Correlation between copy number variation genes (focal events) and molecular subtypes
Lung Adenocarcinoma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C1N015F7
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1N015F7
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 74 focal events and 12 molecular subtypes across 515 patients, 301 significant findings detected with P value < 0.05 and Q value < 0.25.

  • amp_1p34.3 cnv correlated to 'CN_CNMF'.

  • amp_1p22.3 cnv correlated to 'CN_CNMF'.

  • amp_1q21.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • amp_3q26.2 cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_4q12 cnv correlated to 'CN_CNMF'.

  • amp_5p15.33 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_5p13.1 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_6p21.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • amp_7p11.2 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_7q31.2 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_8p11.23 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • amp_8p11.21 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_8q11.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_8q24.21 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_10p15.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_11q13.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • amp_12q14.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_12q15 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_13q33.3 cnv correlated to 'METHLYATION_CNMF'.

  • amp_14q13.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_16p11.2 cnv correlated to 'CN_CNMF'.

  • amp_17q12 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_17q23.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_18q11.2 cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_19q12 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • amp_22q11.22 cnv correlated to 'CN_CNMF'.

  • amp_xq28 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_1p36.13 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_1p13.1 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_2q22.1 cnv correlated to 'CN_CNMF'.

  • del_3p26.2 cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_3p21.31 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_3q29 cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_4p16.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_4q34.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_5q12.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_5q31.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_6q22.31 cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • del_6q26 cnv correlated to 'CN_CNMF'.

  • del_8p23.2 cnv correlated to 'CN_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_8p11.21 cnv correlated to 'CN_CNMF'.

  • del_9p23 cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

  • del_9p21.3 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_9q21.11 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_10p15.3 cnv correlated to 'CN_CNMF'.

  • del_10q26.3 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_11p15.5 cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • del_11q23.2 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • del_11q25 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • del_12q12 cnv correlated to 'CN_CNMF'.

  • del_12q24.33 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_13q12.11 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_13q12.13 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_13q14.2 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_13q34 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_15q11.2 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • del_17p13.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_18q21.32 cnv correlated to 'CN_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_18q23 cnv correlated to 'CN_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_19p13.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_19p13.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_19q13.33 cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_20p13 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_21q11.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_22q13.32 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_xp22.2 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 74 focal events and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 301 significant findings detected.

