
(0.0207) 		0.0165
(0.0796) 		0.044
(0.152) 		0.0142
(0.0723) 		0.371
(0.611) 		0.378
(0.616) 		0.733
(0.863)
del 15q11 2 300 (52%) 279 0.00099
(0.0092) 		0.0237
(0.102) 		0.00809
(0.048) 		0.00809
(0.048) 		1e-05
(0.000165) 		1e-05
(0.000165) 		0.17
(0.364) 		0.507
(0.72) 		0.00077
(0.00772) 		0.195
(0.401) 		0.254
(0.478) 		0.00983
(0.0561) 		0.047
(0.157) 		0.592
(0.781)
amp 12p12 1 312 (54%) 267 0.00136
(0.0118) 		0.268
(0.492) 		0.845
(0.946) 		0.0341
(0.131) 		1e-05
(0.000165) 		1e-05
(0.000165) 		0.205
(0.414) 		0.607
(0.792) 		0.00183
(0.015) 		0.00478
(0.0319) 		0.661
(0.817) 		0.00314
(0.0228) 		0.0662
(0.197) 		0.0348
(0.131)
del 3p26 2 210 (36%) 369 1e-05
(0.000165) 		0.00019
(0.00237) 		0.0116
(0.0635) 		0.00278
(0.0207) 		1e-05
(0.000165) 		1e-05
(0.000165) 		0.389
(0.627) 		0.105
(0.269) 		0.00112
(0.0103) 		0.00083
(0.00808) 		0.607
(0.792) 		0.0942
(0.251) 		0.106
(0.27) 		0.718
(0.854)
del 12q24 33 220 (38%) 359 0.00183
(0.015) 		0.0992
(0.26) 		0.182
(0.381) 		0.014
(0.0716) 		1e-05
(0.000165) 		0.00876
(0.0509) 		0.147
(0.338) 		0.407
(0.645) 		0.0443
(0.153) 		0.0263
(0.108) 		0.0129
(0.0685) 		0.00477
(0.0319) 		0.635
(0.803) 		0.87
(0.957)
del 22q13 32 504 (87%) 75 0.0183
(0.0852) 		0.126
(0.302) 		0.00267
(0.0202) 		0.305
(0.533) 		0.00013
(0.00166) 		0.00495
(0.0326) 		0.0263
(0.108) 		0.0264
(0.108) 		0.117
(0.288) 		0.0233
(0.102) 		0.0389
(0.143) 		0.597
(0.784)
amp 8q24 21 460 (79%) 119 7e-05
(0.000941) 		1e-05
(0.000165) 		0.378
(0.616) 		0.00198
(0.0161) 		1e-05
(0.000165) 		0.0449
(0.153) 		0.594
(0.781) 		0.0554
(0.175) 		1e-05
(0.000165) 		1e-05
(0.000165) 		0.265
(0.49) 		0.0991
(0.26) 		0.458
(0.684) 		0.636
(0.803)
amp 12q15 222 (38%) 357 4e-05
(0.00056) 		0.247
(0.472) 		0.594
(0.781) 		0.00243
(0.0188) 		1e-05
(0.000165) 		1e-05
(0.000165) 		0.065
(0.195) 		0.621
(0.795) 		0.00604
(0.0385) 		0.00275
(0.0207) 		0.512
(0.722) 		0.1
(0.261) 		0.0435
(0.151) 		0.25
(0.473)
del 9p24 3 261 (45%) 318 0.00076
(0.00772) 		5e-05
(0.000691) 		0.29
(0.515) 		0.0143
(0.0723) 		0.0117
(0.0641) 		1e-05
(0.000165) 		0.452
(0.682) 		0.167
(0.361) 		0.026
(0.108) 		0.235
(0.455) 		0.0207
(0.0926) 		0.125
(0.301) 		0.566
(0.76) 		0.198
(0.404)
del 10q25 1 239 (41%) 340 0.00085
(0.0082) 		0.0159
(0.078) 		0.00661
(0.0407) 		0.0348
(0.131) 		0.0001
(0.00133) 		0.0936
(0.25) 		0.0804
(0.225) 		0.0472
(0.157) 		0.778
(0.895) 		0.964
(1.00) 		0.00031
(0.00368) 		0.475
(0.696) 		0.938
(0.987) 		1
(1.00)
del 19q13 33 299 (52%) 280 0.00035
(0.00397) 		0.00241
(0.0188) 		0.107
(0.27) 		0.0205
(0.0922) 		0.0516
(0.168) 		0.0237
(0.102) 		0.0772
(0.219) 		0.033
(0.129) 		0.015
(0.075) 		0.0163
(0.0795) 		0.635
(0.803) 		0.129
(0.307) 		0.938
(0.987) 		0.0704
(0.204)
amp 1q42 2 322 (56%) 257 0.0121
(0.0654) 		0.0263
(0.108) 		0.125
(0.301) 		0.0078
(0.0469) 		1e-05
(0.000165) 		1e-05
(0.000165) 		0.107
(0.27) 		0.808
(0.92) 		0.0715
(0.207) 		0.0662
(0.197) 		0.873
(0.957) 		0.0023
(0.0182) 		0.668
(0.821) 		0.352
(0.593)
amp 2q31 2 261 (45%) 318 0.00136
(0.0118) 		0.177
(0.374) 		0.0171
(0.0815) 		0.0248
(0.106) 		1e-05
(0.000165) 		0.00091
(0.00861) 		0.034
(0.131) 		0.925
(0.983) 		0.199
(0.406) 		0.121
(0.295) 		0.102
(0.264) 		0.0845
(0.233) 		0.416
(0.652) 		0.866
(0.957)
amp 12p13 33 330 (57%) 249 0.0018
(0.015) 		0.0034
(0.0241) 		0.211
(0.423) 		0.0543
(0.174) 		1e-05
(0.000165) 		4e-05
(0.00056) 		0.123
(0.299) 		0.304
(0.532) 		0.0126
(0.0678) 		0.149
(0.34) 		0.164
(0.359) 		0.00775
(0.0469) 		0.287
(0.511) 		0.37
(0.611)
amp 19p13 12 315 (54%) 264 6e-05
(0.000818) 		0.00024
(0.00292) 		0.081
(0.226) 		0.25
(0.473) 		1e-05
(0.000165) 		1e-05
(0.000165) 		4e-05
(0.00056) 		0.00143
(0.0123) 		0.0603
(0.184) 		0.189
(0.391) 		0.448
(0.682) 		0.096
(0.255) 		0.938
(0.987) 		0.852
(0.95)
amp 19q12 323 (56%) 256 0.0135
(0.0705) 		0.0109
(0.0608) 		0.00645
(0.0401) 		0.524
(0.723) 		1e-05
(0.000165) 		1e-05
(0.000165) 		0.0185
(0.0852) 		0.78
(0.896) 		0.714
(0.852) 		0.212
(0.423) 		0.303
(0.532) 		0.0597
(0.183) 		0.939
(0.987) 		0.572
(0.763)
del 6q27 380 (66%) 199 0.0163
(0.0795) 		0.0626
(0.189) 		0.452
(0.682) 		0.104
(0.267) 		1e-05
(0.000165) 		0.00046
(0.005) 		0.917
(0.983) 		0.9
(0.976) 		0.00055
(0.00586) 		0.00183
(0.015) 		0.569
(0.761) 		0.0258
(0.108) 		0.111
(0.28) 		0.17
(0.364)
del 15q15 1 363 (63%) 216 0.00058
(0.00611) 		0.0597
(0.183) 		0.0574
(0.179) 		0.0032
(0.023) 		1e-05
(0.000165) 		1e-05
(0.000165) 		0.0591
(0.183) 		0.219
(0.433) 		0.0241
(0.103) 		0.375
(0.616) 		0.117
(0.287) 		0.00208
(0.0167) 		0.566
(0.76) 		0.201
(0.409)
amp 1q21 3 367 (63%) 212 0.175
(0.372) 		0.163
(0.359) 		0.242
(0.466) 		0.395
(0.629) 		1e-05
(0.000165) 		3e-05
(0.000438) 		0.0269
(0.109) 		0.0138
(0.0715) 		0.464
(0.689) 		0.118
(0.289) 		0.138
(0.326) 		0.00597
(0.0385) 		0.262
(0.486) 		0.924
(0.983)
amp 2p23 2 251 (43%) 328 0.00624
(0.0394) 		0.0108
(0.0605) 		0.137
(0.323) 		0.141
(0.33) 		1e-05
(0.000165) 		0.0303
(0.121) 		0.185
(0.385) 		0.517
(0.723) 		0.0641
(0.193) 		0.00039
(0.00438) 		0.844
(0.946) 		0.202
(0.411) 		0.885
(0.963) 		0.519
(0.723)
amp 6p22 3 305 (53%) 274 1e-05
(0.000165) 		0.0344
(0.131) 		0.234
(0.455) 		0.0886
(0.241) 		1e-05
(0.000165) 		0.00449
(0.0308) 		0.23
(0.45) 		0.63
(0.802) 		0.294
(0.521) 		0.148
(0.34) 		0.646
(0.808) 		0.613
(0.793) 		0.025
(0.106) 		0.475
(0.696)
amp 10p15 3 252 (44%) 327 0.0164
(0.0795) 		0.1
(0.261) 		0.0253
(0.107) 		0.165
(0.36) 		1e-05
(0.000165) 		1e-05
(0.000165) 		0.409
(0.646) 		0.986
(1.00) 		0.0335
(0.13) 		0.0967
(0.257) 		0.828
(0.937) 		0.067
(0.199) 		0.451
(0.682) 		0.491
(0.709)
amp 22q12 2 91 (16%) 488 0.182
(0.381) 		0.156
(0.351) 		0.0986
(0.26) 		0.0345
(0.131) 		0.00461
(0.0314) 		0.0304
(0.121) 		0.672
(0.821) 		0.0013
(0.0116) 		0.141
(0.33) 		0.0776
(0.22) 		0.144
(0.333) 		0.0144
(0.0724) 		1
(1.00) 		0.127
(0.303)
del 4q34 3 421 (73%) 158 0.171
(0.365) 		0.00076
(0.00772) 		0.118
(0.29) 		0.0278
(0.112) 		0.0212
(0.0944) 		0.0749
(0.214) 		0.836
(0.943) 		0.166
(0.361) 		0.0395
(0.143) 		0.046
(0.156) 		0.529
(0.726) 		0.53
(0.727) 		0.83
(0.939) 		1
(1.00)
del 9q34 13 342 (59%) 237 0.124
(0.3) 		0.00092
(0.00863) 		0.874
(0.957) 		0.407
(0.645) 		1e-05
(0.000165) 		0.00569
(0.037) 		0.687
(0.832) 		0.0465
(0.156) 		0.15
(0.342) 		0.0085
(0.0496) 		0.388
(0.626) 		0.102
(0.264) 		0.277
(0.5) 		0.879
(0.961)
del 10q23 31 223 (39%) 356 0.151
(0.343) 		0.0137
(0.0709) 		0.00032
(0.00372) 		0.0558
(0.176) 		1e-05
(0.000165) 		0.0351
(0.132) 		0.308
(0.537) 		0.144
(0.333) 		0.777
(0.895) 		0.462
(0.688) 		0.0422
(0.148) 		0.331
(0.565) 		0.754
(0.879) 		0.703
(0.846)
del 16q22 1 461 (80%) 118 0.526
(0.724) 		0.706
(0.846) 		0.0393
(0.143) 		0.452
(0.682) 		0.0004
(0.00444) 		0.00151
(0.0129) 		0.345
(0.584) 		0.0499
(0.163) 		0.365
(0.606) 		0.912
(0.98) 		0.0838
(0.231) 		0.0464
(0.156) 		0.454
(0.682) 		0.766
(0.886)
amp 3q26 2 485 (84%) 94 0.00044
(0.00484) 		0.0256
(0.108) 		0.614
(0.793) 		0.277
(0.5) 		1e-05
(0.000165) 		1e-05
(0.000165) 		0.9
(0.976) 		0.0555
(0.175) 		0.161
(0.358) 		0.44
(0.677) 		0.489
(0.707) 		0.0689
(0.202) 		0.235
(0.455) 		0.153
(0.347)
amp 5p15 33 308 (53%) 271 0.76
(0.88) 		0.0353
(0.132) 		0.567
(0.761) 		0.236
(0.458) 		1e-05
(0.000165) 		0.00034
(0.0039) 		0.516
(0.723) 		0.155
(0.35) 		0.615
(0.793) 		0.0293
(0.118) 		0.0543
(0.174) 		0.188
(0.391) 		1
(1.00) 		0.131
(0.31)
amp 11q14 1 255 (44%) 324 0.114
(0.284) 		0.00252
(0.0194) 		0.993
(1.00) 		0.353
(0.593) 		2e-05
(0.000305) 		0.0101
(0.057) 		0.41
(0.646) 		0.571
(0.763) 		0.257
(0.481) 		0.02
(0.0907) 		0.522
(0.723) 		0.921
(0.983) 		0.353
(0.593) 		0.663
(0.817)
amp 14q11 2 147 (25%) 432 0.0195
(0.0888) 		0.0889
(0.241) 		0.451
(0.682) 		0.0108
(0.0605) 		0.0187
(0.0857) 		0.0344
(0.131) 		0.963
(1.00) 		0.257
(0.481) 		0.238
(0.459) 		0.273
(0.497) 		0.28
(0.502) 		0.822
(0.931) 		0.47
(0.693) 		0.578
(0.769)
amp 19q13 2 245 (42%) 334 0.0407
(0.146) 		0.538
(0.734) 		0.944
(0.988) 		0.39
(0.627) 		1e-05
(0.000165) 		1e-05
(0.000165) 		0.0537
(0.173) 		0.47
(0.693) 		0.533
(0.729) 		0.0257
(0.108) 		0.563
(0.759) 		0.552
(0.747) 		0.566
(0.76) 		0.792
(0.906)
del 2q37 3 175 (30%) 404 0.00079
(0.00784) 		0.524
(0.723) 		0.884
(0.963) 		0.0169
(0.0808) 		3e-05
(0.000438) 		0.113
(0.282) 		0.949
(0.989) 		0.415
(0.65) 		0.0702
(0.204) 		0.408
(0.645) 		0.0513
(0.167) 		0.0156
(0.0773) 		0.446
(0.682) 		0.871
(0.957)
del 8p23 3 388 (67%) 191 0.00648
(0.0401) 		0.15
(0.341) 		0.646
(0.808) 		0.0112
(0.0621) 		1e-05
(0.000165) 		0.0067
(0.041) 		0.84
(0.945) 		0.116
(0.286) 		0.746
(0.872) 		0.904
(0.977) 		0.285
(0.51) 		0.249
(0.473)
del 8p21 2 406 (70%) 173 0.00599
(0.0385) 		0.0905
(0.244) 		0.175
(0.372) 		0.00559
(0.0366) 		1e-05
(0.000165) 		0.0135
(0.0705) 		0.783
(0.899) 		0.703
(0.846) 		0.145
(0.335) 		0.681
(0.827) 		0.776
(0.895) 		0.514
(0.722)
del 19p13 3 512 (88%) 67 0.0376
(0.139) 		0.0917
(0.247) 		0.914
(0.981) 		0.543
(0.739) 		0.00032
(0.00372) 		0.0069
(0.042) 		0.00406
(0.0286) 		0.159
(0.356) 		0.751
(0.876) 		0.0553
(0.175) 		0.233
(0.454) 		0.733
(0.863)
amp 1p34 3 292 (50%) 287 0.438
(0.675) 		0.0823
(0.229) 		0.0424
(0.148) 		0.089
(0.241) 		2e-05
(0.000305) 		0.00211
(0.0168) 		0.273
(0.497) 		0.365
(0.606) 		0.732
(0.863) 		0.76
(0.88) 		0.103
(0.266) 		0.165
(0.36) 		0.0746
(0.214) 		0.356
(0.595)
amp 4p16 3 163 (28%) 416 0.353
(0.593) 		0.385
(0.624) 		0.0396
(0.143) 		0.448
(0.682) 		0.0009
(0.0086) 		0.136
(0.322) 		0.245
(0.47) 		0.465
(0.689) 		0.454
(0.682) 		0.715
(0.852) 		0.467
(0.69) 		0.0144
(0.0723) 		0.673
(0.822) 		0.714
(0.852)
amp 8p11 21 210 (36%) 369 0.204
(0.412) 		0.322
(0.554) 		0.0154
(0.0765) 		0.503
(0.717) 		1e-05
(0.000165) 		0.00029
(0.00349) 		0.06
(0.184) 		0.387
(0.626) 		0.162
(0.359) 		0.273
(0.497) 		0.981
(1.00) 		0.326
(0.559) 		0.458
(0.684) 		0.977
(1.00)
amp 17q25 3 215 (37%) 364 0.705
(0.846) 		0.0594
(0.183) 		0.936
(0.987) 		0.665
(0.818) 		0.00816
(0.048) 		0.518
(0.723) 		0.473
(0.696) 		0.0127
(0.0678) 		0.0185
(0.0852) 		0.365
(0.606) 		0.412
(0.647) 		0.127
(0.303) 		0.589
(0.779) 		0.519
(0.723)
amp 18q11 2 142 (25%) 437 0.139
(0.328) 		0.744
(0.871) 		0.904
(0.977) 		0.262
(0.486) 		2e-05
(0.000305) 		1e-05
(0.000165) 		0.163
(0.359) 		0.848
(0.948) 		0.505
(0.72) 		0.611
(0.792) 		0.167
(0.361) 		0.514
(0.722) 		0.0275
(0.112) 		0.378
(0.616)
amp xp11 23 159 (27%) 420 0.495
(0.711) 		0.867
(0.957) 		0.306
(0.533) 		0.632
(0.802) 		1e-05
(0.000165) 		0.0236
(0.102) 		0.584
(0.776) 		0.453
(0.682) 		0.498
(0.714) 		0.68
(0.827) 		0.919
(0.983) 		0.0318
(0.125) 		0.378
(0.616) 		0.86
(0.955)
del 1p36 11 269 (46%) 310 0.701
(0.844) 		0.0701
(0.204) 		0.0696
(0.204) 		0.116
(0.286) 		0.00895
(0.0517) 		0.0135
(0.0705) 		0.0482
(0.159) 		0.207
(0.416) 		0.157
(0.353) 		0.194
(0.4) 		0.338
(0.573) 		0.171
(0.366) 		1
(1.00) 		0.732
(0.863)
del 3q13 31 84 (15%) 495 0.0127
(0.0678) 		0.227
(0.446) 		0.907
(0.979) 		0.628
(0.802) 		0.116
(0.286) 		0.0803
(0.225) 		0.237
(0.458) 		0.0378
(0.139) 		0.0421
(0.148) 		0.0886
(0.241) 		0.693
(0.838) 		0.523
(0.723)
del 7p22 2 253 (44%) 326 0.00023
(0.00283) 		0.489
(0.707) 		0.284
(0.509) 		0.026
(0.108) 		1e-05
(0.000165) 		0.818
(0.929) 		0.94
(0.987) 		0.756
(0.879) 		0.424
(0.66) 		0.803
(0.916) 		0.357
(0.596) 		0.988
(1.00) 		0.458
(0.684) 		0.852
(0.95)
del 10p15 3 120 (21%) 459 0.0466
(0.156) 		0.707
(0.846) 		0.178
(0.374) 		0.32
(0.551) 		0.0183
(0.0852) 		0.057
(0.178) 		0.328
(0.561) 		0.484
(0.704) 		0.843
(0.946) 		0.982
(1.00) 		0.332
(0.566) 		0.265
(0.489) 		0.429
(0.663) 		0.0346
(0.131)
del 11p15 5 346 (60%) 233 0.39
(0.627) 		0.969
(1.00) 		0.856
(0.952) 		0.086
(0.236) 		1e-05
(0.000165) 		0.395
(0.629) 		0.083
(0.231) 		0.659
(0.817) 		0.735
(0.864) 		0.485
(0.705) 		0.142
(0.331) 		0.00925
(0.0531) 		0.214
(0.426) 		0.0176
(0.083)
del 16p13 3 313 (54%) 266 0.289
(0.515) 		0.072
(0.207) 		0.0566
(0.177) 		0.0303
(0.121) 		0.00492
(0.0326) 		0.277
(0.5) 		0.0417
(0.148) 		0.452
(0.682) 		0.924
(0.983) 		0.988
(1.00) 		0.214
(0.426) 		0.482
(0.703) 		0.93
(0.985) 		0.493
(0.709)
del 16q23 1 452 (78%) 127 0.08
(0.225) 		0.245
(0.47) 		0.0994
(0.26) 		0.0631
(0.19) 		1e-05
(0.000165) 		1e-05
(0.000165) 		0.481
(0.702) 		0.374
(0.615) 		0.125
(0.302) 		0.413
(0.648) 		0.177
(0.374) 		0.0478
(0.158) 		0.267
(0.492) 		0.944
(0.988)
del 19q13 43 285 (49%) 294 0.0221
(0.0974) 		0.0835
(0.231) 		0.641
(0.806) 		0.387
(0.626) 		0.00633
(0.0397) 		0.0412
(0.147) 		0.18
(0.377) 		0.397
(0.63) 		0.611
(0.792) 		0.059
(0.183) 		0.928
(0.985) 		0.119
(0.291) 		0.455
(0.683) 		0.0525
(0.17)
amp 4q13 3 113 (20%) 466 0.617
(0.794) 		0.466
(0.69) 		0.352
(0.593) 		0.986
(1.00) 		0.00011
(0.00144) 		0.00242
(0.0188) 		0.885
(0.963) 		0.882
(0.963) 		0.739
(0.867) 		0.588
(0.779) 		0.707
(0.846) 		0.695
(0.839) 		0.219
(0.433) 		0.377
(0.616)
amp 10q22 3 183 (32%) 396 0.54
(0.735) 		0.225
(0.443) 		0.61
(0.792) 		0.948
(0.989) 		0.0428
(0.149) 		0.00019
(0.00237) 		0.864
(0.957) 		0.885
(0.963) 		0.552
(0.747) 		0.573
(0.763) 		0.686
(0.831) 		0.645
(0.808) 		1
(1.00) 		0.52
(0.723)
amp 14q32 33 156 (27%) 423 0.568
(0.761) 		0.655
(0.815) 		0.902
(0.976) 		0.0172
(0.0815) 		3e-05
(0.000438) 		0.328
(0.561) 		0.911
(0.98) 		0.807
(0.92) 		0.112
(0.282) 		0.0936
(0.25) 		0.671
(0.821) 		0.422
(0.66) 		0.233
(0.455) 		0.0784
(0.221)
amp xq28 220 (38%) 359 0.0681
(0.2) 		0.846
(0.947) 		0.394
(0.629) 		0.126
(0.302) 		0.00126
(0.0114) 		0.936
(0.987) 		0.533
(0.729) 		0.425
(0.66) 		0.722
(0.856) 		0.377
(0.616) 		0.91
(0.98) 		0.807
(0.92) 		0.00818
(0.048) 		0.249
(0.473)
del 2q22 1 136 (23%) 443 0.25
(0.473) 		0.303
(0.532) 		0.104
(0.267) 		0.00408
(0.0286) 		0.0474
(0.157) 		0.303
(0.532) 		0.976
(1.00) 		0.949
(0.989) 		0.426
(0.661) 		0.791
(0.905) 		0.775
(0.895) 		0.588
(0.779) 		0.923
(0.983) 		0.514
(0.722)
del 4q22 1 394 (68%) 185 0.261
(0.486) 		0.0233
(0.102) 		0.681
(0.827) 		0.164
(0.359) 		0.00054
(0.00581) 		0.897
(0.974) 		0.0623
(0.189) 		0.916
(0.983) 		0.742
(0.87) 		0.721
(0.856) 		0.196
(0.401) 		0.256
(0.481) 		0.67
(0.821) 		0.492
(0.709)
del 5q12 1 355 (61%) 224 0.0719
(0.207) 		0.872
(0.957) 		0.278
(0.5) 		0.0549
(0.175) 		1e-05
(0.000165) 		0.0361
(0.134) 		0.76
(0.88) 		0.791
(0.905) 		0.297
(0.523) 		0.31
(0.539) 		0.159
(0.356) 		0.253
(0.478) 		0.316
(0.547) 		0.188
(0.39)
del 18q23 381 (66%) 198 0.479
(0.7) 		0.854
(0.95) 		0.523
(0.723) 		0.956
(0.995) 		0.00127
(0.0114) 		0.441
(0.678) 		0.22
(0.435) 		0.274
(0.497) 		0.717
(0.853) 		0.0455
(0.155) 		0.609
(0.792) 		0.495
(0.711) 		0.446
(0.682) 		0.872
(0.957)
amp 7q36 3 319 (55%) 260 0.161
(0.358) 		0.194
(0.4) 		0.304
(0.532) 		0.991
(1.00) 		1e-05
(0.000165) 		0.0675
(0.199) 		0.259
(0.482) 		0.145
(0.335) 		0.924
(0.983) 		0.653
(0.813) 		0.283
(0.507) 		0.502
(0.717) 		0.715
(0.852) 		0.864
(0.957)
amp 15q26 3 163 (28%) 416 0.394
(0.629) 		0.424
(0.66) 		0.584
(0.776) 		0.428
(0.663) 		1e-05
(0.000165) 		0.861
(0.955) 		0.968
(1.00) 		0.735
(0.864) 		0.318
(0.549) 		0.939
(0.987) 		0.169
(0.364) 		0.0661
(0.197) 		0.0748
(0.214) 		0.616
(0.793)
del 1q41 97 (17%) 482 0.908
(0.979) 		0.622
(0.795) 		0.652
(0.813) 		0.838
(0.944) 		1e-05
(0.000165) 		0.101
(0.261) 		0.397
(0.63) 		0.543
(0.739) 		0.608
(0.792) 		0.93
(0.985) 		0.633
(0.803) 		0.97
(1.00)
del 5q13 2 419 (72%) 160 0.424
(0.66) 		0.621
(0.795) 		0.75
(0.876) 		0.258
(0.482) 		1e-05
(0.000165) 		0.171
(0.365) 		0.5
(0.716) 		0.969
(1.00) 		0.366
(0.606) 		0.0896
(0.242) 		0.451
(0.682) 		0.107
(0.27) 		0.876
(0.958) 		0.268
(0.492)
del 11q25 201 (35%) 378 0.164
(0.359) 		0.652
(0.813) 		0.1
(0.261) 		0.0537
(0.173) 		0.00606
(0.0385) 		0.147
(0.338) 		0.489
(0.707) 		0.393
(0.629) 		0.842
(0.946) 		0.16
(0.356) 		0.85
(0.95) 		0.27
(0.494) 		0.675
(0.824) 		0.533
(0.729)
del 14q23 3 305 (53%) 274 0.176
(0.373) 		0.506
(0.72) 		0.23
(0.45) 		0.612
(0.792) 		2e-05
(0.000305) 		0.621
(0.795) 		0.659
(0.817) 		0.32
(0.551) 		0.263
(0.486) 		0.515
(0.722) 		0.475
(0.696) 		0.591
(0.781) 		0.204
(0.412) 		0.143
(0.333)
del 17q11 2 472 (82%) 107 0.432
(0.667) 		0.192
(0.397) 		0.756
(0.879) 		0.219
(0.433) 		0.0196
(0.089) 		0.355
(0.594) 		0.671
(0.821) 		0.512
(0.722) 		0.511
(0.722) 		0.522
(0.723) 		0.173
(0.368) 		0.164
(0.359) 		1
(1.00) 		0.87
(0.957)
del 21q22 3 227 (39%) 352 0.447
(0.682) 		0.0417
(0.148) 		0.817
(0.929) 		0.207
(0.417) 		0.105
(0.267) 		0.512
(0.722) 		0.61
(0.792) 		0.593
(0.781) 		0.638
(0.804) 		0.487
(0.706) 		0.277
(0.5) 		0.727
(0.861) 		0.0861
(0.236) 		0.256
(0.481)
del xp21 1 358 (62%) 221 0.293
(0.52) 		0.513
(0.722) 		0.338
(0.573) 		0.786
(0.901) 		0.193
(0.399) 		0.0755
(0.215) 		0.643
(0.807) 		0.0614
(0.187) 		0.524
(0.723) 		0.549
(0.744) 		0.0391
(0.143) 		0.622
(0.795) 		0.632
(0.802) 		0.945
(0.988)
del 2p25 3 120 (21%) 459 0.369
(0.611) 		0.269
(0.493) 		0.312
(0.54) 		0.158
(0.356) 		0.629
(0.802) 		0.732
(0.863) 		0.525
(0.723) 		0.832
(0.939) 		0.115
(0.286) 		0.662
(0.817) 		0.561
(0.757) 		0.95
(0.99) 		0.383
(0.623) 		0.927
(0.984)
del 17p12 491 (85%) 88 0.393
(0.629) 		0.337
(0.573) 		0.544
(0.739) 		0.69
(0.835) 		0.293
(0.519) 		0.599
(0.784) 		0.87
(0.957) 		0.66
(0.817) 		0.444
(0.682) 		0.46
(0.685) 		0.647
(0.808) 		0.21
(0.422)
'amp_1p34.3' versus 'MIR_CNMF'