Clinical
Features 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
amp 3q26 2 170 (33%) 345 0.00029
(0.174) 		0.00145
(0.795) 		1e-05
(0.00888) 		1e-05
(0.00888) 		0.474
(1.00) 		0.0174
(1.00) 		1e-05
(0.00888) 		1e-05
(0.00888) 		1e-05
(0.00888) 		1e-05
(0.00888) 		0.463
(1.00) 		2e-05
(0.0136)
amp 7p11 2 273 (53%) 242 0.959
(1.00) 		0.902
(1.00) 		1e-05
(0.00888) 		0.00132
(0.73) 		0.0016
(0.87) 		0.0061
(1.00) 		1e-05
(0.00888) 		1e-05
(0.00888) 		1e-05
(0.00888) 		1e-05
(0.00888) 		7e-05
(0.0447) 		1e-05
(0.00888)
amp 8p11 21 174 (34%) 341 0.253
(1.00) 		0.445
(1.00) 		1e-05
(0.00888) 		0.00032
(0.19) 		0.3
(1.00) 		0.927
(1.00) 		1e-05
(0.00888) 		2e-05
(0.0136) 		0.0003
(0.179) 		0.0001
(0.0626) 		0.0194
(1.00) 		0.00019
(0.116)
amp 8q11 1 234 (45%) 281 0.0049
(1.00) 		0.0393
(1.00) 		1e-05
(0.00888) 		1e-05
(0.00888) 		0.255
(1.00) 		0.958
(1.00) 		1e-05
(0.00888) 		1e-05
(0.00888) 		2e-05
(0.0136) 		0.00014
(0.0868) 		0.00111
(0.617) 		1e-05
(0.00888)
amp 11q13 3 174 (34%) 341 0.00662
(1.00) 		0.00265
(1.00) 		1e-05
(0.00888) 		1e-05
(0.00888) 		0.0303
(1.00) 		0.911
(1.00) 		1e-05
(0.00888) 		1e-05
(0.00888) 		1e-05
(0.00888) 		1e-05
(0.00888) 		0.571
(1.00) 		0.00017
(0.105)
amp 12p12 1 179 (35%) 336 0.196
(1.00) 		0.0382
(1.00) 		1e-05
(0.00888) 		1e-05
(0.00888) 		0.038
(1.00) 		0.447
(1.00) 		1e-05
(0.00888) 		1e-05
(0.00888) 		2e-05
(0.0136) 		3e-05
(0.0199) 		0.677
(1.00) 		1e-05
(0.00888)
amp 12q14 1 170 (33%) 345 0.408
(1.00) 		0.286
(1.00) 		1e-05
(0.00888) 		1e-05
(0.00888) 		0.338
(1.00) 		0.551
(1.00) 		1e-05
(0.00888) 		1e-05
(0.00888) 		1e-05
(0.00888) 		1e-05
(0.00888) 		0.348
(1.00) 		1e-05
(0.00888)
amp 12q15 171 (33%) 344 0.222
(1.00) 		0.137
(1.00) 		1e-05
(0.00888) 		1e-05
(0.00888) 		0.209
(1.00) 		0.0971
(1.00) 		1e-05
(0.00888) 		1e-05
(0.00888) 		1e-05
(0.00888) 		1e-05
(0.00888) 		0.352
(1.00) 		1e-05
(0.00888)
amp 14q13 3 230 (45%) 285 0.797
(1.00) 		0.539
(1.00) 		1e-05
(0.00888) 		1e-05
(0.00888) 		0.0571
(1.00) 		0.866
(1.00) 		1e-05
(0.00888) 		1e-05
(0.00888) 		2e-05
(0.0136) 		1e-05
(0.00888) 		0.185
(1.00) 		0.00013
(0.0809)
amp 17q12 227 (44%) 288 0.0901
(1.00) 		0.0334
(1.00) 		1e-05
(0.00888) 		1e-05
(0.00888) 		0.31
(1.00) 		0.0169
(1.00) 		1e-05
(0.00888) 		1e-05
(0.00888) 		1e-05
(0.00888) 		1e-05
(0.00888) 		0.543
(1.00) 		1e-05
(0.00888)
amp 17q23 1 249 (48%) 266 0.0788
(1.00) 		0.303
(1.00) 		1e-05
(0.00888) 		1e-05
(0.00888) 		0.241
(1.00) 		0.0566
(1.00) 		1e-05
(0.00888) 		1e-05
(0.00888) 		1e-05
(0.00888) 		3e-05
(0.0199) 		0.701
(1.00) 		3e-05
(0.0199)
amp 19q12 139 (27%) 376 0.0509
(1.00) 		0.0104
(1.00) 		8e-05
(0.0506) 		1e-05
(0.00888) 		0.766
(1.00) 		0.353
(1.00) 		0.0002
(0.122) 		1e-05
(0.00888) 		1e-05
(0.00888) 		0.00032
(0.19) 		0.0611
(1.00) 		4e-05
(0.0261)
amp 20q13 33 250 (49%) 265 0.00555
(1.00) 		0.0447
(1.00) 		1e-05
(0.00888) 		3e-05
(0.0199) 		0.0435
(1.00) 		0.363
(1.00) 		1e-05
(0.00888) 		1e-05
(0.00888) 		1e-05
(0.00888) 		1e-05
(0.00888) 		0.0587
(1.00) 		3e-05
(0.0199)
del 4p16 3 130 (25%) 385 0.596
(1.00) 		0.309
(1.00) 		1e-05
(0.00888) 		1e-05
(0.00888) 		0.837
(1.00) 		0.398
(1.00) 		2e-05
(0.0136) 		2e-05
(0.0136) 		1e-05
(0.00888) 		1e-05
(0.00888) 		0.611
(1.00) 		0.00035
(0.207)
del 4q34 3 186 (36%) 329 0.00193
(1.00) 		0.00309
(1.00) 		1e-05
(0.00888) 		1e-05
(0.00888) 		0.136
(1.00) 		0.255
(1.00) 		1e-05
(0.00888) 		1e-05
(0.00888) 		1e-05
(0.00888) 		1e-05
(0.00888) 		0.0239
(1.00) 		1e-05
(0.00888)
del 5q12 1 179 (35%) 336 0.26
(1.00) 		0.166
(1.00) 		1e-05
(0.00888) 		1e-05
(0.00888) 		0.0301
(1.00) 		0.405
(1.00) 		1e-05
(0.00888) 		1e-05
(0.00888) 		1e-05
(0.00888) 		1e-05
(0.00888) 		0.0228
(1.00) 		1e-05
(0.00888)
del 5q31 1 210 (41%) 305 0.093
(1.00) 		0.242
(1.00) 		1e-05
(0.00888) 		1e-05
(0.00888) 		0.0836
(1.00) 		0.429
(1.00) 		1e-05
(0.00888) 		1e-05
(0.00888) 		1e-05
(0.00888) 		1e-05
(0.00888) 		0.359
(1.00) 		1e-05
(0.00888)
del 19p13 3 275 (53%) 240 0.573
(1.00) 		0.813
(1.00) 		1e-05
(0.00888) 		1e-05
(0.00888) 		0.511
(1.00) 		0.235
(1.00) 		1e-05
(0.00888) 		1e-05
(0.00888) 		1e-05
(0.00888) 		1e-05
(0.00888) 		0.12
(1.00) 		0.00031
(0.185)
del 19p13 2 268 (52%) 247 0.693
(1.00) 		1
(1.00) 		1e-05
(0.00888) 		1e-05
(0.00888) 		0.895
(1.00) 		0.0822
(1.00) 		2e-05
(0.0136) 		1e-05
(0.00888) 		1e-05
(0.00888) 		1e-05
(0.00888) 		0.0557
(1.00) 		0.00012
(0.0749)
del 21q11 2 176 (34%) 339 0.0606
(1.00) 		0.0475
(1.00) 		1e-05
(0.00888) 		0.00022
(0.133) 		0.0124
(1.00) 		0.233
(1.00) 		1e-05
(0.00888) 		1e-05
(0.00888) 		1e-05
(0.00888) 		2e-05
(0.0136) 		0.49
(1.00) 		1e-05
(0.00888)
del 22q13 32 250 (49%) 265 0.0255
(1.00) 		0.0808
(1.00) 		1e-05
(0.00888) 		1e-05
(0.00888) 		0.739
(1.00) 		0.443
(1.00) 		1e-05
(0.00888) 		1e-05
(0.00888) 		1e-05
(0.00888) 		1e-05
(0.00888) 		0.016
(1.00) 		1e-05
(0.00888)
amp 5p13 1 304 (59%) 211 0.262
(1.00) 		1
(1.00) 		1e-05
(0.00888) 		0.00487
(1.00) 		0.101
(1.00) 		0.0496
(1.00) 		1e-05
(0.00888) 		1e-05
(0.00888) 		0.0001
(0.0626) 		0.00026
(0.156) 		0.225
(1.00) 		1e-05
(0.00888)
amp 8q24 21 324 (63%) 191 0.0349
(1.00) 		0.0878
(1.00) 		1e-05
(0.00888) 		1e-05
(0.00888) 		0.505
(1.00) 		0.79
(1.00) 		1e-05
(0.00888) 		1e-05
(0.00888) 		1e-05
(0.00888) 		0.00102
(0.571) 		0.0743
(1.00) 		1e-05
(0.00888)
amp 10p15 1 141 (27%) 374 0.0229
(1.00) 		0.0159
(1.00) 		1e-05
(0.00888) 		1e-05
(0.00888) 		0.00682
(1.00) 		0.0556
(1.00) 		4e-05
(0.0261) 		1e-05
(0.00888) 		5e-05
(0.0324) 		2e-05
(0.0136) 		0.0379
(1.00) 		0.00068
(0.388)
amp 18q11 2 104 (20%) 411 0.194
(1.00) 		0.0196
(1.00) 		0.001
(0.561) 		1e-05
(0.00888) 		0.0785
(1.00) 		0.232
(1.00) 		8e-05
(0.0506) 		0.00012
(0.0749) 		0.00014
(0.0868) 		5e-05
(0.0324) 		0.457
(1.00) 		7e-05
(0.0447)
del 3p21 31 247 (48%) 268 0.133
(1.00) 		0.348
(1.00) 		1e-05
(0.00888) 		1e-05
(0.00888) 		0.0345
(1.00) 		0.219
(1.00) 		0.0169
(1.00) 		1e-05
(0.00888) 		1e-05
(0.00888) 		1e-05
(0.00888) 		0.66
(1.00) 		2e-05
(0.0136)
del 8p23 2 252 (49%) 263 0.00497
(1.00) 		0.00981
(1.00) 		1e-05
(0.00888) 		0.00061
(0.35) 		0.0224
(1.00) 		0.00038
(0.223) 		1e-05
(0.00888) 		1e-05
(0.00888) 		5e-05
(0.0324) 		0.00448
(1.00) 		0.0137
(1.00) 		0.00017
(0.105)
del 9q21 11 257 (50%) 258 0.0337
(1.00) 		0.484
(1.00) 		3e-05
(0.0199) 		6e-05
(0.0385) 		0.242
(1.00) 		0.0417
(1.00) 		0.00264
(1.00) 		6e-05
(0.0385) 		5e-05
(0.0324) 		1e-05
(0.00888) 		0.219
(1.00) 		0.00019
(0.116)
del 3p26 2 232 (45%) 283 0.0942
(1.00) 		0.241
(1.00) 		2e-05
(0.0136) 		0.00045
(0.263) 		0.0551
(1.00) 		0.377
(1.00) 		0.0933
(1.00) 		1e-05
(0.00888) 		3e-05
(0.0199) 		0.00013
(0.0809) 		0.813
(1.00) 		0.00026
(0.156)
del 10q26 3 147 (29%) 368 0.616
(1.00) 		0.339
(1.00) 		1e-05
(0.00888) 		0.014
(1.00) 		0.00131
(0.726) 		0.00316
(1.00) 		3e-05
(0.0199) 		1e-05
(0.00888) 		0.00791
(1.00) 		0.00021
(0.127) 		0.0229
(1.00) 		0.00031
(0.185)
del 15q11 2 263 (51%) 252 0.168
(1.00) 		0.3
(1.00) 		1e-05
(0.00888) 		0.00052
(0.3) 		0.036
(1.00) 		0.00177
(0.954) 		1e-05
(0.00888) 		1e-05
(0.00888) 		2e-05
(0.0136) 		0.0154
(1.00) 		0.271
(1.00) 		1e-05
(0.00888)
amp 5p15 33 334 (65%) 181 0.878
(1.00) 		0.805
(1.00) 		1e-05
(0.00888) 		0.0691
(1.00) 		0.0154
(1.00) 		0.0125
(1.00) 		1e-05
(0.00888) 		1e-05
(0.00888) 		0.00132
(0.73) 		0.00094
(0.528) 		0.406
(1.00) 		1e-05
(0.00888)
amp 7q31 2 216 (42%) 299 0.482
(1.00) 		0.311
(1.00) 		1e-05
(0.00888) 		0.00148
(0.808) 		0.0828
(1.00) 		0.12
(1.00) 		1e-05
(0.00888) 		1e-05
(0.00888) 		0.00056
(0.322) 		0.00305
(1.00) 		0.144
(1.00) 		1e-05
(0.00888)
amp 8p11 23 137 (27%) 378 0.294
(1.00) 		0.101
(1.00) 		1e-05
(0.00888) 		1e-05
(0.00888) 		0.692
(1.00) 		0.96
(1.00) 		1e-05
(0.00888) 		0.00017
(0.105) 		0.0168
(1.00) 		0.00514
(1.00) 		0.504
(1.00) 		0.0174
(1.00)
amp xq28 158 (31%) 357 0.299
(1.00) 		0.243
(1.00) 		1e-05
(0.00888) 		7e-05
(0.0447) 		0.32
(1.00) 		0.552
(1.00) 		5e-05
(0.0324) 		4e-05
(0.0261) 		0.0101
(1.00) 		0.0896
(1.00) 		0.26
(1.00) 		0.0005
(0.289)
del 13q14 2 282 (55%) 233 0.00867
(1.00) 		0.0649
(1.00) 		1e-05
(0.00888) 		0.0234
(1.00) 		0.00478
(1.00) 		0.00148
(0.808) 		1e-05
(0.00888) 		1e-05
(0.00888) 		0.00168
(0.909) 		0.00698
(1.00) 		0.0492
(1.00) 		9e-05
(0.0566)
del 16q23 1 169 (33%) 346 0.0603
(1.00) 		0.877
(1.00) 		2e-05
(0.0136) 		9e-05
(0.0566) 		0.219
(1.00) 		0.00092
(0.518) 		1e-05
(0.00888) 		1e-05
(0.00888) 		0.0278
(1.00) 		0.00255
(1.00) 		0.861
(1.00) 		0.0006
(0.344)
del 17p13 3 278 (54%) 237 0.385
(1.00) 		0.787
(1.00) 		1e-05
(0.00888) 		1e-05
(0.00888) 		0.00049
(0.284) 		0.00063
(0.36) 		1e-05
(0.00888) 		1e-05
(0.00888) 		0.00879
(1.00) 		0.0182
(1.00) 		0.603
(1.00) 		0.00113
(0.627)
del 18q21 32 254 (49%) 261 0.113
(1.00) 		0.0795
(1.00) 		1e-05
(0.00888) 		0.768
(1.00) 		0.0193
(1.00) 		0.00016
(0.0987) 		3e-05
(0.0199) 		6e-05
(0.0385) 		0.0109
(1.00) 		0.165
(1.00) 		0.862
(1.00) 		0.0555
(1.00)
del 18q23 249 (48%) 266 0.0292
(1.00) 		0.0255
(1.00) 		1e-05
(0.00888) 		0.596
(1.00) 		0.0072
(1.00) 		7e-05
(0.0447) 		1e-05
(0.00888) 		4e-05
(0.0261) 		0.00747
(1.00) 		0.183
(1.00) 		0.804
(1.00) 		0.057
(1.00)
del 19q13 33 194 (38%) 321 0.274
(1.00) 		0.256
(1.00) 		1e-05
(0.00888) 		0.00067
(0.383) 		0.204
(1.00) 		0.212
(1.00) 		0.00192
(1.00) 		2e-05
(0.0136) 		2e-05
(0.0136) 		1e-05
(0.00888) 		0.577
(1.00) 		0.0119
(1.00)
amp 1q21 3 376 (73%) 139 0.361
(1.00) 		0.521
(1.00) 		1e-05
(0.00888) 		1e-05
(0.00888) 		0.11
(1.00) 		0.0293
(1.00) 		0.00464
(1.00) 		1e-05
(0.00888) 		0.00396
(1.00) 		0.00073
(0.415) 		0.00441
(1.00) 		0.24
(1.00)
del 1p36 13 120 (23%) 395 0.796
(1.00) 		0.381
(1.00) 		1e-05
(0.00888) 		0.0025
(1.00) 		0.695
(1.00) 		0.103
(1.00) 		9e-05
(0.0566) 		1e-05
(0.00888) 		0.0113
(1.00) 		0.134
(1.00) 		0.011
(1.00) 		0.0245
(1.00)
del 1p13 1 151 (29%) 364 0.619
(1.00) 		0.454
(1.00) 		1e-05
(0.00888) 		0.00091
(0.513) 		0.126
(1.00) 		0.0547
(1.00) 		0.00017
(0.105) 		0.00024
(0.144) 		0.156
(1.00) 		0.00222
(1.00) 		0.841
(1.00) 		0.777
(1.00)
del 3q29 135 (26%) 380 0.711
(1.00) 		0.616
(1.00) 		0.125
(1.00) 		0.00021
(0.127) 		0.139
(1.00) 		0.0281
(1.00) 		8e-05
(0.0506) 		1e-05
(0.00888) 		0.853
(1.00) 		0.0426
(1.00) 		0.147
(1.00) 		0.246
(1.00)
del 9p21 3 292 (57%) 223 0.522
(1.00) 		0.804
(1.00) 		0.00023
(0.139) 		0.132
(1.00) 		0.511
(1.00) 		0.0294
(1.00) 		2e-05
(0.0136) 		2e-05
(0.0136) 		0.14
(1.00) 		0.0024
(1.00) 		0.0442
(1.00) 		0.106
(1.00)
del 11p15 5 142 (28%) 373 0.265
(1.00) 		0.0318
(1.00) 		1e-05
(0.00888) 		0.00139
(0.764) 		0.624
(1.00) 		0.334
(1.00) 		0.00043
(0.252) 		1e-05
(0.00888) 		0.00019
(0.116) 		0.00043
(0.252) 		0.0695
(1.00) 		0.00046
(0.268)
del 12q24 33 130 (25%) 385 0.0624
(1.00) 		0.0716
(1.00) 		1e-05
(0.00888) 		0.0686
(1.00) 		0.0626
(1.00) 		0.185
(1.00) 		4e-05
(0.0261) 		1e-05
(0.00888) 		0.147
(1.00) 		0.018
(1.00) 		0.554
(1.00) 		0.463
(1.00)
del 13q12 11 293 (57%) 222 0.00106
(0.593) 		0.0384
(1.00) 		1e-05
(0.00888) 		0.0114
(1.00) 		0.00667
(1.00) 		0.00047
(0.274) 		1e-05
(0.00888) 		1e-05
(0.00888) 		0.00319
(1.00) 		0.00375
(1.00) 		0.245
(1.00) 		0.00047
(0.274)
del 13q12 13 292 (57%) 223 0.00865
(1.00) 		0.0638
(1.00) 		1e-05
(0.00888) 		0.00482
(1.00) 		0.00883
(1.00) 		0.00083
(0.47) 		1e-05
(0.00888) 		1e-05
(0.00888) 		0.00442
(1.00) 		0.00568
(1.00) 		0.213
(1.00) 		0.00054
(0.311)
del 13q34 241 (47%) 274 0.0358
(1.00) 		0.112
(1.00) 		1e-05
(0.00888) 		0.166
(1.00) 		0.00133
(0.733) 		0.0148
(1.00) 		1e-05
(0.00888) 		1e-05
(0.00888) 		0.00978
(1.00) 		0.0271
(1.00) 		0.226
(1.00) 		0.0177
(1.00)
del 20p13 130 (25%) 385 0.106
(1.00) 		0.223
(1.00) 		1e-05
(0.00888) 		0.00236
(1.00) 		0.00344
(1.00) 		0.00044
(0.257) 		2e-05
(0.0136) 		1e-05
(0.00888) 		0.954
(1.00) 		0.706
(1.00) 		0.368
(1.00) 		0.0157
(1.00)
del xp22 2 144 (28%) 371 0.689
(1.00) 		0.892
(1.00) 		1e-05
(0.00888) 		0.00205
(1.00) 		0.092
(1.00) 		0.0114
(1.00) 		0.00017
(0.105) 		0.0003
(0.179) 		0.341
(1.00) 		0.586
(1.00) 		0.962
(1.00) 		0.104
(1.00)
amp 6p21 1 189 (37%) 326 0.674
(1.00) 		0.254
(1.00) 		1e-05
(0.00888) 		1e-05
(0.00888) 		0.1
(1.00) 		0.467
(1.00) 		0.00357
(1.00) 		0.0008
(0.454) 		0.0258
(1.00) 		0.00471
(1.00) 		0.349
(1.00) 		0.0275
(1.00)
del 6q22 31 255 (50%) 260 0.542
(1.00) 		0.141
(1.00) 		0.00483
(1.00) 		1e-05
(0.00888) 		0.129
(1.00) 		0.0161
(1.00) 		0.0274
(1.00) 		0.00015
(0.0927) 		0.706
(1.00) 		0.00147
(0.804) 		0.666
(1.00) 		0.287
(1.00)
del 11q23 2 120 (23%) 395 0.431
(1.00) 		0.846
(1.00) 		1e-05
(0.00888) 		0.00441
(1.00) 		0.0376
(1.00) 		0.336
(1.00) 		7e-05
(0.0447) 		0.00289
(1.00) 		0.00199
(1.00) 		0.0407
(1.00) 		0.0456
(1.00) 		0.31
(1.00)
del 11q25 116 (23%) 399 0.107
(1.00) 		0.485
(1.00) 		3e-05
(0.0199) 		0.011
(1.00) 		0.00419
(1.00) 		0.148
(1.00) 		0.00023
(0.139) 		0.0111
(1.00) 		0.086
(1.00) 		0.175
(1.00) 		0.119
(1.00) 		0.456
(1.00)
amp 1p34 3 138 (27%) 377 0.552
(1.00) 		0.58
(1.00) 		1e-05
(0.00888) 		0.26
(1.00) 		0.011
(1.00) 		0.16
(1.00) 		0.0524
(1.00) 		0.00191
(1.00) 		0.114
(1.00) 		0.00944
(1.00) 		0.305
(1.00) 		0.00652
(1.00)
amp 1p22 3 141 (27%) 374 0.876
(1.00) 		1
(1.00) 		1e-05
(0.00888) 		0.125
(1.00) 		0.0166
(1.00) 		0.508
(1.00) 		0.0419
(1.00) 		0.0157
(1.00) 		0.123
(1.00) 		0.0379
(1.00) 		0.424
(1.00) 		0.176
(1.00)
amp 4q12 96 (19%) 419 0.704
(1.00) 		0.256
(1.00) 		1e-05
(0.00888) 		0.117
(1.00) 		0.141
(1.00) 		0.0145
(1.00) 		0.00428
(1.00) 		0.00739
(1.00) 		0.00695
(1.00) 		0.00169
(0.913) 		0.827
(1.00) 		0.0011
(0.613)
amp 13q33 3 77 (15%) 438 0.464
(1.00) 		0.52
(1.00) 		0.0902
(1.00) 		8e-05
(0.0506) 		0.194
(1.00) 		0.923
(1.00) 		0.474
(1.00) 		0.0211
(1.00) 		0.152
(1.00) 		0.12
(1.00) 		0.652
(1.00) 		0.0415
(1.00)
amp 16p11 2 168 (33%) 347 0.802
(1.00) 		0.392
(1.00) 		1e-05
(0.00888) 		0.00704
(1.00) 		0.155
(1.00) 		0.226
(1.00) 		0.331
(1.00) 		0.0587
(1.00) 		0.0345
(1.00) 		0.105
(1.00) 		0.406
(1.00) 		0.182
(1.00)
amp 22q11 22 90 (17%) 425 0.27
(1.00) 		0.127
(1.00) 		1e-05
(0.00888) 		0.362
(1.00) 		0.0129
(1.00) 		0.211
(1.00) 		0.561
(1.00) 		0.0619
(1.00) 		0.0398
(1.00) 		0.0419
(1.00) 		0.729
(1.00) 		0.0166
(1.00)
del 2q22 1 45 (9%) 470 0.869
(1.00) 		0.781
(1.00) 		0.00036
(0.212) 		0.0113
(1.00) 		0.186
(1.00) 		0.449
(1.00) 		0.0241
(1.00) 		0.00517
(1.00) 		0.0169
(1.00) 		0.00468
(1.00) 		0.948
(1.00) 		0.038
(1.00)
del 6q26 257 (50%) 258 0.369
(1.00) 		0.334
(1.00) 		0.00037
(0.218) 		0.0007
(0.398) 		0.0753
(1.00) 		0.0823
(1.00) 		0.103
(1.00) 		0.00489
(1.00) 		0.771
(1.00) 		0.0135
(1.00) 		0.516
(1.00) 		0.191
(1.00)
del 8p11 21 125 (24%) 390 0.794
(1.00) 		0.508
(1.00) 		1e-05
(0.00888) 		0.175
(1.00) 		0.78
(1.00) 		0.0351
(1.00) 		0.00836
(1.00) 		0.059
(1.00) 		0.152
(1.00) 		0.573
(1.00) 		0.541
(1.00) 		0.13
(1.00)
del 9p23 286 (56%) 229 0.522
(1.00) 		0.806
(1.00) 		0.00047
(0.274) 		0.262
(1.00) 		0.794
(1.00) 		0.243
(1.00) 		0.00353
(1.00) 		6e-05
(0.0385) 		0.12
(1.00) 		0.0281
(1.00) 		0.285
(1.00) 		0.215
(1.00)
del 10p15 3 125 (24%) 390 1
(1.00) 		0.845
(1.00) 		5e-05
(0.0324) 		0.0107
(1.00) 		0.138
(1.00) 		0.121
(1.00) 		0.00531
(1.00) 		0.00084
(0.475) 		0.00142
(0.78) 		0.0166
(1.00) 		0.0325
(1.00) 		0.0126
(1.00)
del 12q12 98 (19%) 417 0.6
(1.00) 		0.751
(1.00) 		0.00033
(0.195) 		0.117
(1.00) 		0.136
(1.00) 		0.0676
(1.00) 		0.00637
(1.00) 		0.0229
(1.00) 		0.0562
(1.00) 		0.212
(1.00) 		0.902
(1.00) 		0.0263
(1.00)
del 3q11 1 139 (27%) 376 0.612
(1.00) 		0.686
(1.00) 		0.13
(1.00) 		0.022
(1.00) 		0.77
(1.00) 		0.766
(1.00) 		0.0844
(1.00) 		0.0016
(0.87) 		0.215
(1.00) 		0.694
(1.00) 		0.603
(1.00) 		0.859
(1.00)
del 6q11 1 139 (27%) 376 0.953
(1.00) 		1
(1.00) 		0.312
(1.00) 		0.0885
(1.00) 		0.394
(1.00) 		0.924
(1.00) 		0.664
(1.00) 		0.835
(1.00) 		0.0308
(1.00) 		0.201
(1.00) 		0.732
(1.00) 		0.0774
(1.00)
del 12p13 2 139 (27%) 376 0.256
(1.00) 		0.899
(1.00) 		0.00106
(0.593) 		0.00529
(1.00) 		0.166
(1.00) 		0.0633
(1.00) 		0.00163
(0.883) 		0.00292
(1.00) 		0.802
(1.00) 		0.977
(1.00) 		0.491
(1.00) 		0.0852
(1.00)
del 14q32 33 150 (29%) 365 0.701
(1.00) 		0.286
(1.00) 		0.00472
(1.00) 		0.738
(1.00) 		0.771
(1.00) 		0.347
(1.00) 		0.213
(1.00) 		0.0971
(1.00) 		0.021
(1.00) 		0.287
(1.00) 		0.218
(1.00) 		0.0722
(1.00)
del 20q13 12 82 (16%) 433 0.171
(1.00) 		0.579
(1.00) 		0.45
(1.00) 		0.264
(1.00) 		0.11
(1.00) 		0.129
(1.00) 		0.185
(1.00) 		0.0415
(1.00) 		0.147
(1.00) 		0.158
(1.00) 		0.044
(1.00) 		0.257
(1.00)
'amp_1p34.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
AMP PEAK 1(1P34.3) MUTATED 84 39 15
AMP PEAK 1(1P34.3) WILD-TYPE 107 190 80

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

'amp_1p22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S2.  Gene #2: 'amp_1p22.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
AMP PEAK 2(1P22.3) MUTATED 84 41 16
AMP PEAK 2(1P22.3) WILD-TYPE 107 188 79

Figure S2.  Get High-res Image Gene #2: 'amp_1p22.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1q21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S3.  Gene #3: 'amp_1q21.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
AMP PEAK 3(1Q21.3) MUTATED 153 140 83
AMP PEAK 3(1Q21.3) WILD-TYPE 38 89 12

Figure S3.  Get High-res Image Gene #3: 'amp_1q21.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1q21.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S4.  Gene #3: 'amp_1q21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 125 108 116
AMP PEAK 3(1Q21.3) MUTATED 66 113 85 63
AMP PEAK 3(1Q21.3) WILD-TYPE 30 12 23 53

Figure S4.  Get High-res Image Gene #3: 'amp_1q21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_1q21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S5.  Gene #3: 'amp_1q21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
AMP PEAK 3(1Q21.3) MUTATED 65 39 23 60 44 43 38 5 36
AMP PEAK 3(1Q21.3) WILD-TYPE 18 18 21 24 2 8 11 13 18

Figure S5.  Get High-res Image Gene #3: 'amp_1q21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_3q26.2' versus 'MRNA_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.17

Table S6.  Gene #4: 'amp_3q26.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 5 9 12 6
AMP PEAK 4(3Q26.2) MUTATED 0 6 0 4
AMP PEAK 4(3Q26.2) WILD-TYPE 5 3 12 2

Figure S6.  Get High-res Image Gene #4: 'amp_3q26.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_3q26.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S7.  Gene #4: 'amp_3q26.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
AMP PEAK 4(3Q26.2) MUTATED 85 44 41
AMP PEAK 4(3Q26.2) WILD-TYPE 106 185 54

Figure S7.  Get High-res Image Gene #4: 'amp_3q26.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_3q26.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S8.  Gene #4: 'amp_3q26.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 125 108 116
AMP PEAK 4(3Q26.2) MUTATED 7 58 37 40
AMP PEAK 4(3Q26.2) WILD-TYPE 89 67 71 76

Figure S8.  Get High-res Image Gene #4: 'amp_3q26.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_3q26.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S9.  Gene #4: 'amp_3q26.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
AMP PEAK 4(3Q26.2) MUTATED 56 7 32 50 17
AMP PEAK 4(3Q26.2) WILD-TYPE 82 105 44 56 37

Figure S9.  Get High-res Image Gene #4: 'amp_3q26.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_3q26.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S10.  Gene #4: 'amp_3q26.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
AMP PEAK 4(3Q26.2) MUTATED 23 5 20 57 5 17 18 5 12
AMP PEAK 4(3Q26.2) WILD-TYPE 60 52 24 27 41 34 31 13 42

Figure S10.  Get High-res Image Gene #4: 'amp_3q26.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_3q26.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S11.  Gene #4: 'amp_3q26.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
AMP PEAK 4(3Q26.2) MUTATED 41 103 24
AMP PEAK 4(3Q26.2) WILD-TYPE 148 125 69

Figure S11.  Get High-res Image Gene #4: 'amp_3q26.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_3q26.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S12.  Gene #4: 'amp_3q26.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
AMP PEAK 4(3Q26.2) MUTATED 12 67 35 54
AMP PEAK 4(3Q26.2) WILD-TYPE 59 131 106 46

Figure S12.  Get High-res Image Gene #4: 'amp_3q26.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_3q26.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S13.  Gene #4: 'amp_3q26.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
AMP PEAK 4(3Q26.2) MUTATED 15 101 25
AMP PEAK 4(3Q26.2) WILD-TYPE 88 147 58

Figure S13.  Get High-res Image Gene #4: 'amp_3q26.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_4q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S14.  Gene #5: 'amp_4q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
AMP PEAK 5(4Q12) MUTATED 62 21 13
AMP PEAK 5(4Q12) WILD-TYPE 129 208 82

Figure S14.  Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_5p15.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S15.  Gene #6: 'amp_5p15.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
AMP PEAK 6(5P15.33) MUTATED 171 110 53
AMP PEAK 6(5P15.33) WILD-TYPE 20 119 42

Figure S15.  Get High-res Image Gene #6: 'amp_5p15.33' versus Molecular Subtype #3: 'CN_CNMF'

'amp_5p15.33' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S16.  Gene #6: 'amp_5p15.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
AMP PEAK 6(5P15.33) MUTATED 111 63 33 73 33
AMP PEAK 6(5P15.33) WILD-TYPE 27 49 43 33 21

Figure S16.  Get High-res Image Gene #6: 'amp_5p15.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_5p15.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S17.  Gene #6: 'amp_5p15.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
AMP PEAK 6(5P15.33) MUTATED 65 33 28 70 20 34 30 0 33
AMP PEAK 6(5P15.33) WILD-TYPE 18 24 16 14 26 17 19 18 21

Figure S17.  Get High-res Image Gene #6: 'amp_5p15.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S18.  Gene #6: 'amp_5p15.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
AMP PEAK 6(5P15.33) MUTATED 43 187 56
AMP PEAK 6(5P15.33) WILD-TYPE 60 61 27

Figure S18.  Get High-res Image Gene #6: 'amp_5p15.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_5p13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S19.  Gene #7: 'amp_5p13.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
AMP PEAK 7(5P13.1) MUTATED 154 96 54
AMP PEAK 7(5P13.1) WILD-TYPE 37 133 41

Figure S19.  Get High-res Image Gene #7: 'amp_5p13.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_5p13.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S20.  Gene #7: 'amp_5p13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
AMP PEAK 7(5P13.1) MUTATED 94 55 29 76 31
AMP PEAK 7(5P13.1) WILD-TYPE 44 57 47 30 23

Figure S20.  Get High-res Image Gene #7: 'amp_5p13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_5p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S21.  Gene #7: 'amp_5p13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
AMP PEAK 7(5P13.1) MUTATED 59 29 22 67 18 36 24 0 30
AMP PEAK 7(5P13.1) WILD-TYPE 24 28 22 17 28 15 25 18 24

Figure S21.  Get High-res Image Gene #7: 'amp_5p13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_5p13.1' versus 'MIRSEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.063

Table S22.  Gene #7: 'amp_5p13.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
AMP PEAK 7(5P13.1) MUTATED 90 156 57
AMP PEAK 7(5P13.1) WILD-TYPE 99 72 36

Figure S22.  Get High-res Image Gene #7: 'amp_5p13.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_5p13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.16

Table S23.  Gene #7: 'amp_5p13.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
AMP PEAK 7(5P13.1) MUTATED 41 126 64 72
AMP PEAK 7(5P13.1) WILD-TYPE 30 72 77 28

Figure S23.  Get High-res Image Gene #7: 'amp_5p13.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_5p13.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S24.  Gene #7: 'amp_5p13.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
AMP PEAK 7(5P13.1) MUTATED 37 175 50
AMP PEAK 7(5P13.1) WILD-TYPE 66 73 33

Figure S24.  Get High-res Image Gene #7: 'amp_5p13.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_6p21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S25.  Gene #8: 'amp_6p21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
AMP PEAK 8(6P21.1) MUTATED 80 58 51
AMP PEAK 8(6P21.1) WILD-TYPE 111 171 44

Figure S25.  Get High-res Image Gene #8: 'amp_6p21.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_6p21.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S26.  Gene #8: 'amp_6p21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 125 108 116
AMP PEAK 8(6P21.1) MUTATED 33 76 42 18
AMP PEAK 8(6P21.1) WILD-TYPE 63 49 66 98

Figure S26.  Get High-res Image Gene #8: 'amp_6p21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_7p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S27.  Gene #9: 'amp_7p11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
AMP PEAK 9(7P11.2) MUTATED 145 89 39
AMP PEAK 9(7P11.2) WILD-TYPE 46 140 56

Figure S27.  Get High-res Image Gene #9: 'amp_7p11.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_7p11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S28.  Gene #9: 'amp_7p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
AMP PEAK 9(7P11.2) MUTATED 106 36 40 46 28
AMP PEAK 9(7P11.2) WILD-TYPE 32 76 36 60 26

Figure S28.  Get High-res Image Gene #9: 'amp_7p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_7p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S29.  Gene #9: 'amp_7p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
AMP PEAK 9(7P11.2) MUTATED 53 23 35 48 9 23 32 2 31
AMP PEAK 9(7P11.2) WILD-TYPE 30 34 9 36 37 28 17 16 23

Figure S29.  Get High-res Image Gene #9: 'amp_7p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_7p11.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S30.  Gene #9: 'amp_7p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
AMP PEAK 9(7P11.2) MUTATED 71 134 65
AMP PEAK 9(7P11.2) WILD-TYPE 118 94 28

Figure S30.  Get High-res Image Gene #9: 'amp_7p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_7p11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S31.  Gene #9: 'amp_7p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
AMP PEAK 9(7P11.2) MUTATED 22 127 64 57
AMP PEAK 9(7P11.2) WILD-TYPE 49 71 77 43

Figure S31.  Get High-res Image Gene #9: 'amp_7p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_7p11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.045

Table S32.  Gene #9: 'amp_7p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 198 91
AMP PEAK 9(7P11.2) MUTATED 62 107 65
AMP PEAK 9(7P11.2) WILD-TYPE 83 91 26

Figure S32.  Get High-res Image Gene #9: 'amp_7p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_7p11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S33.  Gene #9: 'amp_7p11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
AMP PEAK 9(7P11.2) MUTATED 31 154 49
AMP PEAK 9(7P11.2) WILD-TYPE 72 94 34

Figure S33.  Get High-res Image Gene #9: 'amp_7p11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7q31.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S34.  Gene #10: 'amp_7q31.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
AMP PEAK 10(7Q31.2) MUTATED 116 63 37
AMP PEAK 10(7Q31.2) WILD-TYPE 75 166 58

Figure S34.  Get High-res Image Gene #10: 'amp_7q31.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_7q31.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S35.  Gene #10: 'amp_7q31.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
AMP PEAK 10(7Q31.2) MUTATED 86 24 33 36 23
AMP PEAK 10(7Q31.2) WILD-TYPE 52 88 43 70 31

Figure S35.  Get High-res Image Gene #10: 'amp_7q31.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_7q31.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S36.  Gene #10: 'amp_7q31.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
AMP PEAK 10(7Q31.2) MUTATED 46 15 33 39 5 15 23 2 24
AMP PEAK 10(7Q31.2) WILD-TYPE 37 42 11 45 41 36 26 16 30

Figure S36.  Get High-res Image Gene #10: 'amp_7q31.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_7q31.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S37.  Gene #10: 'amp_7q31.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
AMP PEAK 10(7Q31.2) MUTATED 22 124 37
AMP PEAK 10(7Q31.2) WILD-TYPE 81 124 46

Figure S37.  Get High-res Image Gene #10: 'amp_7q31.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8p11.23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S38.  Gene #11: 'amp_8p11.23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
AMP PEAK 11(8P11.23) MUTATED 39 36 62
AMP PEAK 11(8P11.23) WILD-TYPE 152 193 33

Figure S38.  Get High-res Image Gene #11: 'amp_8p11.23' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8p11.23' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S39.  Gene #11: 'amp_8p11.23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 125 108 116
AMP PEAK 11(8P11.23) MUTATED 18 54 25 22
AMP PEAK 11(8P11.23) WILD-TYPE 78 71 83 94

Figure S39.  Get High-res Image Gene #11: 'amp_8p11.23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8p11.23' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S40.  Gene #11: 'amp_8p11.23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
AMP PEAK 11(8P11.23) MUTATED 28 16 25 49 12
AMP PEAK 11(8P11.23) WILD-TYPE 110 96 51 57 42

Figure S40.  Get High-res Image Gene #11: 'amp_8p11.23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8p11.23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.1

Table S41.  Gene #11: 'amp_8p11.23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
AMP PEAK 11(8P11.23) MUTATED 22 7 10 27 12 23 19 0 10
AMP PEAK 11(8P11.23) WILD-TYPE 61 50 34 57 34 28 30 18 44

Figure S41.  Get High-res Image Gene #11: 'amp_8p11.23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8p11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S42.  Gene #12: 'amp_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
AMP PEAK 12(8P11.21) MUTATED 55 46 73
AMP PEAK 12(8P11.21) WILD-TYPE 136 183 22

Figure S42.  Get High-res Image Gene #12: 'amp_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8p11.21' versus 'METHLYATION_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.19

Table S43.  Gene #12: 'amp_8p11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 125 108 116
AMP PEAK 12(8P11.21) MUTATED 21 61 37 33
AMP PEAK 12(8P11.21) WILD-TYPE 75 64 71 83

Figure S43.  Get High-res Image Gene #12: 'amp_8p11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8p11.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S44.  Gene #12: 'amp_8p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
AMP PEAK 12(8P11.21) MUTATED 44 19 25 63 14
AMP PEAK 12(8P11.21) WILD-TYPE 94 93 51 43 40

Figure S44.  Get High-res Image Gene #12: 'amp_8p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8p11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S45.  Gene #12: 'amp_8p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
AMP PEAK 12(8P11.21) MUTATED 26 9 20 35 15 30 18 0 12
AMP PEAK 12(8P11.21) WILD-TYPE 57 48 24 49 31 21 31 18 42

Figure S45.  Get High-res Image Gene #12: 'amp_8p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8p11.21' versus 'MIRSEQ_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.18

Table S46.  Gene #12: 'amp_8p11.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
AMP PEAK 12(8P11.21) MUTATED 45 97 31
AMP PEAK 12(8P11.21) WILD-TYPE 144 131 62

Figure S46.  Get High-res Image Gene #12: 'amp_8p11.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_8p11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.063

Table S47.  Gene #12: 'amp_8p11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
AMP PEAK 12(8P11.21) MUTATED 18 75 32 48
AMP PEAK 12(8P11.21) WILD-TYPE 53 123 109 52

Figure S47.  Get High-res Image Gene #12: 'amp_8p11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_8p11.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.12

Table S48.  Gene #12: 'amp_8p11.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
AMP PEAK 12(8P11.21) MUTATED 19 102 27
AMP PEAK 12(8P11.21) WILD-TYPE 84 146 56