P value = 0.0424 (Fisher's exact test), Q value = 0.15

Table S1.  Gene #1: 'amp_1p34.3' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 131 243
AMP PEAK 1(1P34.3) MUTATED 91 55 135
AMP PEAK 1(1P34.3) WILD-TYPE 90 76 108

Figure S1.  Get High-res Image Gene #1: 'amp_1p34.3' versus Molecular Subtype #3: 'MIR_CNMF'

'amp_1p34.3' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00031

Table S2.  Gene #1: 'amp_1p34.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
AMP PEAK 1(1P34.3) MUTATED 141 43 108
AMP PEAK 1(1P34.3) WILD-TYPE 101 87 99

Figure S2.  Get High-res Image Gene #1: 'amp_1p34.3' versus Molecular Subtype #5: 'CN_CNMF'

'amp_1p34.3' versus 'METHLYATION_CNMF'

P value = 0.00211 (Fisher's exact test), Q value = 0.017

Table S3.  Gene #1: 'amp_1p34.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
AMP PEAK 1(1P34.3) MUTATED 60 52 74 101
AMP PEAK 1(1P34.3) WILD-TYPE 53 46 113 69

Figure S3.  Get High-res Image Gene #1: 'amp_1p34.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_1q21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S4.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
AMP PEAK 2(1Q21.3) MUTATED 195 60 112
AMP PEAK 2(1Q21.3) WILD-TYPE 47 70 95

Figure S4.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #5: 'CN_CNMF'

'amp_1q21.3' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00044

Table S5.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
AMP PEAK 2(1Q21.3) MUTATED 75 70 93 123
AMP PEAK 2(1Q21.3) WILD-TYPE 38 28 94 47

Figure S5.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_1q21.3' versus 'RPPA_CNMF'

P value = 0.0269 (Fisher's exact test), Q value = 0.11

Table S6.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 189 76
AMP PEAK 2(1Q21.3) MUTATED 85 132 42
AMP PEAK 2(1Q21.3) WILD-TYPE 61 57 34

Figure S6.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #7: 'RPPA_CNMF'

'amp_1q21.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0138 (Fisher's exact test), Q value = 0.071

Table S7.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 54 60 154
AMP PEAK 2(1Q21.3) MUTATED 79 43 40 97
AMP PEAK 2(1Q21.3) WILD-TYPE 64 11 20 57

Figure S7.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'amp_1q21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00597 (Fisher's exact test), Q value = 0.038

Table S8.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
AMP PEAK 2(1Q21.3) MUTATED 54 42 119 68
AMP PEAK 2(1Q21.3) WILD-TYPE 51 29 46 38

Figure S8.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'amp_1q42.2' versus 'MRNA_CNMF'

P value = 0.0121 (Fisher's exact test), Q value = 0.065

Table S9.  Gene #3: 'amp_1q42.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 112 118 151
AMP PEAK 3(1Q42.2) MUTATED 114 59 57 75
AMP PEAK 3(1Q42.2) WILD-TYPE 62 53 61 76

Figure S9.  Get High-res Image Gene #3: 'amp_1q42.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_1q42.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.0263 (Fisher's exact test), Q value = 0.11

Table S10.  Gene #3: 'amp_1q42.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
AMP PEAK 3(1Q42.2) MUTATED 174 74 57
AMP PEAK 3(1Q42.2) WILD-TYPE 136 84 32

Figure S10.  Get High-res Image Gene #3: 'amp_1q42.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_1q42.2' versus 'MIR_CHIERARCHICAL'

P value = 0.0078 (Fisher's exact test), Q value = 0.047

Table S11.  Gene #3: 'amp_1q42.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
AMP PEAK 3(1Q42.2) MUTATED 45 30 36 43 13 44 21 22 37 13
AMP PEAK 3(1Q42.2) WILD-TYPE 40 27 22 39 21 31 13 14 15 29

Figure S11.  Get High-res Image Gene #3: 'amp_1q42.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'amp_1q42.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S12.  Gene #3: 'amp_1q42.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
AMP PEAK 3(1Q42.2) MUTATED 174 62 86
AMP PEAK 3(1Q42.2) WILD-TYPE 68 68 121

Figure S12.  Get High-res Image Gene #3: 'amp_1q42.2' versus Molecular Subtype #5: 'CN_CNMF'

'amp_1q42.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S13.  Gene #3: 'amp_1q42.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
AMP PEAK 3(1Q42.2) MUTATED 58 69 75 112
AMP PEAK 3(1Q42.2) WILD-TYPE 55 29 112 58

Figure S13.  Get High-res Image Gene #3: 'amp_1q42.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_1q42.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0023 (Fisher's exact test), Q value = 0.018

Table S14.  Gene #3: 'amp_1q42.2' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
AMP PEAK 3(1Q42.2) MUTATED 41 43 101 59
AMP PEAK 3(1Q42.2) WILD-TYPE 64 28 64 47

Figure S14.  Get High-res Image Gene #3: 'amp_1q42.2' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'amp_2p23.2' versus 'MRNA_CNMF'

P value = 0.00624 (Fisher's exact test), Q value = 0.039

Table S15.  Gene #4: 'amp_2p23.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 112 118 151
AMP PEAK 4(2P23.2) MUTATED 94 47 46 53
AMP PEAK 4(2P23.2) WILD-TYPE 82 65 72 98

Figure S15.  Get High-res Image Gene #4: 'amp_2p23.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_2p23.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.0108 (Fisher's exact test), Q value = 0.06

Table S16.  Gene #4: 'amp_2p23.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
AMP PEAK 4(2P23.2) MUTATED 122 67 51
AMP PEAK 4(2P23.2) WILD-TYPE 188 91 38

Figure S16.  Get High-res Image Gene #4: 'amp_2p23.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_2p23.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S17.  Gene #4: 'amp_2p23.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
AMP PEAK 4(2P23.2) MUTATED 132 34 85
AMP PEAK 4(2P23.2) WILD-TYPE 110 96 122

Figure S17.  Get High-res Image Gene #4: 'amp_2p23.2' versus Molecular Subtype #5: 'CN_CNMF'

'amp_2p23.2' versus 'METHLYATION_CNMF'

P value = 0.0303 (Fisher's exact test), Q value = 0.12

Table S18.  Gene #4: 'amp_2p23.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
AMP PEAK 4(2P23.2) MUTATED 51 40 66 86
AMP PEAK 4(2P23.2) WILD-TYPE 62 58 121 84

Figure S18.  Get High-res Image Gene #4: 'amp_2p23.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_2p23.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00039 (Fisher's exact test), Q value = 0.0044

Table S19.  Gene #4: 'amp_2p23.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
AMP PEAK 4(2P23.2) MUTATED 55 40 44
AMP PEAK 4(2P23.2) WILD-TYPE 91 19 51

Figure S19.  Get High-res Image Gene #4: 'amp_2p23.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_2q31.2' versus 'MRNA_CNMF'

P value = 0.00136 (Fisher's exact test), Q value = 0.012

Table S20.  Gene #5: 'amp_2q31.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 112 118 151
AMP PEAK 5(2Q31.2) MUTATED 99 42 42 68
AMP PEAK 5(2Q31.2) WILD-TYPE 77 70 76 83

Figure S20.  Get High-res Image Gene #5: 'amp_2q31.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_2q31.2' versus 'MIR_CNMF'

P value = 0.0171 (Fisher's exact test), Q value = 0.081

Table S21.  Gene #5: 'amp_2q31.2' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 131 243
AMP PEAK 5(2Q31.2) MUTATED 79 47 124
AMP PEAK 5(2Q31.2) WILD-TYPE 102 84 119

Figure S21.  Get High-res Image Gene #5: 'amp_2q31.2' versus Molecular Subtype #3: 'MIR_CNMF'

'amp_2q31.2' versus 'MIR_CHIERARCHICAL'

P value = 0.0248 (Fisher's exact test), Q value = 0.11

Table S22.  Gene #5: 'amp_2q31.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
AMP PEAK 5(2Q31.2) MUTATED 30 20 32 42 14 36 18 14 31 13
AMP PEAK 5(2Q31.2) WILD-TYPE 55 37 26 40 20 39 16 22 21 29

Figure S22.  Get High-res Image Gene #5: 'amp_2q31.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'amp_2q31.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S23.  Gene #5: 'amp_2q31.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
AMP PEAK 5(2Q31.2) MUTATED 143 21 97
AMP PEAK 5(2Q31.2) WILD-TYPE 99 109 110

Figure S23.  Get High-res Image Gene #5: 'amp_2q31.2' versus Molecular Subtype #5: 'CN_CNMF'

'amp_2q31.2' versus 'METHLYATION_CNMF'

P value = 0.00091 (Fisher's exact test), Q value = 0.0086

Table S24.  Gene #5: 'amp_2q31.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
AMP PEAK 5(2Q31.2) MUTATED 51 48 64 94
AMP PEAK 5(2Q31.2) WILD-TYPE 62 50 123 76

Figure S24.  Get High-res Image Gene #5: 'amp_2q31.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_2q31.2' versus 'RPPA_CNMF'

P value = 0.034 (Fisher's exact test), Q value = 0.13

Table S25.  Gene #5: 'amp_2q31.2' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 189 76
AMP PEAK 5(2Q31.2) MUTATED 64 95 25
AMP PEAK 5(2Q31.2) WILD-TYPE 82 94 51

Figure S25.  Get High-res Image Gene #5: 'amp_2q31.2' versus Molecular Subtype #7: 'RPPA_CNMF'

'amp_3q26.2' versus 'MRNA_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.0048

Table S26.  Gene #6: 'amp_3q26.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 112 118 151
AMP PEAK 6(3Q26.2) MUTATED 147 96 85 138
AMP PEAK 6(3Q26.2) WILD-TYPE 29 16 33 13

Figure S26.  Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_3q26.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.0256 (Fisher's exact test), Q value = 0.11

Table S27.  Gene #6: 'amp_3q26.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
AMP PEAK 6(3Q26.2) MUTATED 257 141 68
AMP PEAK 6(3Q26.2) WILD-TYPE 53 17 21

Figure S27.  Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_3q26.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S28.  Gene #6: 'amp_3q26.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
AMP PEAK 6(3Q26.2) MUTATED 224 80 181
AMP PEAK 6(3Q26.2) WILD-TYPE 18 50 26

Figure S28.  Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #5: 'CN_CNMF'

'amp_3q26.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S29.  Gene #6: 'amp_3q26.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
AMP PEAK 6(3Q26.2) MUTATED 107 78 137 153
AMP PEAK 6(3Q26.2) WILD-TYPE 6 20 50 17

Figure S29.  Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_4p16.3' versus 'MIR_CNMF'

P value = 0.0396 (Fisher's exact test), Q value = 0.14

Table S30.  Gene #7: 'amp_4p16.3' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 131 243
AMP PEAK 7(4P16.3) MUTATED 52 26 78
AMP PEAK 7(4P16.3) WILD-TYPE 129 105 165

Figure S30.  Get High-res Image Gene #7: 'amp_4p16.3' versus Molecular Subtype #3: 'MIR_CNMF'

'amp_4p16.3' versus 'CN_CNMF'

P value = 9e-04 (Fisher's exact test), Q value = 0.0086

Table S31.  Gene #7: 'amp_4p16.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
AMP PEAK 7(4P16.3) MUTATED 65 23 75
AMP PEAK 7(4P16.3) WILD-TYPE 177 107 132

Figure S31.  Get High-res Image Gene #7: 'amp_4p16.3' versus Molecular Subtype #5: 'CN_CNMF'

'amp_4p16.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0144 (Fisher's exact test), Q value = 0.072

Table S32.  Gene #7: 'amp_4p16.3' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
AMP PEAK 7(4P16.3) MUTATED 23 25 58 22
AMP PEAK 7(4P16.3) WILD-TYPE 82 46 107 84

Figure S32.  Get High-res Image Gene #7: 'amp_4p16.3' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'amp_4q13.3' versus 'CN_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.0014

Table S33.  Gene #8: 'amp_4q13.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
AMP PEAK 8(4Q13.3) MUTATED 44 12 57
AMP PEAK 8(4Q13.3) WILD-TYPE 198 118 150

Figure S33.  Get High-res Image Gene #8: 'amp_4q13.3' versus Molecular Subtype #5: 'CN_CNMF'

'amp_4q13.3' versus 'METHLYATION_CNMF'

P value = 0.00242 (Fisher's exact test), Q value = 0.019

Table S34.  Gene #8: 'amp_4q13.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
AMP PEAK 8(4Q13.3) MUTATED 22 15 24 48
AMP PEAK 8(4Q13.3) WILD-TYPE 91 83 163 122

Figure S34.  Get High-res Image Gene #8: 'amp_4q13.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_5p15.33' versus 'MRNA_CHIERARCHICAL'

P value = 0.0353 (Fisher's exact test), Q value = 0.13

Table S35.  Gene #9: 'amp_5p15.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
AMP PEAK 9(5P15.33) MUTATED 177 83 37
AMP PEAK 9(5P15.33) WILD-TYPE 133 75 52

Figure S35.  Get High-res Image Gene #9: 'amp_5p15.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_5p15.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S36.  Gene #9: 'amp_5p15.33' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
AMP PEAK 9(5P15.33) MUTATED 146 41 121
AMP PEAK 9(5P15.33) WILD-TYPE 96 89 86

Figure S36.  Get High-res Image Gene #9: 'amp_5p15.33' versus Molecular Subtype #5: 'CN_CNMF'

'amp_5p15.33' versus 'METHLYATION_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.0039

Table S37.  Gene #9: 'amp_5p15.33' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
AMP PEAK 9(5P15.33) MUTATED 74 44 83 102
AMP PEAK 9(5P15.33) WILD-TYPE 39 54 104 68

Figure S37.  Get High-res Image Gene #9: 'amp_5p15.33' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_5p15.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0293 (Fisher's exact test), Q value = 0.12

Table S38.  Gene #9: 'amp_5p15.33' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
AMP PEAK 9(5P15.33) MUTATED 91 26 47
AMP PEAK 9(5P15.33) WILD-TYPE 55 33 48

Figure S38.  Get High-res Image Gene #9: 'amp_5p15.33' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_6p22.3' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S39.  Gene #10: 'amp_6p22.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 112 118 151
AMP PEAK 10(6P22.3) MUTATED 114 50 41 87
AMP PEAK 10(6P22.3) WILD-TYPE 62 62 77 64

Figure S39.  Get High-res Image Gene #10: 'amp_6p22.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_6p22.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.0344 (Fisher's exact test), Q value = 0.13

Table S40.  Gene #10: 'amp_6p22.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
AMP PEAK 10(6P22.3) MUTATED 166 71 55
AMP PEAK 10(6P22.3) WILD-TYPE 144 87 34

Figure S40.  Get High-res Image Gene #10: 'amp_6p22.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_6p22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S41.  Gene #10: 'amp_6p22.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
AMP PEAK 10(6P22.3) MUTATED 147 37 121
AMP PEAK 10(6P22.3) WILD-TYPE 95 93 86

Figure S41.  Get High-res Image Gene #10: 'amp_6p22.3' versus Molecular Subtype #5: 'CN_CNMF'

'amp_6p22.3' versus 'METHLYATION_CNMF'

P value = 0.00449 (Fisher's exact test), Q value = 0.031

Table S42.  Gene #10: 'amp_6p22.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
AMP PEAK 10(6P22.3) MUTATED 64 52 79 103
AMP PEAK 10(6P22.3) WILD-TYPE 49 46 108 67

Figure S42.  Get High-res Image Gene #10: 'amp_6p22.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_6p22.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.025 (Fisher's exact test), Q value = 0.11

Table S43.  Gene #10: 'amp_6p22.3' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 6 6 5 5
AMP PEAK 10(6P22.3) MUTATED 2 5 1 5
AMP PEAK 10(6P22.3) WILD-TYPE 4 1 4 0

Figure S43.  Get High-res Image Gene #10: 'amp_6p22.3' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'amp_7q36.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S44.  Gene #11: 'amp_7q36.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
AMP PEAK 11(7Q36.3) MUTATED 155 44 120
AMP PEAK 11(7Q36.3) WILD-TYPE 87 86 87

Figure S44.  Get High-res Image Gene #11: 'amp_7q36.3' versus Molecular Subtype #5: 'CN_CNMF'

'amp_8p11.21' versus 'MIR_CNMF'

P value = 0.0154 (Fisher's exact test), Q value = 0.076

Table S45.  Gene #12: 'amp_8p11.21' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 131 243
AMP PEAK 12(8P11.21) MUTATED 55 40 103
AMP PEAK 12(8P11.21) WILD-TYPE 126 91 140

Figure S45.  Get High-res Image Gene #12: 'amp_8p11.21' versus Molecular Subtype #3: 'MIR_CNMF'

'amp_8p11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S46.  Gene #12: 'amp_8p11.21' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
AMP PEAK 12(8P11.21) MUTATED 114 27 69
AMP PEAK 12(8P11.21) WILD-TYPE 128 103 138

Figure S46.  Get High-res Image Gene #12: 'amp_8p11.21' versus Molecular Subtype #5: 'CN_CNMF'

'amp_8p11.21' versus 'METHLYATION_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.0035

Table S47.  Gene #12: 'amp_8p11.21' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
AMP PEAK 12(8P11.21) MUTATED 49 44 45 68
AMP PEAK 12(8P11.21) WILD-TYPE 64 54 142 102

Figure S47.  Get High-res Image Gene #12: 'amp_8p11.21' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'MRNA_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00094

Table S48.  Gene #13: 'amp_8q24.21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 112 118 151
AMP PEAK 13(8Q24.21) MUTATED 120 99 93 129
AMP PEAK 13(8Q24.21) WILD-TYPE 56 13 25 22

Figure S48.  Get High-res Image Gene #13: 'amp_8q24.21' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_8q24.21' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S49.  Gene #13: 'amp_8q24.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
AMP PEAK 13(8Q24.21) MUTATED 244 144 53
AMP PEAK 13(8Q24.21) WILD-TYPE 66 14 36

Figure S49.  Get High-res Image Gene #13: 'amp_8q24.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_8q24.21' versus 'MIR_CHIERARCHICAL'

P value = 0.00198 (Fisher's exact test), Q value = 0.016

Table S50.  Gene #13: 'amp_8q24.21' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
AMP PEAK 13(8Q24.21) MUTATED 71 46 43 67 31 64 24 26 30 38
AMP PEAK 13(8Q24.21) WILD-TYPE 14 11 15 15 3 11 10 10 22 4

Figure S50.  Get High-res Image Gene #13: 'amp_8q24.21' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'amp_8q24.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S51.  Gene #13: 'amp_8q24.21' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
AMP PEAK 13(8Q24.21) MUTATED 175 83 202
AMP PEAK 13(8Q24.21) WILD-TYPE 67 47 5

Figure S51.  Get High-res Image Gene #13: 'amp_8q24.21' versus Molecular Subtype #5: 'CN_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

P value = 0.0449 (Fisher's exact test), Q value = 0.15

Table S52.  Gene #13: 'amp_8q24.21' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
AMP PEAK 13(8Q24.21) MUTATED 94 67 152 136
AMP PEAK 13(8Q24.21) WILD-TYPE 19 31 35 34

Figure S52.  Get High-res Image Gene #13: 'amp_8q24.21' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S53.  Gene #13: 'amp_8q24.21' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 109 112
AMP PEAK 13(8Q24.21) MUTATED 71 72 105
AMP PEAK 13(8Q24.21) WILD-TYPE 8 37 7

Figure S53.  Get High-res Image Gene #13: 'amp_8q24.21' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S54.  Gene #13: 'amp_8q24.21' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
AMP PEAK 13(8Q24.21) MUTATED 120 38 90
AMP PEAK 13(8Q24.21) WILD-TYPE 26 21 5

Figure S54.  Get High-res Image Gene #13: 'amp_8q24.21' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_10p15.3' versus 'MRNA_CNMF'

P value = 0.0164 (Fisher's exact test), Q value = 0.079

Table S55.  Gene #14: 'amp_10p15.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 112 118 151
AMP PEAK 14(10P15.3) MUTATED 87 49 37 70
AMP PEAK 14(10P15.3) WILD-TYPE 89 63 81 81

Figure S55.  Get High-res Image Gene #14: 'amp_10p15.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_10p15.3' versus 'MIR_CNMF'

P value = 0.0253 (Fisher's exact test), Q value = 0.11

Table S56.  Gene #14: 'amp_10p15.3' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 131 243
AMP PEAK 14(10P15.3) MUTATED 82 44 116
AMP PEAK 14(10P15.3) WILD-TYPE 99 87 127

Figure S56.  Get High-res Image Gene #14: 'amp_10p15.3' versus Molecular Subtype #3: 'MIR_CNMF'

'amp_10p15.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S57.  Gene #14: 'amp_10p15.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
AMP PEAK 14(10P15.3) MUTATED 146 30 76
AMP PEAK 14(10P15.3) WILD-TYPE 96 100 131

Figure S57.  Get High-res Image Gene #14: 'amp_10p15.3' versus Molecular Subtype #5: 'CN_CNMF'

'amp_10p15.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S58.  Gene #14: 'amp_10p15.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
AMP PEAK 14(10P15.3) MUTATED 56 46 49 94
AMP PEAK 14(10P15.3) WILD-TYPE 57 52 138 76

Figure S58.  Get High-res Image Gene #14: 'amp_10p15.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_10p15.3' versus 'MRNASEQ_CNMF'

P value = 0.0335 (Fisher's exact test), Q value = 0.13

Table S59.  Gene #14: 'amp_10p15.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 109 112
AMP PEAK 14(10P15.3) MUTATED 25 55 45
AMP PEAK 14(10P15.3) WILD-TYPE 54 54 67

Figure S59.  Get High-res Image Gene #14: 'amp_10p15.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_10q22.3' versus 'CN_CNMF'

P value = 0.0428 (Fisher's exact test), Q value = 0.15

Table S60.  Gene #15: 'amp_10q22.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
AMP PEAK 15(10Q22.3) MUTATED 86 30 67
AMP PEAK 15(10Q22.3) WILD-TYPE 156 100 140

Figure S60.  Get High-res Image Gene #15: 'amp_10q22.3' versus Molecular Subtype #5: 'CN_CNMF'

'amp_10q22.3' versus 'METHLYATION_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.0024

Table S61.  Gene #15: 'amp_10q22.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
AMP PEAK 15(10Q22.3) MUTATED 53 34 43 49
AMP PEAK 15(10Q22.3) WILD-TYPE 60 64 144 121

Figure S61.  Get High-res Image Gene #15: 'amp_10q22.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_11q14.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00252 (Fisher's exact test), Q value = 0.019

Table S62.  Gene #16: 'amp_11q14.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
AMP PEAK 16(11Q14.1) MUTATED 153 66 26
AMP PEAK 16(11Q14.1) WILD-TYPE 157 92 63

Figure S62.  Get High-res Image Gene #16: 'amp_11q14.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_11q14.1' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00031

Table S63.  Gene #16: 'amp_11q14.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
AMP PEAK 16(11Q14.1) MUTATED 108 34 113
AMP PEAK 16(11Q14.1) WILD-TYPE 134 96 94

Figure S63.  Get High-res Image Gene #16: 'amp_11q14.1' versus Molecular Subtype #5: 'CN_CNMF'

'amp_11q14.1' versus 'METHLYATION_CNMF'

P value = 0.0101 (Fisher's exact test), Q value = 0.057

Table S64.  Gene #16: 'amp_11q14.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
AMP PEAK 16(11Q14.1) MUTATED 56 30 79 85
AMP PEAK 16(11Q14.1) WILD-TYPE 57 68 108 85

Figure S64.  Get High-res Image Gene #16: 'amp_11q14.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_11q14.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.02 (Fisher's exact test), Q value = 0.091

Table S65.  Gene #16: 'amp_11q14.1' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
AMP PEAK 16(11Q14.1) MUTATED 75 18 47
AMP PEAK 16(11Q14.1) WILD-TYPE 71 41 48

Figure S65.  Get High-res Image Gene #16: 'amp_11q14.1' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_12p13.33' versus 'MRNA_CNMF'

P value = 0.0018 (Fisher's exact test), Q value = 0.015

Table S66.  Gene #17: 'amp_12p13.33' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 112 118 151
AMP PEAK 17(12P13.33) MUTATED 120 59 57 79
AMP PEAK 17(12P13.33) WILD-TYPE 56 53 61 72

Figure S66.  Get High-res Image Gene #17: 'amp_12p13.33' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_12p13.33' versus 'MRNA_CHIERARCHICAL'

P value = 0.0034 (Fisher's exact test), Q value = 0.024

Table S67.  Gene #17: 'amp_12p13.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
AMP PEAK 17(12P13.33) MUTATED 175 77 63
AMP PEAK 17(12P13.33) WILD-TYPE 135 81 26

Figure S67.  Get High-res Image Gene #17: 'amp_12p13.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_12p13.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S68.  Gene #17: 'amp_12p13.33' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
AMP PEAK 17(12P13.33) MUTATED 174 50 106
AMP PEAK 17(12P13.33) WILD-TYPE 68 80 101

Figure S68.  Get High-res Image Gene #17: 'amp_12p13.33' versus Molecular Subtype #5: 'CN_CNMF'

'amp_12p13.33' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00056

Table S69.  Gene #17: 'amp_12p13.33' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
AMP PEAK 17(12P13.33) MUTATED 65 65 79 114
AMP PEAK 17(12P13.33) WILD-TYPE 48 33 108 56

Figure S69.  Get High-res Image Gene #17: 'amp_12p13.33' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_12p13.33' versus 'MRNASEQ_CNMF'

P value = 0.0126 (Fisher's exact test), Q value = 0.068

Table S70.  Gene #17: 'amp_12p13.33' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 109 112
AMP PEAK 17(12P13.33) MUTATED 37 72 56
AMP PEAK 17(12P13.33) WILD-TYPE 42 37 56

Figure S70.  Get High-res Image Gene #17: 'amp_12p13.33' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_12p13.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00775 (Fisher's exact test), Q value = 0.047

Table S71.  Gene #17: 'amp_12p13.33' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
AMP PEAK 17(12P13.33) MUTATED 45 45 103 57
AMP PEAK 17(12P13.33) WILD-TYPE 60 26 62 49

Figure S71.  Get High-res Image Gene #17: 'amp_12p13.33' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'amp_12p12.1' versus 'MRNA_CNMF'

P value = 0.00136 (Fisher's exact test), Q value = 0.012

Table S72.  Gene #18: 'amp_12p12.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 112 118 151
AMP PEAK 18(12P12.1) MUTATED 112 62 49 74
AMP PEAK 18(12P12.1) WILD-TYPE 64 50 69 77

Figure S72.  Get High-res Image Gene #18: 'amp_12p12.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_12p12.1' versus 'MIR_CHIERARCHICAL'