Figure S48.  Get High-res Image Gene #12: 'amp_8p11.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8q11.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S49.  Gene #13: 'amp_8q11.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
AMP PEAK 13(8Q11.1) MUTATED 102 58 74
AMP PEAK 13(8Q11.1) WILD-TYPE 89 171 21

Figure S49.  Get High-res Image Gene #13: 'amp_8q11.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8q11.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S50.  Gene #13: 'amp_8q11.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 125 108 116
AMP PEAK 13(8Q11.1) MUTATED 28 78 57 41
AMP PEAK 13(8Q11.1) WILD-TYPE 68 47 51 75

Figure S50.  Get High-res Image Gene #13: 'amp_8q11.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8q11.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S51.  Gene #13: 'amp_8q11.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
AMP PEAK 13(8Q11.1) MUTATED 67 28 32 71 21
AMP PEAK 13(8Q11.1) WILD-TYPE 71 84 44 35 33

Figure S51.  Get High-res Image Gene #13: 'amp_8q11.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8q11.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S52.  Gene #13: 'amp_8q11.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
AMP PEAK 13(8Q11.1) MUTATED 35 16 26 42 18 37 24 0 21
AMP PEAK 13(8Q11.1) WILD-TYPE 48 41 18 42 28 14 25 18 33

Figure S52.  Get High-res Image Gene #13: 'amp_8q11.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8q11.1' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S53.  Gene #13: 'amp_8q11.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
AMP PEAK 13(8Q11.1) MUTATED 59 127 46
AMP PEAK 13(8Q11.1) WILD-TYPE 130 101 47

Figure S53.  Get High-res Image Gene #13: 'amp_8q11.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_8q11.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.087

Table S54.  Gene #13: 'amp_8q11.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
AMP PEAK 13(8Q11.1) MUTATED 28 102 44 58
AMP PEAK 13(8Q11.1) WILD-TYPE 43 96 97 42

Figure S54.  Get High-res Image Gene #13: 'amp_8q11.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_8q11.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S55.  Gene #13: 'amp_8q11.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
AMP PEAK 13(8Q11.1) MUTATED 27 136 35
AMP PEAK 13(8Q11.1) WILD-TYPE 76 112 48

Figure S55.  Get High-res Image Gene #13: 'amp_8q11.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8q24.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S56.  Gene #14: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
AMP PEAK 14(8Q24.21) MUTATED 142 98 84
AMP PEAK 14(8Q24.21) WILD-TYPE 49 131 11

Figure S56.  Get High-res Image Gene #14: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S57.  Gene #14: 'amp_8q24.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 125 108 116
AMP PEAK 14(8Q24.21) MUTATED 43 97 80 61
AMP PEAK 14(8Q24.21) WILD-TYPE 53 28 28 55

Figure S57.  Get High-res Image Gene #14: 'amp_8q24.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S58.  Gene #14: 'amp_8q24.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
AMP PEAK 14(8Q24.21) MUTATED 103 49 39 86 26
AMP PEAK 14(8Q24.21) WILD-TYPE 35 63 37 20 28

Figure S58.  Get High-res Image Gene #14: 'amp_8q24.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S59.  Gene #14: 'amp_8q24.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
AMP PEAK 14(8Q24.21) MUTATED 52 25 39 57 27 45 30 0 28
AMP PEAK 14(8Q24.21) WILD-TYPE 31 32 5 27 19 6 19 18 26

Figure S59.  Get High-res Image Gene #14: 'amp_8q24.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S60.  Gene #14: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
AMP PEAK 14(8Q24.21) MUTATED 92 166 63
AMP PEAK 14(8Q24.21) WILD-TYPE 97 62 30

Figure S60.  Get High-res Image Gene #14: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S61.  Gene #14: 'amp_8q24.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
AMP PEAK 14(8Q24.21) MUTATED 42 176 53
AMP PEAK 14(8Q24.21) WILD-TYPE 61 72 30

Figure S61.  Get High-res Image Gene #14: 'amp_8q24.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_10p15.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S62.  Gene #15: 'amp_10p15.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
AMP PEAK 15(10P15.1) MUTATED 59 37 45
AMP PEAK 15(10P15.1) WILD-TYPE 132 192 50

Figure S62.  Get High-res Image Gene #15: 'amp_10p15.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_10p15.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S63.  Gene #15: 'amp_10p15.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 125 108 116
AMP PEAK 15(10P15.1) MUTATED 8 51 39 23
AMP PEAK 15(10P15.1) WILD-TYPE 88 74 69 93

Figure S63.  Get High-res Image Gene #15: 'amp_10p15.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_10p15.1' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.026

Table S64.  Gene #15: 'amp_10p15.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
AMP PEAK 15(10P15.1) MUTATED 37 17 27 45 8
AMP PEAK 15(10P15.1) WILD-TYPE 101 95 49 61 46

Figure S64.  Get High-res Image Gene #15: 'amp_10p15.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_10p15.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S65.  Gene #15: 'amp_10p15.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
AMP PEAK 15(10P15.1) MUTATED 22 4 13 22 14 23 25 0 11
AMP PEAK 15(10P15.1) WILD-TYPE 61 53 31 62 32 28 24 18 43

Figure S65.  Get High-res Image Gene #15: 'amp_10p15.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_10p15.1' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.032

Table S66.  Gene #15: 'amp_10p15.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
AMP PEAK 15(10P15.1) MUTATED 32 84 22
AMP PEAK 15(10P15.1) WILD-TYPE 157 144 71

Figure S66.  Get High-res Image Gene #15: 'amp_10p15.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_10p15.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S67.  Gene #15: 'amp_10p15.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
AMP PEAK 15(10P15.1) MUTATED 16 69 18 35
AMP PEAK 15(10P15.1) WILD-TYPE 55 129 123 65

Figure S67.  Get High-res Image Gene #15: 'amp_10p15.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_11q13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S68.  Gene #16: 'amp_11q13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
AMP PEAK 16(11Q13.3) MUTATED 93 34 47
AMP PEAK 16(11Q13.3) WILD-TYPE 98 195 48

Figure S68.  Get High-res Image Gene #16: 'amp_11q13.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_11q13.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S69.  Gene #16: 'amp_11q13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 125 108 116
AMP PEAK 16(11Q13.3) MUTATED 15 56 48 30
AMP PEAK 16(11Q13.3) WILD-TYPE 81 69 60 86

Figure S69.  Get High-res Image Gene #16: 'amp_11q13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_11q13.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S70.  Gene #16: 'amp_11q13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
AMP PEAK 16(11Q13.3) MUTATED 58 21 17 56 12
AMP PEAK 16(11Q13.3) WILD-TYPE 80 91 59 50 42

Figure S70.  Get High-res Image Gene #16: 'amp_11q13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_11q13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S71.  Gene #16: 'amp_11q13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
AMP PEAK 16(11Q13.3) MUTATED 31 15 18 33 4 34 15 2 12
AMP PEAK 16(11Q13.3) WILD-TYPE 52 42 26 51 42 17 34 16 42

Figure S71.  Get High-res Image Gene #16: 'amp_11q13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_11q13.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S72.  Gene #16: 'amp_11q13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
AMP PEAK 16(11Q13.3) MUTATED 35 105 31
AMP PEAK 16(11Q13.3) WILD-TYPE 154 123 62

Figure S72.  Get High-res Image Gene #16: 'amp_11q13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_11q13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S73.  Gene #16: 'amp_11q13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
AMP PEAK 16(11Q13.3) MUTATED 11 83 30 47
AMP PEAK 16(11Q13.3) WILD-TYPE 60 115 111 53

Figure S73.  Get High-res Image Gene #16: 'amp_11q13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_11q13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.1

Table S74.  Gene #16: 'amp_11q13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
AMP PEAK 16(11Q13.3) MUTATED 18 98 30
AMP PEAK 16(11Q13.3) WILD-TYPE 85 150 53

Figure S74.  Get High-res Image Gene #16: 'amp_11q13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12p12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S75.  Gene #17: 'amp_12p12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
AMP PEAK 17(12P12.1) MUTATED 74 51 54
AMP PEAK 17(12P12.1) WILD-TYPE 117 178 41

Figure S75.  Get High-res Image Gene #17: 'amp_12p12.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_12p12.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S76.  Gene #17: 'amp_12p12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 125 108 116
AMP PEAK 17(12P12.1) MUTATED 10 57 43 40
AMP PEAK 17(12P12.1) WILD-TYPE 86 68 65 76

Figure S76.  Get High-res Image Gene #17: 'amp_12p12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_12p12.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S77.  Gene #17: 'amp_12p12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
AMP PEAK 17(12P12.1) MUTATED 55 10 38 53 16
AMP PEAK 17(12P12.1) WILD-TYPE 83 102 38 53 38

Figure S77.  Get High-res Image Gene #17: 'amp_12p12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_12p12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S78.  Gene #17: 'amp_12p12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
AMP PEAK 17(12P12.1) MUTATED 28 7 21 31 5 32 28 5 15
AMP PEAK 17(12P12.1) WILD-TYPE 55 50 23 53 41 19 21 13 39

Figure S78.  Get High-res Image Gene #17: 'amp_12p12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_12p12.1' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S79.  Gene #17: 'amp_12p12.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
AMP PEAK 17(12P12.1) MUTATED 44 103 29
AMP PEAK 17(12P12.1) WILD-TYPE 145 125 64

Figure S79.  Get High-res Image Gene #17: 'amp_12p12.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_12p12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S80.  Gene #17: 'amp_12p12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
AMP PEAK 17(12P12.1) MUTATED 13 81 35 47
AMP PEAK 17(12P12.1) WILD-TYPE 58 117 106 53

Figure S80.  Get High-res Image Gene #17: 'amp_12p12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_12p12.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S81.  Gene #17: 'amp_12p12.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
AMP PEAK 17(12P12.1) MUTATED 17 107 25
AMP PEAK 17(12P12.1) WILD-TYPE 86 141 58

Figure S81.  Get High-res Image Gene #17: 'amp_12p12.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12q14.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S82.  Gene #18: 'amp_12q14.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
AMP PEAK 18(12Q14.1) MUTATED 67 48 55
AMP PEAK 18(12Q14.1) WILD-TYPE 124 181 40

Figure S82.  Get High-res Image Gene #18: 'amp_12q14.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_12q14.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S83.  Gene #18: 'amp_12q14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 125 108 116
AMP PEAK 18(12Q14.1) MUTATED 11 63 33 38
AMP PEAK 18(12Q14.1) WILD-TYPE 85 62 75 78

Figure S83.  Get High-res Image Gene #18: 'amp_12q14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_12q14.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S84.  Gene #18: 'amp_12q14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
AMP PEAK 18(12Q14.1) MUTATED 42 13 34 58 12
AMP PEAK 18(12Q14.1) WILD-TYPE 96 99 42 48 42

Figure S84.  Get High-res Image Gene #18: 'amp_12q14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_12q14.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S85.  Gene #18: 'amp_12q14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
AMP PEAK 18(12Q14.1) MUTATED 18 11 18 28 6 36 30 2 10
AMP PEAK 18(12Q14.1) WILD-TYPE 65 46 26 56 40 15 19 16 44

Figure S85.  Get High-res Image Gene #18: 'amp_12q14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_12q14.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S86.  Gene #18: 'amp_12q14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
AMP PEAK 18(12Q14.1) MUTATED 34 107 27
AMP PEAK 18(12Q14.1) WILD-TYPE 155 121 66

Figure S86.  Get High-res Image Gene #18: 'amp_12q14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_12q14.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S87.  Gene #18: 'amp_12q14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
AMP PEAK 18(12Q14.1) MUTATED 13 79 25 51
AMP PEAK 18(12Q14.1) WILD-TYPE 58 119 116 49

Figure S87.  Get High-res Image Gene #18: 'amp_12q14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_12q14.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S88.  Gene #18: 'amp_12q14.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
AMP PEAK 18(12Q14.1) MUTATED 11 108 24
AMP PEAK 18(12Q14.1) WILD-TYPE 92 140 59

Figure S88.  Get High-res Image Gene #18: 'amp_12q14.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12q15' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S89.  Gene #19: 'amp_12q15' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
AMP PEAK 19(12Q15) MUTATED 65 51 55
AMP PEAK 19(12Q15) WILD-TYPE 126 178 40

Figure S89.  Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #3: 'CN_CNMF'

'amp_12q15' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S90.  Gene #19: 'amp_12q15' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 125 108 116
AMP PEAK 19(12Q15) MUTATED 11 64 36 35
AMP PEAK 19(12Q15) WILD-TYPE 85 61 72 81

Figure S90.  Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_12q15' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S91.  Gene #19: 'amp_12q15' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
AMP PEAK 19(12Q15) MUTATED 41 13 35 58 12
AMP PEAK 19(12Q15) WILD-TYPE 97 99 41 48 42

Figure S91.  Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_12q15' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S92.  Gene #19: 'amp_12q15' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
AMP PEAK 19(12Q15) MUTATED 18 11 17 28 6 36 29 4 10
AMP PEAK 19(12Q15) WILD-TYPE 65 46 27 56 40 15 20 14 44

Figure S92.  Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_12q15' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S93.  Gene #19: 'amp_12q15' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
AMP PEAK 19(12Q15) MUTATED 35 110 25
AMP PEAK 19(12Q15) WILD-TYPE 154 118 68

Figure S93.  Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_12q15' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S94.  Gene #19: 'amp_12q15' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
AMP PEAK 19(12Q15) MUTATED 12 77 29 52
AMP PEAK 19(12Q15) WILD-TYPE 59 121 112 48

Figure S94.  Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_12q15' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S95.  Gene #19: 'amp_12q15' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
AMP PEAK 19(12Q15) MUTATED 13 106 26
AMP PEAK 19(12Q15) WILD-TYPE 90 142 57

Figure S95.  Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_13q33.3' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.051

Table S96.  Gene #20: 'amp_13q33.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 125 108 116
AMP PEAK 20(13Q33.3) MUTATED 13 34 11 8
AMP PEAK 20(13Q33.3) WILD-TYPE 83 91 97 108

Figure S96.  Get High-res Image Gene #20: 'amp_13q33.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_14q13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S97.  Gene #21: 'amp_14q13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
AMP PEAK 21(14Q13.3) MUTATED 103 63 64
AMP PEAK 21(14Q13.3) WILD-TYPE 88 166 31

Figure S97.  Get High-res Image Gene #21: 'amp_14q13.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_14q13.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S98.  Gene #21: 'amp_14q13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 125 108 116
AMP PEAK 21(14Q13.3) MUTATED 29 77 54 38
AMP PEAK 21(14Q13.3) WILD-TYPE 67 48 54 78

Figure S98.  Get High-res Image Gene #21: 'amp_14q13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_14q13.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S99.  Gene #21: 'amp_14q13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
AMP PEAK 21(14Q13.3) MUTATED 81 39 10 74 15
AMP PEAK 21(14Q13.3) WILD-TYPE 57 73 66 32 39

Figure S99.  Get High-res Image Gene #21: 'amp_14q13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_14q13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S100.  Gene #21: 'amp_14q13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
AMP PEAK 21(14Q13.3) MUTATED 47 25 21 55 9 40 8 0 14
AMP PEAK 21(14Q13.3) WILD-TYPE 36 32 23 29 37 11 41 18 40