P value = 0.0341 (Fisher's exact test), Q value = 0.13

Table S73.  Gene #18: 'amp_12p12.1' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
AMP PEAK 18(12P12.1) MUTATED 40 27 31 47 20 37 21 17 39 17
AMP PEAK 18(12P12.1) WILD-TYPE 45 30 27 35 14 38 13 19 13 25

Figure S73.  Get High-res Image Gene #18: 'amp_12p12.1' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'amp_12p12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S74.  Gene #18: 'amp_12p12.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
AMP PEAK 18(12P12.1) MUTATED 173 46 93
AMP PEAK 18(12P12.1) WILD-TYPE 69 84 114

Figure S74.  Get High-res Image Gene #18: 'amp_12p12.1' versus Molecular Subtype #5: 'CN_CNMF'

'amp_12p12.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S75.  Gene #18: 'amp_12p12.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
AMP PEAK 18(12P12.1) MUTATED 72 64 64 105
AMP PEAK 18(12P12.1) WILD-TYPE 41 34 123 65

Figure S75.  Get High-res Image Gene #18: 'amp_12p12.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_12p12.1' versus 'MRNASEQ_CNMF'

P value = 0.00183 (Fisher's exact test), Q value = 0.015

Table S76.  Gene #18: 'amp_12p12.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 109 112
AMP PEAK 18(12P12.1) MUTATED 31 71 62
AMP PEAK 18(12P12.1) WILD-TYPE 48 38 50

Figure S76.  Get High-res Image Gene #18: 'amp_12p12.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_12p12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00478 (Fisher's exact test), Q value = 0.032

Table S77.  Gene #18: 'amp_12p12.1' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
AMP PEAK 18(12P12.1) MUTATED 68 42 54
AMP PEAK 18(12P12.1) WILD-TYPE 78 17 41

Figure S77.  Get High-res Image Gene #18: 'amp_12p12.1' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_12p12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00314 (Fisher's exact test), Q value = 0.023

Table S78.  Gene #18: 'amp_12p12.1' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
AMP PEAK 18(12P12.1) MUTATED 42 44 100 52
AMP PEAK 18(12P12.1) WILD-TYPE 63 27 65 54

Figure S78.  Get High-res Image Gene #18: 'amp_12p12.1' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'amp_12p12.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0348 (Fisher's exact test), Q value = 0.13

Table S79.  Gene #18: 'amp_12p12.1' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 5 2 2 4 5 4
AMP PEAK 18(12P12.1) MUTATED 3 0 0 1 5 3
AMP PEAK 18(12P12.1) WILD-TYPE 2 2 2 3 0 1

Figure S79.  Get High-res Image Gene #18: 'amp_12p12.1' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12q15' versus 'MRNA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00056

Table S80.  Gene #19: 'amp_12q15' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 112 118 151
AMP PEAK 19(12Q15) MUTATED 92 41 27 51
AMP PEAK 19(12Q15) WILD-TYPE 84 71 91 100

Figure S80.  Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_12q15' versus 'MIR_CHIERARCHICAL'

P value = 0.00243 (Fisher's exact test), Q value = 0.019

Table S81.  Gene #19: 'amp_12q15' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
AMP PEAK 19(12Q15) MUTATED 31 13 23 29 15 24 15 16 33 11
AMP PEAK 19(12Q15) WILD-TYPE 54 44 35 53 19 51 19 20 19 31

Figure S81.  Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'amp_12q15' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S82.  Gene #19: 'amp_12q15' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
AMP PEAK 19(12Q15) MUTATED 130 39 53
AMP PEAK 19(12Q15) WILD-TYPE 112 91 154

Figure S82.  Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #5: 'CN_CNMF'

'amp_12q15' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S83.  Gene #19: 'amp_12q15' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
AMP PEAK 19(12Q15) MUTATED 54 51 37 75
AMP PEAK 19(12Q15) WILD-TYPE 59 47 150 95

Figure S83.  Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_12q15' versus 'MRNASEQ_CNMF'

P value = 0.00604 (Fisher's exact test), Q value = 0.038

Table S84.  Gene #19: 'amp_12q15' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 109 112
AMP PEAK 19(12Q15) MUTATED 24 56 39
AMP PEAK 19(12Q15) WILD-TYPE 55 53 73

Figure S84.  Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_12q15' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00275 (Fisher's exact test), Q value = 0.021

Table S85.  Gene #19: 'amp_12q15' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
AMP PEAK 19(12Q15) MUTATED 53 35 31
AMP PEAK 19(12Q15) WILD-TYPE 93 24 64

Figure S85.  Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_12q15' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0435 (Fisher's exact test), Q value = 0.15

Table S86.  Gene #19: 'amp_12q15' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 6 6 5 5
AMP PEAK 19(12Q15) MUTATED 2 1 2 5
AMP PEAK 19(12Q15) WILD-TYPE 4 5 3 0

Figure S86.  Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'amp_14q11.2' versus 'MRNA_CNMF'

P value = 0.0195 (Fisher's exact test), Q value = 0.089

Table S87.  Gene #20: 'amp_14q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 112 118 151
AMP PEAK 20(14Q11.2) MUTATED 59 21 31 32
AMP PEAK 20(14Q11.2) WILD-TYPE 117 91 87 119

Figure S87.  Get High-res Image Gene #20: 'amp_14q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_14q11.2' versus 'MIR_CHIERARCHICAL'

P value = 0.0108 (Fisher's exact test), Q value = 0.06

Table S88.  Gene #20: 'amp_14q11.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
AMP PEAK 20(14Q11.2) MUTATED 26 16 15 21 10 8 10 11 20 5
AMP PEAK 20(14Q11.2) WILD-TYPE 59 41 43 61 24 67 24 25 32 37

Figure S88.  Get High-res Image Gene #20: 'amp_14q11.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'amp_14q11.2' versus 'CN_CNMF'

P value = 0.0187 (Fisher's exact test), Q value = 0.086

Table S89.  Gene #20: 'amp_14q11.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
AMP PEAK 20(14Q11.2) MUTATED 73 22 52
AMP PEAK 20(14Q11.2) WILD-TYPE 169 108 155

Figure S89.  Get High-res Image Gene #20: 'amp_14q11.2' versus Molecular Subtype #5: 'CN_CNMF'

'amp_14q11.2' versus 'METHLYATION_CNMF'

P value = 0.0344 (Fisher's exact test), Q value = 0.13

Table S90.  Gene #20: 'amp_14q11.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
AMP PEAK 20(14Q11.2) MUTATED 34 30 34 47
AMP PEAK 20(14Q11.2) WILD-TYPE 79 68 153 123

Figure S90.  Get High-res Image Gene #20: 'amp_14q11.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_14q32.33' versus 'MIR_CHIERARCHICAL'

P value = 0.0172 (Fisher's exact test), Q value = 0.081

Table S91.  Gene #21: 'amp_14q32.33' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
AMP PEAK 21(14Q32.33) MUTATED 25 12 12 26 11 11 5 15 17 16
AMP PEAK 21(14Q32.33) WILD-TYPE 60 45 46 56 23 64 29 21 35 26

Figure S91.  Get High-res Image Gene #21: 'amp_14q32.33' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'amp_14q32.33' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00044

Table S92.  Gene #21: 'amp_14q32.33' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
AMP PEAK 21(14Q32.33) MUTATED 45 32 79
AMP PEAK 21(14Q32.33) WILD-TYPE 197 98 128

Figure S92.  Get High-res Image Gene #21: 'amp_14q32.33' versus Molecular Subtype #5: 'CN_CNMF'

'amp_15q26.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S93.  Gene #22: 'amp_15q26.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
AMP PEAK 22(15Q26.3) MUTATED 50 25 88
AMP PEAK 22(15Q26.3) WILD-TYPE 192 105 119

Figure S93.  Get High-res Image Gene #22: 'amp_15q26.3' versus Molecular Subtype #5: 'CN_CNMF'

'amp_17q25.3' versus 'CN_CNMF'

P value = 0.00816 (Fisher's exact test), Q value = 0.048

Table S94.  Gene #23: 'amp_17q25.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
AMP PEAK 23(17Q25.3) MUTATED 81 40 94
AMP PEAK 23(17Q25.3) WILD-TYPE 161 90 113

Figure S94.  Get High-res Image Gene #23: 'amp_17q25.3' versus Molecular Subtype #5: 'CN_CNMF'

'amp_17q25.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0127 (Fisher's exact test), Q value = 0.068

Table S95.  Gene #23: 'amp_17q25.3' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 54 60 154
AMP PEAK 23(17Q25.3) MUTATED 62 24 27 43
AMP PEAK 23(17Q25.3) WILD-TYPE 81 30 33 111

Figure S95.  Get High-res Image Gene #23: 'amp_17q25.3' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'amp_17q25.3' versus 'MRNASEQ_CNMF'

P value = 0.0185 (Fisher's exact test), Q value = 0.085

Table S96.  Gene #23: 'amp_17q25.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 109 112
AMP PEAK 23(17Q25.3) MUTATED 37 31 48
AMP PEAK 23(17Q25.3) WILD-TYPE 42 78 64

Figure S96.  Get High-res Image Gene #23: 'amp_17q25.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_18q11.2' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00031

Table S97.  Gene #24: 'amp_18q11.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
AMP PEAK 24(18Q11.2) MUTATED 83 17 42
AMP PEAK 24(18Q11.2) WILD-TYPE 159 113 165

Figure S97.  Get High-res Image Gene #24: 'amp_18q11.2' versus Molecular Subtype #5: 'CN_CNMF'

'amp_18q11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S98.  Gene #24: 'amp_18q11.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
AMP PEAK 24(18Q11.2) MUTATED 39 18 23 61
AMP PEAK 24(18Q11.2) WILD-TYPE 74 80 164 109

Figure S98.  Get High-res Image Gene #24: 'amp_18q11.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_18q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0275 (Fisher's exact test), Q value = 0.11

Table S99.  Gene #24: 'amp_18q11.2' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 6 6 5 5
AMP PEAK 24(18Q11.2) MUTATED 1 0 2 4
AMP PEAK 24(18Q11.2) WILD-TYPE 5 6 3 1

Figure S99.  Get High-res Image Gene #24: 'amp_18q11.2' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'amp_19p13.12' versus 'MRNA_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00082

Table S100.  Gene #25: 'amp_19p13.12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 112 118 151
AMP PEAK 25(19P13.12) MUTATED 114 43 70 75
AMP PEAK 25(19P13.12) WILD-TYPE 62 69 48 76

Figure S100.  Get High-res Image Gene #25: 'amp_19p13.12' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_19p13.12' versus 'MRNA_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.0029

Table S101.  Gene #25: 'amp_19p13.12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
AMP PEAK 25(19P13.12) MUTATED 186 64 52
AMP PEAK 25(19P13.12) WILD-TYPE 124 94 37

Figure S101.  Get High-res Image Gene #25: 'amp_19p13.12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_19p13.12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S102.  Gene #25: 'amp_19p13.12' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
AMP PEAK 25(19P13.12) MUTATED 170 49 96
AMP PEAK 25(19P13.12) WILD-TYPE 72 81 111

Figure S102.  Get High-res Image Gene #25: 'amp_19p13.12' versus Molecular Subtype #5: 'CN_CNMF'

'amp_19p13.12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S103.  Gene #25: 'amp_19p13.12' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
AMP PEAK 25(19P13.12) MUTATED 58 58 69 122
AMP PEAK 25(19P13.12) WILD-TYPE 55 40 118 48

Figure S103.  Get High-res Image Gene #25: 'amp_19p13.12' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_19p13.12' versus 'RPPA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00056

Table S104.  Gene #25: 'amp_19p13.12' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 189 76
AMP PEAK 25(19P13.12) MUTATED 70 126 30
AMP PEAK 25(19P13.12) WILD-TYPE 76 63 46

Figure S104.  Get High-res Image Gene #25: 'amp_19p13.12' versus Molecular Subtype #7: 'RPPA_CNMF'

'amp_19p13.12' versus 'RPPA_CHIERARCHICAL'

P value = 0.00143 (Fisher's exact test), Q value = 0.012

Table S105.  Gene #25: 'amp_19p13.12' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 54 60 154
AMP PEAK 25(19P13.12) MUTATED 64 26 43 93
AMP PEAK 25(19P13.12) WILD-TYPE 79 28 17 61

Figure S105.  Get High-res Image Gene #25: 'amp_19p13.12' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'amp_19q12' versus 'MRNA_CNMF'

P value = 0.0135 (Fisher's exact test), Q value = 0.071

Table S106.  Gene #26: 'amp_19q12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 112 118 151
AMP PEAK 26(19Q12) MUTATED 111 53 58 92
AMP PEAK 26(19Q12) WILD-TYPE 65 59 60 59

Figure S106.  Get High-res Image Gene #26: 'amp_19q12' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_19q12' versus 'MRNA_CHIERARCHICAL'

P value = 0.0109 (Fisher's exact test), Q value = 0.061

Table S107.  Gene #26: 'amp_19q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
AMP PEAK 26(19Q12) MUTATED 187 73 54
AMP PEAK 26(19Q12) WILD-TYPE 123 85 35

Figure S107.  Get High-res Image Gene #26: 'amp_19q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_19q12' versus 'MIR_CNMF'

P value = 0.00645 (Fisher's exact test), Q value = 0.04

Table S108.  Gene #26: 'amp_19q12' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 131 243
AMP PEAK 26(19Q12) MUTATED 106 58 148
AMP PEAK 26(19Q12) WILD-TYPE 75 73 95

Figure S108.  Get High-res Image Gene #26: 'amp_19q12' versus Molecular Subtype #3: 'MIR_CNMF'

'amp_19q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S109.  Gene #26: 'amp_19q12' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
AMP PEAK 26(19Q12) MUTATED 195 40 88
AMP PEAK 26(19Q12) WILD-TYPE 47 90 119

Figure S109.  Get High-res Image Gene #26: 'amp_19q12' versus Molecular Subtype #5: 'CN_CNMF'

'amp_19q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S110.  Gene #26: 'amp_19q12' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
AMP PEAK 26(19Q12) MUTATED 71 50 69 130
AMP PEAK 26(19Q12) WILD-TYPE 42 48 118 40

Figure S110.  Get High-res Image Gene #26: 'amp_19q12' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_19q12' versus 'RPPA_CNMF'

P value = 0.0185 (Fisher's exact test), Q value = 0.085

Table S111.  Gene #26: 'amp_19q12' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 189 76
AMP PEAK 26(19Q12) MUTATED 72 117 35
AMP PEAK 26(19Q12) WILD-TYPE 74 72 41

Figure S111.  Get High-res Image Gene #26: 'amp_19q12' versus Molecular Subtype #7: 'RPPA_CNMF'

'amp_19q13.2' versus 'MRNA_CNMF'

P value = 0.0407 (Fisher's exact test), Q value = 0.15

Table S112.  Gene #27: 'amp_19q13.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 112 118 151
AMP PEAK 27(19Q13.2) MUTATED 82 48 37 70
AMP PEAK 27(19Q13.2) WILD-TYPE 94 64 81 81

Figure S112.  Get High-res Image Gene #27: 'amp_19q13.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_19q13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S113.  Gene #27: 'amp_19q13.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
AMP PEAK 27(19Q13.2) MUTATED 148 29 68
AMP PEAK 27(19Q13.2) WILD-TYPE 94 101 139

Figure S113.  Get High-res Image Gene #27: 'amp_19q13.2' versus Molecular Subtype #5: 'CN_CNMF'

'amp_19q13.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S114.  Gene #27: 'amp_19q13.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
AMP PEAK 27(19Q13.2) MUTATED 61 38 51 91
AMP PEAK 27(19Q13.2) WILD-TYPE 52 60 136 79

Figure S114.  Get High-res Image Gene #27: 'amp_19q13.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_19q13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0257 (Fisher's exact test), Q value = 0.11

Table S115.  Gene #27: 'amp_19q13.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
AMP PEAK 27(19Q13.2) MUTATED 55 34 37
AMP PEAK 27(19Q13.2) WILD-TYPE 91 25 58

Figure S115.  Get High-res Image Gene #27: 'amp_19q13.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_20p13' versus 'MRNA_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.0017

Table S116.  Gene #28: 'amp_20p13' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 112 118 151
AMP PEAK 28(20P13) MUTATED 118 56 49 78
AMP PEAK 28(20P13) WILD-TYPE 58 56 69 73

Figure S116.  Get High-res Image Gene #28: 'amp_20p13' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20p13' versus 'MRNA_CHIERARCHICAL'

P value = 0.0047 (Fisher's exact test), Q value = 0.032

Table S117.  Gene #28: 'amp_20p13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
AMP PEAK 28(20P13) MUTATED 160 79 62
AMP PEAK 28(20P13) WILD-TYPE 150 79 27

Figure S117.  Get High-res Image Gene #28: 'amp_20p13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20p13' versus 'MIR_CNMF'

P value = 0.0313 (Fisher's exact test), Q value = 0.12

Table S118.  Gene #28: 'amp_20p13' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 131 243
AMP PEAK 28(20P13) MUTATED 97 59 144
AMP PEAK 28(20P13) WILD-TYPE 84 72 99

Figure S118.  Get High-res Image Gene #28: 'amp_20p13' versus Molecular Subtype #3: 'MIR_CNMF'

'amp_20p13' versus 'MIR_CHIERARCHICAL'

P value = 0.0312 (Fisher's exact test), Q value = 0.12

Table S119.  Gene #28: 'amp_20p13' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
AMP PEAK 28(20P13) MUTATED 41 28 36 44 19 44 23 18 34 13
AMP PEAK 28(20P13) WILD-TYPE 44 29 22 38 15 31 11 18 18 29

Figure S119.  Get High-res Image Gene #28: 'amp_20p13' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'amp_20p13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S120.  Gene #28: 'amp_20p13' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
AMP PEAK 28(20P13) MUTATED 181 39 96
AMP PEAK 28(20P13) WILD-TYPE 61 91 111

Figure S120.  Get High-res Image Gene #28: 'amp_20p13' versus Molecular Subtype #5: 'CN_CNMF'

'amp_20p13' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S121.  Gene #28: 'amp_20p13' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
AMP PEAK 28(20P13) MUTATED 64 63 67 112
AMP PEAK 28(20P13) WILD-TYPE 49 35 120 58

Figure S121.  Get High-res Image Gene #28: 'amp_20p13' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_20p13' versus 'MRNASEQ_CNMF'

P value = 0.0216 (Fisher's exact test), Q value = 0.096

Table S122.  Gene #28: 'amp_20p13' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 109 112
AMP PEAK 28(20P13) MUTATED 36 71 59
AMP PEAK 28(20P13) WILD-TYPE 43 38 53

Figure S122.  Get High-res Image Gene #28: 'amp_20p13' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_20p13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0446 (Fisher's exact test), Q value = 0.15