Figure S100.  Get High-res Image Gene #21: 'amp_14q13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_14q13.3' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S101.  Gene #21: 'amp_14q13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
AMP PEAK 21(14Q13.3) MUTATED 55 125 47
AMP PEAK 21(14Q13.3) WILD-TYPE 134 103 46

Figure S101.  Get High-res Image Gene #21: 'amp_14q13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_14q13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S102.  Gene #21: 'amp_14q13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
AMP PEAK 21(14Q13.3) MUTATED 28 112 34 53
AMP PEAK 21(14Q13.3) WILD-TYPE 43 86 107 47

Figure S102.  Get High-res Image Gene #21: 'amp_14q13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_14q13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.081

Table S103.  Gene #21: 'amp_14q13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
AMP PEAK 21(14Q13.3) MUTATED 27 125 41
AMP PEAK 21(14Q13.3) WILD-TYPE 76 123 42

Figure S103.  Get High-res Image Gene #21: 'amp_14q13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_16p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S104.  Gene #22: 'amp_16p11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
AMP PEAK 22(16P11.2) MUTATED 85 49 34
AMP PEAK 22(16P11.2) WILD-TYPE 106 180 61

Figure S104.  Get High-res Image Gene #22: 'amp_16p11.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S105.  Gene #23: 'amp_17q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
AMP PEAK 23(17Q12) MUTATED 122 52 53
AMP PEAK 23(17Q12) WILD-TYPE 69 177 42

Figure S105.  Get High-res Image Gene #23: 'amp_17q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S106.  Gene #23: 'amp_17q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 125 108 116
AMP PEAK 23(17Q12) MUTATED 20 68 61 40
AMP PEAK 23(17Q12) WILD-TYPE 76 57 47 76

Figure S106.  Get High-res Image Gene #23: 'amp_17q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17q12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S107.  Gene #23: 'amp_17q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
AMP PEAK 23(17Q12) MUTATED 84 30 24 57 20
AMP PEAK 23(17Q12) WILD-TYPE 54 82 52 49 34

Figure S107.  Get High-res Image Gene #23: 'amp_17q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S108.  Gene #23: 'amp_17q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
AMP PEAK 23(17Q12) MUTATED 43 20 26 51 8 28 19 1 19
AMP PEAK 23(17Q12) WILD-TYPE 40 37 18 33 38 23 30 17 35

Figure S108.  Get High-res Image Gene #23: 'amp_17q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S109.  Gene #23: 'amp_17q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
AMP PEAK 23(17Q12) MUTATED 58 129 38
AMP PEAK 23(17Q12) WILD-TYPE 131 99 55

Figure S109.  Get High-res Image Gene #23: 'amp_17q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_17q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S110.  Gene #23: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
AMP PEAK 23(17Q12) MUTATED 21 103 40 61
AMP PEAK 23(17Q12) WILD-TYPE 50 95 101 39

Figure S110.  Get High-res Image Gene #23: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S111.  Gene #23: 'amp_17q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
AMP PEAK 23(17Q12) MUTATED 24 125 38
AMP PEAK 23(17Q12) WILD-TYPE 79 123 45

Figure S111.  Get High-res Image Gene #23: 'amp_17q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17q23.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S112.  Gene #24: 'amp_17q23.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
AMP PEAK 24(17Q23.1) MUTATED 130 64 55
AMP PEAK 24(17Q23.1) WILD-TYPE 61 165 40

Figure S112.  Get High-res Image Gene #24: 'amp_17q23.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q23.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S113.  Gene #24: 'amp_17q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 125 108 116
AMP PEAK 24(17Q23.1) MUTATED 22 68 74 46
AMP PEAK 24(17Q23.1) WILD-TYPE 74 57 34 70

Figure S113.  Get High-res Image Gene #24: 'amp_17q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17q23.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S114.  Gene #24: 'amp_17q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
AMP PEAK 24(17Q23.1) MUTATED 95 37 30 54 21
AMP PEAK 24(17Q23.1) WILD-TYPE 43 75 46 52 33

Figure S114.  Get High-res Image Gene #24: 'amp_17q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S115.  Gene #24: 'amp_17q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
AMP PEAK 24(17Q23.1) MUTATED 52 25 30 49 7 28 24 0 22
AMP PEAK 24(17Q23.1) WILD-TYPE 31 32 14 35 39 23 25 18 32

Figure S115.  Get High-res Image Gene #24: 'amp_17q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_17q23.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S116.  Gene #24: 'amp_17q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
AMP PEAK 24(17Q23.1) MUTATED 68 136 43
AMP PEAK 24(17Q23.1) WILD-TYPE 121 92 50

Figure S116.  Get High-res Image Gene #24: 'amp_17q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_17q23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S117.  Gene #24: 'amp_17q23.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
AMP PEAK 24(17Q23.1) MUTATED 26 111 48 62
AMP PEAK 24(17Q23.1) WILD-TYPE 45 87 93 38

Figure S117.  Get High-res Image Gene #24: 'amp_17q23.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_17q23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S118.  Gene #24: 'amp_17q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
AMP PEAK 24(17Q23.1) MUTATED 28 134 43
AMP PEAK 24(17Q23.1) WILD-TYPE 75 114 40

Figure S118.  Get High-res Image Gene #24: 'amp_17q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_18q11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S119.  Gene #25: 'amp_18q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 125 108 116
AMP PEAK 25(18Q11.2) MUTATED 6 51 23 14
AMP PEAK 25(18Q11.2) WILD-TYPE 90 74 85 102

Figure S119.  Get High-res Image Gene #25: 'amp_18q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_18q11.2' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.051

Table S120.  Gene #25: 'amp_18q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
AMP PEAK 25(18Q11.2) MUTATED 24 12 19 37 6
AMP PEAK 25(18Q11.2) WILD-TYPE 114 100 57 69 48

Figure S120.  Get High-res Image Gene #25: 'amp_18q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_18q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.075

Table S121.  Gene #25: 'amp_18q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
AMP PEAK 25(18Q11.2) MUTATED 12 5 7 27 6 21 10 4 6
AMP PEAK 25(18Q11.2) WILD-TYPE 71 52 37 57 40 30 39 14 48

Figure S121.  Get High-res Image Gene #25: 'amp_18q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_18q11.2' versus 'MIRSEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.087

Table S122.  Gene #25: 'amp_18q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
AMP PEAK 25(18Q11.2) MUTATED 21 62 20
AMP PEAK 25(18Q11.2) WILD-TYPE 168 166 73

Figure S122.  Get High-res Image Gene #25: 'amp_18q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_18q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.032

Table S123.  Gene #25: 'amp_18q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
AMP PEAK 25(18Q11.2) MUTATED 6 43 19 35
AMP PEAK 25(18Q11.2) WILD-TYPE 65 155 122 65

Figure S123.  Get High-res Image Gene #25: 'amp_18q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_18q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.045

Table S124.  Gene #25: 'amp_18q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
AMP PEAK 25(18Q11.2) MUTATED 10 70 12
AMP PEAK 25(18Q11.2) WILD-TYPE 93 178 71

Figure S124.  Get High-res Image Gene #25: 'amp_18q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19q12' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.051

Table S125.  Gene #26: 'amp_19q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
AMP PEAK 26(19Q12) MUTATED 56 43 40
AMP PEAK 26(19Q12) WILD-TYPE 135 186 55

Figure S125.  Get High-res Image Gene #26: 'amp_19q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S126.  Gene #26: 'amp_19q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 125 108 116
AMP PEAK 26(19Q12) MUTATED 15 56 22 31
AMP PEAK 26(19Q12) WILD-TYPE 81 69 86 85

Figure S126.  Get High-res Image Gene #26: 'amp_19q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_19q12' versus 'MRNASEQ_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.12

Table S127.  Gene #26: 'amp_19q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
AMP PEAK 26(19Q12) MUTATED 38 17 28 40 8
AMP PEAK 26(19Q12) WILD-TYPE 100 95 48 66 46

Figure S127.  Get High-res Image Gene #26: 'amp_19q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_19q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S128.  Gene #26: 'amp_19q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
AMP PEAK 26(19Q12) MUTATED 18 5 14 32 12 17 23 1 9
AMP PEAK 26(19Q12) WILD-TYPE 65 52 30 52 34 34 26 17 45

Figure S128.  Get High-res Image Gene #26: 'amp_19q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S129.  Gene #26: 'amp_19q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
AMP PEAK 26(19Q12) MUTATED 30 86 23
AMP PEAK 26(19Q12) WILD-TYPE 159 142 70

Figure S129.  Get High-res Image Gene #26: 'amp_19q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_19q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00032 (Fisher's exact test), Q value = 0.19

Table S130.  Gene #26: 'amp_19q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
AMP PEAK 26(19Q12) MUTATED 14 61 24 40
AMP PEAK 26(19Q12) WILD-TYPE 57 137 117 60

Figure S130.  Get High-res Image Gene #26: 'amp_19q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.026

Table S131.  Gene #26: 'amp_19q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
AMP PEAK 26(19Q12) MUTATED 19 89 13
AMP PEAK 26(19Q12) WILD-TYPE 84 159 70

Figure S131.  Get High-res Image Gene #26: 'amp_19q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20q13.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S132.  Gene #27: 'amp_20q13.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
AMP PEAK 27(20Q13.33) MUTATED 106 79 65
AMP PEAK 27(20Q13.33) WILD-TYPE 85 150 30

Figure S132.  Get High-res Image Gene #27: 'amp_20q13.33' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20q13.33' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S133.  Gene #27: 'amp_20q13.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 125 108 116
AMP PEAK 27(20Q13.33) MUTATED 36 83 48 45
AMP PEAK 27(20Q13.33) WILD-TYPE 60 42 60 71

Figure S133.  Get High-res Image Gene #27: 'amp_20q13.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20q13.33' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S134.  Gene #27: 'amp_20q13.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
AMP PEAK 27(20Q13.33) MUTATED 71 41 27 75 19
AMP PEAK 27(20Q13.33) WILD-TYPE 67 71 49 31 35

Figure S134.  Get High-res Image Gene #27: 'amp_20q13.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20q13.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S135.  Gene #27: 'amp_20q13.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
AMP PEAK 27(20Q13.33) MUTATED 34 21 28 56 21 36 17 2 18
AMP PEAK 27(20Q13.33) WILD-TYPE 49 36 16 28 25 15 32 16 36

Figure S135.  Get High-res Image Gene #27: 'amp_20q13.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20q13.33' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S136.  Gene #27: 'amp_20q13.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
AMP PEAK 27(20Q13.33) MUTATED 66 138 42
AMP PEAK 27(20Q13.33) WILD-TYPE 123 90 51

Figure S136.  Get High-res Image Gene #27: 'amp_20q13.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_20q13.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S137.  Gene #27: 'amp_20q13.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
AMP PEAK 27(20Q13.33) MUTATED 24 106 53 63
AMP PEAK 27(20Q13.33) WILD-TYPE 47 92 88 37

Figure S137.  Get High-res Image Gene #27: 'amp_20q13.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20q13.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S138.  Gene #27: 'amp_20q13.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
AMP PEAK 27(20Q13.33) MUTATED 30 140 37
AMP PEAK 27(20Q13.33) WILD-TYPE 73 108 46

Figure S138.  Get High-res Image Gene #27: 'amp_20q13.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_22q11.22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S139.  Gene #28: 'amp_22q11.22' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
AMP PEAK 28(22Q11.22) MUTATED 54 23 13
AMP PEAK 28(22Q11.22) WILD-TYPE 137 206 82

Figure S139.  Get High-res Image Gene #28: 'amp_22q11.22' versus Molecular Subtype #3: 'CN_CNMF'

'amp_xq28' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S140.  Gene #29: 'amp_xq28' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
AMP PEAK 29(XQ28) MUTATED 94 34 30
AMP PEAK 29(XQ28) WILD-TYPE 97 195 65

Figure S140.  Get High-res Image Gene #29: 'amp_xq28' versus Molecular Subtype #3: 'CN_CNMF'

'amp_xq28' versus 'METHLYATION_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.045

Table S141.  Gene #29: 'amp_xq28' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 125 108 116
AMP PEAK 29(XQ28) MUTATED 16 47 44 25
AMP PEAK 29(XQ28) WILD-TYPE 80 78 64 91

Figure S141.  Get High-res Image Gene #29: 'amp_xq28' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_xq28' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.032

Table S142.  Gene #29: 'amp_xq28' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
AMP PEAK 29(XQ28) MUTATED 65 23 17 32 12
AMP PEAK 29(XQ28) WILD-TYPE 73 89 59 74 42

Figure S142.  Get High-res Image Gene #29: 'amp_xq28' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_xq28' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.026

Table S143.  Gene #29: 'amp_xq28' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
AMP PEAK 29(XQ28) MUTATED 32 13 23 34 6 13 13 0 15
AMP PEAK 29(XQ28) WILD-TYPE 51 44 21 50 40 38 36 18 39

Figure S143.  Get High-res Image Gene #29: 'amp_xq28' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S144.  Gene #30: 'del_1p36.13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
DEL PEAK 1(1P36.13) MUTATED 30 45 45
DEL PEAK 1(1P36.13) WILD-TYPE 161 184 50

Figure S144.  Get High-res Image Gene #30: 'del_1p36.13' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p36.13' versus 'MRNASEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.057

Table S145.  Gene #30: 'del_1p36.13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
DEL PEAK 1(1P36.13) MUTATED 31 15 23 38 5
DEL PEAK 1(1P36.13) WILD-TYPE 107 97 53 68 49

Figure S145.  Get High-res Image Gene #30: 'del_1p36.13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p36.13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S146.  Gene #30: 'del_1p36.13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
DEL PEAK 1(1P36.13) MUTATED 12 9 15 17 11 25 17 2 4
DEL PEAK 1(1P36.13) WILD-TYPE 71 48 29 67 35 26 32 16 50

Figure S146.  Get High-res Image Gene #30: 'del_1p36.13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S147.  Gene #31: 'del_1p13.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
DEL PEAK 2(1P13.1) MUTATED 49 47 55
DEL PEAK 2(1P13.1) WILD-TYPE 142 182 40

Figure S147.  Get High-res Image Gene #31: 'del_1p13.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p13.1' versus 'MRNASEQ_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.1

Table S148.  Gene #31: 'del_1p13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
DEL PEAK 2(1P13.1) MUTATED 34 26 23 50 10
DEL PEAK 2(1P13.1) WILD-TYPE 104 86 53 56 44

Figure S148.  Get High-res Image Gene #31: 'del_1p13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.14

Table S149.  Gene #31: 'del_1p13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
DEL PEAK 2(1P13.1) MUTATED 18 15 15 22 20 27 16 2 8
DEL PEAK 2(1P13.1) WILD-TYPE 65 42 29 62 26 24 33 16 46

Figure S149.  Get High-res Image Gene #31: 'del_1p13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_2q22.1' versus 'CN_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.21

Table S150.  Gene #32: 'del_2q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
DEL PEAK 3(2Q22.1) MUTATED 23 8 14
DEL PEAK 3(2Q22.1) WILD-TYPE 168 221 81

Figure S150.  Get High-res Image Gene #32: 'del_2q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p26.2' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S151.  Gene #33: 'del_3p26.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
DEL PEAK 4(3P26.2) MUTATED 103 76 53
DEL PEAK 4(3P26.2) WILD-TYPE 88 153 42