Table S123.  Gene #28: 'amp_20p13' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
AMP PEAK 28(20P13) MUTATED 74 41 51
AMP PEAK 28(20P13) WILD-TYPE 72 18 44

Figure S123.  Get High-res Image Gene #28: 'amp_20p13' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_20p13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00081 (Fisher's exact test), Q value = 0.008

Table S124.  Gene #28: 'amp_20p13' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
AMP PEAK 28(20P13) MUTATED 44 44 106 50
AMP PEAK 28(20P13) WILD-TYPE 61 27 59 56

Figure S124.  Get High-res Image Gene #28: 'amp_20p13' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'amp_20q11.21' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S125.  Gene #29: 'amp_20q11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 112 118 151
AMP PEAK 29(20Q11.21) MUTATED 132 70 46 83
AMP PEAK 29(20Q11.21) WILD-TYPE 44 42 72 68

Figure S125.  Get High-res Image Gene #29: 'amp_20q11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20q11.21' versus 'MRNA_CHIERARCHICAL'

P value = 0.00322 (Fisher's exact test), Q value = 0.023

Table S126.  Gene #29: 'amp_20q11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
AMP PEAK 29(20Q11.21) MUTATED 177 87 67
AMP PEAK 29(20Q11.21) WILD-TYPE 133 71 22

Figure S126.  Get High-res Image Gene #29: 'amp_20q11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20q11.21' versus 'MIR_CNMF'

P value = 0.0392 (Fisher's exact test), Q value = 0.14

Table S127.  Gene #29: 'amp_20q11.21' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 131 243
AMP PEAK 29(20Q11.21) MUTATED 110 66 155
AMP PEAK 29(20Q11.21) WILD-TYPE 71 65 88

Figure S127.  Get High-res Image Gene #29: 'amp_20q11.21' versus Molecular Subtype #3: 'MIR_CNMF'

'amp_20q11.21' versus 'MIR_CHIERARCHICAL'

P value = 0.00299 (Fisher's exact test), Q value = 0.022

Table S128.  Gene #29: 'amp_20q11.21' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
AMP PEAK 29(20Q11.21) MUTATED 45 33 36 44 20 45 29 21 40 18
AMP PEAK 29(20Q11.21) WILD-TYPE 40 24 22 38 14 30 5 15 12 24

Figure S128.  Get High-res Image Gene #29: 'amp_20q11.21' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'amp_20q11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S129.  Gene #29: 'amp_20q11.21' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
AMP PEAK 29(20Q11.21) MUTATED 206 47 94
AMP PEAK 29(20Q11.21) WILD-TYPE 36 83 113

Figure S129.  Get High-res Image Gene #29: 'amp_20q11.21' versus Molecular Subtype #5: 'CN_CNMF'

'amp_20q11.21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S130.  Gene #29: 'amp_20q11.21' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
AMP PEAK 29(20Q11.21) MUTATED 80 65 59 135
AMP PEAK 29(20Q11.21) WILD-TYPE 33 33 128 35

Figure S130.  Get High-res Image Gene #29: 'amp_20q11.21' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_20q11.21' versus 'MRNASEQ_CNMF'

P value = 0.00416 (Fisher's exact test), Q value = 0.029

Table S131.  Gene #29: 'amp_20q11.21' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 109 112
AMP PEAK 29(20Q11.21) MUTATED 37 77 69
AMP PEAK 29(20Q11.21) WILD-TYPE 42 32 43

Figure S131.  Get High-res Image Gene #29: 'amp_20q11.21' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_20q11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00279 (Fisher's exact test), Q value = 0.021

Table S132.  Gene #29: 'amp_20q11.21' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
AMP PEAK 29(20Q11.21) MUTATED 80 47 56
AMP PEAK 29(20Q11.21) WILD-TYPE 66 12 39

Figure S132.  Get High-res Image Gene #29: 'amp_20q11.21' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_20q11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00073 (Fisher's exact test), Q value = 0.0076

Table S133.  Gene #29: 'amp_20q11.21' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
AMP PEAK 29(20Q11.21) MUTATED 52 46 119 57
AMP PEAK 29(20Q11.21) WILD-TYPE 53 25 46 49

Figure S133.  Get High-res Image Gene #29: 'amp_20q11.21' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'amp_20q13.33' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00031

Table S134.  Gene #30: 'amp_20q13.33' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 112 118 151
AMP PEAK 30(20Q13.33) MUTATED 144 78 68 95
AMP PEAK 30(20Q13.33) WILD-TYPE 32 34 50 56

Figure S134.  Get High-res Image Gene #30: 'amp_20q13.33' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20q13.33' versus 'MRNA_CHIERARCHICAL'

P value = 0.00077 (Fisher's exact test), Q value = 0.0077

Table S135.  Gene #30: 'amp_20q13.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
AMP PEAK 30(20Q13.33) MUTATED 206 103 76
AMP PEAK 30(20Q13.33) WILD-TYPE 104 55 13

Figure S135.  Get High-res Image Gene #30: 'amp_20q13.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20q13.33' versus 'MIR_CHIERARCHICAL'

P value = 0.00133 (Fisher's exact test), Q value = 0.012

Table S136.  Gene #30: 'amp_20q13.33' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
AMP PEAK 30(20Q13.33) MUTATED 49 35 41 52 29 54 29 25 45 25
AMP PEAK 30(20Q13.33) WILD-TYPE 36 22 17 30 5 21 5 11 7 17

Figure S136.  Get High-res Image Gene #30: 'amp_20q13.33' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'amp_20q13.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S137.  Gene #30: 'amp_20q13.33' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
AMP PEAK 30(20Q13.33) MUTATED 213 54 134
AMP PEAK 30(20Q13.33) WILD-TYPE 29 76 73

Figure S137.  Get High-res Image Gene #30: 'amp_20q13.33' versus Molecular Subtype #5: 'CN_CNMF'

'amp_20q13.33' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S138.  Gene #30: 'amp_20q13.33' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
AMP PEAK 30(20Q13.33) MUTATED 88 79 91 134
AMP PEAK 30(20Q13.33) WILD-TYPE 25 19 96 36

Figure S138.  Get High-res Image Gene #30: 'amp_20q13.33' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_20q13.33' versus 'MRNASEQ_CNMF'

P value = 0.0375 (Fisher's exact test), Q value = 0.14

Table S139.  Gene #30: 'amp_20q13.33' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 109 112
AMP PEAK 30(20Q13.33) MUTATED 49 86 78
AMP PEAK 30(20Q13.33) WILD-TYPE 30 23 34

Figure S139.  Get High-res Image Gene #30: 'amp_20q13.33' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_20q13.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00264 (Fisher's exact test), Q value = 0.02

Table S140.  Gene #30: 'amp_20q13.33' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
AMP PEAK 30(20Q13.33) MUTATED 95 52 66
AMP PEAK 30(20Q13.33) WILD-TYPE 51 7 29

Figure S140.  Get High-res Image Gene #30: 'amp_20q13.33' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_20q13.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0496 (Fisher's exact test), Q value = 0.16

Table S141.  Gene #30: 'amp_20q13.33' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
AMP PEAK 30(20Q13.33) MUTATED 69 53 128 68
AMP PEAK 30(20Q13.33) WILD-TYPE 36 18 37 38

Figure S141.  Get High-res Image Gene #30: 'amp_20q13.33' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'amp_20q13.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.031 (Fisher's exact test), Q value = 0.12

Table S142.  Gene #30: 'amp_20q13.33' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 5 2 2 4 5 4
AMP PEAK 30(20Q13.33) MUTATED 4 2 0 2 5 4
AMP PEAK 30(20Q13.33) WILD-TYPE 1 0 2 2 0 0

Figure S142.  Get High-res Image Gene #30: 'amp_20q13.33' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_22q12.2' versus 'MIR_CHIERARCHICAL'

P value = 0.0345 (Fisher's exact test), Q value = 0.13

Table S143.  Gene #31: 'amp_22q12.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
AMP PEAK 31(22Q12.2) MUTATED 11 7 15 16 4 16 5 8 3 2
AMP PEAK 31(22Q12.2) WILD-TYPE 74 50 43 66 30 59 29 28 49 40

Figure S143.  Get High-res Image Gene #31: 'amp_22q12.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'amp_22q12.2' versus 'CN_CNMF'

P value = 0.00461 (Fisher's exact test), Q value = 0.031

Table S144.  Gene #31: 'amp_22q12.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
AMP PEAK 31(22Q12.2) MUTATED 45 9 37
AMP PEAK 31(22Q12.2) WILD-TYPE 197 121 170

Figure S144.  Get High-res Image Gene #31: 'amp_22q12.2' versus Molecular Subtype #5: 'CN_CNMF'

'amp_22q12.2' versus 'METHLYATION_CNMF'

P value = 0.0304 (Fisher's exact test), Q value = 0.12

Table S145.  Gene #31: 'amp_22q12.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
AMP PEAK 31(22Q12.2) MUTATED 23 8 25 33
AMP PEAK 31(22Q12.2) WILD-TYPE 90 90 162 137

Figure S145.  Get High-res Image Gene #31: 'amp_22q12.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_22q12.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0013 (Fisher's exact test), Q value = 0.012

Table S146.  Gene #31: 'amp_22q12.2' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 54 60 154
AMP PEAK 31(22Q12.2) MUTATED 22 18 13 16
AMP PEAK 31(22Q12.2) WILD-TYPE 121 36 47 138

Figure S146.  Get High-res Image Gene #31: 'amp_22q12.2' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'amp_22q12.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0144 (Fisher's exact test), Q value = 0.072

Table S147.  Gene #31: 'amp_22q12.2' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
AMP PEAK 31(22Q12.2) MUTATED 15 8 38 10
AMP PEAK 31(22Q12.2) WILD-TYPE 90 63 127 96

Figure S147.  Get High-res Image Gene #31: 'amp_22q12.2' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'amp_xp11.23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S148.  Gene #32: 'amp_xp11.23' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
AMP PEAK 32(XP11.23) MUTATED 92 14 53
AMP PEAK 32(XP11.23) WILD-TYPE 150 116 154

Figure S148.  Get High-res Image Gene #32: 'amp_xp11.23' versus Molecular Subtype #5: 'CN_CNMF'

'amp_xp11.23' versus 'METHLYATION_CNMF'

P value = 0.0236 (Fisher's exact test), Q value = 0.1

Table S149.  Gene #32: 'amp_xp11.23' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
AMP PEAK 32(XP11.23) MUTATED 34 24 38 58
AMP PEAK 32(XP11.23) WILD-TYPE 79 74 149 112

Figure S149.  Get High-res Image Gene #32: 'amp_xp11.23' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_xp11.23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0318 (Fisher's exact test), Q value = 0.12

Table S150.  Gene #32: 'amp_xp11.23' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
AMP PEAK 32(XP11.23) MUTATED 23 27 53 23
AMP PEAK 32(XP11.23) WILD-TYPE 82 44 112 83

Figure S150.  Get High-res Image Gene #32: 'amp_xp11.23' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'amp_xq28' versus 'CN_CNMF'

P value = 0.00126 (Fisher's exact test), Q value = 0.011

Table S151.  Gene #33: 'amp_xq28' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
AMP PEAK 33(XQ28) MUTATED 91 34 95
AMP PEAK 33(XQ28) WILD-TYPE 151 96 112

Figure S151.  Get High-res Image Gene #33: 'amp_xq28' versus Molecular Subtype #5: 'CN_CNMF'

'amp_xq28' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00818 (Fisher's exact test), Q value = 0.048

Table S152.  Gene #33: 'amp_xq28' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 6 6 5 5
AMP PEAK 33(XQ28) MUTATED 3 0 2 5
AMP PEAK 33(XQ28) WILD-TYPE 3 6 3 0

Figure S152.  Get High-res Image Gene #33: 'amp_xq28' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'del_1p36.11' versus 'CN_CNMF'

P value = 0.00895 (Fisher's exact test), Q value = 0.052

Table S153.  Gene #34: 'del_1p36.11' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
DEL PEAK 1(1P36.11) MUTATED 95 71 103
DEL PEAK 1(1P36.11) WILD-TYPE 147 59 104

Figure S153.  Get High-res Image Gene #34: 'del_1p36.11' versus Molecular Subtype #5: 'CN_CNMF'

'del_1p36.11' versus 'METHLYATION_CNMF'

P value = 0.0135 (Fisher's exact test), Q value = 0.071

Table S154.  Gene #34: 'del_1p36.11' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
DEL PEAK 1(1P36.11) MUTATED 57 51 96 62
DEL PEAK 1(1P36.11) WILD-TYPE 56 47 91 108

Figure S154.  Get High-res Image Gene #34: 'del_1p36.11' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_1p36.11' versus 'RPPA_CNMF'

P value = 0.0482 (Fisher's exact test), Q value = 0.16

Table S155.  Gene #34: 'del_1p36.11' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 189 76
DEL PEAK 1(1P36.11) MUTATED 76 75 39
DEL PEAK 1(1P36.11) WILD-TYPE 70 114 37

Figure S155.  Get High-res Image Gene #34: 'del_1p36.11' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_1q41' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S156.  Gene #35: 'del_1q41' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
DEL PEAK 2(1Q41) MUTATED 33 5 59
DEL PEAK 2(1Q41) WILD-TYPE 209 125 148

Figure S156.  Get High-res Image Gene #35: 'del_1q41' versus Molecular Subtype #5: 'CN_CNMF'

'del_2q22.1' versus 'MIR_CHIERARCHICAL'

P value = 0.00408 (Fisher's exact test), Q value = 0.029

Table S157.  Gene #37: 'del_2q22.1' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
DEL PEAK 4(2Q22.1) MUTATED 21 8 8 20 14 18 4 17 12 10
DEL PEAK 4(2Q22.1) WILD-TYPE 64 49 50 62 20 57 30 19 40 32

Figure S157.  Get High-res Image Gene #37: 'del_2q22.1' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_2q22.1' versus 'CN_CNMF'

P value = 0.0474 (Fisher's exact test), Q value = 0.16

Table S158.  Gene #37: 'del_2q22.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
DEL PEAK 4(2Q22.1) MUTATED 55 22 59
DEL PEAK 4(2Q22.1) WILD-TYPE 187 108 148

Figure S158.  Get High-res Image Gene #37: 'del_2q22.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_2q37.3' versus 'MRNA_CNMF'

P value = 0.00079 (Fisher's exact test), Q value = 0.0078

Table S159.  Gene #38: 'del_2q37.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 112 118 151
DEL PEAK 5(2Q37.3) MUTATED 43 35 27 65
DEL PEAK 5(2Q37.3) WILD-TYPE 133 77 91 86

Figure S159.  Get High-res Image Gene #38: 'del_2q37.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_2q37.3' versus 'MIR_CHIERARCHICAL'

P value = 0.0169 (Fisher's exact test), Q value = 0.081

Table S160.  Gene #38: 'del_2q37.3' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
DEL PEAK 5(2Q37.3) MUTATED 23 12 16 31 10 24 5 20 14 15
DEL PEAK 5(2Q37.3) WILD-TYPE 62 45 42 51 24 51 29 16 38 27

Figure S160.  Get High-res Image Gene #38: 'del_2q37.3' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_2q37.3' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00044

Table S161.  Gene #38: 'del_2q37.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
DEL PEAK 5(2Q37.3) MUTATED 68 23 84
DEL PEAK 5(2Q37.3) WILD-TYPE 174 107 123

Figure S161.  Get High-res Image Gene #38: 'del_2q37.3' versus Molecular Subtype #5: 'CN_CNMF'

'del_2q37.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0156 (Fisher's exact test), Q value = 0.077

Table S162.  Gene #38: 'del_2q37.3' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
DEL PEAK 5(2Q37.3) MUTATED 45 18 52 25
DEL PEAK 5(2Q37.3) WILD-TYPE 60 53 113 81

Figure S162.  Get High-res Image Gene #38: 'del_2q37.3' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_3p26.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S163.  Gene #39: 'del_3p26.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 112 118 151
DEL PEAK 6(3P26.2) MUTATED 85 40 22 58
DEL PEAK 6(3P26.2) WILD-TYPE 91 72 96 93

Figure S163.  Get High-res Image Gene #39: 'del_3p26.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_3p26.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.0024

Table S164.  Gene #39: 'del_3p26.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
DEL PEAK 6(3P26.2) MUTATED 101 54 50
DEL PEAK 6(3P26.2) WILD-TYPE 209 104 39

Figure S164.  Get High-res Image Gene #39: 'del_3p26.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_3p26.2' versus 'MIR_CNMF'

P value = 0.0116 (Fisher's exact test), Q value = 0.064

Table S165.  Gene #39: 'del_3p26.2' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 131 243
DEL PEAK 6(3P26.2) MUTATED 62 37 105
DEL PEAK 6(3P26.2) WILD-TYPE 119 94 138

Figure S165.  Get High-res Image Gene #39: 'del_3p26.2' versus Molecular Subtype #3: 'MIR_CNMF'

'del_3p26.2' versus 'MIR_CHIERARCHICAL'

P value = 0.00278 (Fisher's exact test), Q value = 0.021

Table S166.  Gene #39: 'del_3p26.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
DEL PEAK 6(3P26.2) MUTATED 29 20 12 34 13 26 18 16 28 8
DEL PEAK 6(3P26.2) WILD-TYPE 56 37 46 48 21 49 16 20 24 34

Figure S166.  Get High-res Image Gene #39: 'del_3p26.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_3p26.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S167.  Gene #39: 'del_3p26.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
DEL PEAK 6(3P26.2) MUTATED 125 28 57
DEL PEAK 6(3P26.2) WILD-TYPE 117 102 150

Figure S167.  Get High-res Image Gene #39: 'del_3p26.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_3p26.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S168.  Gene #39: 'del_3p26.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
DEL PEAK 6(3P26.2) MUTATED 51 40 41 77
DEL PEAK 6(3P26.2) WILD-TYPE 62 58 146 93

Figure S168.  Get High-res Image Gene #39: 'del_3p26.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_3p26.2' versus 'MRNASEQ_CNMF'

P value = 0.00112 (Fisher's exact test), Q value = 0.01

Table S169.  Gene #39: 'del_3p26.2' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 109 112
DEL PEAK 6(3P26.2) MUTATED 16 46 50
DEL PEAK 6(3P26.2) WILD-TYPE 63 63 62

Figure S169.  Get High-res Image Gene #39: 'del_3p26.2' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_3p26.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00083 (Fisher's exact test), Q value = 0.0081

Table S170.  Gene #39: 'del_3p26.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
DEL PEAK 6(3P26.2) MUTATED 39 29 44
DEL PEAK 6(3P26.2) WILD-TYPE 107 30 51

Figure S170.  Get High-res Image Gene #39: 'del_3p26.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_3q13.31' versus 'MRNA_CNMF'

P value = 0.0127 (Fisher's exact test), Q value = 0.068

Table S171.  Gene #40: 'del_3q13.31' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 112 118 151
DEL PEAK 7(3Q13.31) MUTATED 28 20 23 11
DEL PEAK 7(3Q13.31) WILD-TYPE 148 92 95 140

Figure S171.  Get High-res Image Gene #40: 'del_3q13.31' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_3q13.31' versus 'RPPA_CHIERARCHICAL'

P value = 0.0378 (Fisher's exact test), Q value = 0.14

Table S172.  Gene #40: 'del_3q13.31' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 54 60 154
DEL PEAK 7(3Q13.31) MUTATED 27 7 14 15
DEL PEAK 7(3Q13.31) WILD-TYPE 116 47 46 139

Figure S172.  Get High-res Image Gene #40: 'del_3q13.31' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_3q13.31' versus 'MRNASEQ_CNMF'

P value = 0.0421 (Fisher's exact test), Q value = 0.15

Table S173.  Gene #40: 'del_3q13.31' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 109 112
DEL PEAK 7(3Q13.31) MUTATED 5 16 21
DEL PEAK 7(3Q13.31) WILD-TYPE 74 93 91

Figure S173.  Get High-res Image Gene #40: 'del_3q13.31' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_4q22.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.0233 (Fisher's exact test), Q value = 0.1

Table S174.  Gene #41: 'del_4q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
DEL PEAK 8(4Q22.1) MUTATED 212 96 69
DEL PEAK 8(4Q22.1) WILD-TYPE 98 62 20

Figure S174.  Get High-res Image Gene #41: 'del_4q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_4q22.1' versus 'CN_CNMF'

P value = 0.00054 (Fisher's exact test), Q value = 0.0058

Table S175.  Gene #41: 'del_4q22.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
DEL PEAK 8(4Q22.1) MUTATED 185 85 124
DEL PEAK 8(4Q22.1) WILD-TYPE 57 45 83

Figure S175.  Get High-res Image Gene #41: 'del_4q22.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_4q34.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.00076 (Fisher's exact test), Q value = 0.0077

Table S176.  Gene #42: 'del_4q34.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
DEL PEAK 9(4Q34.3) MUTATED 226 102 77
DEL PEAK 9(4Q34.3) WILD-TYPE 84 56 12

Figure S176.  Get High-res Image Gene #42: 'del_4q34.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_4q34.3' versus 'MIR_CHIERARCHICAL'

P value = 0.0278 (Fisher's exact test), Q value = 0.11

Table S177.  Gene #42: 'del_4q34.3' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
DEL PEAK 9(4Q34.3) MUTATED 66 42 41 65 22 49 29 24 43 23
DEL PEAK 9(4Q34.3) WILD-TYPE 19 15 17 17 12 26 5 12 9 19

Figure S177.  Get High-res Image Gene #42: 'del_4q34.3' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_4q34.3' versus 'CN_CNMF'

P value = 0.0212 (Fisher's exact test), Q value = 0.094

Table S178.  Gene #42: 'del_4q34.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
DEL PEAK 9(4Q34.3) MUTATED 185 82 154
DEL PEAK 9(4Q34.3) WILD-TYPE 57 48 53

Figure S178.  Get High-res Image Gene #42: 'del_4q34.3' versus Molecular Subtype #5: 'CN_CNMF'

'del_4q34.3' versus 'MRNASEQ_CNMF'

P value = 0.0395 (Fisher's exact test), Q value = 0.14

Table S179.  Gene #42: 'del_4q34.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 109 112
DEL PEAK 9(4Q34.3) MUTATED 64 79 72
DEL PEAK 9(4Q34.3) WILD-TYPE 15 30 40

Figure S179.  Get High-res Image Gene #42: 'del_4q34.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_4q34.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.046 (Fisher's exact test), Q value = 0.16

Table S180.  Gene #42: 'del_4q34.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
DEL PEAK 9(4Q34.3) MUTATED 110 46 59
DEL PEAK 9(4Q34.3) WILD-TYPE 36 13 36

Figure S180.  Get High-res Image Gene #42: 'del_4q34.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_5q12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S181.  Gene #43: 'del_5q12.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
DEL PEAK 10(5Q12.1) MUTATED 165 46 144
DEL PEAK 10(5Q12.1) WILD-TYPE 77 84 63

Figure S181.  Get High-res Image Gene #43: 'del_5q12.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_5q12.1' versus 'METHLYATION_CNMF'

P value = 0.0361 (Fisher's exact test), Q value = 0.13

Table S182.  Gene #43: 'del_5q12.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
DEL PEAK 10(5Q12.1) MUTATED 73 51 108 116
DEL PEAK 10(5Q12.1) WILD-TYPE 40 47 79 54

Figure S182.  Get High-res Image Gene #43: 'del_5q12.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_5q13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S183.  Gene #44: 'del_5q13.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
DEL PEAK 11(5Q13.2) MUTATED 177 63 179
DEL PEAK 11(5Q13.2) WILD-TYPE 65 67 28

Figure S183.  Get High-res Image Gene #44: 'del_5q13.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_6q27' versus 'MRNA_CNMF'

P value = 0.0163 (Fisher's exact test), Q value = 0.079

Table S184.  Gene #45: 'del_6q27' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 112 118 151
DEL PEAK 12(6Q27) MUTATED 101 81 86 98
DEL PEAK 12(6Q27) WILD-TYPE 75 31 32 53

Figure S184.  Get High-res Image Gene #45: 'del_6q27' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_6q27' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S185.  Gene #45: 'del_6q27' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
DEL PEAK 12(6Q27) MUTATED 124 91 165
DEL PEAK 12(6Q27) WILD-TYPE 118 39 42

Figure S185.  Get High-res Image Gene #45: 'del_6q27' versus Molecular Subtype #5: 'CN_CNMF'

'del_6q27' versus 'METHLYATION_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.005

Table S186.  Gene #45: 'del_6q27' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
DEL PEAK 12(6Q27) MUTATED 66 66 144 99
DEL PEAK 12(6Q27) WILD-TYPE 47 32 43 71

Figure S186.  Get High-res Image Gene #45: 'del_6q27' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_6q27' versus 'MRNASEQ_CNMF'

P value = 0.00055 (Fisher's exact test), Q value = 0.0059

Table S187.  Gene #45: 'del_6q27' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 109 112
DEL PEAK 12(6Q27) MUTATED 57 52 78
DEL PEAK 12(6Q27) WILD-TYPE 22 57 34

Figure S187.  Get High-res Image Gene #45: 'del_6q27' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_6q27' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00183 (Fisher's exact test), Q value = 0.015

Table S188.  Gene #45: 'del_6q27' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
DEL PEAK 12(6Q27) MUTATED 92 26 69
DEL PEAK 12(6Q27) WILD-TYPE 54 33 26

Figure S188.  Get High-res Image Gene #45: 'del_6q27' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_6q27' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0258 (Fisher's exact test), Q value = 0.11

Table S189.  Gene #45: 'del_6q27' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
DEL PEAK 12(6Q27) MUTATED 79 43 96 72
DEL PEAK 12(6Q27) WILD-TYPE 26 28 69 34

Figure S189.  Get High-res Image Gene #45: 'del_6q27' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_7p22.2' versus 'MRNA_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.0028

Table S190.  Gene #46: 'del_7p22.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 112 118 151
DEL PEAK 13(7P22.2) MUTATED 82 48 32 81
DEL PEAK 13(7P22.2) WILD-TYPE 94 64 86 70

Figure S190.  Get High-res Image Gene #46: 'del_7p22.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_7p22.2' versus 'MIR_CHIERARCHICAL'

P value = 0.026 (Fisher's exact test), Q value = 0.11

Table S191.  Gene #46: 'del_7p22.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
DEL PEAK 13(7P22.2) MUTATED 36 30 24 34 15 28 10 20 18 28
DEL PEAK 13(7P22.2) WILD-TYPE 49 27 34 48 19 47 24 16 34 14

Figure S191.  Get High-res Image Gene #46: 'del_7p22.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_7p22.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S192.  Gene #46: 'del_7p22.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
DEL PEAK 13(7P22.2) MUTATED 87 35 131
DEL PEAK 13(7P22.2) WILD-TYPE 155 95 76

Figure S192.  Get High-res Image Gene #46: 'del_7p22.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_8p23.3' versus 'MRNA_CNMF'

P value = 0.00648 (Fisher's exact test), Q value = 0.04

Table S193.  Gene #47: 'del_8p23.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 112 118 151
DEL PEAK 14(8P23.3) MUTATED 111 76 70 117
DEL PEAK 14(8P23.3) WILD-TYPE 65 36 48 34

Figure S193.  Get High-res Image Gene #47: 'del_8p23.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_8p23.3' versus 'MIR_CHIERARCHICAL'

P value = 0.0112 (Fisher's exact test), Q value = 0.062

Table S194.  Gene #47: 'del_8p23.3' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
DEL PEAK 14(8P23.3) MUTATED 57 36 34 61 30 53 15 27 33 29
DEL PEAK 14(8P23.3) WILD-TYPE 28 21 24 21 4 22 19 9 19 13

Figure S194.  Get High-res Image Gene #47: 'del_8p23.3' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_8p23.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S195.  Gene #47: 'del_8p23.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
DEL PEAK 14(8P23.3) MUTATED 166 59 163
DEL PEAK 14(8P23.3) WILD-TYPE 76 71 44

Figure S195.  Get High-res Image Gene #47: 'del_8p23.3' versus Molecular Subtype #5: 'CN_CNMF'

'del_8p23.3' versus 'METHLYATION_CNMF'

P value = 0.0067 (Fisher's exact test), Q value = 0.041

Table S196.  Gene #47: 'del_8p23.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
DEL PEAK 14(8P23.3) MUTATED 86 59 113 123
DEL PEAK 14(8P23.3) WILD-TYPE 27 39 74 47

Figure S196.  Get High-res Image Gene #47: 'del_8p23.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_8p21.2' versus 'MRNA_CNMF'

P value = 0.00599 (Fisher's exact test), Q value = 0.038

Table S197.  Gene #48: 'del_8p21.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 112 118 151
DEL PEAK 15(8P21.2) MUTATED 115 83 74 120
DEL PEAK 15(8P21.2) WILD-TYPE 61 29 44 31

Figure S197.  Get High-res Image Gene #48: 'del_8p21.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_8p21.2' versus 'MIR_CHIERARCHICAL'

P value = 0.00559 (Fisher's exact test), Q value = 0.037

Table S198.  Gene #48: 'del_8p21.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
DEL PEAK 15(8P21.2) MUTATED 66 35 39 56 30 51 16 30 36 33
DEL PEAK 15(8P21.2) WILD-TYPE 19 22 19 26 4 24 18 6 16 9

Figure S198.  Get High-res Image Gene #48: 'del_8p21.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_8p21.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S199.  Gene #48: 'del_8p21.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
DEL PEAK 15(8P21.2) MUTATED 169 68 169
DEL PEAK 15(8P21.2) WILD-TYPE 73 62 38

Figure S199.  Get High-res Image Gene #48: 'del_8p21.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_8p21.2' versus 'METHLYATION_CNMF'

P value = 0.0135 (Fisher's exact test), Q value = 0.071

Table S200.  Gene #48: 'del_8p21.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
DEL PEAK 15(8P21.2) MUTATED 87 64 119 130
DEL PEAK 15(8P21.2) WILD-TYPE 26 34 68 40

Figure S200.  Get High-res Image Gene #48: 'del_8p21.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_9p24.3' versus 'MRNA_CNMF'

P value = 0.00076 (Fisher's exact test), Q value = 0.0077

Table S201.  Gene #49: 'del_9p24.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 112 118 151
DEL PEAK 16(9P24.3) MUTATED 90 61 48 49
DEL PEAK 16(9P24.3) WILD-TYPE 86 51 70 102

Figure S201.  Get High-res Image Gene #49: 'del_9p24.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_9p24.3' versus 'MRNA_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00069

Table S202.  Gene #49: 'del_9p24.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
DEL PEAK 16(9P24.3) MUTATED 120 69 59
DEL PEAK 16(9P24.3) WILD-TYPE 190 89 30

Figure S202.  Get High-res Image Gene #49: 'del_9p24.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_9p24.3' versus 'MIR_CHIERARCHICAL'

P value = 0.0143 (Fisher's exact test), Q value = 0.072

Table S203.  Gene #49: 'del_9p24.3' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
DEL PEAK 16(9P24.3) MUTATED 34 21 28 30 18 27 16 16 36 20
DEL PEAK 16(9P24.3) WILD-TYPE 51 36 30 52 16 48 18 20 16 22

Figure S203.  Get High-res Image Gene #49: 'del_9p24.3' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_9p24.3' versus 'CN_CNMF'

P value = 0.0117 (Fisher's exact test), Q value = 0.064

Table S204.  Gene #49: 'del_9p24.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
DEL PEAK 16(9P24.3) MUTATED 125 58 78
DEL PEAK 16(9P24.3) WILD-TYPE 117 72 129

Figure S204.  Get High-res Image Gene #49: 'del_9p24.3' versus Molecular Subtype #5: 'CN_CNMF'

'del_9p24.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S205.  Gene #49: 'del_9p24.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
DEL PEAK 16(9P24.3) MUTATED 57 57 58 85
DEL PEAK 16(9P24.3) WILD-TYPE 56 41 129 85

Figure S205.  Get High-res Image Gene #49: 'del_9p24.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_9p24.3' versus 'MRNASEQ_CNMF'

P value = 0.026 (Fisher's exact test), Q value = 0.11

Table S206.  Gene #49: 'del_9p24.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 109 112
DEL PEAK 16(9P24.3) MUTATED 26 57 53
DEL PEAK 16(9P24.3) WILD-TYPE 53 52 59

Figure S206.  Get High-res Image Gene #49: 'del_9p24.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_9p24.3' versus 'MIRSEQ_CNMF'

P value = 0.0207 (Fisher's exact test), Q value = 0.093

Table S207.  Gene #49: 'del_9p24.3' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 135 141 100
DEL PEAK 16(9P24.3) MUTATED 36 46 72 42
DEL PEAK 16(9P24.3) WILD-TYPE 35 89 69 58

Figure S207.  Get High-res Image Gene #49: 'del_9p24.3' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_9q34.13' versus 'MRNA_CHIERARCHICAL'

P value = 0.00092 (Fisher's exact test), Q value = 0.0086

Table S208.  Gene #50: 'del_9q34.13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
DEL PEAK 17(9Q34.13) MUTATED 185 79 66
DEL PEAK 17(9Q34.13) WILD-TYPE 125 79 23

Figure S208.  Get High-res Image Gene #50: 'del_9q34.13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_9q34.13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S209.  Gene #50: 'del_9q34.13' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
DEL PEAK 17(9Q34.13) MUTATED 180 65 97
DEL PEAK 17(9Q34.13) WILD-TYPE 62 65 110

Figure S209.  Get High-res Image Gene #50: 'del_9q34.13' versus Molecular Subtype #5: 'CN_CNMF'

'del_9q34.13' versus 'METHLYATION_CNMF'

P value = 0.00569 (Fisher's exact test), Q value = 0.037

Table S210.  Gene #50: 'del_9q34.13' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
DEL PEAK 17(9Q34.13) MUTATED 66 62 94 116
DEL PEAK 17(9Q34.13) WILD-TYPE 47 36 93 54

Figure S210.  Get High-res Image Gene #50: 'del_9q34.13' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_9q34.13' versus 'RPPA_CHIERARCHICAL'

P value = 0.0465 (Fisher's exact test), Q value = 0.16

Table S211.  Gene #50: 'del_9q34.13' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 54 60 154
DEL PEAK 17(9Q34.13) MUTATED 70 34 31 98
DEL PEAK 17(9Q34.13) WILD-TYPE 73 20 29 56

Figure S211.  Get High-res Image Gene #50: 'del_9q34.13' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_9q34.13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0085 (Fisher's exact test), Q value = 0.05

Table S212.  Gene #50: 'del_9q34.13' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
DEL PEAK 17(9Q34.13) MUTATED 82 46 54
DEL PEAK 17(9Q34.13) WILD-TYPE 64 13 41

Figure S212.  Get High-res Image Gene #50: 'del_9q34.13' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_10p15.3' versus 'MRNA_CNMF'

P value = 0.0466 (Fisher's exact test), Q value = 0.16

Table S213.  Gene #51: 'del_10p15.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 112 118 151
DEL PEAK 18(10P15.3) MUTATED 43 17 32 25
DEL PEAK 18(10P15.3) WILD-TYPE 133 95 86 126

Figure S213.  Get High-res Image Gene #51: 'del_10p15.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_10p15.3' versus 'CN_CNMF'

P value = 0.0183 (Fisher's exact test), Q value = 0.085

Table S214.  Gene #51: 'del_10p15.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
DEL PEAK 18(10P15.3) MUTATED 37 34 49
DEL PEAK 18(10P15.3) WILD-TYPE 205 96 158

Figure S214.  Get High-res Image Gene #51: 'del_10p15.3' versus Molecular Subtype #5: 'CN_CNMF'

'del_10p15.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0346 (Fisher's exact test), Q value = 0.13

Table S215.  Gene #51: 'del_10p15.3' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 5 2 2 4 5 4
DEL PEAK 18(10P15.3) MUTATED 0 0 2 1 0 1
DEL PEAK 18(10P15.3) WILD-TYPE 5 2 0 3 5 3

Figure S215.  Get High-res Image Gene #51: 'del_10p15.3' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q23.31' versus 'MRNA_CHIERARCHICAL'

P value = 0.0137 (Fisher's exact test), Q value = 0.071

Table S216.  Gene #52: 'del_10q23.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
DEL PEAK 19(10Q23.31) MUTATED 136 53 26
DEL PEAK 19(10Q23.31) WILD-TYPE 174 105 63

Figure S216.  Get High-res Image Gene #52: 'del_10q23.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_10q23.31' versus 'MIR_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.0037

Table S217.  Gene #52: 'del_10q23.31' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 131 243
DEL PEAK 19(10Q23.31) MUTATED 73 32 110
DEL PEAK 19(10Q23.31) WILD-TYPE 108 99 133

Figure S217.  Get High-res Image Gene #52: 'del_10q23.31' versus Molecular Subtype #3: 'MIR_CNMF'

'del_10q23.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S218.  Gene #52: 'del_10q23.31' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
DEL PEAK 19(10Q23.31) MUTATED 112 24 87
DEL PEAK 19(10Q23.31) WILD-TYPE 130 106 120

Figure S218.  Get High-res Image Gene #52: 'del_10q23.31' versus Molecular Subtype #5: 'CN_CNMF'

'del_10q23.31' versus 'METHLYATION_CNMF'

P value = 0.0351 (Fisher's exact test), Q value = 0.13

Table S219.  Gene #52: 'del_10q23.31' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
DEL PEAK 19(10Q23.31) MUTATED 48 27 70 76
DEL PEAK 19(10Q23.31) WILD-TYPE 65 71 117 94

Figure S219.  Get High-res Image Gene #52: 'del_10q23.31' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_10q23.31' versus 'MIRSEQ_CNMF'

P value = 0.0422 (Fisher's exact test), Q value = 0.15

Table S220.  Gene #52: 'del_10q23.31' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 135 141 100
DEL PEAK 19(10Q23.31) MUTATED 23 60 48 49
DEL PEAK 19(10Q23.31) WILD-TYPE 48 75 93 51

Figure S220.  Get High-res Image Gene #52: 'del_10q23.31' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_10q25.1' versus 'MRNA_CNMF'

P value = 0.00085 (Fisher's exact test), Q value = 0.0082

Table S221.  Gene #53: 'del_10q25.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 112 118 151
DEL PEAK 20(10Q25.1) MUTATED 74 31 46 79
DEL PEAK 20(10Q25.1) WILD-TYPE 102 81 72 72

Figure S221.  Get High-res Image Gene #53: 'del_10q25.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_10q25.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.0159 (Fisher's exact test), Q value = 0.078

Table S222.  Gene #53: 'del_10q25.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
DEL PEAK 20(10Q25.1) MUTATED 144 58 28
DEL PEAK 20(10Q25.1) WILD-TYPE 166 100 61

Figure S222.  Get High-res Image Gene #53: 'del_10q25.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_10q25.1' versus 'MIR_CNMF'

P value = 0.00661 (Fisher's exact test), Q value = 0.041

Table S223.  Gene #53: 'del_10q25.1' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 131 243
DEL PEAK 20(10Q25.1) MUTATED 80 39 112
DEL PEAK 20(10Q25.1) WILD-TYPE 101 92 131

Figure S223.  Get High-res Image Gene #53: 'del_10q25.1' versus Molecular Subtype #3: 'MIR_CNMF'

'del_10q25.1' versus 'MIR_CHIERARCHICAL'

P value = 0.0348 (Fisher's exact test), Q value = 0.13

Table S224.  Gene #53: 'del_10q25.1' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
DEL PEAK 20(10Q25.1) MUTATED 30 24 27 42 15 26 18 21 15 13
DEL PEAK 20(10Q25.1) WILD-TYPE 55 33 31 40 19 49 16 15 37 29

Figure S224.  Get High-res Image Gene #53: 'del_10q25.1' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_10q25.1' versus 'CN_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.0013

Table S225.  Gene #53: 'del_10q25.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
DEL PEAK 20(10Q25.1) MUTATED 110 33 96
DEL PEAK 20(10Q25.1) WILD-TYPE 132 97 111

Figure S225.  Get High-res Image Gene #53: 'del_10q25.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_10q25.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0472 (Fisher's exact test), Q value = 0.16

Table S226.  Gene #53: 'del_10q25.1' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 54 60 154
DEL PEAK 20(10Q25.1) MUTATED 49 29 28 71
DEL PEAK 20(10Q25.1) WILD-TYPE 94 25 32 83

Figure S226.  Get High-res Image Gene #53: 'del_10q25.1' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_10q25.1' versus 'MIRSEQ_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.0037

Table S227.  Gene #53: 'del_10q25.1' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 135 141 100
DEL PEAK 20(10Q25.1) MUTATED 19 67 50 55
DEL PEAK 20(10Q25.1) WILD-TYPE 52 68 91 45

Figure S227.  Get High-res Image Gene #53: 'del_10q25.1' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_11p15.5' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S228.  Gene #54: 'del_11p15.5' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
DEL PEAK 21(11P15.5) MUTATED 122 62 162
DEL PEAK 21(11P15.5) WILD-TYPE 120 68 45

Figure S228.  Get High-res Image Gene #54: 'del_11p15.5' versus Molecular Subtype #5: 'CN_CNMF'

'del_11p15.5' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00925 (Fisher's exact test), Q value = 0.053

Table S229.  Gene #54: 'del_11p15.5' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
DEL PEAK 21(11P15.5) MUTATED 76 38 91 56
DEL PEAK 21(11P15.5) WILD-TYPE 29 33 74 50

Figure S229.  Get High-res Image Gene #54: 'del_11p15.5' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0176 (Fisher's exact test), Q value = 0.083

Table S230.  Gene #54: 'del_11p15.5' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 5 2 2 4 5 4
DEL PEAK 21(11P15.5) MUTATED 0 0 1 2 1 4
DEL PEAK 21(11P15.5) WILD-TYPE 5 2 1 2 4 0

Figure S230.  Get High-res Image Gene #54: 'del_11p15.5' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11q25' versus 'CN_CNMF'

P value = 0.00606 (Fisher's exact test), Q value = 0.038

Table S231.  Gene #55: 'del_11q25' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
DEL PEAK 22(11Q25) MUTATED 102 36 63
DEL PEAK 22(11Q25) WILD-TYPE 140 94 144

Figure S231.  Get High-res Image Gene #55: 'del_11q25' versus Molecular Subtype #5: 'CN_CNMF'

'del_12q23.1' versus 'MRNA_CNMF'

P value = 0.0101 (Fisher's exact test), Q value = 0.057

Table S232.  Gene #56: 'del_12q23.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 112 118 151
DEL PEAK 23(12Q23.1) MUTATED 44 46 42 60
DEL PEAK 23(12Q23.1) WILD-TYPE 132 66 76 91

Figure S232.  Get High-res Image Gene #56: 'del_12q23.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_12q23.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00413 (Fisher's exact test), Q value = 0.029

Table S233.  Gene #56: 'del_12q23.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
DEL PEAK 23(12Q23.1) MUTATED 104 68 20
DEL PEAK 23(12Q23.1) WILD-TYPE 206 90 69

Figure S233.  Get High-res Image Gene #56: 'del_12q23.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_12q23.1' versus 'MIR_CNMF'

P value = 0.0207 (Fisher's exact test), Q value = 0.093

Table S234.  Gene #56: 'del_12q23.1' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 131 243
DEL PEAK 23(12Q23.1) MUTATED 72 52 69
DEL PEAK 23(12Q23.1) WILD-TYPE 109 79 174

Figure S234.  Get High-res Image Gene #56: 'del_12q23.1' versus Molecular Subtype #3: 'MIR_CNMF'

'del_12q23.1' versus 'MIR_CHIERARCHICAL'

P value = 0.0462 (Fisher's exact test), Q value = 0.16

Table S235.  Gene #56: 'del_12q23.1' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
DEL PEAK 23(12Q23.1) MUTATED 31 23 15 25 14 29 6 18 13 19
DEL PEAK 23(12Q23.1) WILD-TYPE 54 34 43 57 20 46 28 18 39 23

Figure S235.  Get High-res Image Gene #56: 'del_12q23.1' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_12q23.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S236.  Gene #56: 'del_12q23.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
DEL PEAK 23(12Q23.1) MUTATED 58 34 106
DEL PEAK 23(12Q23.1) WILD-TYPE 184 96 101

Figure S236.  Get High-res Image Gene #56: 'del_12q23.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_12q23.1' versus 'METHLYATION_CNMF'

P value = 0.0185 (Fisher's exact test), Q value = 0.085

Table S237.  Gene #56: 'del_12q23.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
DEL PEAK 23(12Q23.1) MUTATED 39 23 78 55
DEL PEAK 23(12Q23.1) WILD-TYPE 74 75 109 115

Figure S237.  Get High-res Image Gene #56: 'del_12q23.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_12q23.1' versus 'RPPA_CNMF'

P value = 0.012 (Fisher's exact test), Q value = 0.065

Table S238.  Gene #56: 'del_12q23.1' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 189 76
DEL PEAK 23(12Q23.1) MUTATED 57 51 33
DEL PEAK 23(12Q23.1) WILD-TYPE 89 138 43

Figure S238.  Get High-res Image Gene #56: 'del_12q23.1' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_12q23.1' versus 'MRNASEQ_CNMF'

P value = 0.0358 (Fisher's exact test), Q value = 0.13

Table S239.  Gene #56: 'del_12q23.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 109 112
DEL PEAK 23(12Q23.1) MUTATED 25 27 46
DEL PEAK 23(12Q23.1) WILD-TYPE 54 82 66

Figure S239.  Get High-res Image Gene #56: 'del_12q23.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_12q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00169 (Fisher's exact test), Q value = 0.014

Table S240.  Gene #56: 'del_12q23.1' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
DEL PEAK 23(12Q23.1) MUTATED 46 10 42
DEL PEAK 23(12Q23.1) WILD-TYPE 100 49 53

Figure S240.  Get High-res Image Gene #56: 'del_12q23.1' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_12q23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0409 (Fisher's exact test), Q value = 0.15

Table S241.  Gene #56: 'del_12q23.1' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
DEL PEAK 23(12Q23.1) MUTATED 43 15 60 34
DEL PEAK 23(12Q23.1) WILD-TYPE 62 56 105 72

Figure S241.  Get High-res Image Gene #56: 'del_12q23.1' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_12q24.33' versus 'MRNA_CNMF'

P value = 0.00183 (Fisher's exact test), Q value = 0.015

Table S242.  Gene #57: 'del_12q24.33' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 112 118 151
DEL PEAK 24(12Q24.33) MUTATED 47 45 53 67
DEL PEAK 24(12Q24.33) WILD-TYPE 129 67 65 84

Figure S242.  Get High-res Image Gene #57: 'del_12q24.33' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_12q24.33' versus 'MIR_CHIERARCHICAL'

P value = 0.014 (Fisher's exact test), Q value = 0.072

Table S243.  Gene #57: 'del_12q24.33' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
DEL PEAK 24(12Q24.33) MUTATED 34 21 19 35 11 34 7 19 11 21
DEL PEAK 24(12Q24.33) WILD-TYPE 51 36 39 47 23 41 27 17 41 21

Figure S243.  Get High-res Image Gene #57: 'del_12q24.33' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_12q24.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S244.  Gene #57: 'del_12q24.33' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
DEL PEAK 24(12Q24.33) MUTATED 66 37 117
DEL PEAK 24(12Q24.33) WILD-TYPE 176 93 90

Figure S244.  Get High-res Image Gene #57: 'del_12q24.33' versus Molecular Subtype #5: 'CN_CNMF'

'del_12q24.33' versus 'METHLYATION_CNMF'

P value = 0.00876 (Fisher's exact test), Q value = 0.051

Table S245.  Gene #57: 'del_12q24.33' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
DEL PEAK 24(12Q24.33) MUTATED 43 31 89 54
DEL PEAK 24(12Q24.33) WILD-TYPE 70 67 98 116

Figure S245.  Get High-res Image Gene #57: 'del_12q24.33' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_12q24.33' versus 'MRNASEQ_CNMF'

P value = 0.0443 (Fisher's exact test), Q value = 0.15

Table S246.  Gene #57: 'del_12q24.33' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 109 112
DEL PEAK 24(12Q24.33) MUTATED 33 29 45
DEL PEAK 24(12Q24.33) WILD-TYPE 46 80 67

Figure S246.  Get High-res Image Gene #57: 'del_12q24.33' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_12q24.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0263 (Fisher's exact test), Q value = 0.11

Table S247.  Gene #57: 'del_12q24.33' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
DEL PEAK 24(12Q24.33) MUTATED 53 13 41
DEL PEAK 24(12Q24.33) WILD-TYPE 93 46 54

Figure S247.  Get High-res Image Gene #57: 'del_12q24.33' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_12q24.33' versus 'MIRSEQ_CNMF'

P value = 0.0129 (Fisher's exact test), Q value = 0.069

Table S248.  Gene #57: 'del_12q24.33' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 135 141 100
DEL PEAK 24(12Q24.33) MUTATED 25 64 40 38
DEL PEAK 24(12Q24.33) WILD-TYPE 46 71 101 62

Figure S248.  Get High-res Image Gene #57: 'del_12q24.33' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_12q24.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00477 (Fisher's exact test), Q value = 0.032

Table S249.  Gene #57: 'del_12q24.33' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
DEL PEAK 24(12Q24.33) MUTATED 54 20 60 33
DEL PEAK 24(12Q24.33) WILD-TYPE 51 51 105 73

Figure S249.  Get High-res Image Gene #57: 'del_12q24.33' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MRNA_CNMF'

P value = 0.014 (Fisher's exact test), Q value = 0.072

Table S250.  Gene #58: 'del_13q14.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 112 118 151
DEL PEAK 25(13Q14.2) MUTATED 114 60 68 108
DEL PEAK 25(13Q14.2) WILD-TYPE 62 52 50 43

Figure S250.  Get High-res Image Gene #58: 'del_13q14.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_13q14.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.0166 (Fisher's exact test), Q value = 0.08

Table S251.  Gene #58: 'del_13q14.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
DEL PEAK 25(13Q14.2) MUTATED 211 88 51
DEL PEAK 25(13Q14.2) WILD-TYPE 99 70 38

Figure S251.  Get High-res Image Gene #58: 'del_13q14.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_13q14.2' versus 'MIR_CHIERARCHICAL'

P value = 0.0427 (Fisher's exact test), Q value = 0.15

Table S252.  Gene #58: 'del_13q14.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
DEL PEAK 25(13Q14.2) MUTATED 52 37 42 52 26 37 16 27 32 29
DEL PEAK 25(13Q14.2) WILD-TYPE 33 20 16 30 8 38 18 9 20 13

Figure S252.  Get High-res Image Gene #58: 'del_13q14.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_13q14.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S253.  Gene #58: 'del_13q14.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
DEL PEAK 25(13Q14.2) MUTATED 149 60 155
DEL PEAK 25(13Q14.2) WILD-TYPE 93 70 52

Figure S253.  Get High-res Image Gene #58: 'del_13q14.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_13q14.2' versus 'RPPA_CNMF'

P value = 0.00124 (Fisher's exact test), Q value = 0.011

Table S254.  Gene #58: 'del_13q14.2' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 189 76
DEL PEAK 25(13Q14.2) MUTATED 76 135 45
DEL PEAK 25(13Q14.2) WILD-TYPE 70 54 31

Figure S254.  Get High-res Image Gene #58: 'del_13q14.2' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_13q14.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00281 (Fisher's exact test), Q value = 0.021

Table S255.  Gene #58: 'del_13q14.2' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 54 60 154
DEL PEAK 25(13Q14.2) MUTATED 73 32 42 109
DEL PEAK 25(13Q14.2) WILD-TYPE 70 22 18 45

Figure S255.  Get High-res Image Gene #58: 'del_13q14.2' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_13q14.2' versus 'MRNASEQ_CNMF'

P value = 0.0165 (Fisher's exact test), Q value = 0.08

Table S256.  Gene #58: 'del_13q14.2' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 109 112
DEL PEAK 25(13Q14.2) MUTATED 55 77 60
DEL PEAK 25(13Q14.2) WILD-TYPE 24 32 52

Figure S256.  Get High-res Image Gene #58: 'del_13q14.2' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_13q14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.044 (Fisher's exact test), Q value = 0.15

Table S257.  Gene #58: 'del_13q14.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
DEL PEAK 25(13Q14.2) MUTATED 101 40 51
DEL PEAK 25(13Q14.2) WILD-TYPE 45 19 44

Figure S257.  Get High-res Image Gene #58: 'del_13q14.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_CNMF'

P value = 0.0142 (Fisher's exact test), Q value = 0.072

Table S258.  Gene #58: 'del_13q14.2' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 135 141 100
DEL PEAK 25(13Q14.2) MUTATED 33 86 89 71
DEL PEAK 25(13Q14.2) WILD-TYPE 38 49 52 29

Figure S258.  Get High-res Image Gene #58: 'del_13q14.2' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_14q23.3' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00031

Table S259.  Gene #59: 'del_14q23.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
DEL PEAK 26(14Q23.3) MUTATED 153 51 101
DEL PEAK 26(14Q23.3) WILD-TYPE 89 79 106

Figure S259.  Get High-res Image Gene #59: 'del_14q23.3' versus Molecular Subtype #5: 'CN_CNMF'

'del_15q11.2' versus 'MRNA_CNMF'

P value = 0.00099 (Fisher's exact test), Q value = 0.0092

Table S260.  Gene #60: 'del_15q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 112 118 151
DEL PEAK 27(15Q11.2) MUTATED 111 53 47 80
DEL PEAK 27(15Q11.2) WILD-TYPE 65 59 71 71

Figure S260.  Get High-res Image Gene #60: 'del_15q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_15q11.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.0237 (Fisher's exact test), Q value = 0.1

Table S261.  Gene #60: 'del_15q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
DEL PEAK 27(15Q11.2) MUTATED 164 71 56
DEL PEAK 27(15Q11.2) WILD-TYPE 146 87 33

Figure S261.  Get High-res Image Gene #60: 'del_15q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_15q11.2' versus 'MIR_CNMF'

P value = 0.00809 (Fisher's exact test), Q value = 0.048

Table S262.  Gene #60: 'del_15q11.2' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 131 243
DEL PEAK 27(15Q11.2) MUTATED 95 54 141
DEL PEAK 27(15Q11.2) WILD-TYPE 86 77 102

Figure S262.  Get High-res Image Gene #60: 'del_15q11.2' versus Molecular Subtype #3: 'MIR_CNMF'

'del_15q11.2' versus 'MIR_CHIERARCHICAL'

P value = 0.00809 (Fisher's exact test), Q value = 0.048

Table S263.  Gene #60: 'del_15q11.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
DEL PEAK 27(15Q11.2) MUTATED 36 28 36 40 19 43 23 21 32 12
DEL PEAK 27(15Q11.2) WILD-TYPE 49 29 22 42 15 32 11 15 20 30

Figure S263.  Get High-res Image Gene #60: 'del_15q11.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_15q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S264.  Gene #60: 'del_15q11.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
DEL PEAK 27(15Q11.2) MUTATED 184 42 74
DEL PEAK 27(15Q11.2) WILD-TYPE 58 88 133

Figure S264.  Get High-res Image Gene #60: 'del_15q11.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_15q11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S265.  Gene #60: 'del_15q11.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
DEL PEAK 27(15Q11.2) MUTATED 67 58 64 108
DEL PEAK 27(15Q11.2) WILD-TYPE 46 40 123 62

Figure S265.  Get High-res Image Gene #60: 'del_15q11.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_15q11.2' versus 'MRNASEQ_CNMF'

P value = 0.00077 (Fisher's exact test), Q value = 0.0077

Table S266.  Gene #60: 'del_15q11.2' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 109 112
DEL PEAK 27(15Q11.2) MUTATED 29 70 54
DEL PEAK 27(15Q11.2) WILD-TYPE 50 39 58

Figure S266.  Get High-res Image Gene #60: 'del_15q11.2' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_15q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00983 (Fisher's exact test), Q value = 0.056

Table S267.  Gene #60: 'del_15q11.2' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
DEL PEAK 27(15Q11.2) MUTATED 43 40 102 58
DEL PEAK 27(15Q11.2) WILD-TYPE 62 31 63 48

Figure S267.  Get High-res Image Gene #60: 'del_15q11.2' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_15q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.047 (Fisher's exact test), Q value = 0.16

Table S268.  Gene #60: 'del_15q11.2' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 6 6 5 5
DEL PEAK 27(15Q11.2) MUTATED 5 4 0 2
DEL PEAK 27(15Q11.2) WILD-TYPE 1 2 5 3

Figure S268.  Get High-res Image Gene #60: 'del_15q11.2' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'del_15q15.1' versus 'MRNA_CNMF'

P value = 0.00058 (Fisher's exact test), Q value = 0.0061

Table S269.  Gene #61: 'del_15q15.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 112 118 151
DEL PEAK 28(15Q15.1) MUTATED 126 68 57 101
DEL PEAK 28(15Q15.1) WILD-TYPE 50 44 61 50

Figure S269.  Get High-res Image Gene #61: 'del_15q15.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_15q15.1' versus 'MIR_CHIERARCHICAL'

P value = 0.0032 (Fisher's exact test), Q value = 0.023

Table S270.  Gene #61: 'del_15q15.1' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
DEL PEAK 28(15Q15.1) MUTATED 43 32 42 51 23 52 23 26 41 18
DEL PEAK 28(15Q15.1) WILD-TYPE 42 25 16 31 11 23 11 10 11 24

Figure S270.  Get High-res Image Gene #61: 'del_15q15.1' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_15q15.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S271.  Gene #61: 'del_15q15.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
DEL PEAK 28(15Q15.1) MUTATED 201 48 114
DEL PEAK 28(15Q15.1) WILD-TYPE 41 82 93

Figure S271.  Get High-res Image Gene #61: 'del_15q15.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_15q15.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S272.  Gene #61: 'del_15q15.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
DEL PEAK 28(15Q15.1) MUTATED 77 67 89 127
DEL PEAK 28(15Q15.1) WILD-TYPE 36 31 98 43

Figure S272.  Get High-res Image Gene #61: 'del_15q15.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_15q15.1' versus 'MRNASEQ_CNMF'

P value = 0.0241 (Fisher's exact test), Q value = 0.1

Table S273.  Gene #61: 'del_15q15.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 109 112
DEL PEAK 28(15Q15.1) MUTATED 42 79 70
DEL PEAK 28(15Q15.1) WILD-TYPE 37 30 42

Figure S273.  Get High-res Image Gene #61: 'del_15q15.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_15q15.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00208 (Fisher's exact test), Q value = 0.017

Table S274.  Gene #61: 'del_15q15.1' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
DEL PEAK 28(15Q15.1) MUTATED 58 48 124 61
DEL PEAK 28(15Q15.1) WILD-TYPE 47 23 41 45

Figure S274.  Get High-res Image Gene #61: 'del_15q15.1' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_16p13.3' versus 'MIR_CHIERARCHICAL'

P value = 0.0303 (Fisher's exact test), Q value = 0.12

Table S275.  Gene #62: 'del_16p13.3' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
DEL PEAK 29(16P13.3) MUTATED 42 29 25 45 21 43 21 29 25 19
DEL PEAK 29(16P13.3) WILD-TYPE 43 28 33 37 13 32 13 7 27 23

Figure S275.  Get High-res Image Gene #62: 'del_16p13.3' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_16p13.3' versus 'CN_CNMF'

P value = 0.00492 (Fisher's exact test), Q value = 0.033

Table S276.  Gene #62: 'del_16p13.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
DEL PEAK 29(16P13.3) MUTATED 145 55 113
DEL PEAK 29(16P13.3) WILD-TYPE 97 75 94

Figure S276.  Get High-res Image Gene #62: 'del_16p13.3' versus Molecular Subtype #5: 'CN_CNMF'

'del_16p13.3' versus 'RPPA_CNMF'

P value = 0.0417 (Fisher's exact test), Q value = 0.15

Table S277.  Gene #62: 'del_16p13.3' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 189 76
DEL PEAK 29(16P13.3) MUTATED 85 104 31
DEL PEAK 29(16P13.3) WILD-TYPE 61 85 45

Figure S277.  Get High-res Image Gene #62: 'del_16p13.3' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_16q22.1' versus 'MIR_CNMF'

P value = 0.0393 (Fisher's exact test), Q value = 0.14

Table S278.  Gene #63: 'del_16q22.1' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 131 243
DEL PEAK 30(16Q22.1) MUTATED 147 94 201
DEL PEAK 30(16Q22.1) WILD-TYPE 34 37 42

Figure S278.  Get High-res Image Gene #63: 'del_16q22.1' versus Molecular Subtype #3: 'MIR_CNMF'

'del_16q22.1' versus 'CN_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.0044

Table S279.  Gene #63: 'del_16q22.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
DEL PEAK 30(16Q22.1) MUTATED 205 87 169
DEL PEAK 30(16Q22.1) WILD-TYPE 37 43 38

Figure S279.  Get High-res Image Gene #63: 'del_16q22.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_16q22.1' versus 'METHLYATION_CNMF'

P value = 0.00151 (Fisher's exact test), Q value = 0.013

Table S280.  Gene #63: 'del_16q22.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
DEL PEAK 30(16Q22.1) MUTATED 99 79 132 142
DEL PEAK 30(16Q22.1) WILD-TYPE 14 19 55 28

Figure S280.  Get High-res Image Gene #63: 'del_16q22.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_16q22.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0499 (Fisher's exact test), Q value = 0.16

Table S281.  Gene #63: 'del_16q22.1' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 54 60 154
DEL PEAK 30(16Q22.1) MUTATED 108 45 54 115
DEL PEAK 30(16Q22.1) WILD-TYPE 35 9 6 39

Figure S281.  Get High-res Image Gene #63: 'del_16q22.1' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_16q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0464 (Fisher's exact test), Q value = 0.16

Table S282.  Gene #63: 'del_16q22.1' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
DEL PEAK 30(16Q22.1) MUTATED 89 50 140 83
DEL PEAK 30(16Q22.1) WILD-TYPE 16 21 25 23

Figure S282.  Get High-res Image Gene #63: 'del_16q22.1' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_16q23.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S283.  Gene #64: 'del_16q23.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
DEL PEAK 31(16Q23.1) MUTATED 205 81 166
DEL PEAK 31(16Q23.1) WILD-TYPE 37 49 41

Figure S283.  Get High-res Image Gene #64: 'del_16q23.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_16q23.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S284.  Gene #64: 'del_16q23.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
DEL PEAK 31(16Q23.1) MUTATED 103 77 125 138
DEL PEAK 31(16Q23.1) WILD-TYPE 10 21 62 32

Figure S284.  Get High-res Image Gene #64: 'del_16q23.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_16q23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0478 (Fisher's exact test), Q value = 0.16

Table S285.  Gene #64: 'del_16q23.1' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
DEL PEAK 31(16Q23.1) MUTATED 87 51 140 79
DEL PEAK 31(16Q23.1) WILD-TYPE 18 20 25 27

Figure S285.  Get High-res Image Gene #64: 'del_16q23.1' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_17q11.2' versus 'CN_CNMF'

P value = 0.0196 (Fisher's exact test), Q value = 0.089

Table S286.  Gene #66: 'del_17q11.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
DEL PEAK 33(17Q11.2) MUTATED 188 103 181
DEL PEAK 33(17Q11.2) WILD-TYPE 54 27 26

Figure S286.  Get High-res Image Gene #66: 'del_17q11.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_18q23' versus 'CN_CNMF'

P value = 0.00127 (Fisher's exact test), Q value = 0.011

Table S287.  Gene #67: 'del_18q23' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
DEL PEAK 34(18Q23) MUTATED 147 78 156
DEL PEAK 34(18Q23) WILD-TYPE 95 52 51

Figure S287.  Get High-res Image Gene #67: 'del_18q23' versus Molecular Subtype #5: 'CN_CNMF'

'del_18q23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0455 (Fisher's exact test), Q value = 0.15

Table S288.  Gene #67: 'del_18q23' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
DEL PEAK 34(18Q23) MUTATED 86 45 65
DEL PEAK 34(18Q23) WILD-TYPE 60 14 30

Figure S288.  Get High-res Image Gene #67: 'del_18q23' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MRNA_CNMF'

P value = 0.0376 (Fisher's exact test), Q value = 0.14

Table S289.  Gene #68: 'del_19p13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 112 118 151
DEL PEAK 35(19P13.3) MUTATED 164 100 100 127
DEL PEAK 35(19P13.3) WILD-TYPE 12 12 18 24

Figure S289.  Get High-res Image Gene #68: 'del_19p13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_19p13.3' versus 'CN_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.0037

Table S290.  Gene #68: 'del_19p13.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
DEL PEAK 35(19P13.3) MUTATED 227 104 181
DEL PEAK 35(19P13.3) WILD-TYPE 15 26 26

Figure S290.  Get High-res Image Gene #68: 'del_19p13.3' versus Molecular Subtype #5: 'CN_CNMF'

'del_19p13.3' versus 'METHLYATION_CNMF'

P value = 0.0069 (Fisher's exact test), Q value = 0.042

Table S291.  Gene #68: 'del_19p13.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
DEL PEAK 35(19P13.3) MUTATED 104 91 152 154
DEL PEAK 35(19P13.3) WILD-TYPE 9 7 35 16

Figure S291.  Get High-res Image Gene #68: 'del_19p13.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_19p13.3' versus 'RPPA_CNMF'

P value = 0.00406 (Fisher's exact test), Q value = 0.029

Table S292.  Gene #68: 'del_19p13.3' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 189 76
DEL PEAK 35(19P13.3) MUTATED 129 175 59
DEL PEAK 35(19P13.3) WILD-TYPE 17 14 17

Figure S292.  Get High-res Image Gene #68: 'del_19p13.3' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_19q13.33' versus 'MRNA_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.004

Table S293.  Gene #69: 'del_19q13.33' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 112 118 151
DEL PEAK 36(19Q13.33) MUTATED 102 39 69 80
DEL PEAK 36(19Q13.33) WILD-TYPE 74 73 49 71

Figure S293.  Get High-res Image Gene #69: 'del_19q13.33' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_19q13.33' versus 'MRNA_CHIERARCHICAL'

P value = 0.00241 (Fisher's exact test), Q value = 0.019

Table S294.  Gene #69: 'del_19q13.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
DEL PEAK 36(19Q13.33) MUTATED 178 64 48
DEL PEAK 36(19Q13.33) WILD-TYPE 132 94 41

Figure S294.  Get High-res Image Gene #69: 'del_19q13.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_19q13.33' versus 'MIR_CHIERARCHICAL'

P value = 0.0205 (Fisher's exact test), Q value = 0.092

Table S295.  Gene #69: 'del_19q13.33' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
DEL PEAK 36(19Q13.33) MUTATED 44 35 36 50 10 32 18 16 23 25
DEL PEAK 36(19Q13.33) WILD-TYPE 41 22 22 32 24 43 16 20 29 17

Figure S295.  Get High-res Image Gene #69: 'del_19q13.33' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_19q13.33' versus 'METHLYATION_CNMF'

P value = 0.0237 (Fisher's exact test), Q value = 0.1

Table S296.  Gene #69: 'del_19q13.33' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
DEL PEAK 36(19Q13.33) MUTATED 57 51 83 103
DEL PEAK 36(19Q13.33) WILD-TYPE 56 47 104 67

Figure S296.  Get High-res Image Gene #69: 'del_19q13.33' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_19q13.33' versus 'RPPA_CHIERARCHICAL'

P value = 0.033 (Fisher's exact test), Q value = 0.13

Table S297.  Gene #69: 'del_19q13.33' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 54 60 154
DEL PEAK 36(19Q13.33) MUTATED 59 33 35 74
DEL PEAK 36(19Q13.33) WILD-TYPE 84 21 25 80

Figure S297.  Get High-res Image Gene #69: 'del_19q13.33' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_19q13.33' versus 'MRNASEQ_CNMF'

P value = 0.015 (Fisher's exact test), Q value = 0.075

Table S298.  Gene #69: 'del_19q13.33' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 109 112
DEL PEAK 36(19Q13.33) MUTATED 39 63 43
DEL PEAK 36(19Q13.33) WILD-TYPE 40 46 69

Figure S298.  Get High-res Image Gene #69: 'del_19q13.33' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_19q13.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0163 (Fisher's exact test), Q value = 0.079

Table S299.  Gene #69: 'del_19q13.33' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
DEL PEAK 36(19Q13.33) MUTATED 71 37 37
DEL PEAK 36(19Q13.33) WILD-TYPE 75 22 58

Figure S299.  Get High-res Image Gene #69: 'del_19q13.33' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_19q13.43' versus 'MRNA_CNMF'

P value = 0.0221 (Fisher's exact test), Q value = 0.097

Table S300.  Gene #70: 'del_19q13.43' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 112 118 151
DEL PEAK 37(19Q13.43) MUTATED 95 41 62 78
DEL PEAK 37(19Q13.43) WILD-TYPE 81 71 56 73

Figure S300.  Get High-res Image Gene #70: 'del_19q13.43' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_19q13.43' versus 'CN_CNMF'

P value = 0.00633 (Fisher's exact test), Q value = 0.04

Table S301.  Gene #70: 'del_19q13.43' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
DEL PEAK 37(19Q13.43) MUTATED 136 64 85
DEL PEAK 37(19Q13.43) WILD-TYPE 106 66 122

Figure S301.  Get High-res Image Gene #70: 'del_19q13.43' versus Molecular Subtype #5: 'CN_CNMF'

'del_19q13.43' versus 'METHLYATION_CNMF'

P value = 0.0412 (Fisher's exact test), Q value = 0.15

Table S302.  Gene #70: 'del_19q13.43' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
DEL PEAK 37(19Q13.43) MUTATED 49 50 83 98
DEL PEAK 37(19Q13.43) WILD-TYPE 64 48 104 72

Figure S302.  Get High-res Image Gene #70: 'del_19q13.43' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_21q22.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.0417 (Fisher's exact test), Q value = 0.15

Table S303.  Gene #71: 'del_21q22.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
DEL PEAK 38(21Q22.3) MUTATED 117 58 46
DEL PEAK 38(21Q22.3) WILD-TYPE 193 100 43

Figure S303.  Get High-res Image Gene #71: 'del_21q22.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_22q13.32' versus 'MRNA_CNMF'

P value = 0.0183 (Fisher's exact test), Q value = 0.085

Table S304.  Gene #72: 'del_22q13.32' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 112 118 151
DEL PEAK 39(22Q13.32) MUTATED 164 94 98 128
DEL PEAK 39(22Q13.32) WILD-TYPE 12 18 20 23

Figure S304.  Get High-res Image Gene #72: 'del_22q13.32' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_22q13.32' versus 'MIR_CNMF'

P value = 0.00267 (Fisher's exact test), Q value = 0.02

Table S305.  Gene #72: 'del_22q13.32' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 181 131 243
DEL PEAK 39(22Q13.32) MUTATED 158 103 222
DEL PEAK 39(22Q13.32) WILD-TYPE 23 28 21

Figure S305.  Get High-res Image Gene #72: 'del_22q13.32' versus Molecular Subtype #3: 'MIR_CNMF'

'del_22q13.32' versus 'CN_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.0017

Table S306.  Gene #72: 'del_22q13.32' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 242 130 207
DEL PEAK 39(22Q13.32) MUTATED 222 98 184
DEL PEAK 39(22Q13.32) WILD-TYPE 20 32 23

Figure S306.  Get High-res Image Gene #72: 'del_22q13.32' versus Molecular Subtype #5: 'CN_CNMF'

'del_22q13.32' versus 'METHLYATION_CNMF'

P value = 0.00495 (Fisher's exact test), Q value = 0.033

Table S307.  Gene #72: 'del_22q13.32' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 98 187 170
DEL PEAK 39(22Q13.32) MUTATED 101 91 149 153
DEL PEAK 39(22Q13.32) WILD-TYPE 12 7 38 17

Figure S307.  Get High-res Image Gene #72: 'del_22q13.32' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_22q13.32' versus 'RPPA_CNMF'

P value = 0.0263 (Fisher's exact test), Q value = 0.11

Table S308.  Gene #72: 'del_22q13.32' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 189 76
DEL PEAK 39(22Q13.32) MUTATED 124 172 60
DEL PEAK 39(22Q13.32) WILD-TYPE 22 17 16

Figure S308.  Get High-res Image Gene #72: 'del_22q13.32' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_22q13.32' versus 'RPPA_CHIERARCHICAL'

P value = 0.0264 (Fisher's exact test), Q value = 0.11

Table S309.  Gene #72: 'del_22q13.32' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 54 60 154
DEL PEAK 39(22Q13.32) MUTATED 115 46 53 142
DEL PEAK 39(22Q13.32) WILD-TYPE 28 8 7 12

Figure S309.  Get High-res Image Gene #72: 'del_22q13.32' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_22q13.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0233 (Fisher's exact test), Q value = 0.1

Table S310.  Gene #72: 'del_22q13.32' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
DEL PEAK 39(22Q13.32) MUTATED 122 57 81
DEL PEAK 39(22Q13.32) WILD-TYPE 24 2 14

Figure S310.  Get High-res Image Gene #72: 'del_22q13.32' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.32' versus 'MIRSEQ_CNMF'

P value = 0.0389 (Fisher's exact test), Q value = 0.14

Table S311.  Gene #72: 'del_22q13.32' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 135 141 100
DEL PEAK 39(22Q13.32) MUTATED 54 120 126 90
DEL PEAK 39(22Q13.32) WILD-TYPE 17 15 15 10

Figure S311.  Get High-res Image Gene #72: 'del_22q13.32' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_xp21.1' versus 'MIRSEQ_CNMF'

P value = 0.0391 (Fisher's exact test), Q value = 0.14

Table S312.  Gene #73: 'del_xp21.1' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 135 141 100
DEL PEAK 40(XP21.1) MUTATED 38 83 87 74
DEL PEAK 40(XP21.1) WILD-TYPE 33 52 54 26

Figure S312.  Get High-res Image Gene #73: 'del_xp21.1' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

Methods & Data
Input

  • Copy number data file = all_lesions.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/OV-TP/22534546/transformed.cor.cli.txt

  • Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/OV-TP/22555032/OV-TP.transferedmergedcluster.txt

  • Number of patients = 579

  • Number of significantly focal cnvs = 73

  • Number of molecular subtypes = 14

  • Exclude genes that fewer than K tumors have alterations, 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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