Figure S151.  Get High-res Image Gene #33: 'del_3p26.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p26.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S152.  Gene #33: 'del_3p26.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
DEL PEAK 4(3P26.2) MUTATED 28 24 17 57 13 35 28 0 18
DEL PEAK 4(3P26.2) WILD-TYPE 55 33 27 27 33 16 21 18 36

Figure S152.  Get High-res Image Gene #33: 'del_3p26.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p26.2' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S153.  Gene #33: 'del_3p26.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
DEL PEAK 4(3P26.2) MUTATED 60 115 53
DEL PEAK 4(3P26.2) WILD-TYPE 129 113 40

Figure S153.  Get High-res Image Gene #33: 'del_3p26.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3p26.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.081

Table S154.  Gene #33: 'del_3p26.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
DEL PEAK 4(3P26.2) MUTATED 30 85 49 64
DEL PEAK 4(3P26.2) WILD-TYPE 41 113 92 36

Figure S154.  Get High-res Image Gene #33: 'del_3p26.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3p26.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.16

Table S155.  Gene #33: 'del_3p26.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
DEL PEAK 4(3P26.2) MUTATED 30 131 37
DEL PEAK 4(3P26.2) WILD-TYPE 73 117 46

Figure S155.  Get High-res Image Gene #33: 'del_3p26.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p21.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S156.  Gene #34: 'del_3p21.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
DEL PEAK 5(3P21.31) MUTATED 110 78 59
DEL PEAK 5(3P21.31) WILD-TYPE 81 151 36

Figure S156.  Get High-res Image Gene #34: 'del_3p21.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p21.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S157.  Gene #34: 'del_3p21.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 125 108 116
DEL PEAK 5(3P21.31) MUTATED 37 85 45 47
DEL PEAK 5(3P21.31) WILD-TYPE 59 40 63 69

Figure S157.  Get High-res Image Gene #34: 'del_3p21.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3p21.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S158.  Gene #34: 'del_3p21.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
DEL PEAK 5(3P21.31) MUTATED 28 25 19 61 13 37 30 1 19
DEL PEAK 5(3P21.31) WILD-TYPE 55 32 25 23 33 14 19 17 35

Figure S158.  Get High-res Image Gene #34: 'del_3p21.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p21.31' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S159.  Gene #34: 'del_3p21.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
DEL PEAK 5(3P21.31) MUTATED 64 125 54
DEL PEAK 5(3P21.31) WILD-TYPE 125 103 39

Figure S159.  Get High-res Image Gene #34: 'del_3p21.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3p21.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S160.  Gene #34: 'del_3p21.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
DEL PEAK 5(3P21.31) MUTATED 32 93 49 69
DEL PEAK 5(3P21.31) WILD-TYPE 39 105 92 31

Figure S160.  Get High-res Image Gene #34: 'del_3p21.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3p21.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S161.  Gene #34: 'del_3p21.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
DEL PEAK 5(3P21.31) MUTATED 31 141 39
DEL PEAK 5(3P21.31) WILD-TYPE 72 107 44

Figure S161.  Get High-res Image Gene #34: 'del_3p21.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3q29' versus 'METHLYATION_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.13

Table S162.  Gene #36: 'del_3q29' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 125 108 116
DEL PEAK 7(3Q29) MUTATED 35 43 30 15
DEL PEAK 7(3Q29) WILD-TYPE 61 82 78 101

Figure S162.  Get High-res Image Gene #36: 'del_3q29' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3q29' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.051

Table S163.  Gene #36: 'del_3q29' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
DEL PEAK 7(3Q29) MUTATED 22 40 13 41 15
DEL PEAK 7(3Q29) WILD-TYPE 116 72 63 65 39

Figure S163.  Get High-res Image Gene #36: 'del_3q29' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3q29' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S164.  Gene #36: 'del_3q29' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
DEL PEAK 7(3Q29) MUTATED 17 19 5 12 22 29 14 0 13
DEL PEAK 7(3Q29) WILD-TYPE 66 38 39 72 24 22 35 18 41

Figure S164.  Get High-res Image Gene #36: 'del_3q29' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4p16.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S165.  Gene #37: 'del_4p16.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
DEL PEAK 8(4P16.3) MUTATED 54 34 42
DEL PEAK 8(4P16.3) WILD-TYPE 137 195 53

Figure S165.  Get High-res Image Gene #37: 'del_4p16.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_4p16.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S166.  Gene #37: 'del_4p16.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 125 108 116
DEL PEAK 8(4P16.3) MUTATED 7 49 25 32
DEL PEAK 8(4P16.3) WILD-TYPE 89 76 83 84

Figure S166.  Get High-res Image Gene #37: 'del_4p16.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4p16.3' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S167.  Gene #37: 'del_4p16.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
DEL PEAK 8(4P16.3) MUTATED 35 12 20 45 13
DEL PEAK 8(4P16.3) WILD-TYPE 103 100 56 61 41

Figure S167.  Get High-res Image Gene #37: 'del_4p16.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4p16.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S168.  Gene #37: 'del_4p16.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
DEL PEAK 8(4P16.3) MUTATED 18 9 9 39 4 23 11 2 10
DEL PEAK 8(4P16.3) WILD-TYPE 65 48 35 45 42 28 38 16 44

Figure S168.  Get High-res Image Gene #37: 'del_4p16.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4p16.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S169.  Gene #37: 'del_4p16.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
DEL PEAK 8(4P16.3) MUTATED 24 80 25
DEL PEAK 8(4P16.3) WILD-TYPE 165 148 68

Figure S169.  Get High-res Image Gene #37: 'del_4p16.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_4p16.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S170.  Gene #37: 'del_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
DEL PEAK 8(4P16.3) MUTATED 6 57 25 41
DEL PEAK 8(4P16.3) WILD-TYPE 65 141 116 59

Figure S170.  Get High-res Image Gene #37: 'del_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4p16.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00035 (Fisher's exact test), Q value = 0.21

Table S171.  Gene #37: 'del_4p16.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
DEL PEAK 8(4P16.3) MUTATED 13 80 18
DEL PEAK 8(4P16.3) WILD-TYPE 90 168 65

Figure S171.  Get High-res Image Gene #37: 'del_4p16.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q34.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S172.  Gene #38: 'del_4q34.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
DEL PEAK 9(4Q34.3) MUTATED 78 49 59
DEL PEAK 9(4Q34.3) WILD-TYPE 113 180 36

Figure S172.  Get High-res Image Gene #38: 'del_4q34.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q34.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S173.  Gene #38: 'del_4q34.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 125 108 116
DEL PEAK 9(4Q34.3) MUTATED 9 75 35 41
DEL PEAK 9(4Q34.3) WILD-TYPE 87 50 73 75

Figure S173.  Get High-res Image Gene #38: 'del_4q34.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q34.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S174.  Gene #38: 'del_4q34.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
DEL PEAK 9(4Q34.3) MUTATED 45 18 37 64 14
DEL PEAK 9(4Q34.3) WILD-TYPE 93 94 39 42 40

Figure S174.  Get High-res Image Gene #38: 'del_4q34.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4q34.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S175.  Gene #38: 'del_4q34.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
DEL PEAK 9(4Q34.3) MUTATED 24 9 6 50 8 36 29 1 15
DEL PEAK 9(4Q34.3) WILD-TYPE 59 48 38 34 38 15 20 17 39

Figure S175.  Get High-res Image Gene #38: 'del_4q34.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S176.  Gene #38: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
DEL PEAK 9(4Q34.3) MUTATED 39 117 29
DEL PEAK 9(4Q34.3) WILD-TYPE 150 111 64

Figure S176.  Get High-res Image Gene #38: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_4q34.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S177.  Gene #38: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
DEL PEAK 9(4Q34.3) MUTATED 12 80 29 64
DEL PEAK 9(4Q34.3) WILD-TYPE 59 118 112 36

Figure S177.  Get High-res Image Gene #38: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S178.  Gene #38: 'del_4q34.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
DEL PEAK 9(4Q34.3) MUTATED 20 119 20
DEL PEAK 9(4Q34.3) WILD-TYPE 83 129 63

Figure S178.  Get High-res Image Gene #38: 'del_4q34.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S179.  Gene #39: 'del_5q12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
DEL PEAK 10(5Q12.1) MUTATED 97 40 42
DEL PEAK 10(5Q12.1) WILD-TYPE 94 189 53

Figure S179.  Get High-res Image Gene #39: 'del_5q12.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q12.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S180.  Gene #39: 'del_5q12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 125 108 116
DEL PEAK 10(5Q12.1) MUTATED 14 63 38 35
DEL PEAK 10(5Q12.1) WILD-TYPE 82 62 70 81

Figure S180.  Get High-res Image Gene #39: 'del_5q12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5q12.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S181.  Gene #39: 'del_5q12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
DEL PEAK 10(5Q12.1) MUTATED 57 19 29 52 12
DEL PEAK 10(5Q12.1) WILD-TYPE 81 93 47 54 42

Figure S181.  Get High-res Image Gene #39: 'del_5q12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_5q12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S182.  Gene #39: 'del_5q12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
DEL PEAK 10(5Q12.1) MUTATED 30 11 13 46 6 24 24 1 14
DEL PEAK 10(5Q12.1) WILD-TYPE 53 46 31 38 40 27 25 17 40

Figure S182.  Get High-res Image Gene #39: 'del_5q12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5q12.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S183.  Gene #39: 'del_5q12.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
DEL PEAK 10(5Q12.1) MUTATED 36 115 25
DEL PEAK 10(5Q12.1) WILD-TYPE 153 113 68

Figure S183.  Get High-res Image Gene #39: 'del_5q12.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_5q12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S184.  Gene #39: 'del_5q12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
DEL PEAK 10(5Q12.1) MUTATED 12 75 33 56
DEL PEAK 10(5Q12.1) WILD-TYPE 59 123 108 44

Figure S184.  Get High-res Image Gene #39: 'del_5q12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_5q12.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S185.  Gene #39: 'del_5q12.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
DEL PEAK 10(5Q12.1) MUTATED 14 113 21
DEL PEAK 10(5Q12.1) WILD-TYPE 89 135 62

Figure S185.  Get High-res Image Gene #39: 'del_5q12.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q31.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S186.  Gene #40: 'del_5q31.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
DEL PEAK 11(5Q31.1) MUTATED 106 53 51
DEL PEAK 11(5Q31.1) WILD-TYPE 85 176 44

Figure S186.  Get High-res Image Gene #40: 'del_5q31.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q31.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S187.  Gene #40: 'del_5q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 125 108 116
DEL PEAK 11(5Q31.1) MUTATED 18 70 47 41
DEL PEAK 11(5Q31.1) WILD-TYPE 78 55 61 75

Figure S187.  Get High-res Image Gene #40: 'del_5q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5q31.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S188.  Gene #40: 'del_5q31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
DEL PEAK 11(5Q31.1) MUTATED 66 23 33 59 15
DEL PEAK 11(5Q31.1) WILD-TYPE 72 89 43 47 39

Figure S188.  Get High-res Image Gene #40: 'del_5q31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_5q31.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S189.  Gene #40: 'del_5q31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
DEL PEAK 11(5Q31.1) MUTATED 36 12 16 47 10 30 26 1 18
DEL PEAK 11(5Q31.1) WILD-TYPE 47 45 28 37 36 21 23 17 36

Figure S189.  Get High-res Image Gene #40: 'del_5q31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5q31.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S190.  Gene #40: 'del_5q31.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
DEL PEAK 11(5Q31.1) MUTATED 46 130 31
DEL PEAK 11(5Q31.1) WILD-TYPE 143 98 62

Figure S190.  Get High-res Image Gene #40: 'del_5q31.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_5q31.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S191.  Gene #40: 'del_5q31.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
DEL PEAK 11(5Q31.1) MUTATED 18 89 36 64
DEL PEAK 11(5Q31.1) WILD-TYPE 53 109 105 36

Figure S191.  Get High-res Image Gene #40: 'del_5q31.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_5q31.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S192.  Gene #40: 'del_5q31.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
DEL PEAK 11(5Q31.1) MUTATED 21 130 28
DEL PEAK 11(5Q31.1) WILD-TYPE 82 118 55

Figure S192.  Get High-res Image Gene #40: 'del_5q31.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q22.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S193.  Gene #42: 'del_6q22.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 125 108 116
DEL PEAK 13(6Q22.31) MUTATED 53 65 70 36
DEL PEAK 13(6Q22.31) WILD-TYPE 43 60 38 80

Figure S193.  Get High-res Image Gene #42: 'del_6q22.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_6q22.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.093

Table S194.  Gene #42: 'del_6q22.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
DEL PEAK 13(6Q22.31) MUTATED 46 24 21 31 34 33 19 4 29
DEL PEAK 13(6Q22.31) WILD-TYPE 37 33 23 53 12 18 30 14 25

Figure S194.  Get High-res Image Gene #42: 'del_6q22.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_6q26' versus 'CN_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.22

Table S195.  Gene #43: 'del_6q26' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
DEL PEAK 14(6Q26) MUTATED 102 94 61
DEL PEAK 14(6Q26) WILD-TYPE 89 135 34

Figure S195.  Get High-res Image Gene #43: 'del_6q26' versus Molecular Subtype #3: 'CN_CNMF'

'del_8p23.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S196.  Gene #44: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
DEL PEAK 15(8P23.2) MUTATED 137 73 42
DEL PEAK 15(8P23.2) WILD-TYPE 54 156 53

Figure S196.  Get High-res Image Gene #44: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_8p23.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00038 (Fisher's exact test), Q value = 0.22

Table S197.  Gene #44: 'del_8p23.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 40 33 45 31 32
DEL PEAK 15(8P23.2) MUTATED 20 9 33 13 11
DEL PEAK 15(8P23.2) WILD-TYPE 20 24 12 18 21

Figure S197.  Get High-res Image Gene #44: 'del_8p23.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_8p23.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S198.  Gene #44: 'del_8p23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
DEL PEAK 15(8P23.2) MUTATED 96 39 32 50 21
DEL PEAK 15(8P23.2) WILD-TYPE 42 73 44 56 33

Figure S198.  Get High-res Image Gene #44: 'del_8p23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_8p23.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S199.  Gene #44: 'del_8p23.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
DEL PEAK 15(8P23.2) MUTATED 49 22 31 56 10 20 24 2 24
DEL PEAK 15(8P23.2) WILD-TYPE 34 35 13 28 36 31 25 16 30

Figure S199.  Get High-res Image Gene #44: 'del_8p23.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.032

Table S200.  Gene #44: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
DEL PEAK 15(8P23.2) MUTATED 68 127 54
DEL PEAK 15(8P23.2) WILD-TYPE 121 101 39

Figure S200.  Get High-res Image Gene #44: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_8p23.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.1

Table S201.  Gene #44: 'del_8p23.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
DEL PEAK 15(8P23.2) MUTATED 32 137 41
DEL PEAK 15(8P23.2) WILD-TYPE 71 111 42

Figure S201.  Get High-res Image Gene #44: 'del_8p23.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S202.  Gene #45: 'del_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
DEL PEAK 16(8P11.21) MUTATED 84 36 5
DEL PEAK 16(8P11.21) WILD-TYPE 107 193 90

Figure S202.  Get High-res Image Gene #45: 'del_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.039

Table S203.  Gene #46: 'del_9p23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
DEL PEAK 17(9P23) MUTATED 41 31 19 54 22 26 42 10 23
DEL PEAK 17(9P23) WILD-TYPE 42 26 25 30 24 25 7 8 31

Figure S203.  Get High-res Image Gene #46: 'del_9p23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'CN_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.14

Table S204.  Gene #47: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
DEL PEAK 18(9P21.3) MUTATED 130 112 50
DEL PEAK 18(9P21.3) WILD-TYPE 61 117 45

Figure S204.  Get High-res Image Gene #47: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S205.  Gene #47: 'del_9p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
DEL PEAK 18(9P21.3) MUTATED 73 60 64 51 27
DEL PEAK 18(9P21.3) WILD-TYPE 65 52 12 55 27

Figure S205.  Get High-res Image Gene #47: 'del_9p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S206.  Gene #47: 'del_9p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
DEL PEAK 18(9P21.3) MUTATED 43 33 21 54 22 24 44 11 23
DEL PEAK 18(9P21.3) WILD-TYPE 40 24 23 30 24 27 5 7 31

Figure S206.  Get High-res Image Gene #47: 'del_9p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9q21.11' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S207.  Gene #48: 'del_9q21.11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
DEL PEAK 19(9Q21.11) MUTATED 106 89 62
DEL PEAK 19(9Q21.11) WILD-TYPE 85 140 33

Figure S207.  Get High-res Image Gene #48: 'del_9q21.11' versus Molecular Subtype #3: 'CN_CNMF'

'del_9q21.11' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.039

Table S208.  Gene #48: 'del_9q21.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 125 108 116
DEL PEAK 19(9Q21.11) MUTATED 37 83 44 54
DEL PEAK 19(9Q21.11) WILD-TYPE 59 42 64 62

Figure S208.  Get High-res Image Gene #48: 'del_9q21.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9q21.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.039

Table S209.  Gene #48: 'del_9q21.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
DEL PEAK 19(9Q21.11) MUTATED 34 27 19 52 15 37 32 4 24
DEL PEAK 19(9Q21.11) WILD-TYPE 49 30 25 32 31 14 17 14 30

Figure S209.  Get High-res Image Gene #48: 'del_9q21.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9q21.11' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.032

Table S210.  Gene #48: 'del_9q21.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
DEL PEAK 19(9Q21.11) MUTATED 70 126 58
DEL PEAK 19(9Q21.11) WILD-TYPE 119 102 35

Figure S210.  Get High-res Image Gene #48: 'del_9q21.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_9q21.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S211.  Gene #48: 'del_9q21.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
DEL PEAK 19(9Q21.11) MUTATED 26 102 55 71
DEL PEAK 19(9Q21.11) WILD-TYPE 45 96 86 29

Figure S211.  Get High-res Image Gene #48: 'del_9q21.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9q21.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.12

Table S212.  Gene #48: 'del_9q21.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
DEL PEAK 19(9Q21.11) MUTATED 34 142 40
DEL PEAK 19(9Q21.11) WILD-TYPE 69 106 43

Figure S212.  Get High-res Image Gene #48: 'del_9q21.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10p15.3' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.032

Table S213.  Gene #49: 'del_10p15.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
DEL PEAK 20(10P15.3) MUTATED 65 37 23
DEL PEAK 20(10P15.3) WILD-TYPE 126 192 72

Figure S213.  Get High-res Image Gene #49: 'del_10p15.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q26.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S214.  Gene #50: 'del_10q26.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
DEL PEAK 21(10Q26.3) MUTATED 79 42 26
DEL PEAK 21(10Q26.3) WILD-TYPE 112 187 69

Figure S214.  Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q26.3' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S215.  Gene #50: 'del_10q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
DEL PEAK 21(10Q26.3) MUTATED 59 19 13 34 16
DEL PEAK 21(10Q26.3) WILD-TYPE 79 93 63 72 38

Figure S215.  Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10q26.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S216.  Gene #50: 'del_10q26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
DEL PEAK 21(10Q26.3) MUTATED 30 16 15 43 1 11 9 2 14
DEL PEAK 21(10Q26.3) WILD-TYPE 53 41 29 41 45 40 40 16 40

Figure S216.  Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10q26.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.13

Table S217.  Gene #50: 'del_10q26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
DEL PEAK 21(10Q26.3) MUTATED 10 60 32 43
DEL PEAK 21(10Q26.3) WILD-TYPE 61 138 109 57

Figure S217.  Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_10q26.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.18

Table S218.  Gene #50: 'del_10q26.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
DEL PEAK 21(10Q26.3) MUTATED 14 84 26
DEL PEAK 21(10Q26.3) WILD-TYPE 89 164 57

Figure S218.  Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11p15.5' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S219.  Gene #51: 'del_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
DEL PEAK 22(11P15.5) MUTATED 79 35 28
DEL PEAK 22(11P15.5) WILD-TYPE 112 194 67

Figure S219.  Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

'del_11p15.5' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S220.  Gene #51: 'del_11p15.5' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
DEL PEAK 22(11P15.5) MUTATED 23 6 11 34 8 13 23 0 13
DEL PEAK 22(11P15.5) WILD-TYPE 60 51 33 50 38 38 26 18 41

Figure S220.  Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.12

Table S221.  Gene #51: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
DEL PEAK 22(11P15.5) MUTATED 35 83 22
DEL PEAK 22(11P15.5) WILD-TYPE 154 145 71

Figure S221.  Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_11q23.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S222.  Gene #52: 'del_11q23.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
DEL PEAK 23(11Q23.2) MUTATED 39 39 42
DEL PEAK 23(11Q23.2) WILD-TYPE 152 190 53

Figure S222.  Get High-res Image Gene #52: 'del_11q23.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_11q23.2' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.045

Table S223.  Gene #52: 'del_11q23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
DEL PEAK 23(11Q23.2) MUTATED 26 13 25 37 10
DEL PEAK 23(11Q23.2) WILD-TYPE 112 99 51 69 44

Figure S223.  Get High-res Image Gene #52: 'del_11q23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_11q25' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S224.  Gene #53: 'del_11q25' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
DEL PEAK 24(11Q25) MUTATED 43 35 38
DEL PEAK 24(11Q25) WILD-TYPE 148 194 57

Figure S224.  Get High-res Image Gene #53: 'del_11q25' versus Molecular Subtype #3: 'CN_CNMF'

'del_11q25' versus 'MRNASEQ_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.14

Table S225.  Gene #53: 'del_11q25' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
DEL PEAK 24(11Q25) MUTATED 24 14 26 35 10
DEL PEAK 24(11Q25) WILD-TYPE 114 98 50 71 44

Figure S225.  Get High-res Image Gene #53: 'del_11q25' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_12q12' versus 'CN_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.2

Table S226.  Gene #55: 'del_12q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
DEL PEAK 26(12Q12) MUTATED 53 35 10
DEL PEAK 26(12Q12) WILD-TYPE 138 194 85

Figure S226.  Get High-res Image Gene #55: 'del_12q12' versus Molecular Subtype #3: 'CN_CNMF'

'del_12q24.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S227.  Gene #56: 'del_12q24.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
DEL PEAK 27(12Q24.33) MUTATED 65 55 10
DEL PEAK 27(12Q24.33) WILD-TYPE 126 174 85

Figure S227.  Get High-res Image Gene #56: 'del_12q24.33' versus Molecular Subtype #3: 'CN_CNMF'

'del_12q24.33' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.026

Table S228.  Gene #56: 'del_12q24.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
DEL PEAK 27(12Q24.33) MUTATED 46 35 7 16 18
DEL PEAK 27(12Q24.33) WILD-TYPE 92 77 69 90 36

Figure S228.  Get High-res Image Gene #56: 'del_12q24.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_12q24.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S229.  Gene #56: 'del_12q24.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
DEL PEAK 27(12Q24.33) MUTATED 31 18 4 24 15 2 6 2 20
DEL PEAK 27(12Q24.33) WILD-TYPE 52 39 40 60 31 49 43 16 34

Figure S229.  Get High-res Image Gene #56: 'del_12q24.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_13q12.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S230.  Gene #57: 'del_13q12.11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
DEL PEAK 28(13Q12.11) MUTATED 147 79 67
DEL PEAK 28(13Q12.11) WILD-TYPE 44 150 28

Figure S230.  Get High-res Image Gene #57: 'del_13q12.11' versus Molecular Subtype #3: 'CN_CNMF'

'del_13q12.11' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S231.  Gene #57: 'del_13q12.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
DEL PEAK 28(13Q12.11) MUTATED 101 45 30 76 27
DEL PEAK 28(13Q12.11) WILD-TYPE 37 67 46 30 27

Figure S231.  Get High-res Image Gene #57: 'del_13q12.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_13q12.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S232.  Gene #57: 'del_13q12.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
DEL PEAK 28(13Q12.11) MUTATED 60 24 29 61 14 37 24 1 29
DEL PEAK 28(13Q12.11) WILD-TYPE 23 33 15 23 32 14 25 17 25

Figure S232.  Get High-res Image Gene #57: 'del_13q12.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_13q12.13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S233.  Gene #58: 'del_13q12.13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
DEL PEAK 29(13Q12.13) MUTATED 147 77 68
DEL PEAK 29(13Q12.13) WILD-TYPE 44 152 27

Figure S233.  Get High-res Image Gene #58: 'del_13q12.13' versus Molecular Subtype #3: 'CN_CNMF'

'del_13q12.13' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S234.  Gene #58: 'del_13q12.13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
DEL PEAK 29(13Q12.13) MUTATED 99 47 29 76 27
DEL PEAK 29(13Q12.13) WILD-TYPE 39 65 47 30 27

Figure S234.  Get High-res Image Gene #58: 'del_13q12.13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_13q12.13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S235.  Gene #58: 'del_13q12.13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
DEL PEAK 29(13Q12.13) MUTATED 60 26 28 58 14 39 23 1 29
DEL PEAK 29(13Q12.13) WILD-TYPE 23 31 16 26 32 12 26 17 25

Figure S235.  Get High-res Image Gene #58: 'del_13q12.13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_13q14.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S236.  Gene #59: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
DEL PEAK 30(13Q14.2) MUTATED 143 72 67
DEL PEAK 30(13Q14.2) WILD-TYPE 48 157 28

Figure S236.  Get High-res Image Gene #59: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_13q14.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S237.  Gene #59: 'del_13q14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
DEL PEAK 30(13Q14.2) MUTATED 98 43 28 74 25
DEL PEAK 30(13Q14.2) WILD-TYPE 40 69 48 32 29

Figure S237.  Get High-res Image Gene #59: 'del_13q14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_13q14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S238.  Gene #59: 'del_13q14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
DEL PEAK 30(13Q14.2) MUTATED 59 24 29 54 11 40 23 1 27
DEL PEAK 30(13Q14.2) WILD-TYPE 24 33 15 30 35 11 26 17 27

Figure S238.  Get High-res Image Gene #59: 'del_13q14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.057

Table S239.  Gene #59: 'del_13q14.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
DEL PEAK 30(13Q14.2) MUTATED 39 157 44
DEL PEAK 30(13Q14.2) WILD-TYPE 64 91 39

Figure S239.  Get High-res Image Gene #59: 'del_13q14.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_13q34' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S240.  Gene #60: 'del_13q34' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
DEL PEAK 31(13Q34) MUTATED 117 62 62
DEL PEAK 31(13Q34) WILD-TYPE 74 167 33

Figure S240.  Get High-res Image Gene #60: 'del_13q34' versus Molecular Subtype #3: 'CN_CNMF'

'del_13q34' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S241.  Gene #60: 'del_13q34' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
DEL PEAK 31(13Q34) MUTATED 80 38 25 65 22
DEL PEAK 31(13Q34) WILD-TYPE 58 74 51 41 32

Figure S241.  Get High-res Image Gene #60: 'del_13q34' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_13q34' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S242.  Gene #60: 'del_13q34' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
DEL PEAK 31(13Q34) MUTATED 53 19 24 43 13 33 21 1 23
DEL PEAK 31(13Q34) WILD-TYPE 30 38 20 41 33 18 28 17 31

Figure S242.  Get High-res Image Gene #60: 'del_13q34' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_15q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S243.  Gene #62: 'del_15q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
DEL PEAK 33(15Q11.2) MUTATED 126 78 59
DEL PEAK 33(15Q11.2) WILD-TYPE 65 151 36

Figure S243.  Get High-res Image Gene #62: 'del_15q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S244.  Gene #62: 'del_15q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
DEL PEAK 33(15Q11.2) MUTATED 96 43 15 68 26
DEL PEAK 33(15Q11.2) WILD-TYPE 42 69 61 38 28

Figure S244.  Get High-res Image Gene #62: 'del_15q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_15q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S245.  Gene #62: 'del_15q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
DEL PEAK 33(15Q11.2) MUTATED 55 26 30 54 11 35 10 0 27
DEL PEAK 33(15Q11.2) WILD-TYPE 28 31 14 30 35 16 39 18 27

Figure S245.  Get High-res Image Gene #62: 'del_15q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_15q11.2' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S246.  Gene #62: 'del_15q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
DEL PEAK 33(15Q11.2) MUTATED 71 134 56
DEL PEAK 33(15Q11.2) WILD-TYPE 118 94 37

Figure S246.  Get High-res Image Gene #62: 'del_15q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_15q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S247.  Gene #62: 'del_15q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
DEL PEAK 33(15Q11.2) MUTATED 32 138 51
DEL PEAK 33(15Q11.2) WILD-TYPE 71 110 32

Figure S247.  Get High-res Image Gene #62: 'del_15q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q23.1' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S248.  Gene #63: 'del_16q23.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
DEL PEAK 34(16Q23.1) MUTATED 79 48 42
DEL PEAK 34(16Q23.1) WILD-TYPE 112 181 53

Figure S248.  Get High-res Image Gene #63: 'del_16q23.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_16q23.1' versus 'METHLYATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.057

Table S249.  Gene #63: 'del_16q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 125 108 116
DEL PEAK 34(16Q23.1) MUTATED 17 47 50 32
DEL PEAK 34(16Q23.1) WILD-TYPE 79 78 58 84

Figure S249.  Get High-res Image Gene #63: 'del_16q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_16q23.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S250.  Gene #63: 'del_16q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
DEL PEAK 34(16Q23.1) MUTATED 69 19 26 40 11
DEL PEAK 34(16Q23.1) WILD-TYPE 69 93 50 66 43

Figure S250.  Get High-res Image Gene #63: 'del_16q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_16q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S251.  Gene #63: 'del_16q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
DEL PEAK 34(16Q23.1) MUTATED 42 10 24 35 9 17 17 0 11
DEL PEAK 34(16Q23.1) WILD-TYPE 41 47 20 49 37 34 32 18 43

Figure S251.  Get High-res Image Gene #63: 'del_16q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_17p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S252.  Gene #64: 'del_17p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
DEL PEAK 35(17P13.3) MUTATED 149 78 51
DEL PEAK 35(17P13.3) WILD-TYPE 42 151 44

Figure S252.  Get High-res Image Gene #64: 'del_17p13.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_17p13.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S253.  Gene #64: 'del_17p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 125 108 116
DEL PEAK 35(17P13.3) MUTATED 34 69 79 55
DEL PEAK 35(17P13.3) WILD-TYPE 62 56 29 61

Figure S253.  Get High-res Image Gene #64: 'del_17p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_17p13.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S254.  Gene #64: 'del_17p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
DEL PEAK 35(17P13.3) MUTATED 98 42 36 61 24
DEL PEAK 35(17P13.3) WILD-TYPE 40 70 40 45 30

Figure S254.  Get High-res Image Gene #64: 'del_17p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_17p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S255.  Gene #64: 'del_17p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
DEL PEAK 35(17P13.3) MUTATED 59 26 27 51 10 33 22 6 27
DEL PEAK 35(17P13.3) WILD-TYPE 24 31 17 33 36 18 27 12 27

Figure S255.  Get High-res Image Gene #64: 'del_17p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_18q21.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S256.  Gene #65: 'del_18q21.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
DEL PEAK 36(18Q21.32) MUTATED 135 87 32
DEL PEAK 36(18Q21.32) WILD-TYPE 56 142 63

Figure S256.  Get High-res Image Gene #65: 'del_18q21.32' versus Molecular Subtype #3: 'CN_CNMF'

'del_18q21.32' versus 'RPPA_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.099

Table S257.  Gene #65: 'del_18q21.32' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 40 33 45 31 32
DEL PEAK 36(18Q21.32) MUTATED 19 10 36 16 14
DEL PEAK 36(18Q21.32) WILD-TYPE 21 23 9 15 18

Figure S257.  Get High-res Image Gene #65: 'del_18q21.32' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_18q21.32' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S258.  Gene #65: 'del_18q21.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
DEL PEAK 36(18Q21.32) MUTATED 91 42 40 42 23
DEL PEAK 36(18Q21.32) WILD-TYPE 47 70 36 64 31

Figure S258.  Get High-res Image Gene #65: 'del_18q21.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_18q21.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.039

Table S259.  Gene #65: 'del_18q21.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
DEL PEAK 36(18Q21.32) MUTATED 44 28 28 51 9 17 30 9 22
DEL PEAK 36(18Q21.32) WILD-TYPE 39 29 16 33 37 34 19 9 32

Figure S259.  Get High-res Image Gene #65: 'del_18q21.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_18q23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S260.  Gene #66: 'del_18q23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
DEL PEAK 37(18Q23) MUTATED 135 84 30
DEL PEAK 37(18Q23) WILD-TYPE 56 145 65

Figure S260.  Get High-res Image Gene #66: 'del_18q23' versus Molecular Subtype #3: 'CN_CNMF'

'del_18q23' versus 'RPPA_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.045

Table S261.  Gene #66: 'del_18q23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 40 33 45 31 32
DEL PEAK 37(18Q23) MUTATED 17 8 35 16 14
DEL PEAK 37(18Q23) WILD-TYPE 23 25 10 15 18

Figure S261.  Get High-res Image Gene #66: 'del_18q23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_18q23' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S262.  Gene #66: 'del_18q23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
DEL PEAK 37(18Q23) MUTATED 92 42 40 38 23
DEL PEAK 37(18Q23) WILD-TYPE 46 70 36 68 31

Figure S262.  Get High-res Image Gene #66: 'del_18q23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_18q23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.026

Table S263.  Gene #66: 'del_18q23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
DEL PEAK 37(18Q23) MUTATED 42 27 29 50 9 17 30 9 22
DEL PEAK 37(18Q23) WILD-TYPE 41 30 15 34 37 34 19 9 32

Figure S263.  Get High-res Image Gene #66: 'del_18q23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S264.  Gene #67: 'del_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
DEL PEAK 38(19P13.3) MUTATED 118 87 70
DEL PEAK 38(19P13.3) WILD-TYPE 73 142 25

Figure S264.  Get High-res Image Gene #67: 'del_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_19p13.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S265.  Gene #67: 'del_19p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 125 108 116
DEL PEAK 38(19P13.3) MUTATED 41 95 48 53
DEL PEAK 38(19P13.3) WILD-TYPE 55 30 60 63

Figure S265.  Get High-res Image Gene #67: 'del_19p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_19p13.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S266.  Gene #67: 'del_19p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
DEL PEAK 38(19P13.3) MUTATED 70 49 50 76 17
DEL PEAK 38(19P13.3) WILD-TYPE 68 63 26 30 37

Figure S266.  Get High-res Image Gene #67: 'del_19p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_19p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S267.  Gene #67: 'del_19p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
DEL PEAK 38(19P13.3) MUTATED 29 20 22 56 37 34 43 4 17
DEL PEAK 38(19P13.3) WILD-TYPE 54 37 22 28 9 17 6 14 37

Figure S267.  Get High-res Image Gene #67: 'del_19p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S268.  Gene #67: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
DEL PEAK 38(19P13.3) MUTATED 78 151 41
DEL PEAK 38(19P13.3) WILD-TYPE 111 77 52

Figure S268.  Get High-res Image Gene #67: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_19p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S269.  Gene #67: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
DEL PEAK 38(19P13.3) MUTATED 35 113 49 73
DEL PEAK 38(19P13.3) WILD-TYPE 36 85 92 27

Figure S269.  Get High-res Image Gene #67: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.18

Table S270.  Gene #67: 'del_19p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
DEL PEAK 38(19P13.3) MUTATED 46 153 33
DEL PEAK 38(19P13.3) WILD-TYPE 57 95 50

Figure S270.  Get High-res Image Gene #67: 'del_19p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19p13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S271.  Gene #68: 'del_19p13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
DEL PEAK 39(19P13.2) MUTATED 117 84 67
DEL PEAK 39(19P13.2) WILD-TYPE 74 145 28

Figure S271.  Get High-res Image Gene #68: 'del_19p13.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_19p13.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S272.  Gene #68: 'del_19p13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 125 108 116
DEL PEAK 39(19P13.2) MUTATED 38 95 50 49
DEL PEAK 39(19P13.2) WILD-TYPE 58 30 58 67

Figure S272.  Get High-res Image Gene #68: 'del_19p13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_19p13.2' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S273.  Gene #68: 'del_19p13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
DEL PEAK 39(19P13.2) MUTATED 71 47 45 77 17
DEL PEAK 39(19P13.2) WILD-TYPE 67 65 31 29 37

Figure S273.  Get High-res Image Gene #68: 'del_19p13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_19p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S274.  Gene #68: 'del_19p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
DEL PEAK 39(19P13.2) MUTATED 31 18 23 48 36 40 39 4 18
DEL PEAK 39(19P13.2) WILD-TYPE 52 39 21 36 10 11 10 14 36

Figure S274.  Get High-res Image Gene #68: 'del_19p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S275.  Gene #68: 'del_19p13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
DEL PEAK 39(19P13.2) MUTATED 76 148 39
DEL PEAK 39(19P13.2) WILD-TYPE 113 80 54

Figure S275.  Get High-res Image Gene #68: 'del_19p13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_19p13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S276.  Gene #68: 'del_19p13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
DEL PEAK 39(19P13.2) MUTATED 36 108 47 72
DEL PEAK 39(19P13.2) WILD-TYPE 35 90 94 28

Figure S276.  Get High-res Image Gene #68: 'del_19p13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_19p13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.075

Table S277.  Gene #68: 'del_19p13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
DEL PEAK 39(19P13.2) MUTATED 43 152 32
DEL PEAK 39(19P13.2) WILD-TYPE 60 96 51

Figure S277.  Get High-res Image Gene #68: 'del_19p13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19q13.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S278.  Gene #69: 'del_19q13.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
DEL PEAK 40(19Q13.33) MUTATED 98 52 44
DEL PEAK 40(19Q13.33) WILD-TYPE 93 177 51

Figure S278.  Get High-res Image Gene #69: 'del_19q13.33' versus Molecular Subtype #3: 'CN_CNMF'

'del_19q13.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S279.  Gene #69: 'del_19q13.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
DEL PEAK 40(19Q13.33) MUTATED 29 16 21 40 22 24 23 0 10
DEL PEAK 40(19Q13.33) WILD-TYPE 54 41 23 44 24 27 26 18 44

Figure S279.  Get High-res Image Gene #69: 'del_19q13.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_19q13.33' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S280.  Gene #69: 'del_19q13.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
DEL PEAK 40(19Q13.33) MUTATED 47 108 35
DEL PEAK 40(19Q13.33) WILD-TYPE 142 120 58

Figure S280.  Get High-res Image Gene #69: 'del_19q13.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_19q13.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S281.  Gene #69: 'del_19q13.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
DEL PEAK 40(19Q13.33) MUTATED 23 87 28 52
DEL PEAK 40(19Q13.33) WILD-TYPE 48 111 113 48

Figure S281.  Get High-res Image Gene #69: 'del_19q13.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_20p13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S282.  Gene #70: 'del_20p13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
DEL PEAK 41(20P13) MUTATED 73 38 19
DEL PEAK 41(20P13) WILD-TYPE 118 191 76

Figure S282.  Get High-res Image Gene #70: 'del_20p13' versus Molecular Subtype #3: 'CN_CNMF'

'del_20p13' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S283.  Gene #70: 'del_20p13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
DEL PEAK 41(20P13) MUTATED 56 23 21 14 12
DEL PEAK 41(20P13) WILD-TYPE 82 89 55 92 42

Figure S283.  Get High-res Image Gene #70: 'del_20p13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_20p13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S284.  Gene #70: 'del_20p13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
DEL PEAK 41(20P13) MUTATED 32 16 20 15 0 10 16 3 14
DEL PEAK 41(20P13) WILD-TYPE 51 41 24 69 46 41 33 15 40

Figure S284.  Get High-res Image Gene #70: 'del_20p13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_21q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S285.  Gene #72: 'del_21q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
DEL PEAK 43(21Q11.2) MUTATED 57 64 55
DEL PEAK 43(21Q11.2) WILD-TYPE 134 165 40

Figure S285.  Get High-res Image Gene #72: 'del_21q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_21q11.2' versus 'METHLYATION_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.13

Table S286.  Gene #72: 'del_21q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 125 108 116
DEL PEAK 43(21Q11.2) MUTATED 16 55 38 37
DEL PEAK 43(21Q11.2) WILD-TYPE 80 70 70 79

Figure S286.  Get High-res Image Gene #72: 'del_21q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_21q11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S287.  Gene #72: 'del_21q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
DEL PEAK 43(21Q11.2) MUTATED 49 13 30 59 12
DEL PEAK 43(21Q11.2) WILD-TYPE 89 99 46 47 42

Figure S287.  Get High-res Image Gene #72: 'del_21q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_21q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S288.  Gene #72: 'del_21q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
DEL PEAK 43(21Q11.2) MUTATED 18 9 18 33 10 34 24 3 14
DEL PEAK 43(21Q11.2) WILD-TYPE 65 48 26 51 36 17 25 15 40

Figure S288.  Get High-res Image Gene #72: 'del_21q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_21q11.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S289.  Gene #72: 'del_21q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
DEL PEAK 43(21Q11.2) MUTATED 41 108 24
DEL PEAK 43(21Q11.2) WILD-TYPE 148 120 69

Figure S289.  Get High-res Image Gene #72: 'del_21q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_21q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S290.  Gene #72: 'del_21q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
DEL PEAK 43(21Q11.2) MUTATED 16 73 32 52
DEL PEAK 43(21Q11.2) WILD-TYPE 55 125 109 48

Figure S290.  Get High-res Image Gene #72: 'del_21q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_21q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S291.  Gene #72: 'del_21q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
DEL PEAK 43(21Q11.2) MUTATED 18 106 23
DEL PEAK 43(21Q11.2) WILD-TYPE 85 142 60

Figure S291.  Get High-res Image Gene #72: 'del_21q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_22q13.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S292.  Gene #73: 'del_22q13.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
DEL PEAK 44(22Q13.32) MUTATED 116 65 69
DEL PEAK 44(22Q13.32) WILD-TYPE 75 164 26

Figure S292.  Get High-res Image Gene #73: 'del_22q13.32' versus Molecular Subtype #3: 'CN_CNMF'

'del_22q13.32' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S293.  Gene #73: 'del_22q13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 125 108 116
DEL PEAK 44(22Q13.32) MUTATED 25 75 67 49
DEL PEAK 44(22Q13.32) WILD-TYPE 71 50 41 67

Figure S293.  Get High-res Image Gene #73: 'del_22q13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_22q13.32' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S294.  Gene #73: 'del_22q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
DEL PEAK 44(22Q13.32) MUTATED 80 33 36 74 12
DEL PEAK 44(22Q13.32) WILD-TYPE 58 79 40 32 42

Figure S294.  Get High-res Image Gene #73: 'del_22q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_22q13.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S295.  Gene #73: 'del_22q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
DEL PEAK 44(22Q13.32) MUTATED 52 14 24 47 14 39 28 4 13
DEL PEAK 44(22Q13.32) WILD-TYPE 31 43 20 37 32 12 21 14 41

Figure S295.  Get High-res Image Gene #73: 'del_22q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.32' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S296.  Gene #73: 'del_22q13.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
DEL PEAK 44(22Q13.32) MUTATED 65 138 44
DEL PEAK 44(22Q13.32) WILD-TYPE 124 90 49

Figure S296.  Get High-res Image Gene #73: 'del_22q13.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_22q13.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S297.  Gene #73: 'del_22q13.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
DEL PEAK 44(22Q13.32) MUTATED 24 116 46 61
DEL PEAK 44(22Q13.32) WILD-TYPE 47 82 95 39

Figure S297.  Get High-res Image Gene #73: 'del_22q13.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_22q13.32' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S298.  Gene #73: 'del_22q13.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
DEL PEAK 44(22Q13.32) MUTATED 32 144 34
DEL PEAK 44(22Q13.32) WILD-TYPE 71 104 49

Figure S298.  Get High-res Image Gene #73: 'del_22q13.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xp22.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S299.  Gene #74: 'del_xp22.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
DEL PEAK 45(XP22.2) MUTATED 82 37 25
DEL PEAK 45(XP22.2) WILD-TYPE 109 192 70

Figure S299.  Get High-res Image Gene #74: 'del_xp22.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_xp22.2' versus 'MRNASEQ_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.1

Table S300.  Gene #74: 'del_xp22.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
DEL PEAK 45(XP22.2) MUTATED 59 28 13 25 10
DEL PEAK 45(XP22.2) WILD-TYPE 79 84 63 81 44

Figure S300.  Get High-res Image Gene #74: 'del_xp22.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_xp22.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.18

Table S301.  Gene #74: 'del_xp22.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
DEL PEAK 45(XP22.2) MUTATED 36 16 18 27 8 8 8 1 13
DEL PEAK 45(XP22.2) WILD-TYPE 47 41 26 57 38 43 41 17 41

Figure S301.  Get High-res Image Gene #74: 'del_xp22.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

Methods & Data
Input

  • Copy number data file = transformed.cor.cli.txt

  • Molecular subtype file = LUAD-TP.transferedmergedcluster.txt

  • Number of patients = 515

  • Number of significantly focal cnvs = 74

  • Number of molecular subtypes = 12

  • 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)
Copyright © 2015 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle