Correlation between copy number variation genes (focal events) and molecular subtypes
Head and Neck Squamous Cell Carcinoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1KP816C
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1KP816C
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 77 focal events and 10 molecular subtypes across 522 patients, 423 significant findings detected with P value < 0.05 and Q value < 0.25.

  • amp_2q11.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • amp_2q31.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_3q26.33 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • amp_5p15.33 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_6p12.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_6q12 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

  • amp_7q21.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_8p11.23 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_8q11.21 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • amp_9p24.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_9p23 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • amp_9p13.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • amp_9q34.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL', and 'MRNASEQ_CHIERARCHICAL'.

  • amp_11p13 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • amp_11q13.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • amp_12p13.33 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • amp_12q15 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • amp_13q22.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • amp_13q34 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • amp_15q26.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CNMF'.

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

  • amp_18p11.31 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • amp_19p13.2 cnv correlated to 'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • amp_20p12.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_20q11.22 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

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

  • del_1p36.21 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_1p13.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • del_1q44 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • del_2q21.2 cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_2q22.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_2q36.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

  • del_3p24.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_3p14.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • del_3p12.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • del_4p15.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_4q21.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • del_4q22.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • del_4q35.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

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

  • del_5q15 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • del_5q35.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • del_6p25.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL', and 'MRNASEQ_CNMF'.

  • del_7q31.1 cnv correlated to 'CN_CNMF'.

  • del_7q36.1 cnv correlated to 'CN_CNMF' and 'RPPA_CNMF'.

  • del_8p23.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_9p23 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • del_9p21.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

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

  • del_9q34.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • del_10p15.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • del_10p11.21 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • del_10q23.31 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_11p15.5 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_11q23.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_12q24.33 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

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

  • del_13q14.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • del_14q11.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • del_14q32.32 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_15q15.1 cnv correlated to 'CN_CNMF'.

  • del_16q23.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_16q23.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_17p11.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • del_17q25.3 cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_18q21.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • del_18q23 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • del_21q22.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • del_xp22.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • del_xp21.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • del_xq21.33 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 77 focal events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 423 significant findings detected.

Clinical
Features 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
del 1p36 21 95 (18%) 427 1e-05
(4.87e-05) 		1e-05
(4.87e-05) 		0.00087
(0.00278) 		0.0056
(0.0145) 		1e-05
(4.87e-05) 		1e-05
(4.87e-05) 		0.00158
(0.00472) 		0.0413
(0.0779) 		0.00109
(0.0034) 		0.0116
(0.0271)
del 1p13 2 133 (25%) 389 1e-05
(4.87e-05) 		1e-05
(4.87e-05) 		0.0246
(0.0502) 		0.00744
(0.0186) 		0.0233
(0.0484) 		2e-05
(8.95e-05) 		0.00182
(0.00531) 		0.00011
(0.000426) 		0.0007
(0.0023) 		0.184
(0.265)
del 4p15 2 208 (40%) 314 1e-05
(4.87e-05) 		1e-05
(4.87e-05) 		0.0111
(0.0261) 		0.334
(0.424) 		8e-05
(0.000313) 		1e-05
(4.87e-05) 		0.00777
(0.0194) 		0.0289
(0.058) 		0.00023
(0.00082) 		0.017
(0.0375)
del 14q32 32 75 (14%) 447 0.0102
(0.0241) 		1e-05
(4.87e-05) 		0.0181
(0.0393) 		0.469
(0.552) 		1e-05
(4.87e-05) 		1e-05
(4.87e-05) 		0.00102
(0.00322) 		0.0292
(0.058) 		1e-05
(4.87e-05) 		0.00082
(0.00265)
amp 8q11 21 310 (59%) 212 1e-05
(4.87e-05) 		1e-05
(4.87e-05) 		0.0973
(0.158) 		0.631
(0.701) 		0.00014
(0.000528) 		1e-05
(4.87e-05) 		0.033
(0.0641) 		0.00526
(0.0137) 		0.00098
(0.00312) 		0.00243
(0.00688)
del 3p26 2 348 (67%) 174 1e-05
(4.87e-05) 		1e-05
(4.87e-05) 		0.529
(0.603) 		0.212
(0.299) 		0.00016
(0.000595) 		1e-05
(4.87e-05) 		0.0181
(0.0394) 		1e-05
(4.87e-05) 		2e-05
(8.95e-05) 		0.00708
(0.0179)
del 3p24 1 368 (70%) 154 1e-05
(4.87e-05) 		1e-05
(4.87e-05) 		0.42
(0.512) 		0.115
(0.182) 		0.00294
(0.00811) 		1e-05
(4.87e-05) 		0.0025
(0.00703) 		3e-05
(0.000128) 		3e-05
(0.000128) 		0.0297
(0.059)
del 8p23 2 304 (58%) 218 1e-05
(4.87e-05) 		1e-05
(4.87e-05) 		0.281
(0.371) 		0.324
(0.414) 		0.00106
(0.00332) 		1e-05
(4.87e-05) 		0.0178
(0.0389) 		0.00372
(0.00991) 		1e-05
(4.87e-05) 		3e-05
(0.000128)
del 11p15 5 163 (31%) 359 1e-05
(4.87e-05) 		1e-05
(4.87e-05) 		0.868
(0.902) 		0.282
(0.371) 		1e-05
(4.87e-05) 		0.0132
(0.0304) 		1e-05
(4.87e-05) 		0.00326
(0.0089) 		0.00013
(0.000498) 		0.00783
(0.0194)
del 16q23 1 98 (19%) 424 2e-05
(8.95e-05) 		1e-05
(4.87e-05) 		0.469
(0.552) 		0.458
(0.543) 		1e-05
(4.87e-05) 		1e-05
(4.87e-05) 		0.008
(0.0197) 		0.0403
(0.0763) 		2e-05
(8.95e-05) 		0.00116
(0.00359)
amp 8q24 21 386 (74%) 136 1e-05
(4.87e-05) 		1e-05
(4.87e-05) 		0.316
(0.409) 		0.45
(0.536) 		0.00182
(0.00531) 		1e-05
(4.87e-05) 		0.0671
(0.117) 		0.00104
(0.00327) 		0.00021
(0.000756) 		0.00817
(0.02)
amp 9p24 1 126 (24%) 396 1e-05
(4.87e-05) 		1e-05
(4.87e-05) 		0.136
(0.208) 		0.248
(0.336) 		0.0153
(0.0342) 		0.0151
(0.0342) 		0.0773
(0.132) 		0.00102
(0.00322) 		0.00017
(0.000629) 		0.0403
(0.0763)
amp 12p13 33 167 (32%) 355 1e-05
(4.87e-05) 		1e-05
(4.87e-05) 		0.0416
(0.078) 		0.521
(0.596) 		0.0033
(0.00895) 		0.00011
(0.000426) 		0.00175
(0.00516) 		0.0897
(0.148) 		0.00166
(0.00494) 		0.38
(0.47)
amp 17q12 91 (17%) 431 1e-05
(4.87e-05) 		2e-05
(8.95e-05) 		0.188
(0.27) 		0.722
(0.776) 		0.00614
(0.0157) 		2e-05
(8.95e-05) 		0.00326
(0.0089) 		5e-05
(0.000203) 		0.00797
(0.0197) 		0.648
(0.716)
del 1q44 48 (9%) 474 0.00055
(0.00185) 		0.0171
(0.0375) 		0.731
(0.78) 		0.908
(0.929) 		0.0132
(0.0304) 		0.0097
(0.0232) 		0.00174
(0.00515) 		0.0468
(0.0855) 		0.0182
(0.0395) 		0.44
(0.528)
del 10q23 31 138 (26%) 384 1e-05
(4.87e-05) 		1e-05
(4.87e-05) 		0.134
(0.204) 		0.98
(0.986) 		0.0006
(0.002) 		0.00284
(0.00792) 		0.0228
(0.0475) 		0.462
(0.546) 		0.00021
(0.000756) 		0.0324
(0.0632)
del 16q23 3 105 (20%) 417 4e-05
(0.000163) 		1e-05
(4.87e-05) 		0.163
(0.242) 		0.232
(0.323) 		1e-05
(4.87e-05) 		1e-05
(4.87e-05) 		0.0225
(0.0473) 		0.165
(0.243) 		4e-05
(0.000163) 		0.00366
(0.00982)
del 18q21 2 268 (51%) 254 1e-05
(4.87e-05) 		1e-05
(4.87e-05) 		0.9
(0.924) 		0.38
(0.47) 		0.0116
(0.0271) 		1e-05
(4.87e-05) 		0.0332
(0.0643) 		1e-05
(4.87e-05) 		7e-05
(0.000279) 		0.0813
(0.137)
del 18q23 288 (55%) 234 1e-05
(4.87e-05) 		1e-05
(4.87e-05) 		0.257
(0.344) 		0.248
(0.335) 		0.00635
(0.0161) 		1e-05
(4.87e-05) 		0.0627
(0.11) 		1e-05
(4.87e-05) 		1e-05
(4.87e-05) 		0.0211
(0.0447)
del xp22 2 157 (30%) 365 1e-05
(4.87e-05) 		1e-05
(4.87e-05) 		0.318
(0.41) 		0.00265
(0.00742) 		0.0455
(0.0836) 		0.0172
(0.0375) 		0.0054
(0.014) 		0.157
(0.236) 		0.0044
(0.0116) 		0.336
(0.424)
del xq21 33 80 (15%) 442 1e-05
(4.87e-05) 		1e-05
(4.87e-05) 		0.342
(0.43) 		0.126
(0.196) 		0.00066
(0.00218) 		0.00349
(0.00943) 		0.00014
(0.000528) 		0.0124
(0.0288) 		0.0414
(0.0779) 		0.174
(0.253)
amp 2q11 2 107 (20%) 415 1e-05
(4.87e-05) 		1e-05
(4.87e-05) 		0.508
(0.585) 		0.542
(0.617) 		0.0816
(0.137) 		1e-05
(4.87e-05) 		0.0247
(0.0502) 		0.00077
(0.0025) 		0.00222
(0.0064) 		0.0782
(0.132)
amp 2q31 2 112 (21%) 410 1e-05
(4.87e-05) 		1e-05
(4.87e-05) 		0.24
(0.329) 		0.313
(0.406) 		0.236
(0.327) 		1e-05
(4.87e-05) 		0.0778
(0.132) 		0.00658
(0.0167) 		0.00065
(0.00216) 		0.00862
(0.0208)
amp 3q26 33 380 (73%) 142 1e-05
(4.87e-05) 		1e-05
(4.87e-05) 		0.131
(0.202) 		0.308
(0.401) 		1e-05
(4.87e-05) 		0.00031
(0.00107) 		0.00043
(0.00147) 		0.593
(0.664) 		0.00025
(0.000883) 		0.162
(0.242)
amp 7p11 2 222 (43%) 300 1e-05
(4.87e-05) 		1e-05
(4.87e-05) 		0.997
(0.998) 		0.672
(0.735) 		0.0267
(0.0539) 		1e-05
(4.87e-05) 		0.487
(0.566) 		1e-05
(4.87e-05) 		0.00153
(0.00462) 		0.124
(0.193)
amp 9p23 124 (24%) 398 1e-05
(4.87e-05) 		1e-05
(4.87e-05) 		0.389
(0.48) 		0.423
(0.514) 		0.0184
(0.0397) 		0.02
(0.0426) 		0.0759
(0.13) 		0.00245
(0.00691) 		0.00133
(0.00406) 		0.212
(0.299)
amp 9p13 3 139 (27%) 383 1e-05
(4.87e-05) 		0.00242
(0.00688) 		0.487
(0.566) 		0.124
(0.193) 		0.00187
(0.00543) 		0.00126
(0.00387) 		0.0138
(0.0314) 		0.0598
(0.107) 		0.0424
(0.079) 		0.42
(0.512)
amp 18p11 31 156 (30%) 366 1e-05
(4.87e-05) 		1e-05
(4.87e-05) 		0.522
(0.596) 		0.517
(0.594) 		0.0977
(0.158) 		4e-05
(0.000163) 		0.328
(0.419) 		0.00021
(0.000756) 		1e-05
(4.87e-05) 		0.0301
(0.0596)
amp 18q11 2 106 (20%) 416 2e-05
(8.95e-05) 		8e-05
(0.000313) 		0.519
(0.595) 		0.205
(0.292) 		0.428
(0.517) 		0.0128
(0.0297) 		0.0127
(0.0295) 		0.0291
(0.058) 		0.0168
(0.0371) 		0.203
(0.289)
del 2q21 2 78 (15%) 444 0.913
(0.932) 		0.0204
(0.0432) 		0.703
(0.761) 		0.211
(0.299) 		0.0434
(0.08) 		0.00024
(0.000852) 		0.00225
(0.00646) 		0.258
(0.345) 		0.0392
(0.0752) 		0.0355
(0.0684)
del 2q22 1 121 (23%) 401 0.0197
(0.0421) 		2e-05
(8.95e-05) 		0.347
(0.434) 		0.835
(0.873) 		0.24
(0.329) 		0.00894
(0.0215) 		0.161
(0.24) 		0.00116
(0.00359) 		0.0305
(0.0602) 		0.0402
(0.0763)
del 3p14 2 372 (71%) 150 1e-05
(4.87e-05) 		1e-05
(4.87e-05) 		0.61
(0.683) 		0.175
(0.255) 		0.0157
(0.0349) 		1e-05
(4.87e-05) 		0.0886
(0.147) 		0.00034
(0.00116) 		1e-05
(4.87e-05) 		0.316
(0.409)
del 3p12 1 343 (66%) 179 1e-05
(4.87e-05) 		1e-05
(4.87e-05) 		0.829
(0.871) 		0.902
(0.924) 		0.0233
(0.0484) 		1e-05
(4.87e-05) 		0.0605
(0.108) 		0.00046
(0.00156) 		1e-05
(4.87e-05) 		0.519
(0.595)
del 4q21 3 156 (30%) 366 1e-05
(4.87e-05) 		1e-05
(4.87e-05) 		0.287
(0.377) 		0.046
(0.0843) 		0.00847
(0.0206) 		3e-05
(0.000128) 		0.402
(0.493) 		0.0307
(0.0605) 		0.196
(0.281) 		0.937
(0.952)
del 5q12 1 215 (41%) 307 1e-05
(4.87e-05) 		1e-05
(4.87e-05) 		0.0896
(0.148) 		0.359
(0.448) 		0.0621
(0.109) 		1e-05
(4.87e-05) 		0.0867
(0.144) 		4e-05
(0.000163) 		0.00052
(0.00176) 		0.0479
(0.0873)
del 5q35 3 199 (38%) 323 1e-05
(4.87e-05) 		1e-05
(4.87e-05) 		0.242
(0.329) 		0.722
(0.776) 		0.0312
(0.0612) 		1e-05
(4.87e-05) 		0.239
(0.329) 		4e-05
(0.000163) 		0.0003
(0.00104) 		0.116
(0.183)
del 10p11 21 162 (31%) 360 1e-05
(4.87e-05) 		1e-05
(4.87e-05) 		0.449
(0.536) 		0.169
(0.248) 		0.236
(0.328) 		0.0258
(0.0521) 		0.0425
(0.0791) 		0.0152
(0.0342) 		0.0235
(0.0487) 		0.708
(0.765)
del 11q23 1 246 (47%) 276 1e-05
(4.87e-05) 		1e-05
(4.87e-05) 		0.0902
(0.148) 		0.165
(0.243) 		2e-05
(8.95e-05) 		1e-05
(4.87e-05) 		0.00802
(0.0197) 		0.0135
(0.0309) 		0.0734
(0.127) 		0.244
(0.331)
del 13q12 11 233 (45%) 289 1e-05
(4.87e-05) 		1e-05
(4.87e-05) 		0.159
(0.238) 		0.242
(0.329) 		0.0254
(0.0514) 		1e-05
(4.87e-05) 		0.474
(0.557) 		0.0312
(0.0612) 		0.00983
(0.0234) 		0.885
(0.914)
del 13q14 2 217 (42%) 305 1e-05
(4.87e-05) 		1e-05
(4.87e-05) 		0.109
(0.173) 		0.57
(0.642) 		1e-05
(4.87e-05) 		8e-05
(0.000313) 		0.00119
(0.00367) 		0.215
(0.302) 		0.00156
(0.00467) 		0.131
(0.202)
del 19p13 3 175 (34%) 347 1e-05
(4.87e-05) 		1e-05
(4.87e-05) 		0.305
(0.398) 		0.369
(0.459) 		0.0189
(0.0406) 		0.0006
(0.002) 		0.119
(0.187) 		0.00012
(0.000462) 		2e-05
(8.95e-05) 		0.0879
(0.146)
del 21q22 3 208 (40%) 314 1e-05
(4.87e-05) 		1e-05
(4.87e-05) 		0.552
(0.626) 		0.729
(0.78) 		0.00819
(0.02) 		2e-05
(8.95e-05) 		0.336
(0.424) 		4e-05
(0.000163) 		0.00015
(0.000563) 		0.132
(0.202)
amp 7q21 3 169 (32%) 353 1e-05
(4.87e-05) 		1e-05
(4.87e-05) 		0.331
(0.42) 		0.44
(0.528) 		0.205
(0.292) 		1e-05
(4.87e-05) 		0.0434
(0.08) 		0.00018
(0.00066) 		0.0617
(0.109) 		0.872
(0.905)
amp 11q13 3 229 (44%) 293 1e-05
(4.87e-05) 		1e-05
(4.87e-05) 		0.834
(0.873) 		0.73
(0.78) 		0.345
(0.433) 		0.032
(0.0625) 		0.783
(0.829) 		0.00449
(0.0118) 		0.00149
(0.00452) 		0.0607
(0.108)
amp 13q34 106 (20%) 416 1e-05
(4.87e-05) 		6e-05
(0.000241) 		0.226
(0.316) 		0.487
(0.566) 		0.016
(0.0354) 		0.00416
(0.011) 		0.0963
(0.157) 		0.132
(0.202) 		0.016
(0.0354) 		0.125
(0.194)
amp 19p13 2 60 (11%) 462 0.164
(0.242) 		1e-05
(4.87e-05) 		0.0403
(0.0763) 		1
(1.00) 		0.00075
(0.00245) 		0.011
(0.0259) 		0.0213
(0.0448) 		0.231
(0.322) 		0.253
(0.34) 		0.181
(0.261)
amp 20p12 2 191 (37%) 331 2e-05
(8.95e-05) 		6e-05
(0.000241) 		0.874
(0.905) 		0.932
(0.948) 		0.0741
(0.127) 		0.0043
(0.0114) 		0.11
(0.174) 		0.0225
(0.0473) 		0.663
(0.728) 		0.0432
(0.08)
del 4q22 1 169 (32%) 353 1e-05
(4.87e-05) 		1e-05
(4.87e-05) 		0.244
(0.331) 		0.0758
(0.13) 		0.00829
(0.0202) 		0.00028
(0.00098) 		0.261
(0.348) 		0.04
(0.0763) 		0.09
(0.148) 		0.394
(0.485)
del 4q35 2 213 (41%) 309 1e-05
(4.87e-05) 		1e-05
(4.87e-05) 		0.845
(0.882) 		0.187
(0.269) 		0.029
(0.058) 		0.0002
(0.00073) 		0.151
(0.228) 		0.00581
(0.015) 		0.121
(0.189) 		0.242
(0.329)
del 5q15 226 (43%) 296 1e-05
(4.87e-05) 		1e-05
(4.87e-05) 		0.144
(0.219) 		0.43
(0.519) 		0.0989
(0.16) 		1e-05
(4.87e-05) 		0.109
(0.173) 		3e-05
(0.000128) 		0.00016
(0.000595) 		0.341
(0.43)
del 6p25 3 96 (18%) 426 2e-05
(8.95e-05) 		1e-05
(4.87e-05) 		0.0417
(0.078) 		0.0101
(0.0241) 		0.00294
(0.00811) 		0.172
(0.251) 		0.176
(0.255) 		0.727
(0.78) 		0.23
(0.321) 		0.663
(0.728)
del 9p23 239 (46%) 283 1e-05
(4.87e-05) 		1e-05
(4.87e-05) 		0.281
(0.371) 		0.112
(0.178) 		0.974
(0.983) 		1e-05
(4.87e-05) 		0.405
(0.497) 		0.00014
(0.000528) 		1e-05
(4.87e-05) 		0.309
(0.401)
del 9p21 3 302 (58%) 220 1e-05
(4.87e-05) 		1e-05
(4.87e-05) 		0.672
(0.735) 		0.364
(0.455) 		0.279
(0.37) 		1e-05
(4.87e-05) 		0.441
(0.528) 		1e-05
(4.87e-05) 		1e-05
(4.87e-05) 		0.14
(0.213)
del 9q21 11 108 (21%) 414 1e-05
(4.87e-05) 		1e-05
(4.87e-05) 		0.983
(0.988) 		0.236
(0.328) 		0.748
(0.797) 		0.0227
(0.0474) 		0.793
(0.837) 		0.00073
(0.00239) 		0.00329
(0.00895) 		0.92
(0.938)
del 10p15 3 170 (33%) 352 1e-05
(4.87e-05) 		1e-05
(4.87e-05) 		0.475
(0.557) 		0.71
(0.765) 		0.208
(0.295) 		0.00306
(0.00841) 		0.0146
(0.0333) 		0.0805
(0.136) 		0.0003
(0.00104) 		0.344
(0.432)
del 14q11 2 75 (14%) 447 0.00023
(0.00082) 		0.0149
(0.0339) 		0.322
(0.413) 		0.899
(0.924) 		0.104
(0.166) 		0.149
(0.226) 		0.00724
(0.0182) 		0.0331
(0.0643) 		0.00142
(0.00432) 		0.126
(0.196)
amp 5p15 33 240 (46%) 282 1e-05
(4.87e-05) 		1e-05
(4.87e-05) 		0.854
(0.89) 		0.829
(0.871) 		0.0423
(0.079) 		0.681
(0.742) 		0.494
(0.572) 		0.0337
(0.065) 		0.485
(0.566) 		0.984
(0.988)
amp 6p12 1 110 (21%) 412 1e-05
(4.87e-05) 		4e-05
(0.000163) 		0.459
(0.544) 		0.952
(0.965) 		0.702
(0.761) 		0.0362
(0.0694) 		0.427
(0.517) 		0.00242
(0.00688) 		0.0718
(0.124) 		0.171
(0.25)
amp 8p11 23 161 (31%) 361 1e-05
(4.87e-05) 		0.0044
(0.0116) 		0.811
(0.854) 		0.874
(0.905) 		0.0933
(0.152) 		0.17
(0.249) 		0.00227
(0.0065) 		0.0103
(0.0243) 		0.222
(0.311) 		0.131
(0.202)
amp 9q34 3 177 (34%) 345 1e-05
(4.87e-05) 		0.0153
(0.0342) 		0.239
(0.329) 		0.0244
(0.0498) 		0.771
(0.818) 		0.00489
(0.0128) 		0.576
(0.647) 		0.0848
(0.142) 		0.626
(0.697) 		0.319
(0.41)
amp 20q11 22 227 (43%) 295 1e-05
(4.87e-05) 		4e-05
(0.000163) 		0.502
(0.58) 		0.831
(0.872) 		0.0582
(0.104) 		0.0278
(0.0559) 		0.297
(0.389) 		0.0239
(0.0491) 		0.834
(0.873) 		0.0721
(0.124)
del 2q36 2 157 (30%) 365 1e-05
(4.87e-05) 		1e-05
(4.87e-05) 		0.0905
(0.148) 		0.856
(0.891) 		0.0193
(0.0412) 		0.0661
(0.115) 		0.0607
(0.108) 		0.0242
(0.0496) 		0.298
(0.389) 		0.0503
(0.0912)
del 9q34 3 79 (15%) 443 8e-05
(0.000313) 		0.00083
(0.00266) 		0.615
(0.687) 		0.369
(0.459) 		0.775
(0.822) 		0.444
(0.531) 		0.493
(0.571) 		0.00944
(0.0226) 		0.00353
(0.0095) 		0.957
(0.969)
del 17q25 3 71 (14%) 451 0.242
(0.329) 		3e-05
(0.000128) 		0.434
(0.523) 		0.691
(0.753) 		0.0188
(0.0405) 		0.0832
(0.14) 		0.00856
(0.0207) 		0.0503
(0.0912) 		0.0683
(0.119) 		0.00371
(0.00991)
del xp21 3 159 (30%) 363 1e-05
(4.87e-05) 		1e-05
(4.87e-05) 		0.56
(0.633) 		0.0568
(0.102) 		0.508
(0.585) 		0.0238
(0.0491) 		0.108
(0.172) 		0.0852
(0.142) 		0.0136
(0.0311) 		0.252
(0.34)
amp 6q12 96 (18%) 426 1e-05
(4.87e-05) 		0.00018
(0.00066) 		0.274
(0.364) 		0.901
(0.924) 		0.694
(0.753) 		0.00593
(0.0152) 		0.308
(0.401) 		0.239
(0.329) 		0.165
(0.243) 		0.416
(0.508)
amp 11p13 102 (20%) 420 0.00289
(0.00803) 		0.00083
(0.00266) 		0.461
(0.545) 		0.178
(0.258) 		0.902
(0.924) 		0.565
(0.638) 		0.752
(0.8) 		0.491
(0.569) 		0.00583
(0.015) 		0.149
(0.226)
amp 12q15 103 (20%) 419 3e-05
(0.000128) 		0.00034
(0.00116) 		0.0649
(0.114) 		0.205
(0.292) 		0.0896
(0.148) 		0.00154
(0.00463) 		0.743
(0.793) 		0.322
(0.413) 		0.959
(0.97) 		0.369
(0.459)
amp 13q22 1 105 (20%) 417 1e-05
(4.87e-05) 		1e-05
(4.87e-05) 		0.149
(0.225) 		0.154
(0.232) 		0.0966
(0.157) 		0.0776
(0.132) 		0.213
(0.299) 		0.16
(0.24) 		0.0152
(0.0342) 		0.266
(0.354)
amp 15q26 3 105 (20%) 417 2e-05
(8.95e-05) 		0.0072
(0.0181) 		0.454
(0.54) 		0.329
(0.419) 		0.426
(0.517) 		0.0756
(0.13) 		0.163
(0.242) 		0.0507
(0.0916) 		0.0478
(0.0872) 		0.542
(0.617)
del 17p11 2 99 (19%) 423 1e-05
(4.87e-05) 		0.0018
(0.00529) 		0.89
(0.918) 		0.973
(0.983) 		0.297
(0.389) 		0.101
(0.162) 		0.475
(0.557) 		0.127
(0.197) 		0.0239
(0.0491) 		0.929
(0.946)
del 19q13 43 97 (19%) 425 1e-05
(4.87e-05) 		1e-05
(4.87e-05) 		0.33
(0.42) 		0.59
(0.662) 		0.613
(0.685) 		4e-05
(0.000163) 		0.435
(0.524) 		0.0659
(0.115) 		0.239
(0.329) 		0.65
(0.717)
amp xq28 150 (29%) 372 1e-05
(4.87e-05) 		3e-05
(0.000128) 		0.644
(0.712) 		0.198
(0.284) 		0.255
(0.342) 		0.317
(0.409) 		0.255
(0.342) 		0.0929
(0.152) 		0.26
(0.347) 		0.062
(0.109)
del 7q36 1 132 (25%) 390 0.00027
(0.000949) 		0.394
(0.485) 		0.0432
(0.08) 		0.677
(0.739) 		0.888
(0.916) 		0.807
(0.851) 		0.791
(0.837) 		0.331
(0.42) 		0.993
(0.995) 		0.979
(0.986)
del 12q24 33 63 (12%) 459 1e-05
(4.87e-05) 		1e-05
(4.87e-05) 		0.617
(0.688) 		0.457
(0.543) 		0.652
(0.718) 		0.104
(0.167) 		0.48
(0.561) 		0.121
(0.189) 		0.127
(0.196) 		0.556
(0.629)
del 7q31 1 77 (15%) 445 0.00219
(0.00634) 		0.283
(0.373) 		0.57
(0.642) 		0.38
(0.47) 		0.422
(0.513) 		0.552
(0.626) 		0.725
(0.779) 		0.176
(0.255) 		0.479
(0.561) 		0.693
(0.753)
del 15q15 1 124 (24%) 398 1e-05
(4.87e-05) 		0.118
(0.186) 		0.668
(0.733) 		0.412
(0.504) 		0.0534
(0.0964) 		0.0623
(0.11) 		0.704
(0.762) 		0.639
(0.708) 		0.06
(0.107) 		0.632
(0.701)
'amp_2q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S1.  Gene #1: 'amp_2q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
AMP PEAK 1(2Q11.2) MUTATED 36 59 10 2
AMP PEAK 1(2Q11.2) WILD-TYPE 119 76 179 41

Figure S1.  Get High-res Image Gene #1: 'amp_2q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_2q11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S2.  Gene #1: 'amp_2q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
AMP PEAK 1(2Q11.2) MUTATED 6 32 20 39 2 4 4
AMP PEAK 1(2Q11.2) WILD-TYPE 78 47 76 53 76 71 14

Figure S2.  Get High-res Image Gene #1: 'amp_2q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_2q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S3.  Gene #1: 'amp_2q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
AMP PEAK 1(2Q11.2) MUTATED 32 44 28 2
AMP PEAK 1(2Q11.2) WILD-TYPE 144 59 142 63

Figure S3.  Get High-res Image Gene #1: 'amp_2q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_2q11.2' versus 'MIRSEQ_CNMF'

P value = 0.0247 (Fisher's exact test), Q value = 0.05

Table S4.  Gene #1: 'amp_2q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 221 152 145
AMP PEAK 1(2Q11.2) MUTATED 57 23 25
AMP PEAK 1(2Q11.2) WILD-TYPE 164 129 120

Figure S4.  Get High-res Image Gene #1: 'amp_2q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_2q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00077 (Fisher's exact test), Q value = 0.0025

Table S5.  Gene #1: 'amp_2q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
AMP PEAK 1(2Q11.2) MUTATED 35 44 26
AMP PEAK 1(2Q11.2) WILD-TYPE 155 98 160

Figure S5.  Get High-res Image Gene #1: 'amp_2q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_2q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00222 (Fisher's exact test), Q value = 0.0064

Table S6.  Gene #1: 'amp_2q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
AMP PEAK 1(2Q11.2) MUTATED 18 22 31 22 3
AMP PEAK 1(2Q11.2) WILD-TYPE 54 118 67 94 44

Figure S6.  Get High-res Image Gene #1: 'amp_2q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_2q31.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S7.  Gene #2: 'amp_2q31.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
AMP PEAK 2(2Q31.2) MUTATED 37 63 10 2
AMP PEAK 2(2Q31.2) WILD-TYPE 118 72 179 41

Figure S7.  Get High-res Image Gene #2: 'amp_2q31.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_2q31.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S8.  Gene #2: 'amp_2q31.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
AMP PEAK 2(2Q31.2) MUTATED 8 25 18 49 5 4 3
AMP PEAK 2(2Q31.2) WILD-TYPE 76 54 78 43 73 71 15

Figure S8.  Get High-res Image Gene #2: 'amp_2q31.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_2q31.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S9.  Gene #2: 'amp_2q31.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
AMP PEAK 2(2Q31.2) MUTATED 35 41 32 4
AMP PEAK 2(2Q31.2) WILD-TYPE 141 62 138 61

Figure S9.  Get High-res Image Gene #2: 'amp_2q31.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_2q31.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00658 (Fisher's exact test), Q value = 0.017

Table S10.  Gene #2: 'amp_2q31.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
AMP PEAK 2(2Q31.2) MUTATED 40 42 28
AMP PEAK 2(2Q31.2) WILD-TYPE 150 100 158

Figure S10.  Get High-res Image Gene #2: 'amp_2q31.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_2q31.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00065 (Fisher's exact test), Q value = 0.0022

Table S11.  Gene #2: 'amp_2q31.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
AMP PEAK 2(2Q31.2) MUTATED 22 25 30 24 2
AMP PEAK 2(2Q31.2) WILD-TYPE 50 115 68 92 45

Figure S11.  Get High-res Image Gene #2: 'amp_2q31.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_2q31.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00862 (Fisher's exact test), Q value = 0.021

Table S12.  Gene #2: 'amp_2q31.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 244 89
AMP PEAK 2(2Q31.2) MUTATED 41 51 11
AMP PEAK 2(2Q31.2) WILD-TYPE 99 193 78

Figure S12.  Get High-res Image Gene #2: 'amp_2q31.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_3q26.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S13.  Gene #3: 'amp_3q26.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
AMP PEAK 3(3Q26.33) MUTATED 130 125 94 31
AMP PEAK 3(3Q26.33) WILD-TYPE 25 10 95 12

Figure S13.  Get High-res Image Gene #3: 'amp_3q26.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3q26.33' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S14.  Gene #3: 'amp_3q26.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
AMP PEAK 3(3Q26.33) MUTATED 49 66 77 85 62 28 13
AMP PEAK 3(3Q26.33) WILD-TYPE 35 13 19 7 16 47 5

Figure S14.  Get High-res Image Gene #3: 'amp_3q26.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_3q26.33' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S15.  Gene #3: 'amp_3q26.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
AMP PEAK 3(3Q26.33) MUTATED 105 177 94
AMP PEAK 3(3Q26.33) WILD-TYPE 36 35 67

Figure S15.  Get High-res Image Gene #3: 'amp_3q26.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_3q26.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.0011

Table S16.  Gene #3: 'amp_3q26.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
AMP PEAK 3(3Q26.33) MUTATED 130 89 107 50
AMP PEAK 3(3Q26.33) WILD-TYPE 46 14 63 15

Figure S16.  Get High-res Image Gene #3: 'amp_3q26.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_3q26.33' versus 'MIRSEQ_CNMF'

P value = 0.00043 (Fisher's exact test), Q value = 0.0015

Table S17.  Gene #3: 'amp_3q26.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 221 152 145
AMP PEAK 3(3Q26.33) MUTATED 178 95 103
AMP PEAK 3(3Q26.33) WILD-TYPE 43 57 42

Figure S17.  Get High-res Image Gene #3: 'amp_3q26.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_3q26.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.00088

Table S18.  Gene #3: 'amp_3q26.33' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
AMP PEAK 3(3Q26.33) MUTATED 57 84 84 80 32
AMP PEAK 3(3Q26.33) WILD-TYPE 15 56 14 36 15

Figure S18.  Get High-res Image Gene #3: 'amp_3q26.33' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_5p15.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S19.  Gene #4: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
AMP PEAK 4(5P15.33) MUTATED 93 88 44 15
AMP PEAK 4(5P15.33) WILD-TYPE 62 47 145 28

Figure S19.  Get High-res Image Gene #4: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5p15.33' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S20.  Gene #4: 'amp_5p15.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
AMP PEAK 4(5P15.33) MUTATED 29 45 54 52 35 15 10
AMP PEAK 4(5P15.33) WILD-TYPE 55 34 42 40 43 60 8

Figure S20.  Get High-res Image Gene #4: 'amp_5p15.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_5p15.33' versus 'MRNASEQ_CNMF'

P value = 0.0423 (Fisher's exact test), Q value = 0.079

Table S21.  Gene #4: 'amp_5p15.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
AMP PEAK 4(5P15.33) MUTATED 73 104 62
AMP PEAK 4(5P15.33) WILD-TYPE 68 108 99

Figure S21.  Get High-res Image Gene #4: 'amp_5p15.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_5p15.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0337 (Fisher's exact test), Q value = 0.065

Table S22.  Gene #4: 'amp_5p15.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
AMP PEAK 4(5P15.33) MUTATED 86 77 74
AMP PEAK 4(5P15.33) WILD-TYPE 104 65 112

Figure S22.  Get High-res Image Gene #4: 'amp_5p15.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_6p12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S23.  Gene #5: 'amp_6p12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
AMP PEAK 5(6P12.1) MUTATED 46 37 16 11
AMP PEAK 5(6P12.1) WILD-TYPE 109 98 173 32

Figure S23.  Get High-res Image Gene #5: 'amp_6p12.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6p12.1' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00016

Table S24.  Gene #5: 'amp_6p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
AMP PEAK 5(6P12.1) MUTATED 10 26 32 23 7 8 4
AMP PEAK 5(6P12.1) WILD-TYPE 74 53 64 69 71 67 14

Figure S24.  Get High-res Image Gene #5: 'amp_6p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6p12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0362 (Fisher's exact test), Q value = 0.069

Table S25.  Gene #5: 'amp_6p12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
AMP PEAK 5(6P12.1) MUTATED 39 28 35 6
AMP PEAK 5(6P12.1) WILD-TYPE 137 75 135 59

Figure S25.  Get High-res Image Gene #5: 'amp_6p12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_6p12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00242 (Fisher's exact test), Q value = 0.0069

Table S26.  Gene #5: 'amp_6p12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
AMP PEAK 5(6P12.1) MUTATED 48 37 24
AMP PEAK 5(6P12.1) WILD-TYPE 142 105 162

Figure S26.  Get High-res Image Gene #5: 'amp_6p12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_6q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S27.  Gene #6: 'amp_6q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
AMP PEAK 6(6Q12) MUTATED 44 30 12 10
AMP PEAK 6(6Q12) WILD-TYPE 111 105 177 33

Figure S27.  Get High-res Image Gene #6: 'amp_6q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6q12' versus 'METHLYATION_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.00066

Table S28.  Gene #6: 'amp_6q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
AMP PEAK 6(6Q12) MUTATED 10 18 26 25 4 9 4
AMP PEAK 6(6Q12) WILD-TYPE 74 61 70 67 74 66 14

Figure S28.  Get High-res Image Gene #6: 'amp_6q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00593 (Fisher's exact test), Q value = 0.015

Table S29.  Gene #6: 'amp_6q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
AMP PEAK 6(6Q12) MUTATED 31 24 35 3
AMP PEAK 6(6Q12) WILD-TYPE 145 79 135 62

Figure S29.  Get High-res Image Gene #6: 'amp_6q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_7p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S30.  Gene #7: 'amp_7p11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
AMP PEAK 7(7P11.2) MUTATED 90 72 41 19
AMP PEAK 7(7P11.2) WILD-TYPE 65 63 148 24

Figure S30.  Get High-res Image Gene #7: 'amp_7p11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7p11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S31.  Gene #7: 'amp_7p11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
AMP PEAK 7(7P11.2) MUTATED 30 43 52 56 6 24 11
AMP PEAK 7(7P11.2) WILD-TYPE 54 36 44 36 72 51 7

Figure S31.  Get High-res Image Gene #7: 'amp_7p11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7p11.2' versus 'MRNASEQ_CNMF'

P value = 0.0267 (Fisher's exact test), Q value = 0.054

Table S32.  Gene #7: 'amp_7p11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
AMP PEAK 7(7P11.2) MUTATED 64 76 79
AMP PEAK 7(7P11.2) WILD-TYPE 77 136 82

Figure S32.  Get High-res Image Gene #7: 'amp_7p11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_7p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S33.  Gene #7: 'amp_7p11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
AMP PEAK 7(7P11.2) MUTATED 76 57 81 5
AMP PEAK 7(7P11.2) WILD-TYPE 100 46 89 60

Figure S33.  Get High-res Image Gene #7: 'amp_7p11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_7p11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S34.  Gene #7: 'amp_7p11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
AMP PEAK 7(7P11.2) MUTATED 84 83 52
AMP PEAK 7(7P11.2) WILD-TYPE 106 59 134

Figure S34.  Get High-res Image Gene #7: 'amp_7p11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_7p11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00153 (Fisher's exact test), Q value = 0.0046

Table S35.  Gene #7: 'amp_7p11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
AMP PEAK 7(7P11.2) MUTATED 39 62 34 56 10
AMP PEAK 7(7P11.2) WILD-TYPE 33 78 64 60 37

Figure S35.  Get High-res Image Gene #7: 'amp_7p11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_7q21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S36.  Gene #8: 'amp_7q21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
AMP PEAK 8(7Q21.3) MUTATED 52 78 25 14
AMP PEAK 8(7Q21.3) WILD-TYPE 103 57 164 29

Figure S36.  Get High-res Image Gene #8: 'amp_7q21.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7q21.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S37.  Gene #8: 'amp_7q21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
AMP PEAK 8(7Q21.3) MUTATED 14 35 29 62 9 13 7
AMP PEAK 8(7Q21.3) WILD-TYPE 70 44 67 30 69 62 11

Figure S37.  Get High-res Image Gene #8: 'amp_7q21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7q21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S38.  Gene #8: 'amp_7q21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
AMP PEAK 8(7Q21.3) MUTATED 47 52 60 8
AMP PEAK 8(7Q21.3) WILD-TYPE 129 51 110 57

Figure S38.  Get High-res Image Gene #8: 'amp_7q21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_7q21.3' versus 'MIRSEQ_CNMF'

P value = 0.0434 (Fisher's exact test), Q value = 0.08

Table S39.  Gene #8: 'amp_7q21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 221 152 145
AMP PEAK 8(7Q21.3) MUTATED 84 43 39
AMP PEAK 8(7Q21.3) WILD-TYPE 137 109 106

Figure S39.  Get High-res Image Gene #8: 'amp_7q21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_7q21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.00066

Table S40.  Gene #8: 'amp_7q21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
AMP PEAK 8(7Q21.3) MUTATED 56 65 45
AMP PEAK 8(7Q21.3) WILD-TYPE 134 77 141

Figure S40.  Get High-res Image Gene #8: 'amp_7q21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_8p11.23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S41.  Gene #9: 'amp_8p11.23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
AMP PEAK 9(8P11.23) MUTATED 34 70 47 10
AMP PEAK 9(8P11.23) WILD-TYPE 121 65 142 33

Figure S41.  Get High-res Image Gene #9: 'amp_8p11.23' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8p11.23' versus 'METHLYATION_CNMF'

P value = 0.0044 (Fisher's exact test), Q value = 0.012

Table S42.  Gene #9: 'amp_8p11.23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
AMP PEAK 9(8P11.23) MUTATED 19 31 27 36 26 13 9
AMP PEAK 9(8P11.23) WILD-TYPE 65 48 69 56 52 62 9

Figure S42.  Get High-res Image Gene #9: 'amp_8p11.23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8p11.23' versus 'MIRSEQ_CNMF'

P value = 0.00227 (Fisher's exact test), Q value = 0.0065

Table S43.  Gene #9: 'amp_8p11.23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 221 152 145
AMP PEAK 9(8P11.23) MUTATED 86 36 37
AMP PEAK 9(8P11.23) WILD-TYPE 135 116 108

Figure S43.  Get High-res Image Gene #9: 'amp_8p11.23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_8p11.23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0103 (Fisher's exact test), Q value = 0.024

Table S44.  Gene #9: 'amp_8p11.23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
AMP PEAK 9(8P11.23) MUTATED 47 57 55
AMP PEAK 9(8P11.23) WILD-TYPE 143 85 131

Figure S44.  Get High-res Image Gene #9: 'amp_8p11.23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_8q11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S45.  Gene #10: 'amp_8q11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
AMP PEAK 10(8Q11.21) MUTATED 117 79 80 34
AMP PEAK 10(8Q11.21) WILD-TYPE 38 56 109 9

Figure S45.  Get High-res Image Gene #10: 'amp_8q11.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q11.21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S46.  Gene #10: 'amp_8q11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
AMP PEAK 10(8Q11.21) MUTATED 54 43 80 51 29 40 13
AMP PEAK 10(8Q11.21) WILD-TYPE 30 36 16 41 49 35 5

Figure S46.  Get High-res Image Gene #10: 'amp_8q11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8q11.21' versus 'MRNASEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00053

Table S47.  Gene #10: 'amp_8q11.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
AMP PEAK 10(8Q11.21) MUTATED 98 104 103
AMP PEAK 10(8Q11.21) WILD-TYPE 43 108 58

Figure S47.  Get High-res Image Gene #10: 'amp_8q11.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_8q11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S48.  Gene #10: 'amp_8q11.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
AMP PEAK 10(8Q11.21) MUTATED 123 51 109 22
AMP PEAK 10(8Q11.21) WILD-TYPE 53 52 61 43

Figure S48.  Get High-res Image Gene #10: 'amp_8q11.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_8q11.21' versus 'MIRSEQ_CNMF'

P value = 0.033 (Fisher's exact test), Q value = 0.064

Table S49.  Gene #10: 'amp_8q11.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 221 152 145
AMP PEAK 10(8Q11.21) MUTATED 118 93 97
AMP PEAK 10(8Q11.21) WILD-TYPE 103 59 48

Figure S49.  Get High-res Image Gene #10: 'amp_8q11.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_8q11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00526 (Fisher's exact test), Q value = 0.014

Table S50.  Gene #10: 'amp_8q11.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
AMP PEAK 10(8Q11.21) MUTATED 129 83 96
AMP PEAK 10(8Q11.21) WILD-TYPE 61 59 90

Figure S50.  Get High-res Image Gene #10: 'amp_8q11.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_8q11.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00098 (Fisher's exact test), Q value = 0.0031

Table S51.  Gene #10: 'amp_8q11.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
AMP PEAK 10(8Q11.21) MUTATED 45 92 51 76 16
AMP PEAK 10(8Q11.21) WILD-TYPE 27 48 47 40 31

Figure S51.  Get High-res Image Gene #10: 'amp_8q11.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_8q11.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00243 (Fisher's exact test), Q value = 0.0069

Table S52.  Gene #10: 'amp_8q11.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 244 89
AMP PEAK 10(8Q11.21) MUTATED 92 126 62
AMP PEAK 10(8Q11.21) WILD-TYPE 48 118 27

Figure S52.  Get High-res Image Gene #10: 'amp_8q11.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8q24.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S53.  Gene #11: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
AMP PEAK 11(8Q24.21) MUTATED 139 105 105 37
AMP PEAK 11(8Q24.21) WILD-TYPE 16 30 84 6

Figure S53.  Get High-res Image Gene #11: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S54.  Gene #11: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
AMP PEAK 11(8Q24.21) MUTATED 65 58 87 73 35 51 17
AMP PEAK 11(8Q24.21) WILD-TYPE 19 21 9 19 43 24 1

Figure S54.  Get High-res Image Gene #11: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CNMF'

P value = 0.00182 (Fisher's exact test), Q value = 0.0053

Table S55.  Gene #11: 'amp_8q24.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
AMP PEAK 11(8Q24.21) MUTATED 116 140 124
AMP PEAK 11(8Q24.21) WILD-TYPE 25 72 37

Figure S55.  Get High-res Image Gene #11: 'amp_8q24.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S56.  Gene #11: 'amp_8q24.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
AMP PEAK 11(8Q24.21) MUTATED 142 75 136 27
AMP PEAK 11(8Q24.21) WILD-TYPE 34 28 34 38

Figure S56.  Get High-res Image Gene #11: 'amp_8q24.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00104 (Fisher's exact test), Q value = 0.0033

Table S57.  Gene #11: 'amp_8q24.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
AMP PEAK 11(8Q24.21) MUTATED 154 109 120
AMP PEAK 11(8Q24.21) WILD-TYPE 36 33 66

Figure S57.  Get High-res Image Gene #11: 'amp_8q24.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.00076

Table S58.  Gene #11: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
AMP PEAK 11(8Q24.21) MUTATED 54 114 68 91 22
AMP PEAK 11(8Q24.21) WILD-TYPE 18 26 30 25 25

Figure S58.  Get High-res Image Gene #11: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00817 (Fisher's exact test), Q value = 0.02

Table S59.  Gene #11: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 244 89
AMP PEAK 11(8Q24.21) MUTATED 113 165 71
AMP PEAK 11(8Q24.21) WILD-TYPE 27 79 18

Figure S59.  Get High-res Image Gene #11: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_9p24.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S60.  Gene #12: 'amp_9p24.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
AMP PEAK 12(9P24.1) MUTATED 26 21 41 38
AMP PEAK 12(9P24.1) WILD-TYPE 129 114 148 5

Figure S60.  Get High-res Image Gene #12: 'amp_9p24.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_9p24.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S61.  Gene #12: 'amp_9p24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
AMP PEAK 12(9P24.1) MUTATED 16 8 21 19 20 39 3
AMP PEAK 12(9P24.1) WILD-TYPE 68 71 75 73 58 36 15

Figure S61.  Get High-res Image Gene #12: 'amp_9p24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_9p24.1' versus 'MRNASEQ_CNMF'

P value = 0.0153 (Fisher's exact test), Q value = 0.034

Table S62.  Gene #12: 'amp_9p24.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
AMP PEAK 12(9P24.1) MUTATED 31 40 51
AMP PEAK 12(9P24.1) WILD-TYPE 110 172 110

Figure S62.  Get High-res Image Gene #12: 'amp_9p24.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_9p24.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0151 (Fisher's exact test), Q value = 0.034

Table S63.  Gene #12: 'amp_9p24.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
AMP PEAK 12(9P24.1) MUTATED 40 17 54 11
AMP PEAK 12(9P24.1) WILD-TYPE 136 86 116 54

Figure S63.  Get High-res Image Gene #12: 'amp_9p24.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_9p24.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00102 (Fisher's exact test), Q value = 0.0032

Table S64.  Gene #12: 'amp_9p24.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
AMP PEAK 12(9P24.1) MUTATED 43 22 61
AMP PEAK 12(9P24.1) WILD-TYPE 147 120 125

Figure S64.  Get High-res Image Gene #12: 'amp_9p24.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_9p24.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.00063

Table S65.  Gene #12: 'amp_9p24.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
AMP PEAK 12(9P24.1) MUTATED 11 47 12 36 14
AMP PEAK 12(9P24.1) WILD-TYPE 61 93 86 80 33

Figure S65.  Get High-res Image Gene #12: 'amp_9p24.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_9p24.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0403 (Fisher's exact test), Q value = 0.076

Table S66.  Gene #12: 'amp_9p24.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 244 89
AMP PEAK 12(9P24.1) MUTATED 25 68 27
AMP PEAK 12(9P24.1) WILD-TYPE 115 176 62

Figure S66.  Get High-res Image Gene #12: 'amp_9p24.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_9p23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S67.  Gene #13: 'amp_9p23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
AMP PEAK 13(9P23) MUTATED 23 23 40 38
AMP PEAK 13(9P23) WILD-TYPE 132 112 149 5

Figure S67.  Get High-res Image Gene #13: 'amp_9p23' versus Molecular Subtype #1: 'CN_CNMF'

'amp_9p23' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S68.  Gene #13: 'amp_9p23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
AMP PEAK 13(9P23) MUTATED 17 7 20 20 19 38 3
AMP PEAK 13(9P23) WILD-TYPE 67 72 76 72 59 37 15

Figure S68.  Get High-res Image Gene #13: 'amp_9p23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_9p23' versus 'MRNASEQ_CNMF'

P value = 0.0184 (Fisher's exact test), Q value = 0.04

Table S69.  Gene #13: 'amp_9p23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
AMP PEAK 13(9P23) MUTATED 34 38 49
AMP PEAK 13(9P23) WILD-TYPE 107 174 112

Figure S69.  Get High-res Image Gene #13: 'amp_9p23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_9p23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.02 (Fisher's exact test), Q value = 0.043

Table S70.  Gene #13: 'amp_9p23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
AMP PEAK 13(9P23) MUTATED 42 16 52 11
AMP PEAK 13(9P23) WILD-TYPE 134 87 118 54

Figure S70.  Get High-res Image Gene #13: 'amp_9p23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_9p23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00245 (Fisher's exact test), Q value = 0.0069

Table S71.  Gene #13: 'amp_9p23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
AMP PEAK 13(9P23) MUTATED 45 21 58
AMP PEAK 13(9P23) WILD-TYPE 145 121 128

Figure S71.  Get High-res Image Gene #13: 'amp_9p23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_9p23' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00133 (Fisher's exact test), Q value = 0.0041

Table S72.  Gene #13: 'amp_9p23' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
AMP PEAK 13(9P23) MUTATED 12 47 12 32 13
AMP PEAK 13(9P23) WILD-TYPE 60 93 86 84 34

Figure S72.  Get High-res Image Gene #13: 'amp_9p23' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_9p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S73.  Gene #14: 'amp_9p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
AMP PEAK 14(9P13.3) MUTATED 37 31 36 35
AMP PEAK 14(9P13.3) WILD-TYPE 118 104 153 8

Figure S73.  Get High-res Image Gene #14: 'amp_9p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_9p13.3' versus 'METHLYATION_CNMF'

P value = 0.00242 (Fisher's exact test), Q value = 0.0069

Table S74.  Gene #14: 'amp_9p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
AMP PEAK 14(9P13.3) MUTATED 19 15 27 25 14 35 4
AMP PEAK 14(9P13.3) WILD-TYPE 65 64 69 67 64 40 14

Figure S74.  Get High-res Image Gene #14: 'amp_9p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_9p13.3' versus 'MRNASEQ_CNMF'

P value = 0.00187 (Fisher's exact test), Q value = 0.0054

Table S75.  Gene #14: 'amp_9p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
AMP PEAK 14(9P13.3) MUTATED 43 39 54
AMP PEAK 14(9P13.3) WILD-TYPE 98 173 107

Figure S75.  Get High-res Image Gene #14: 'amp_9p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_9p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00126 (Fisher's exact test), Q value = 0.0039

Table S76.  Gene #14: 'amp_9p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
AMP PEAK 14(9P13.3) MUTATED 51 24 55 6
AMP PEAK 14(9P13.3) WILD-TYPE 125 79 115 59

Figure S76.  Get High-res Image Gene #14: 'amp_9p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_9p13.3' versus 'MIRSEQ_CNMF'

P value = 0.0138 (Fisher's exact test), Q value = 0.031

Table S77.  Gene #14: 'amp_9p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 221 152 145
AMP PEAK 14(9P13.3) MUTATED 45 47 47
AMP PEAK 14(9P13.3) WILD-TYPE 176 105 98

Figure S77.  Get High-res Image Gene #14: 'amp_9p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_9p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0424 (Fisher's exact test), Q value = 0.079

Table S78.  Gene #14: 'amp_9p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
AMP PEAK 14(9P13.3) MUTATED 17 45 18 40 10
AMP PEAK 14(9P13.3) WILD-TYPE 55 95 80 76 37

Figure S78.  Get High-res Image Gene #14: 'amp_9p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_9q34.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S79.  Gene #15: 'amp_9q34.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
AMP PEAK 15(9Q34.3) MUTATED 42 57 43 35
AMP PEAK 15(9Q34.3) WILD-TYPE 113 78 146 8

Figure S79.  Get High-res Image Gene #15: 'amp_9q34.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_9q34.3' versus 'METHLYATION_CNMF'

P value = 0.0153 (Fisher's exact test), Q value = 0.034

Table S80.  Gene #15: 'amp_9q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
AMP PEAK 15(9Q34.3) MUTATED 21 21 31 38 22 36 8
AMP PEAK 15(9Q34.3) WILD-TYPE 63 58 65 54 56 39 10

Figure S80.  Get High-res Image Gene #15: 'amp_9q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_9q34.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0244 (Fisher's exact test), Q value = 0.05

Table S81.  Gene #15: 'amp_9q34.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 82 48
AMP PEAK 15(9Q34.3) MUTATED 36 32 11
AMP PEAK 15(9Q34.3) WILD-TYPE 40 50 37

Figure S81.  Get High-res Image Gene #15: 'amp_9q34.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_9q34.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00489 (Fisher's exact test), Q value = 0.013

Table S82.  Gene #15: 'amp_9q34.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
AMP PEAK 15(9Q34.3) MUTATED 60 33 70 11
AMP PEAK 15(9Q34.3) WILD-TYPE 116 70 100 54

Figure S82.  Get High-res Image Gene #15: 'amp_9q34.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_11p13' versus 'CN_CNMF'

P value = 0.00289 (Fisher's exact test), Q value = 0.008

Table S83.  Gene #16: 'amp_11p13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
AMP PEAK 16(11P13) MUTATED 43 22 25 12
AMP PEAK 16(11P13) WILD-TYPE 112 113 164 31

Figure S83.  Get High-res Image Gene #16: 'amp_11p13' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11p13' versus 'METHLYATION_CNMF'

P value = 0.00083 (Fisher's exact test), Q value = 0.0027

Table S84.  Gene #16: 'amp_11p13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
AMP PEAK 16(11P13) MUTATED 9 9 30 24 9 16 5
AMP PEAK 16(11P13) WILD-TYPE 75 70 66 68 69 59 13

Figure S84.  Get High-res Image Gene #16: 'amp_11p13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_11p13' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00583 (Fisher's exact test), Q value = 0.015

Table S85.  Gene #16: 'amp_11p13' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
AMP PEAK 16(11P13) MUTATED 6 35 13 30 8
AMP PEAK 16(11P13) WILD-TYPE 66 105 85 86 39

Figure S85.  Get High-res Image Gene #16: 'amp_11p13' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_11q13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S86.  Gene #17: 'amp_11q13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
AMP PEAK 17(11Q13.3) MUTATED 90 85 37 17
AMP PEAK 17(11Q13.3) WILD-TYPE 65 50 152 26

Figure S86.  Get High-res Image Gene #17: 'amp_11q13.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11q13.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S87.  Gene #17: 'amp_11q13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
AMP PEAK 17(11Q13.3) MUTATED 31 31 62 55 15 21 14
AMP PEAK 17(11Q13.3) WILD-TYPE 53 48 34 37 63 54 4

Figure S87.  Get High-res Image Gene #17: 'amp_11q13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_11q13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.032 (Fisher's exact test), Q value = 0.062

Table S88.  Gene #17: 'amp_11q13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
AMP PEAK 17(11Q13.3) MUTATED 82 42 84 19
AMP PEAK 17(11Q13.3) WILD-TYPE 94 61 86 46

Figure S88.  Get High-res Image Gene #17: 'amp_11q13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_11q13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00449 (Fisher's exact test), Q value = 0.012

Table S89.  Gene #17: 'amp_11q13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
AMP PEAK 17(11Q13.3) MUTATED 91 72 64
AMP PEAK 17(11Q13.3) WILD-TYPE 99 70 122

Figure S89.  Get High-res Image Gene #17: 'amp_11q13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_11q13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00149 (Fisher's exact test), Q value = 0.0045

Table S90.  Gene #17: 'amp_11q13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
AMP PEAK 17(11Q13.3) MUTATED 30 67 36 62 10
AMP PEAK 17(11Q13.3) WILD-TYPE 42 73 62 54 37

Figure S90.  Get High-res Image Gene #17: 'amp_11q13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_12p13.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S91.  Gene #18: 'amp_12p13.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
AMP PEAK 18(12P13.33) MUTATED 60 70 22 15
AMP PEAK 18(12P13.33) WILD-TYPE 95 65 167 28

Figure S91.  Get High-res Image Gene #18: 'amp_12p13.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12p13.33' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S92.  Gene #18: 'amp_12p13.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
AMP PEAK 18(12P13.33) MUTATED 14 36 33 46 23 11 4
AMP PEAK 18(12P13.33) WILD-TYPE 70 43 63 46 55 64 14

Figure S92.  Get High-res Image Gene #18: 'amp_12p13.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_12p13.33' versus 'RPPA_CNMF'

P value = 0.0416 (Fisher's exact test), Q value = 0.078

Table S93.  Gene #18: 'amp_12p13.33' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 53 51 37 65
AMP PEAK 18(12P13.33) MUTATED 23 23 12 15
AMP PEAK 18(12P13.33) WILD-TYPE 30 28 25 50

Figure S93.  Get High-res Image Gene #18: 'amp_12p13.33' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_12p13.33' versus 'MRNASEQ_CNMF'

P value = 0.0033 (Fisher's exact test), Q value = 0.0089

Table S94.  Gene #18: 'amp_12p13.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
AMP PEAK 18(12P13.33) MUTATED 49 81 36
AMP PEAK 18(12P13.33) WILD-TYPE 92 131 125

Figure S94.  Get High-res Image Gene #18: 'amp_12p13.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_12p13.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.00043

Table S95.  Gene #18: 'amp_12p13.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
AMP PEAK 18(12P13.33) MUTATED 61 50 39 16
AMP PEAK 18(12P13.33) WILD-TYPE 115 53 131 49

Figure S95.  Get High-res Image Gene #18: 'amp_12p13.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_12p13.33' versus 'MIRSEQ_CNMF'

P value = 0.00175 (Fisher's exact test), Q value = 0.0052

Table S96.  Gene #18: 'amp_12p13.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 221 152 145
AMP PEAK 18(12P13.33) MUTATED 84 32 50
AMP PEAK 18(12P13.33) WILD-TYPE 137 120 95

Figure S96.  Get High-res Image Gene #18: 'amp_12p13.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_12p13.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00166 (Fisher's exact test), Q value = 0.0049

Table S97.  Gene #18: 'amp_12p13.33' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
AMP PEAK 18(12P13.33) MUTATED 30 33 44 33 11
AMP PEAK 18(12P13.33) WILD-TYPE 42 107 54 83 36

Figure S97.  Get High-res Image Gene #18: 'amp_12p13.33' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_12q15' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00013

Table S98.  Gene #19: 'amp_12q15' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
AMP PEAK 19(12Q15) MUTATED 34 40 17 12
AMP PEAK 19(12Q15) WILD-TYPE 121 95 172 31

Figure S98.  Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12q15' versus 'METHLYATION_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.0012

Table S99.  Gene #19: 'amp_12q15' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
AMP PEAK 19(12Q15) MUTATED 8 21 22 30 13 7 2
AMP PEAK 19(12Q15) WILD-TYPE 76 58 74 62 65 68 16

Figure S99.  Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_12q15' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00154 (Fisher's exact test), Q value = 0.0046

Table S100.  Gene #19: 'amp_12q15' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
AMP PEAK 19(12Q15) MUTATED 35 34 25 8
AMP PEAK 19(12Q15) WILD-TYPE 141 69 145 57

Figure S100.  Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_13q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S101.  Gene #20: 'amp_13q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
AMP PEAK 20(13Q22.1) MUTATED 61 27 14 3
AMP PEAK 20(13Q22.1) WILD-TYPE 94 108 175 40

Figure S101.  Get High-res Image Gene #20: 'amp_13q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_13q22.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S102.  Gene #20: 'amp_13q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
AMP PEAK 20(13Q22.1) MUTATED 8 20 35 18 12 5 7
AMP PEAK 20(13Q22.1) WILD-TYPE 76 59 61 74 66 70 11

Figure S102.  Get High-res Image Gene #20: 'amp_13q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_13q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0152 (Fisher's exact test), Q value = 0.034

Table S103.  Gene #20: 'amp_13q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
AMP PEAK 20(13Q22.1) MUTATED 9 31 15 32 4
AMP PEAK 20(13Q22.1) WILD-TYPE 63 109 83 84 43

Figure S103.  Get High-res Image Gene #20: 'amp_13q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_13q34' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S104.  Gene #21: 'amp_13q34' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
AMP PEAK 21(13Q34) MUTATED 59 22 18 7
AMP PEAK 21(13Q34) WILD-TYPE 96 113 171 36

Figure S104.  Get High-res Image Gene #21: 'amp_13q34' versus Molecular Subtype #1: 'CN_CNMF'

'amp_13q34' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00024

Table S105.  Gene #21: 'amp_13q34' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
AMP PEAK 21(13Q34) MUTATED 11 18 34 20 10 6 7
AMP PEAK 21(13Q34) WILD-TYPE 73 61 62 72 68 69 11

Figure S105.  Get High-res Image Gene #21: 'amp_13q34' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_13q34' versus 'MRNASEQ_CNMF'

P value = 0.016 (Fisher's exact test), Q value = 0.035

Table S106.  Gene #21: 'amp_13q34' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
AMP PEAK 21(13Q34) MUTATED 32 31 42
AMP PEAK 21(13Q34) WILD-TYPE 109 181 119

Figure S106.  Get High-res Image Gene #21: 'amp_13q34' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_13q34' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00416 (Fisher's exact test), Q value = 0.011

Table S107.  Gene #21: 'amp_13q34' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
AMP PEAK 21(13Q34) MUTATED 46 22 33 4
AMP PEAK 21(13Q34) WILD-TYPE 130 81 137 61

Figure S107.  Get High-res Image Gene #21: 'amp_13q34' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_13q34' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.016 (Fisher's exact test), Q value = 0.035

Table S108.  Gene #21: 'amp_13q34' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
AMP PEAK 21(13Q34) MUTATED 10 37 14 30 5
AMP PEAK 21(13Q34) WILD-TYPE 62 103 84 86 42

Figure S108.  Get High-res Image Gene #21: 'amp_13q34' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_15q26.3' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9e-05

Table S109.  Gene #22: 'amp_15q26.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
AMP PEAK 22(15Q26.3) MUTATED 39 42 17 7
AMP PEAK 22(15Q26.3) WILD-TYPE 116 93 172 36

Figure S109.  Get High-res Image Gene #22: 'amp_15q26.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_15q26.3' versus 'METHLYATION_CNMF'

P value = 0.0072 (Fisher's exact test), Q value = 0.018

Table S110.  Gene #22: 'amp_15q26.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
AMP PEAK 22(15Q26.3) MUTATED 9 19 23 26 8 14 6
AMP PEAK 22(15Q26.3) WILD-TYPE 75 60 73 66 70 61 12

Figure S110.  Get High-res Image Gene #22: 'amp_15q26.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_15q26.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0478 (Fisher's exact test), Q value = 0.087

Table S111.  Gene #22: 'amp_15q26.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
AMP PEAK 22(15Q26.3) MUTATED 11 24 26 28 4
AMP PEAK 22(15Q26.3) WILD-TYPE 61 116 72 88 43

Figure S111.  Get High-res Image Gene #22: 'amp_15q26.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_17q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S112.  Gene #23: 'amp_17q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
AMP PEAK 23(17Q12) MUTATED 26 48 9 8
AMP PEAK 23(17Q12) WILD-TYPE 129 87 180 35

Figure S112.  Get High-res Image Gene #23: 'amp_17q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q12' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9e-05

Table S113.  Gene #23: 'amp_17q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
AMP PEAK 23(17Q12) MUTATED 7 21 21 29 6 6 1
AMP PEAK 23(17Q12) WILD-TYPE 77 58 75 63 72 69 17

Figure S113.  Get High-res Image Gene #23: 'amp_17q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_17q12' versus 'MRNASEQ_CNMF'

P value = 0.00614 (Fisher's exact test), Q value = 0.016

Table S114.  Gene #23: 'amp_17q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
AMP PEAK 23(17Q12) MUTATED 22 50 18
AMP PEAK 23(17Q12) WILD-TYPE 119 162 143

Figure S114.  Get High-res Image Gene #23: 'amp_17q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_17q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 9e-05

Table S115.  Gene #23: 'amp_17q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
AMP PEAK 23(17Q12) MUTATED 24 36 23 7
AMP PEAK 23(17Q12) WILD-TYPE 152 67 147 58

Figure S115.  Get High-res Image Gene #23: 'amp_17q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_CNMF'

P value = 0.00326 (Fisher's exact test), Q value = 0.0089

Table S116.  Gene #23: 'amp_17q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 221 152 145
AMP PEAK 23(17Q12) MUTATED 53 18 19
AMP PEAK 23(17Q12) WILD-TYPE 168 134 126

Figure S116.  Get High-res Image Gene #23: 'amp_17q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_17q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 2e-04

Table S117.  Gene #23: 'amp_17q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
AMP PEAK 23(17Q12) MUTATED 31 41 18
AMP PEAK 23(17Q12) WILD-TYPE 159 101 168

Figure S117.  Get High-res Image Gene #23: 'amp_17q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00797 (Fisher's exact test), Q value = 0.02

Table S118.  Gene #23: 'amp_17q12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
AMP PEAK 23(17Q12) MUTATED 12 22 29 18 3
AMP PEAK 23(17Q12) WILD-TYPE 60 118 69 98 44

Figure S118.  Get High-res Image Gene #23: 'amp_17q12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_18p11.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S119.  Gene #24: 'amp_18p11.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
AMP PEAK 24(18P11.31) MUTATED 61 63 23 9
AMP PEAK 24(18P11.31) WILD-TYPE 94 72 166 34

Figure S119.  Get High-res Image Gene #24: 'amp_18p11.31' versus Molecular Subtype #1: 'CN_CNMF'

'amp_18p11.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S120.  Gene #24: 'amp_18p11.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
AMP PEAK 24(18P11.31) MUTATED 9 45 33 34 21 10 4
AMP PEAK 24(18P11.31) WILD-TYPE 75 34 63 58 57 65 14

Figure S120.  Get High-res Image Gene #24: 'amp_18p11.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_18p11.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00016

Table S121.  Gene #24: 'amp_18p11.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
AMP PEAK 24(18P11.31) MUTATED 46 52 39 17
AMP PEAK 24(18P11.31) WILD-TYPE 130 51 131 48

Figure S121.  Get High-res Image Gene #24: 'amp_18p11.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_18p11.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.00076

Table S122.  Gene #24: 'amp_18p11.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
AMP PEAK 24(18P11.31) MUTATED 49 62 44
AMP PEAK 24(18P11.31) WILD-TYPE 141 80 142

Figure S122.  Get High-res Image Gene #24: 'amp_18p11.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_18p11.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S123.  Gene #24: 'amp_18p11.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
AMP PEAK 24(18P11.31) MUTATED 25 28 47 30 7
AMP PEAK 24(18P11.31) WILD-TYPE 47 112 51 86 40

Figure S123.  Get High-res Image Gene #24: 'amp_18p11.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_18p11.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0301 (Fisher's exact test), Q value = 0.06

Table S124.  Gene #24: 'amp_18p11.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 244 89
AMP PEAK 24(18P11.31) MUTATED 42 79 16
AMP PEAK 24(18P11.31) WILD-TYPE 98 165 73

Figure S124.  Get High-res Image Gene #24: 'amp_18p11.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_18q11.2' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9e-05

Table S125.  Gene #25: 'amp_18q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
AMP PEAK 25(18Q11.2) MUTATED 42 40 19 5
AMP PEAK 25(18Q11.2) WILD-TYPE 113 95 170 38

Figure S125.  Get High-res Image Gene #25: 'amp_18q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_18q11.2' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00031

Table S126.  Gene #25: 'amp_18q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
AMP PEAK 25(18Q11.2) MUTATED 6 24 24 26 17 6 3
AMP PEAK 25(18Q11.2) WILD-TYPE 78 55 72 66 61 69 15

Figure S126.  Get High-res Image Gene #25: 'amp_18q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_18q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0128 (Fisher's exact test), Q value = 0.03

Table S127.  Gene #25: 'amp_18q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
AMP PEAK 25(18Q11.2) MUTATED 29 33 29 14
AMP PEAK 25(18Q11.2) WILD-TYPE 147 70 141 51

Figure S127.  Get High-res Image Gene #25: 'amp_18q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_18q11.2' versus 'MIRSEQ_CNMF'

P value = 0.0127 (Fisher's exact test), Q value = 0.03

Table S128.  Gene #25: 'amp_18q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 221 152 145
AMP PEAK 25(18Q11.2) MUTATED 58 22 25
AMP PEAK 25(18Q11.2) WILD-TYPE 163 130 120

Figure S128.  Get High-res Image Gene #25: 'amp_18q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_18q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0291 (Fisher's exact test), Q value = 0.058

Table S129.  Gene #25: 'amp_18q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
AMP PEAK 25(18Q11.2) MUTATED 33 40 32
AMP PEAK 25(18Q11.2) WILD-TYPE 157 102 154

Figure S129.  Get High-res Image Gene #25: 'amp_18q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_18q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0168 (Fisher's exact test), Q value = 0.037

Table S130.  Gene #25: 'amp_18q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
AMP PEAK 25(18Q11.2) MUTATED 13 20 31 22 6
AMP PEAK 25(18Q11.2) WILD-TYPE 59 120 67 94 41

Figure S130.  Get High-res Image Gene #25: 'amp_18q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_19p13.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S131.  Gene #26: 'amp_19p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
AMP PEAK 26(19P13.2) MUTATED 4 9 4 20 20 2 1
AMP PEAK 26(19P13.2) WILD-TYPE 80 70 92 72 58 73 17

Figure S131.  Get High-res Image Gene #26: 'amp_19p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_19p13.2' versus 'RPPA_CNMF'

P value = 0.0403 (Fisher's exact test), Q value = 0.076

Table S132.  Gene #26: 'amp_19p13.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 53 51 37 65
AMP PEAK 26(19P13.2) MUTATED 4 9 5 2
AMP PEAK 26(19P13.2) WILD-TYPE 49 42 32 63

Figure S132.  Get High-res Image Gene #26: 'amp_19p13.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_19p13.2' versus 'MRNASEQ_CNMF'

P value = 0.00075 (Fisher's exact test), Q value = 0.0024

Table S133.  Gene #26: 'amp_19p13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
AMP PEAK 26(19P13.2) MUTATED 12 37 9
AMP PEAK 26(19P13.2) WILD-TYPE 129 175 152

Figure S133.  Get High-res Image Gene #26: 'amp_19p13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_19p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.011 (Fisher's exact test), Q value = 0.026

Table S134.  Gene #26: 'amp_19p13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
AMP PEAK 26(19P13.2) MUTATED 13 17 15 13
AMP PEAK 26(19P13.2) WILD-TYPE 163 86 155 52

Figure S134.  Get High-res Image Gene #26: 'amp_19p13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_19p13.2' versus 'MIRSEQ_CNMF'

P value = 0.0213 (Fisher's exact test), Q value = 0.045

Table S135.  Gene #26: 'amp_19p13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 221 152 145
AMP PEAK 26(19P13.2) MUTATED 35 14 10
AMP PEAK 26(19P13.2) WILD-TYPE 186 138 135

Figure S135.  Get High-res Image Gene #26: 'amp_19p13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_20p12.2' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9e-05

Table S136.  Gene #27: 'amp_20p12.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
AMP PEAK 27(20P12.2) MUTATED 80 46 48 17
AMP PEAK 27(20P12.2) WILD-TYPE 75 89 141 26

Figure S136.  Get High-res Image Gene #27: 'amp_20p12.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20p12.2' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00024

Table S137.  Gene #27: 'amp_20p12.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
AMP PEAK 27(20P12.2) MUTATED 28 25 54 39 21 16 8
AMP PEAK 27(20P12.2) WILD-TYPE 56 54 42 53 57 59 10

Figure S137.  Get High-res Image Gene #27: 'amp_20p12.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_20p12.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0043 (Fisher's exact test), Q value = 0.011

Table S138.  Gene #27: 'amp_20p12.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
AMP PEAK 27(20P12.2) MUTATED 80 34 59 14
AMP PEAK 27(20P12.2) WILD-TYPE 96 69 111 51

Figure S138.  Get High-res Image Gene #27: 'amp_20p12.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_20p12.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0225 (Fisher's exact test), Q value = 0.047

Table S139.  Gene #27: 'amp_20p12.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
AMP PEAK 27(20P12.2) MUTATED 84 50 57
AMP PEAK 27(20P12.2) WILD-TYPE 106 92 129

Figure S139.  Get High-res Image Gene #27: 'amp_20p12.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_20p12.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0432 (Fisher's exact test), Q value = 0.08

Table S140.  Gene #27: 'amp_20p12.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 244 89
AMP PEAK 27(20P12.2) MUTATED 61 76 35
AMP PEAK 27(20P12.2) WILD-TYPE 79 168 54

Figure S140.  Get High-res Image Gene #27: 'amp_20p12.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20q11.22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S141.  Gene #28: 'amp_20q11.22' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
AMP PEAK 28(20Q11.22) MUTATED 94 60 53 20
AMP PEAK 28(20Q11.22) WILD-TYPE 61 75 136 23

Figure S141.  Get High-res Image Gene #28: 'amp_20q11.22' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20q11.22' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00016

Table S142.  Gene #28: 'amp_20q11.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
AMP PEAK 28(20Q11.22) MUTATED 31 38 59 45 27 18 9
AMP PEAK 28(20Q11.22) WILD-TYPE 53 41 37 47 51 57 9

Figure S142.  Get High-res Image Gene #28: 'amp_20q11.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_20q11.22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0278 (Fisher's exact test), Q value = 0.056

Table S143.  Gene #28: 'amp_20q11.22' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
AMP PEAK 28(20Q11.22) MUTATED 90 44 69 20
AMP PEAK 28(20Q11.22) WILD-TYPE 86 59 101 45

Figure S143.  Get High-res Image Gene #28: 'amp_20q11.22' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_20q11.22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0239 (Fisher's exact test), Q value = 0.049

Table S144.  Gene #28: 'amp_20q11.22' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
AMP PEAK 28(20Q11.22) MUTATED 96 61 68
AMP PEAK 28(20Q11.22) WILD-TYPE 94 81 118

Figure S144.  Get High-res Image Gene #28: 'amp_20q11.22' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_xq28' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S145.  Gene #29: 'amp_xq28' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
AMP PEAK 29(XQ28) MUTATED 66 46 26 12
AMP PEAK 29(XQ28) WILD-TYPE 89 89 163 31

Figure S145.  Get High-res Image Gene #29: 'amp_xq28' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xq28' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00013

Table S146.  Gene #29: 'amp_xq28' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
AMP PEAK 29(XQ28) MUTATED 11 20 42 37 20 13 7
AMP PEAK 29(XQ28) WILD-TYPE 73 59 54 55 58 62 11

Figure S146.  Get High-res Image Gene #29: 'amp_xq28' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p36.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S147.  Gene #30: 'del_1p36.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
DEL PEAK 1(1P36.21) MUTATED 26 50 15 4
DEL PEAK 1(1P36.21) WILD-TYPE 129 85 174 39

Figure S147.  Get High-res Image Gene #30: 'del_1p36.21' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S148.  Gene #30: 'del_1p36.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
DEL PEAK 1(1P36.21) MUTATED 4 17 8 48 8 8 2
DEL PEAK 1(1P36.21) WILD-TYPE 80 62 88 44 70 67 16

Figure S148.  Get High-res Image Gene #30: 'del_1p36.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p36.21' versus 'RPPA_CNMF'

P value = 0.00087 (Fisher's exact test), Q value = 0.0028

Table S149.  Gene #30: 'del_1p36.21' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 53 51 37 65
DEL PEAK 1(1P36.21) MUTATED 9 22 4 10
DEL PEAK 1(1P36.21) WILD-TYPE 44 29 33 55

Figure S149.  Get High-res Image Gene #30: 'del_1p36.21' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_1p36.21' versus 'RPPA_CHIERARCHICAL'

P value = 0.0056 (Fisher's exact test), Q value = 0.014

Table S150.  Gene #30: 'del_1p36.21' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 82 48
DEL PEAK 1(1P36.21) MUTATED 15 26 4
DEL PEAK 1(1P36.21) WILD-TYPE 61 56 44

Figure S150.  Get High-res Image Gene #30: 'del_1p36.21' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_1p36.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S151.  Gene #30: 'del_1p36.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
DEL PEAK 1(1P36.21) MUTATED 22 60 12
DEL PEAK 1(1P36.21) WILD-TYPE 119 152 149

Figure S151.  Get High-res Image Gene #30: 'del_1p36.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_1p36.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S152.  Gene #30: 'del_1p36.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 1(1P36.21) MUTATED 27 43 17 7
DEL PEAK 1(1P36.21) WILD-TYPE 149 60 153 58

Figure S152.  Get High-res Image Gene #30: 'del_1p36.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.21' versus 'MIRSEQ_CNMF'

P value = 0.00158 (Fisher's exact test), Q value = 0.0047

Table S153.  Gene #30: 'del_1p36.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 221 152 145
DEL PEAK 1(1P36.21) MUTATED 55 19 18
DEL PEAK 1(1P36.21) WILD-TYPE 166 133 127

Figure S153.  Get High-res Image Gene #30: 'del_1p36.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_1p36.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0413 (Fisher's exact test), Q value = 0.078

Table S154.  Gene #30: 'del_1p36.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
DEL PEAK 1(1P36.21) MUTATED 27 35 30
DEL PEAK 1(1P36.21) WILD-TYPE 163 107 156

Figure S154.  Get High-res Image Gene #30: 'del_1p36.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00109 (Fisher's exact test), Q value = 0.0034

Table S155.  Gene #30: 'del_1p36.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
DEL PEAK 1(1P36.21) MUTATED 14 13 29 21 5
DEL PEAK 1(1P36.21) WILD-TYPE 58 127 69 95 42

Figure S155.  Get High-res Image Gene #30: 'del_1p36.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_1p36.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0116 (Fisher's exact test), Q value = 0.027

Table S156.  Gene #30: 'del_1p36.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 244 89
DEL PEAK 1(1P36.21) MUTATED 23 52 7
DEL PEAK 1(1P36.21) WILD-TYPE 117 192 82

Figure S156.  Get High-res Image Gene #30: 'del_1p36.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S157.  Gene #31: 'del_1p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
DEL PEAK 2(1P13.2) MUTATED 51 61 11 10
DEL PEAK 2(1P13.2) WILD-TYPE 104 74 178 33

Figure S157.  Get High-res Image Gene #31: 'del_1p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p13.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S158.  Gene #31: 'del_1p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
DEL PEAK 2(1P13.2) MUTATED 13 25 20 55 6 8 6
DEL PEAK 2(1P13.2) WILD-TYPE 71 54 76 37 72 67 12

Figure S158.  Get High-res Image Gene #31: 'del_1p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p13.2' versus 'RPPA_CNMF'

P value = 0.0246 (Fisher's exact test), Q value = 0.05

Table S159.  Gene #31: 'del_1p13.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 53 51 37 65
DEL PEAK 2(1P13.2) MUTATED 8 21 10 21
DEL PEAK 2(1P13.2) WILD-TYPE 45 30 27 44

Figure S159.  Get High-res Image Gene #31: 'del_1p13.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_1p13.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00744 (Fisher's exact test), Q value = 0.019

Table S160.  Gene #31: 'del_1p13.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 82 48
DEL PEAK 2(1P13.2) MUTATED 17 34 9
DEL PEAK 2(1P13.2) WILD-TYPE 59 48 39

Figure S160.  Get High-res Image Gene #31: 'del_1p13.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_1p13.2' versus 'MRNASEQ_CNMF'

P value = 0.0233 (Fisher's exact test), Q value = 0.048

Table S161.  Gene #31: 'del_1p13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
DEL PEAK 2(1P13.2) MUTATED 35 66 30
DEL PEAK 2(1P13.2) WILD-TYPE 106 146 131

Figure S161.  Get High-res Image Gene #31: 'del_1p13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_1p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 9e-05

Table S162.  Gene #31: 'del_1p13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 2(1P13.2) MUTATED 43 45 37 6
DEL PEAK 2(1P13.2) WILD-TYPE 133 58 133 59

Figure S162.  Get High-res Image Gene #31: 'del_1p13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1p13.2' versus 'MIRSEQ_CNMF'

P value = 0.00182 (Fisher's exact test), Q value = 0.0053

Table S163.  Gene #31: 'del_1p13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 221 152 145
DEL PEAK 2(1P13.2) MUTATED 73 27 31
DEL PEAK 2(1P13.2) WILD-TYPE 148 125 114

Figure S163.  Get High-res Image Gene #31: 'del_1p13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_1p13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.00043

Table S164.  Gene #31: 'del_1p13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
DEL PEAK 2(1P13.2) MUTATED 47 53 31
DEL PEAK 2(1P13.2) WILD-TYPE 143 89 155

Figure S164.  Get High-res Image Gene #31: 'del_1p13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_1p13.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 7e-04 (Fisher's exact test), Q value = 0.0023

Table S165.  Gene #31: 'del_1p13.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
DEL PEAK 2(1P13.2) MUTATED 29 28 34 24 6
DEL PEAK 2(1P13.2) WILD-TYPE 43 112 64 92 41

Figure S165.  Get High-res Image Gene #31: 'del_1p13.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_1q44' versus 'CN_CNMF'

P value = 0.00055 (Fisher's exact test), Q value = 0.0018

Table S166.  Gene #32: 'del_1q44' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
DEL PEAK 3(1Q44) MUTATED 25 10 7 6
DEL PEAK 3(1Q44) WILD-TYPE 130 125 182 37

Figure S166.  Get High-res Image Gene #32: 'del_1q44' versus Molecular Subtype #1: 'CN_CNMF'

'del_1q44' versus 'METHLYATION_CNMF'

P value = 0.0171 (Fisher's exact test), Q value = 0.038

Table S167.  Gene #32: 'del_1q44' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
DEL PEAK 3(1Q44) MUTATED 7 6 16 8 1 7 3
DEL PEAK 3(1Q44) WILD-TYPE 77 73 80 84 77 68 15

Figure S167.  Get High-res Image Gene #32: 'del_1q44' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1q44' versus 'MRNASEQ_CNMF'

P value = 0.0132 (Fisher's exact test), Q value = 0.03

Table S168.  Gene #32: 'del_1q44' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
DEL PEAK 3(1Q44) MUTATED 17 10 19
DEL PEAK 3(1Q44) WILD-TYPE 124 202 142

Figure S168.  Get High-res Image Gene #32: 'del_1q44' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_1q44' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0097 (Fisher's exact test), Q value = 0.023

Table S169.  Gene #32: 'del_1q44' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 3(1Q44) MUTATED 25 8 12 1
DEL PEAK 3(1Q44) WILD-TYPE 151 95 158 64

Figure S169.  Get High-res Image Gene #32: 'del_1q44' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1q44' versus 'MIRSEQ_CNMF'

P value = 0.00174 (Fisher's exact test), Q value = 0.0052

Table S170.  Gene #32: 'del_1q44' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 221 152 145
DEL PEAK 3(1Q44) MUTATED 9 20 18
DEL PEAK 3(1Q44) WILD-TYPE 212 132 127

Figure S170.  Get High-res Image Gene #32: 'del_1q44' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_1q44' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0468 (Fisher's exact test), Q value = 0.086

Table S171.  Gene #32: 'del_1q44' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
DEL PEAK 3(1Q44) MUTATED 25 11 11
DEL PEAK 3(1Q44) WILD-TYPE 165 131 175

Figure S171.  Get High-res Image Gene #32: 'del_1q44' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_1q44' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0182 (Fisher's exact test), Q value = 0.039

Table S172.  Gene #32: 'del_1q44' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
DEL PEAK 3(1Q44) MUTATED 6 20 2 10 4
DEL PEAK 3(1Q44) WILD-TYPE 66 120 96 106 43

Figure S172.  Get High-res Image Gene #32: 'del_1q44' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_2q21.2' versus 'METHLYATION_CNMF'

P value = 0.0204 (Fisher's exact test), Q value = 0.043

Table S173.  Gene #33: 'del_2q21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
DEL PEAK 4(2Q21.2) MUTATED 6 7 19 17 9 18 2
DEL PEAK 4(2Q21.2) WILD-TYPE 78 72 77 75 69 57 16

Figure S173.  Get High-res Image Gene #33: 'del_2q21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q21.2' versus 'MRNASEQ_CNMF'

P value = 0.0434 (Fisher's exact test), Q value = 0.08

Table S174.  Gene #33: 'del_2q21.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
DEL PEAK 4(2Q21.2) MUTATED 16 26 33
DEL PEAK 4(2Q21.2) WILD-TYPE 125 186 128

Figure S174.  Get High-res Image Gene #33: 'del_2q21.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2q21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.00085

Table S175.  Gene #33: 'del_2q21.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 4(2Q21.2) MUTATED 24 6 40 5
DEL PEAK 4(2Q21.2) WILD-TYPE 152 97 130 60

Figure S175.  Get High-res Image Gene #33: 'del_2q21.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_2q21.2' versus 'MIRSEQ_CNMF'

P value = 0.00225 (Fisher's exact test), Q value = 0.0065

Table S176.  Gene #33: 'del_2q21.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 221 152 145
DEL PEAK 4(2Q21.2) MUTATED 33 33 11
DEL PEAK 4(2Q21.2) WILD-TYPE 188 119 134

Figure S176.  Get High-res Image Gene #33: 'del_2q21.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_2q21.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0392 (Fisher's exact test), Q value = 0.075

Table S177.  Gene #33: 'del_2q21.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
DEL PEAK 4(2Q21.2) MUTATED 6 30 12 17 3
DEL PEAK 4(2Q21.2) WILD-TYPE 66 110 86 99 44

Figure S177.  Get High-res Image Gene #33: 'del_2q21.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_2q21.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0355 (Fisher's exact test), Q value = 0.068

Table S178.  Gene #33: 'del_2q21.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 244 89
DEL PEAK 4(2Q21.2) MUTATED 14 34 20
DEL PEAK 4(2Q21.2) WILD-TYPE 126 210 69

Figure S178.  Get High-res Image Gene #33: 'del_2q21.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_2q22.1' versus 'CN_CNMF'

P value = 0.0197 (Fisher's exact test), Q value = 0.042

Table S179.  Gene #34: 'del_2q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
DEL PEAK 5(2Q22.1) MUTATED 42 39 30 10
DEL PEAK 5(2Q22.1) WILD-TYPE 113 96 159 33

Figure S179.  Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q22.1' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9e-05

Table S180.  Gene #34: 'del_2q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
DEL PEAK 5(2Q22.1) MUTATED 10 16 23 38 11 22 1
DEL PEAK 5(2Q22.1) WILD-TYPE 74 63 73 54 67 53 17

Figure S180.  Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00894 (Fisher's exact test), Q value = 0.022

Table S181.  Gene #34: 'del_2q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 5(2Q22.1) MUTATED 34 30 47 7
DEL PEAK 5(2Q22.1) WILD-TYPE 142 73 123 58

Figure S181.  Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_2q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00116 (Fisher's exact test), Q value = 0.0036

Table S182.  Gene #34: 'del_2q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
DEL PEAK 5(2Q22.1) MUTATED 39 49 33
DEL PEAK 5(2Q22.1) WILD-TYPE 151 93 153

Figure S182.  Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_2q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0305 (Fisher's exact test), Q value = 0.06

Table S183.  Gene #34: 'del_2q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
DEL PEAK 5(2Q22.1) MUTATED 19 38 23 29 3
DEL PEAK 5(2Q22.1) WILD-TYPE 53 102 75 87 44

Figure S183.  Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_2q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0402 (Fisher's exact test), Q value = 0.076

Table S184.  Gene #34: 'del_2q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 244 89
DEL PEAK 5(2Q22.1) MUTATED 24 60 28
DEL PEAK 5(2Q22.1) WILD-TYPE 116 184 61

Figure S184.  Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_2q36.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S185.  Gene #35: 'del_2q36.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
DEL PEAK 6(2Q36.2) MUTATED 48 64 32 13
DEL PEAK 6(2Q36.2) WILD-TYPE 107 71 157 30

Figure S185.  Get High-res Image Gene #35: 'del_2q36.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q36.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S186.  Gene #35: 'del_2q36.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
DEL PEAK 6(2Q36.2) MUTATED 7 25 26 49 24 21 5
DEL PEAK 6(2Q36.2) WILD-TYPE 77 54 70 43 54 54 13

Figure S186.  Get High-res Image Gene #35: 'del_2q36.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q36.2' versus 'MRNASEQ_CNMF'

P value = 0.0193 (Fisher's exact test), Q value = 0.041

Table S187.  Gene #35: 'del_2q36.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
DEL PEAK 6(2Q36.2) MUTATED 35 78 41
DEL PEAK 6(2Q36.2) WILD-TYPE 106 134 120

Figure S187.  Get High-res Image Gene #35: 'del_2q36.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2q36.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0242 (Fisher's exact test), Q value = 0.05

Table S188.  Gene #35: 'del_2q36.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
DEL PEAK 6(2Q36.2) MUTATED 49 55 50
DEL PEAK 6(2Q36.2) WILD-TYPE 141 87 136

Figure S188.  Get High-res Image Gene #35: 'del_2q36.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p26.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S189.  Gene #36: 'del_3p26.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
DEL PEAK 7(3P26.2) MUTATED 144 115 60 29
DEL PEAK 7(3P26.2) WILD-TYPE 11 20 129 14

Figure S189.  Get High-res Image Gene #36: 'del_3p26.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p26.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S190.  Gene #36: 'del_3p26.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
DEL PEAK 7(3P26.2) MUTATED 50 67 87 77 19 31 17
DEL PEAK 7(3P26.2) WILD-TYPE 34 12 9 15 59 44 1

Figure S190.  Get High-res Image Gene #36: 'del_3p26.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p26.2' versus 'MRNASEQ_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 6e-04

Table S191.  Gene #36: 'del_3p26.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
DEL PEAK 7(3P26.2) MUTATED 113 125 105
DEL PEAK 7(3P26.2) WILD-TYPE 28 87 56

Figure S191.  Get High-res Image Gene #36: 'del_3p26.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p26.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S192.  Gene #36: 'del_3p26.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 7(3P26.2) MUTATED 134 83 107 19
DEL PEAK 7(3P26.2) WILD-TYPE 42 20 63 46

Figure S192.  Get High-res Image Gene #36: 'del_3p26.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p26.2' versus 'MIRSEQ_CNMF'

P value = 0.0181 (Fisher's exact test), Q value = 0.039

Table S193.  Gene #36: 'del_3p26.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 221 152 145
DEL PEAK 7(3P26.2) MUTATED 146 91 109
DEL PEAK 7(3P26.2) WILD-TYPE 75 61 36

Figure S193.  Get High-res Image Gene #36: 'del_3p26.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3p26.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S194.  Gene #36: 'del_3p26.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
DEL PEAK 7(3P26.2) MUTATED 144 106 96
DEL PEAK 7(3P26.2) WILD-TYPE 46 36 90

Figure S194.  Get High-res Image Gene #36: 'del_3p26.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p26.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9e-05

Table S195.  Gene #36: 'del_3p26.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
DEL PEAK 7(3P26.2) MUTATED 57 91 64 86 17
DEL PEAK 7(3P26.2) WILD-TYPE 15 49 34 30 30

Figure S195.  Get High-res Image Gene #36: 'del_3p26.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_3p26.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00708 (Fisher's exact test), Q value = 0.018

Table S196.  Gene #36: 'del_3p26.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 244 89
DEL PEAK 7(3P26.2) MUTATED 106 147 62
DEL PEAK 7(3P26.2) WILD-TYPE 34 97 27

Figure S196.  Get High-res Image Gene #36: 'del_3p26.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p24.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S197.  Gene #37: 'del_3p24.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
DEL PEAK 8(3P24.1) MUTATED 145 124 69 30
DEL PEAK 8(3P24.1) WILD-TYPE 10 11 120 13

Figure S197.  Get High-res Image Gene #37: 'del_3p24.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p24.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S198.  Gene #37: 'del_3p24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
DEL PEAK 8(3P24.1) MUTATED 51 71 87 82 29 31 17
DEL PEAK 8(3P24.1) WILD-TYPE 33 8 9 10 49 44 1

Figure S198.  Get High-res Image Gene #37: 'del_3p24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p24.1' versus 'MRNASEQ_CNMF'

P value = 0.00294 (Fisher's exact test), Q value = 0.0081

Table S199.  Gene #37: 'del_3p24.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
DEL PEAK 8(3P24.1) MUTATED 115 142 106
DEL PEAK 8(3P24.1) WILD-TYPE 26 70 55

Figure S199.  Get High-res Image Gene #37: 'del_3p24.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p24.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S200.  Gene #37: 'del_3p24.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 8(3P24.1) MUTATED 137 91 108 27
DEL PEAK 8(3P24.1) WILD-TYPE 39 12 62 38

Figure S200.  Get High-res Image Gene #37: 'del_3p24.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p24.1' versus 'MIRSEQ_CNMF'

P value = 0.0025 (Fisher's exact test), Q value = 0.007

Table S201.  Gene #37: 'del_3p24.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 221 152 145
DEL PEAK 8(3P24.1) MUTATED 162 91 112
DEL PEAK 8(3P24.1) WILD-TYPE 59 61 33

Figure S201.  Get High-res Image Gene #37: 'del_3p24.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3p24.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00013

Table S202.  Gene #37: 'del_3p24.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
DEL PEAK 8(3P24.1) MUTATED 147 110 108
DEL PEAK 8(3P24.1) WILD-TYPE 43 32 78

Figure S202.  Get High-res Image Gene #37: 'del_3p24.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p24.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00013

Table S203.  Gene #37: 'del_3p24.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
DEL PEAK 8(3P24.1) MUTATED 60 91 72 89 20
DEL PEAK 8(3P24.1) WILD-TYPE 12 49 26 27 27

Figure S203.  Get High-res Image Gene #37: 'del_3p24.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_3p24.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0297 (Fisher's exact test), Q value = 0.059

Table S204.  Gene #37: 'del_3p24.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 244 89
DEL PEAK 8(3P24.1) MUTATED 109 159 64
DEL PEAK 8(3P24.1) WILD-TYPE 31 85 25

Figure S204.  Get High-res Image Gene #37: 'del_3p24.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p14.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S205.  Gene #38: 'del_3p14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
DEL PEAK 9(3P14.2) MUTATED 146 128 67 31
DEL PEAK 9(3P14.2) WILD-TYPE 9 7 122 12

Figure S205.  Get High-res Image Gene #38: 'del_3p14.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p14.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S206.  Gene #38: 'del_3p14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
DEL PEAK 9(3P14.2) MUTATED 51 72 85 84 34 29 17
DEL PEAK 9(3P14.2) WILD-TYPE 33 7 11 8 44 46 1

Figure S206.  Get High-res Image Gene #38: 'del_3p14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p14.2' versus 'MRNASEQ_CNMF'

P value = 0.0157 (Fisher's exact test), Q value = 0.035

Table S207.  Gene #38: 'del_3p14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
DEL PEAK 9(3P14.2) MUTATED 113 148 106
DEL PEAK 9(3P14.2) WILD-TYPE 28 64 55

Figure S207.  Get High-res Image Gene #38: 'del_3p14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S208.  Gene #38: 'del_3p14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 9(3P14.2) MUTATED 135 93 108 31
DEL PEAK 9(3P14.2) WILD-TYPE 41 10 62 34

Figure S208.  Get High-res Image Gene #38: 'del_3p14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p14.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00034 (Fisher's exact test), Q value = 0.0012

Table S209.  Gene #38: 'del_3p14.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
DEL PEAK 9(3P14.2) MUTATED 145 111 113
DEL PEAK 9(3P14.2) WILD-TYPE 45 31 73

Figure S209.  Get High-res Image Gene #38: 'del_3p14.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p14.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S210.  Gene #38: 'del_3p14.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
DEL PEAK 9(3P14.2) MUTATED 58 91 77 90 19
DEL PEAK 9(3P14.2) WILD-TYPE 14 49 21 26 28

Figure S210.  Get High-res Image Gene #38: 'del_3p14.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_3p12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S211.  Gene #39: 'del_3p12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
DEL PEAK 10(3P12.1) MUTATED 139 124 52 28
DEL PEAK 10(3P12.1) WILD-TYPE 16 11 137 15

Figure S211.  Get High-res Image Gene #39: 'del_3p12.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p12.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S212.  Gene #39: 'del_3p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
DEL PEAK 10(3P12.1) MUTATED 47 69 77 83 24 27 16
DEL PEAK 10(3P12.1) WILD-TYPE 37 10 19 9 54 48 2

Figure S212.  Get High-res Image Gene #39: 'del_3p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p12.1' versus 'MRNASEQ_CNMF'

P value = 0.0233 (Fisher's exact test), Q value = 0.048

Table S213.  Gene #39: 'del_3p12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
DEL PEAK 10(3P12.1) MUTATED 105 138 96
DEL PEAK 10(3P12.1) WILD-TYPE 36 74 65

Figure S213.  Get High-res Image Gene #39: 'del_3p12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S214.  Gene #39: 'del_3p12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 10(3P12.1) MUTATED 124 88 104 23
DEL PEAK 10(3P12.1) WILD-TYPE 52 15 66 42

Figure S214.  Get High-res Image Gene #39: 'del_3p12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00046 (Fisher's exact test), Q value = 0.0016

Table S215.  Gene #39: 'del_3p12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
DEL PEAK 10(3P12.1) MUTATED 130 107 103
DEL PEAK 10(3P12.1) WILD-TYPE 60 35 83

Figure S215.  Get High-res Image Gene #39: 'del_3p12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p12.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S216.  Gene #39: 'del_3p12.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
DEL PEAK 10(3P12.1) MUTATED 56 84 69 83 15
DEL PEAK 10(3P12.1) WILD-TYPE 16 56 29 33 32

Figure S216.  Get High-res Image Gene #39: 'del_3p12.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_4p15.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S217.  Gene #40: 'del_4p15.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
DEL PEAK 11(4P15.2) MUTATED 71 94 29 14
DEL PEAK 11(4P15.2) WILD-TYPE 84 41 160 29

Figure S217.  Get High-res Image Gene #40: 'del_4p15.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_4p15.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S218.  Gene #40: 'del_4p15.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
DEL PEAK 11(4P15.2) MUTATED 21 46 29 66 21 15 10
DEL PEAK 11(4P15.2) WILD-TYPE 63 33 67 26 57 60 8

Figure S218.  Get High-res Image Gene #40: 'del_4p15.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4p15.2' versus 'RPPA_CNMF'

P value = 0.0111 (Fisher's exact test), Q value = 0.026

Table S219.  Gene #40: 'del_4p15.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 53 51 37 65
DEL PEAK 11(4P15.2) MUTATED 26 31 12 22
DEL PEAK 11(4P15.2) WILD-TYPE 27 20 25 43

Figure S219.  Get High-res Image Gene #40: 'del_4p15.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_4p15.2' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00031

Table S220.  Gene #40: 'del_4p15.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
DEL PEAK 11(4P15.2) MUTATED 63 100 42
DEL PEAK 11(4P15.2) WILD-TYPE 78 112 119

Figure S220.  Get High-res Image Gene #40: 'del_4p15.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4p15.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S221.  Gene #40: 'del_4p15.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 11(4P15.2) MUTATED 74 64 49 18
DEL PEAK 11(4P15.2) WILD-TYPE 102 39 121 47

Figure S221.  Get High-res Image Gene #40: 'del_4p15.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4p15.2' versus 'MIRSEQ_CNMF'

P value = 0.00777 (Fisher's exact test), Q value = 0.019

Table S222.  Gene #40: 'del_4p15.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 221 152 145
DEL PEAK 11(4P15.2) MUTATED 105 50 51
DEL PEAK 11(4P15.2) WILD-TYPE 116 102 94

Figure S222.  Get High-res Image Gene #40: 'del_4p15.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_4p15.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0289 (Fisher's exact test), Q value = 0.058

Table S223.  Gene #40: 'del_4p15.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
DEL PEAK 11(4P15.2) MUTATED 76 68 62
DEL PEAK 11(4P15.2) WILD-TYPE 114 74 124

Figure S223.  Get High-res Image Gene #40: 'del_4p15.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_4p15.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.00082

Table S224.  Gene #40: 'del_4p15.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
DEL PEAK 11(4P15.2) MUTATED 38 40 48 48 11
DEL PEAK 11(4P15.2) WILD-TYPE 34 100 50 68 36

Figure S224.  Get High-res Image Gene #40: 'del_4p15.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_4p15.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.017 (Fisher's exact test), Q value = 0.038

Table S225.  Gene #40: 'del_4p15.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 244 89
DEL PEAK 11(4P15.2) MUTATED 64 97 24
DEL PEAK 11(4P15.2) WILD-TYPE 76 147 65

Figure S225.  Get High-res Image Gene #40: 'del_4p15.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S226.  Gene #41: 'del_4q21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
DEL PEAK 12(4Q21.3) MUTATED 54 68 21 13
DEL PEAK 12(4Q21.3) WILD-TYPE 101 67 168 30

Figure S226.  Get High-res Image Gene #41: 'del_4q21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q21.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S227.  Gene #41: 'del_4q21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
DEL PEAK 12(4Q21.3) MUTATED 15 29 29 49 17 14 3
DEL PEAK 12(4Q21.3) WILD-TYPE 69 50 67 43 61 61 15

Figure S227.  Get High-res Image Gene #41: 'del_4q21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q21.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.046 (Fisher's exact test), Q value = 0.084

Table S228.  Gene #41: 'del_4q21.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 82 48
DEL PEAK 12(4Q21.3) MUTATED 21 32 9
DEL PEAK 12(4Q21.3) WILD-TYPE 55 50 39

Figure S228.  Get High-res Image Gene #41: 'del_4q21.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_4q21.3' versus 'MRNASEQ_CNMF'

P value = 0.00847 (Fisher's exact test), Q value = 0.021

Table S229.  Gene #41: 'del_4q21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
DEL PEAK 12(4Q21.3) MUTATED 48 71 33
DEL PEAK 12(4Q21.3) WILD-TYPE 93 141 128

Figure S229.  Get High-res Image Gene #41: 'del_4q21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4q21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00013

Table S230.  Gene #41: 'del_4q21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 12(4Q21.3) MUTATED 63 44 30 15
DEL PEAK 12(4Q21.3) WILD-TYPE 113 59 140 50

Figure S230.  Get High-res Image Gene #41: 'del_4q21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0307 (Fisher's exact test), Q value = 0.061

Table S231.  Gene #41: 'del_4q21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
DEL PEAK 12(4Q21.3) MUTATED 63 48 42
DEL PEAK 12(4Q21.3) WILD-TYPE 127 94 144

Figure S231.  Get High-res Image Gene #41: 'del_4q21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_4q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S232.  Gene #42: 'del_4q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
DEL PEAK 13(4Q22.1) MUTATED 62 73 21 13
DEL PEAK 13(4Q22.1) WILD-TYPE 93 62 168 30

Figure S232.  Get High-res Image Gene #42: 'del_4q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q22.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S233.  Gene #42: 'del_4q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
DEL PEAK 13(4Q22.1) MUTATED 12 31 29 59 18 15 5
DEL PEAK 13(4Q22.1) WILD-TYPE 72 48 67 33 60 60 13

Figure S233.  Get High-res Image Gene #42: 'del_4q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q22.1' versus 'MRNASEQ_CNMF'

P value = 0.00829 (Fisher's exact test), Q value = 0.02

Table S234.  Gene #42: 'del_4q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
DEL PEAK 13(4Q22.1) MUTATED 51 78 37
DEL PEAK 13(4Q22.1) WILD-TYPE 90 134 124

Figure S234.  Get High-res Image Gene #42: 'del_4q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 0.00098

Table S235.  Gene #42: 'del_4q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 13(4Q22.1) MUTATED 63 48 40 15
DEL PEAK 13(4Q22.1) WILD-TYPE 113 55 130 50

Figure S235.  Get High-res Image Gene #42: 'del_4q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.04 (Fisher's exact test), Q value = 0.076

Table S236.  Gene #42: 'del_4q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
DEL PEAK 13(4Q22.1) MUTATED 66 53 47
DEL PEAK 13(4Q22.1) WILD-TYPE 124 89 139

Figure S236.  Get High-res Image Gene #42: 'del_4q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_4q35.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S237.  Gene #43: 'del_4q35.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
DEL PEAK 14(4Q35.2) MUTATED 90 73 31 19
DEL PEAK 14(4Q35.2) WILD-TYPE 65 62 158 24

Figure S237.  Get High-res Image Gene #43: 'del_4q35.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q35.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S238.  Gene #43: 'del_4q35.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
DEL PEAK 14(4Q35.2) MUTATED 23 39 44 56 20 23 8
DEL PEAK 14(4Q35.2) WILD-TYPE 61 40 52 36 58 52 10

Figure S238.  Get High-res Image Gene #43: 'del_4q35.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q35.2' versus 'MRNASEQ_CNMF'

P value = 0.029 (Fisher's exact test), Q value = 0.058

Table S239.  Gene #43: 'del_4q35.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
DEL PEAK 14(4Q35.2) MUTATED 66 90 52
DEL PEAK 14(4Q35.2) WILD-TYPE 75 122 109

Figure S239.  Get High-res Image Gene #43: 'del_4q35.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4q35.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.00073

Table S240.  Gene #43: 'del_4q35.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 14(4Q35.2) MUTATED 79 55 59 15
DEL PEAK 14(4Q35.2) WILD-TYPE 97 48 111 50

Figure S240.  Get High-res Image Gene #43: 'del_4q35.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q35.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00581 (Fisher's exact test), Q value = 0.015

Table S241.  Gene #43: 'del_4q35.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
DEL PEAK 14(4Q35.2) MUTATED 84 68 59
DEL PEAK 14(4Q35.2) WILD-TYPE 106 74 127

Figure S241.  Get High-res Image Gene #43: 'del_4q35.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_5q12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S242.  Gene #44: 'del_5q12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
DEL PEAK 15(5Q12.1) MUTATED 86 96 22 11
DEL PEAK 15(5Q12.1) WILD-TYPE 69 39 167 32

Figure S242.  Get High-res Image Gene #44: 'del_5q12.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q12.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S243.  Gene #44: 'del_5q12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
DEL PEAK 15(5Q12.1) MUTATED 17 52 53 63 10 10 10
DEL PEAK 15(5Q12.1) WILD-TYPE 67 27 43 29 68 65 8

Figure S243.  Get High-res Image Gene #44: 'del_5q12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S244.  Gene #44: 'del_5q12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 15(5Q12.1) MUTATED 81 70 48 14
DEL PEAK 15(5Q12.1) WILD-TYPE 95 33 122 51

Figure S244.  Get High-res Image Gene #44: 'del_5q12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_5q12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00016

Table S245.  Gene #44: 'del_5q12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
DEL PEAK 15(5Q12.1) MUTATED 84 75 53
DEL PEAK 15(5Q12.1) WILD-TYPE 106 67 133

Figure S245.  Get High-res Image Gene #44: 'del_5q12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_5q12.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00052 (Fisher's exact test), Q value = 0.0018

Table S246.  Gene #44: 'del_5q12.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
DEL PEAK 15(5Q12.1) MUTATED 31 55 54 48 8
DEL PEAK 15(5Q12.1) WILD-TYPE 41 85 44 68 39

Figure S246.  Get High-res Image Gene #44: 'del_5q12.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_5q12.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0479 (Fisher's exact test), Q value = 0.087

Table S247.  Gene #44: 'del_5q12.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 244 89
DEL PEAK 15(5Q12.1) MUTATED 70 91 35
DEL PEAK 15(5Q12.1) WILD-TYPE 70 153 54

Figure S247.  Get High-res Image Gene #44: 'del_5q12.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q15' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S248.  Gene #45: 'del_5q15' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
DEL PEAK 16(5Q15) MUTATED 88 98 28 12
DEL PEAK 16(5Q15) WILD-TYPE 67 37 161 31

Figure S248.  Get High-res Image Gene #45: 'del_5q15' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q15' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S249.  Gene #45: 'del_5q15' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
DEL PEAK 16(5Q15) MUTATED 19 54 52 66 12 12 11
DEL PEAK 16(5Q15) WILD-TYPE 65 25 44 26 66 63 7

Figure S249.  Get High-res Image Gene #45: 'del_5q15' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q15' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S250.  Gene #45: 'del_5q15' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 16(5Q15) MUTATED 82 71 54 16
DEL PEAK 16(5Q15) WILD-TYPE 94 32 116 49

Figure S250.  Get High-res Image Gene #45: 'del_5q15' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_5q15' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00013

Table S251.  Gene #45: 'del_5q15' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
DEL PEAK 16(5Q15) MUTATED 86 80 57
DEL PEAK 16(5Q15) WILD-TYPE 104 62 129

Figure S251.  Get High-res Image Gene #45: 'del_5q15' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_5q15' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 6e-04

Table S252.  Gene #45: 'del_5q15' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
DEL PEAK 16(5Q15) MUTATED 31 58 57 51 8
DEL PEAK 16(5Q15) WILD-TYPE 41 82 41 65 39

Figure S252.  Get High-res Image Gene #45: 'del_5q15' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_5q35.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S253.  Gene #46: 'del_5q35.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
DEL PEAK 17(5Q35.3) MUTATED 68 93 25 13
DEL PEAK 17(5Q35.3) WILD-TYPE 87 42 164 30

Figure S253.  Get High-res Image Gene #46: 'del_5q35.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q35.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S254.  Gene #46: 'del_5q35.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
DEL PEAK 17(5Q35.3) MUTATED 19 57 45 51 11 6 10
DEL PEAK 17(5Q35.3) WILD-TYPE 65 22 51 41 67 69 8

Figure S254.  Get High-res Image Gene #46: 'del_5q35.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q35.3' versus 'MRNASEQ_CNMF'

P value = 0.0312 (Fisher's exact test), Q value = 0.061

Table S255.  Gene #46: 'del_5q35.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
DEL PEAK 17(5Q35.3) MUTATED 62 87 49
DEL PEAK 17(5Q35.3) WILD-TYPE 79 125 112

Figure S255.  Get High-res Image Gene #46: 'del_5q35.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_5q35.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S256.  Gene #46: 'del_5q35.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 17(5Q35.3) MUTATED 76 69 39 14
DEL PEAK 17(5Q35.3) WILD-TYPE 100 34 131 51

Figure S256.  Get High-res Image Gene #46: 'del_5q35.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_5q35.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00016

Table S257.  Gene #46: 'del_5q35.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
DEL PEAK 17(5Q35.3) MUTATED 79 70 47
DEL PEAK 17(5Q35.3) WILD-TYPE 111 72 139

Figure S257.  Get High-res Image Gene #46: 'del_5q35.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_5q35.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.001

Table S258.  Gene #46: 'del_5q35.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
DEL PEAK 17(5Q35.3) MUTATED 28 51 52 41 7
DEL PEAK 17(5Q35.3) WILD-TYPE 44 89 46 75 40

Figure S258.  Get High-res Image Gene #46: 'del_5q35.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_6p25.3' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9e-05

Table S259.  Gene #47: 'del_6p25.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
DEL PEAK 18(6P25.3) MUTATED 30 41 19 6
DEL PEAK 18(6P25.3) WILD-TYPE 125 94 170 37

Figure S259.  Get High-res Image Gene #47: 'del_6p25.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_6p25.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S260.  Gene #47: 'del_6p25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
DEL PEAK 18(6P25.3) MUTATED 11 12 17 37 11 5 3
DEL PEAK 18(6P25.3) WILD-TYPE 73 67 79 55 67 70 15

Figure S260.  Get High-res Image Gene #47: 'del_6p25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6p25.3' versus 'RPPA_CNMF'

P value = 0.0417 (Fisher's exact test), Q value = 0.078

Table S261.  Gene #47: 'del_6p25.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 53 51 37 65
DEL PEAK 18(6P25.3) MUTATED 14 13 2 15
DEL PEAK 18(6P25.3) WILD-TYPE 39 38 35 50

Figure S261.  Get High-res Image Gene #47: 'del_6p25.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_6p25.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0101 (Fisher's exact test), Q value = 0.024

Table S262.  Gene #47: 'del_6p25.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 82 48
DEL PEAK 18(6P25.3) MUTATED 15 25 4
DEL PEAK 18(6P25.3) WILD-TYPE 61 57 44

Figure S262.  Get High-res Image Gene #47: 'del_6p25.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_6p25.3' versus 'MRNASEQ_CNMF'

P value = 0.00294 (Fisher's exact test), Q value = 0.0081

Table S263.  Gene #47: 'del_6p25.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
DEL PEAK 18(6P25.3) MUTATED 31 47 16
DEL PEAK 18(6P25.3) WILD-TYPE 110 165 145

Figure S263.  Get High-res Image Gene #47: 'del_6p25.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_7q31.1' versus 'CN_CNMF'

P value = 0.00219 (Fisher's exact test), Q value = 0.0063

Table S264.  Gene #48: 'del_7q31.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
DEL PEAK 19(7Q31.1) MUTATED 34 20 15 8
DEL PEAK 19(7Q31.1) WILD-TYPE 121 115 174 35

Figure S264.  Get High-res Image Gene #48: 'del_7q31.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_7q36.1' versus 'CN_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.00095

Table S265.  Gene #49: 'del_7q36.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
DEL PEAK 20(7Q36.1) MUTATED 50 39 28 15
DEL PEAK 20(7Q36.1) WILD-TYPE 105 96 161 28

Figure S265.  Get High-res Image Gene #49: 'del_7q36.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_7q36.1' versus 'RPPA_CNMF'

P value = 0.0432 (Fisher's exact test), Q value = 0.08

Table S266.  Gene #49: 'del_7q36.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 53 51 37 65
DEL PEAK 20(7Q36.1) MUTATED 16 21 8 12
DEL PEAK 20(7Q36.1) WILD-TYPE 37 30 29 53

Figure S266.  Get High-res Image Gene #49: 'del_7q36.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_8p23.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S267.  Gene #50: 'del_8p23.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
DEL PEAK 21(8P23.2) MUTATED 125 78 74 27
DEL PEAK 21(8P23.2) WILD-TYPE 30 57 115 16

Figure S267.  Get High-res Image Gene #50: 'del_8p23.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p23.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S268.  Gene #50: 'del_8p23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
DEL PEAK 21(8P23.2) MUTATED 50 40 71 63 16 51 13
DEL PEAK 21(8P23.2) WILD-TYPE 34 39 25 29 62 24 5

Figure S268.  Get High-res Image Gene #50: 'del_8p23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_8p23.2' versus 'MRNASEQ_CNMF'

P value = 0.00106 (Fisher's exact test), Q value = 0.0033

Table S269.  Gene #50: 'del_8p23.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
DEL PEAK 21(8P23.2) MUTATED 94 103 102
DEL PEAK 21(8P23.2) WILD-TYPE 47 109 59

Figure S269.  Get High-res Image Gene #50: 'del_8p23.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_8p23.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S270.  Gene #50: 'del_8p23.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 21(8P23.2) MUTATED 114 62 112 11
DEL PEAK 21(8P23.2) WILD-TYPE 62 41 58 54

Figure S270.  Get High-res Image Gene #50: 'del_8p23.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_CNMF'

P value = 0.0178 (Fisher's exact test), Q value = 0.039

Table S271.  Gene #50: 'del_8p23.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 221 152 145
DEL PEAK 21(8P23.2) MUTATED 113 97 92
DEL PEAK 21(8P23.2) WILD-TYPE 108 55 53

Figure S271.  Get High-res Image Gene #50: 'del_8p23.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_8p23.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00372 (Fisher's exact test), Q value = 0.0099

Table S272.  Gene #50: 'del_8p23.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
DEL PEAK 21(8P23.2) MUTATED 124 87 91
DEL PEAK 21(8P23.2) WILD-TYPE 66 55 95

Figure S272.  Get High-res Image Gene #50: 'del_8p23.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S273.  Gene #50: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
DEL PEAK 21(8P23.2) MUTATED 47 95 44 75 14
DEL PEAK 21(8P23.2) WILD-TYPE 25 45 54 41 33

Figure S273.  Get High-res Image Gene #50: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_8p23.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00013

Table S274.  Gene #50: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 244 89
DEL PEAK 21(8P23.2) MUTATED 96 117 62
DEL PEAK 21(8P23.2) WILD-TYPE 44 127 27

Figure S274.  Get High-res Image Gene #50: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S275.  Gene #51: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
DEL PEAK 22(9P23) MUTATED 103 94 41 1
DEL PEAK 22(9P23) WILD-TYPE 52 41 148 42

Figure S275.  Get High-res Image Gene #51: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p23' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S276.  Gene #51: 'del_9p23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
DEL PEAK 22(9P23) MUTATED 27 57 52 65 9 18 11
DEL PEAK 22(9P23) WILD-TYPE 57 22 44 27 69 57 7

Figure S276.  Get High-res Image Gene #51: 'del_9p23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S277.  Gene #51: 'del_9p23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 22(9P23) MUTATED 77 68 80 12
DEL PEAK 22(9P23) WILD-TYPE 99 35 90 53

Figure S277.  Get High-res Image Gene #51: 'del_9p23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.00053

Table S278.  Gene #51: 'del_9p23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
DEL PEAK 22(9P23) MUTATED 85 85 66
DEL PEAK 22(9P23) WILD-TYPE 105 57 120

Figure S278.  Get High-res Image Gene #51: 'del_9p23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S279.  Gene #51: 'del_9p23' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
DEL PEAK 22(9P23) MUTATED 44 56 58 51 6
DEL PEAK 22(9P23) WILD-TYPE 28 84 40 65 41

Figure S279.  Get High-res Image Gene #51: 'del_9p23' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_9p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S280.  Gene #52: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
DEL PEAK 23(9P21.3) MUTATED 110 109 69 14
DEL PEAK 23(9P21.3) WILD-TYPE 45 26 120 29

Figure S280.  Get High-res Image Gene #52: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S281.  Gene #52: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
DEL PEAK 23(9P21.3) MUTATED 42 66 67 69 11 35 12
DEL PEAK 23(9P21.3) WILD-TYPE 42 13 29 23 67 40 6

Figure S281.  Get High-res Image Gene #52: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S282.  Gene #52: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 23(9P21.3) MUTATED 103 75 107 15
DEL PEAK 23(9P21.3) WILD-TYPE 73 28 63 50

Figure S282.  Get High-res Image Gene #52: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S283.  Gene #52: 'del_9p21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
DEL PEAK 23(9P21.3) MUTATED 113 108 79
DEL PEAK 23(9P21.3) WILD-TYPE 77 34 107

Figure S283.  Get High-res Image Gene #52: 'del_9p21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S284.  Gene #52: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
DEL PEAK 23(9P21.3) MUTATED 54 77 66 63 12
DEL PEAK 23(9P21.3) WILD-TYPE 18 63 32 53 35

Figure S284.  Get High-res Image Gene #52: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_9q21.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S285.  Gene #53: 'del_9q21.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
DEL PEAK 24(9Q21.11) MUTATED 51 35 21 1
DEL PEAK 24(9Q21.11) WILD-TYPE 104 100 168 42

Figure S285.  Get High-res Image Gene #53: 'del_9q21.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_9q21.11' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S286.  Gene #53: 'del_9q21.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
DEL PEAK 24(9Q21.11) MUTATED 12 30 20 28 4 5 9
DEL PEAK 24(9Q21.11) WILD-TYPE 72 49 76 64 74 70 9

Figure S286.  Get High-res Image Gene #53: 'del_9q21.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9q21.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0227 (Fisher's exact test), Q value = 0.047

Table S287.  Gene #53: 'del_9q21.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 24(9Q21.11) MUTATED 33 28 40 6
DEL PEAK 24(9Q21.11) WILD-TYPE 143 75 130 59

Figure S287.  Get High-res Image Gene #53: 'del_9q21.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9q21.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00073 (Fisher's exact test), Q value = 0.0024

Table S288.  Gene #53: 'del_9q21.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
DEL PEAK 24(9Q21.11) MUTATED 33 45 28
DEL PEAK 24(9Q21.11) WILD-TYPE 157 97 158

Figure S288.  Get High-res Image Gene #53: 'del_9q21.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_9q21.11' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00329 (Fisher's exact test), Q value = 0.0089

Table S289.  Gene #53: 'del_9q21.11' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
DEL PEAK 24(9Q21.11) MUTATED 21 27 27 22 2
DEL PEAK 24(9Q21.11) WILD-TYPE 51 113 71 94 45

Figure S289.  Get High-res Image Gene #53: 'del_9q21.11' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_9q34.3' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00031

Table S290.  Gene #54: 'del_9q34.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
DEL PEAK 25(9Q34.3) MUTATED 38 22 18 1
DEL PEAK 25(9Q34.3) WILD-TYPE 117 113 171 42

Figure S290.  Get High-res Image Gene #54: 'del_9q34.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9q34.3' versus 'METHLYATION_CNMF'

P value = 0.00083 (Fisher's exact test), Q value = 0.0027

Table S291.  Gene #54: 'del_9q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
DEL PEAK 25(9Q34.3) MUTATED 5 23 18 15 7 7 4
DEL PEAK 25(9Q34.3) WILD-TYPE 79 56 78 77 71 68 14

Figure S291.  Get High-res Image Gene #54: 'del_9q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9q34.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00944 (Fisher's exact test), Q value = 0.023

Table S292.  Gene #54: 'del_9q34.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
DEL PEAK 25(9Q34.3) MUTATED 28 32 19
DEL PEAK 25(9Q34.3) WILD-TYPE 162 110 167

Figure S292.  Get High-res Image Gene #54: 'del_9q34.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_9q34.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00353 (Fisher's exact test), Q value = 0.0095

Table S293.  Gene #54: 'del_9q34.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
DEL PEAK 25(9Q34.3) MUTATED 18 17 20 19 1
DEL PEAK 25(9Q34.3) WILD-TYPE 54 123 78 97 46

Figure S293.  Get High-res Image Gene #54: 'del_9q34.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_10p15.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S294.  Gene #55: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
DEL PEAK 26(10P15.3) MUTATED 77 48 29 16
DEL PEAK 26(10P15.3) WILD-TYPE 78 87 160 27

Figure S294.  Get High-res Image Gene #55: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10p15.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S295.  Gene #55: 'del_10p15.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
DEL PEAK 26(10P15.3) MUTATED 18 23 43 43 10 22 11
DEL PEAK 26(10P15.3) WILD-TYPE 66 56 53 49 68 53 7

Figure S295.  Get High-res Image Gene #55: 'del_10p15.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10p15.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00306 (Fisher's exact test), Q value = 0.0084

Table S296.  Gene #55: 'del_10p15.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 26(10P15.3) MUTATED 66 33 60 9
DEL PEAK 26(10P15.3) WILD-TYPE 110 70 110 56

Figure S296.  Get High-res Image Gene #55: 'del_10p15.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10p15.3' versus 'MIRSEQ_CNMF'

P value = 0.0146 (Fisher's exact test), Q value = 0.033

Table S297.  Gene #55: 'del_10p15.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 221 152 145
DEL PEAK 26(10P15.3) MUTATED 73 37 58
DEL PEAK 26(10P15.3) WILD-TYPE 148 115 87

Figure S297.  Get High-res Image Gene #55: 'del_10p15.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_10p15.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.001

Table S298.  Gene #55: 'del_10p15.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
DEL PEAK 26(10P15.3) MUTATED 29 42 24 53 7
DEL PEAK 26(10P15.3) WILD-TYPE 43 98 74 63 40

Figure S298.  Get High-res Image Gene #55: 'del_10p15.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_10p11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S299.  Gene #56: 'del_10p11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
DEL PEAK 27(10P11.21) MUTATED 74 50 24 14
DEL PEAK 27(10P11.21) WILD-TYPE 81 85 165 29

Figure S299.  Get High-res Image Gene #56: 'del_10p11.21' versus Molecular Subtype #1: 'CN_CNMF'

'del_10p11.21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S300.  Gene #56: 'del_10p11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
DEL PEAK 27(10P11.21) MUTATED 14 24 42 42 12 19 9
DEL PEAK 27(10P11.21) WILD-TYPE 70 55 54 50 66 56 9

Figure S300.  Get High-res Image Gene #56: 'del_10p11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10p11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0258 (Fisher's exact test), Q value = 0.052

Table S301.  Gene #56: 'del_10p11.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 27(10P11.21) MUTATED 60 34 56 10
DEL PEAK 27(10P11.21) WILD-TYPE 116 69 114 55

Figure S301.  Get High-res Image Gene #56: 'del_10p11.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10p11.21' versus 'MIRSEQ_CNMF'

P value = 0.0425 (Fisher's exact test), Q value = 0.079

Table S302.  Gene #56: 'del_10p11.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 221 152 145
DEL PEAK 27(10P11.21) MUTATED 75 35 50
DEL PEAK 27(10P11.21) WILD-TYPE 146 117 95

Figure S302.  Get High-res Image Gene #56: 'del_10p11.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_10p11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0152 (Fisher's exact test), Q value = 0.034

Table S303.  Gene #56: 'del_10p11.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
DEL PEAK 27(10P11.21) MUTATED 62 54 44
DEL PEAK 27(10P11.21) WILD-TYPE 128 88 142

Figure S303.  Get High-res Image Gene #56: 'del_10p11.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_10p11.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0235 (Fisher's exact test), Q value = 0.049

Table S304.  Gene #56: 'del_10p11.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
DEL PEAK 27(10P11.21) MUTATED 23 40 28 50 9
DEL PEAK 27(10P11.21) WILD-TYPE 49 100 70 66 38

Figure S304.  Get High-res Image Gene #56: 'del_10p11.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_10q23.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S305.  Gene #57: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
DEL PEAK 28(10Q23.31) MUTATED 46 58 27 7
DEL PEAK 28(10Q23.31) WILD-TYPE 109 77 162 36

Figure S305.  Get High-res Image Gene #57: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q23.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S306.  Gene #57: 'del_10q23.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
DEL PEAK 28(10Q23.31) MUTATED 8 25 30 38 24 8 5
DEL PEAK 28(10Q23.31) WILD-TYPE 76 54 66 54 54 67 13

Figure S306.  Get High-res Image Gene #57: 'del_10q23.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q23.31' versus 'MRNASEQ_CNMF'

P value = 6e-04 (Fisher's exact test), Q value = 0.002

Table S307.  Gene #57: 'del_10q23.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
DEL PEAK 28(10Q23.31) MUTATED 36 73 27
DEL PEAK 28(10Q23.31) WILD-TYPE 105 139 134

Figure S307.  Get High-res Image Gene #57: 'del_10q23.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00284 (Fisher's exact test), Q value = 0.0079

Table S308.  Gene #57: 'del_10q23.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 28(10Q23.31) MUTATED 45 39 31 21
DEL PEAK 28(10Q23.31) WILD-TYPE 131 64 139 44

Figure S308.  Get High-res Image Gene #57: 'del_10q23.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_CNMF'

P value = 0.0228 (Fisher's exact test), Q value = 0.047

Table S309.  Gene #57: 'del_10q23.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 221 152 145
DEL PEAK 28(10Q23.31) MUTATED 70 29 36
DEL PEAK 28(10Q23.31) WILD-TYPE 151 123 109

Figure S309.  Get High-res Image Gene #57: 'del_10q23.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_10q23.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.00076

Table S310.  Gene #57: 'del_10q23.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
DEL PEAK 28(10Q23.31) MUTATED 21 24 42 24 14
DEL PEAK 28(10Q23.31) WILD-TYPE 51 116 56 92 33

Figure S310.  Get High-res Image Gene #57: 'del_10q23.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_10q23.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0324 (Fisher's exact test), Q value = 0.063

Table S311.  Gene #57: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 244 89
DEL PEAK 28(10Q23.31) MUTATED 39 72 14
DEL PEAK 28(10Q23.31) WILD-TYPE 101 172 75

Figure S311.  Get High-res Image Gene #57: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11p15.5' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S312.  Gene #58: 'del_11p15.5' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
DEL PEAK 29(11P15.5) MUTATED 42 80 35 6
DEL PEAK 29(11P15.5) WILD-TYPE 113 55 154 37

Figure S312.  Get High-res Image Gene #58: 'del_11p15.5' versus Molecular Subtype #1: 'CN_CNMF'

'del_11p15.5' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S313.  Gene #58: 'del_11p15.5' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
DEL PEAK 29(11P15.5) MUTATED 20 30 24 53 26 6 4
DEL PEAK 29(11P15.5) WILD-TYPE 64 49 72 39 52 69 14

Figure S313.  Get High-res Image Gene #58: 'del_11p15.5' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11p15.5' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S314.  Gene #58: 'del_11p15.5' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
DEL PEAK 29(11P15.5) MUTATED 39 90 32
DEL PEAK 29(11P15.5) WILD-TYPE 102 122 129

Figure S314.  Get High-res Image Gene #58: 'del_11p15.5' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_11p15.5' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0132 (Fisher's exact test), Q value = 0.03

Table S315.  Gene #58: 'del_11p15.5' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 29(11P15.5) MUTATED 42 43 52 24
DEL PEAK 29(11P15.5) WILD-TYPE 134 60 118 41

Figure S315.  Get High-res Image Gene #58: 'del_11p15.5' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S316.  Gene #58: 'del_11p15.5' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 221 152 145
DEL PEAK 29(11P15.5) MUTATED 98 25 40
DEL PEAK 29(11P15.5) WILD-TYPE 123 127 105

Figure S316.  Get High-res Image Gene #58: 'del_11p15.5' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_11p15.5' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00326 (Fisher's exact test), Q value = 0.0089

Table S317.  Gene #58: 'del_11p15.5' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
DEL PEAK 29(11P15.5) MUTATED 46 59 58
DEL PEAK 29(11P15.5) WILD-TYPE 144 83 128

Figure S317.  Get High-res Image Gene #58: 'del_11p15.5' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 5e-04

Table S318.  Gene #58: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
DEL PEAK 29(11P15.5) MUTATED 25 27 47 31 16
DEL PEAK 29(11P15.5) WILD-TYPE 47 113 51 85 31

Figure S318.  Get High-res Image Gene #58: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_11p15.5' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00783 (Fisher's exact test), Q value = 0.019

Table S319.  Gene #58: 'del_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 244 89
DEL PEAK 29(11P15.5) MUTATED 38 90 18
DEL PEAK 29(11P15.5) WILD-TYPE 102 154 71

Figure S319.  Get High-res Image Gene #58: 'del_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11q23.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S320.  Gene #59: 'del_11q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
DEL PEAK 30(11Q23.1) MUTATED 72 89 66 19
DEL PEAK 30(11Q23.1) WILD-TYPE 83 46 123 24

Figure S320.  Get High-res Image Gene #59: 'del_11q23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q23.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S321.  Gene #59: 'del_11q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
DEL PEAK 30(11Q23.1) MUTATED 27 33 49 49 65 13 10
DEL PEAK 30(11Q23.1) WILD-TYPE 57 46 47 43 13 62 8

Figure S321.  Get High-res Image Gene #59: 'del_11q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11q23.1' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9e-05

Table S322.  Gene #59: 'del_11q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
DEL PEAK 30(11Q23.1) MUTATED 61 126 55
DEL PEAK 30(11Q23.1) WILD-TYPE 80 86 106

Figure S322.  Get High-res Image Gene #59: 'del_11q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_11q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S323.  Gene #59: 'del_11q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 30(11Q23.1) MUTATED 74 42 71 55
DEL PEAK 30(11Q23.1) WILD-TYPE 102 61 99 10

Figure S323.  Get High-res Image Gene #59: 'del_11q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11q23.1' versus 'MIRSEQ_CNMF'

P value = 0.00802 (Fisher's exact test), Q value = 0.02

Table S324.  Gene #59: 'del_11q23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 221 152 145
DEL PEAK 30(11Q23.1) MUTATED 121 59 65
DEL PEAK 30(11Q23.1) WILD-TYPE 100 93 80

Figure S324.  Get High-res Image Gene #59: 'del_11q23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_11q23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0135 (Fisher's exact test), Q value = 0.031

Table S325.  Gene #59: 'del_11q23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
DEL PEAK 30(11Q23.1) MUTATED 80 61 104
DEL PEAK 30(11Q23.1) WILD-TYPE 110 81 82

Figure S325.  Get High-res Image Gene #59: 'del_11q23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_12q24.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S326.  Gene #60: 'del_12q24.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
DEL PEAK 31(12Q24.33) MUTATED 26 28 6 3
DEL PEAK 31(12Q24.33) WILD-TYPE 129 107 183 40

Figure S326.  Get High-res Image Gene #60: 'del_12q24.33' versus Molecular Subtype #1: 'CN_CNMF'

'del_12q24.33' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S327.  Gene #60: 'del_12q24.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
DEL PEAK 31(12Q24.33) MUTATED 5 13 13 23 4 1 4
DEL PEAK 31(12Q24.33) WILD-TYPE 79 66 83 69 74 74 14

Figure S327.  Get High-res Image Gene #60: 'del_12q24.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_13q12.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S328.  Gene #61: 'del_13q12.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
DEL PEAK 32(13Q12.11) MUTATED 80 98 37 18
DEL PEAK 32(13Q12.11) WILD-TYPE 75 37 152 25

Figure S328.  Get High-res Image Gene #61: 'del_13q12.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q12.11' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S329.  Gene #61: 'del_13q12.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
DEL PEAK 32(13Q12.11) MUTATED 22 53 48 61 25 17 7
DEL PEAK 32(13Q12.11) WILD-TYPE 62 26 48 31 53 58 11

Figure S329.  Get High-res Image Gene #61: 'del_13q12.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_13q12.11' versus 'MRNASEQ_CNMF'

P value = 0.0254 (Fisher's exact test), Q value = 0.051

Table S330.  Gene #61: 'del_13q12.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
DEL PEAK 32(13Q12.11) MUTATED 67 105 58
DEL PEAK 32(13Q12.11) WILD-TYPE 74 107 103

Figure S330.  Get High-res Image Gene #61: 'del_13q12.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_13q12.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S331.  Gene #61: 'del_13q12.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 32(13Q12.11) MUTATED 83 66 62 19
DEL PEAK 32(13Q12.11) WILD-TYPE 93 37 108 46

Figure S331.  Get High-res Image Gene #61: 'del_13q12.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_13q12.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0312 (Fisher's exact test), Q value = 0.061

Table S332.  Gene #61: 'del_13q12.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
DEL PEAK 32(13Q12.11) MUTATED 86 75 71
DEL PEAK 32(13Q12.11) WILD-TYPE 104 67 115

Figure S332.  Get High-res Image Gene #61: 'del_13q12.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_13q12.11' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00983 (Fisher's exact test), Q value = 0.023

Table S333.  Gene #61: 'del_13q12.11' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
DEL PEAK 32(13Q12.11) MUTATED 42 58 52 49 14
DEL PEAK 32(13Q12.11) WILD-TYPE 30 82 46 67 33

Figure S333.  Get High-res Image Gene #61: 'del_13q12.11' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_13q14.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S334.  Gene #62: 'del_13q14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
DEL PEAK 33(13Q14.2) MUTATED 53 92 55 17
DEL PEAK 33(13Q14.2) WILD-TYPE 102 43 134 26

Figure S334.  Get High-res Image Gene #62: 'del_13q14.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q14.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S335.  Gene #62: 'del_13q14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
DEL PEAK 33(13Q14.2) MUTATED 18 46 39 51 44 16 3
DEL PEAK 33(13Q14.2) WILD-TYPE 66 33 57 41 34 59 15

Figure S335.  Get High-res Image Gene #62: 'del_13q14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_13q14.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S336.  Gene #62: 'del_13q14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
DEL PEAK 33(13Q14.2) MUTATED 55 116 44
DEL PEAK 33(13Q14.2) WILD-TYPE 86 96 117

Figure S336.  Get High-res Image Gene #62: 'del_13q14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_13q14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00031

Table S337.  Gene #62: 'del_13q14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 33(13Q14.2) MUTATED 70 55 52 38
DEL PEAK 33(13Q14.2) WILD-TYPE 106 48 118 27

Figure S337.  Get High-res Image Gene #62: 'del_13q14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_CNMF'

P value = 0.00119 (Fisher's exact test), Q value = 0.0037

Table S338.  Gene #62: 'del_13q14.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 221 152 145
DEL PEAK 33(13Q14.2) MUTATED 112 50 54
DEL PEAK 33(13Q14.2) WILD-TYPE 109 102 91

Figure S338.  Get High-res Image Gene #62: 'del_13q14.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_13q14.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00156 (Fisher's exact test), Q value = 0.0047

Table S339.  Gene #62: 'del_13q14.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
DEL PEAK 33(13Q14.2) MUTATED 35 49 56 38 20
DEL PEAK 33(13Q14.2) WILD-TYPE 37 91 42 78 27

Figure S339.  Get High-res Image Gene #62: 'del_13q14.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_14q11.2' versus 'CN_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.00082

Table S340.  Gene #63: 'del_14q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
DEL PEAK 34(14Q11.2) MUTATED 27 31 15 2
DEL PEAK 34(14Q11.2) WILD-TYPE 128 104 174 41

Figure S340.  Get High-res Image Gene #63: 'del_14q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q11.2' versus 'METHLYATION_CNMF'

P value = 0.0149 (Fisher's exact test), Q value = 0.034

Table S341.  Gene #63: 'del_14q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
DEL PEAK 34(14Q11.2) MUTATED 5 19 12 18 9 8 4
DEL PEAK 34(14Q11.2) WILD-TYPE 79 60 84 74 69 67 14

Figure S341.  Get High-res Image Gene #63: 'del_14q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_14q11.2' versus 'MIRSEQ_CNMF'

P value = 0.00724 (Fisher's exact test), Q value = 0.018

Table S342.  Gene #63: 'del_14q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 221 152 145
DEL PEAK 34(14Q11.2) MUTATED 43 16 13
DEL PEAK 34(14Q11.2) WILD-TYPE 178 136 132

Figure S342.  Get High-res Image Gene #63: 'del_14q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_14q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0331 (Fisher's exact test), Q value = 0.064

Table S343.  Gene #63: 'del_14q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
DEL PEAK 34(14Q11.2) MUTATED 20 29 23
DEL PEAK 34(14Q11.2) WILD-TYPE 170 113 163

Figure S343.  Get High-res Image Gene #63: 'del_14q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_14q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00142 (Fisher's exact test), Q value = 0.0043

Table S344.  Gene #63: 'del_14q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
DEL PEAK 34(14Q11.2) MUTATED 10 9 25 18 5
DEL PEAK 34(14Q11.2) WILD-TYPE 62 131 73 98 42

Figure S344.  Get High-res Image Gene #63: 'del_14q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_14q32.32' versus 'CN_CNMF'

P value = 0.0102 (Fisher's exact test), Q value = 0.024

Table S345.  Gene #64: 'del_14q32.32' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
DEL PEAK 35(14Q32.32) MUTATED 11 26 32 6
DEL PEAK 35(14Q32.32) WILD-TYPE 144 109 157 37

Figure S345.  Get High-res Image Gene #64: 'del_14q32.32' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q32.32' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S346.  Gene #64: 'del_14q32.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
DEL PEAK 35(14Q32.32) MUTATED 3 11 7 18 32 3 1
DEL PEAK 35(14Q32.32) WILD-TYPE 81 68 89 74 46 72 17

Figure S346.  Get High-res Image Gene #64: 'del_14q32.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_14q32.32' versus 'RPPA_CNMF'

P value = 0.0181 (Fisher's exact test), Q value = 0.039

Table S347.  Gene #64: 'del_14q32.32' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 53 51 37 65
DEL PEAK 35(14Q32.32) MUTATED 8 14 2 6
DEL PEAK 35(14Q32.32) WILD-TYPE 45 37 35 59

Figure S347.  Get High-res Image Gene #64: 'del_14q32.32' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_14q32.32' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S348.  Gene #64: 'del_14q32.32' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
DEL PEAK 35(14Q32.32) MUTATED 17 49 7
DEL PEAK 35(14Q32.32) WILD-TYPE 124 163 154

Figure S348.  Get High-res Image Gene #64: 'del_14q32.32' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_14q32.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S349.  Gene #64: 'del_14q32.32' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 35(14Q32.32) MUTATED 21 15 9 28
DEL PEAK 35(14Q32.32) WILD-TYPE 155 88 161 37

Figure S349.  Get High-res Image Gene #64: 'del_14q32.32' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_14q32.32' versus 'MIRSEQ_CNMF'

P value = 0.00102 (Fisher's exact test), Q value = 0.0032

Table S350.  Gene #64: 'del_14q32.32' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 221 152 145
DEL PEAK 35(14Q32.32) MUTATED 46 12 16
DEL PEAK 35(14Q32.32) WILD-TYPE 175 140 129

Figure S350.  Get High-res Image Gene #64: 'del_14q32.32' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_14q32.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0292 (Fisher's exact test), Q value = 0.058

Table S351.  Gene #64: 'del_14q32.32' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
DEL PEAK 35(14Q32.32) MUTATED 21 16 37
DEL PEAK 35(14Q32.32) WILD-TYPE 169 126 149

Figure S351.  Get High-res Image Gene #64: 'del_14q32.32' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_14q32.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S352.  Gene #64: 'del_14q32.32' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
DEL PEAK 35(14Q32.32) MUTATED 11 8 28 5 15
DEL PEAK 35(14Q32.32) WILD-TYPE 61 132 70 111 32

Figure S352.  Get High-res Image Gene #64: 'del_14q32.32' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_14q32.32' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00082 (Fisher's exact test), Q value = 0.0027

Table S353.  Gene #64: 'del_14q32.32' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 244 89
DEL PEAK 35(14Q32.32) MUTATED 19 45 3
DEL PEAK 35(14Q32.32) WILD-TYPE 121 199 86

Figure S353.  Get High-res Image Gene #64: 'del_14q32.32' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_15q15.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S354.  Gene #65: 'del_15q15.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
DEL PEAK 36(15Q15.1) MUTATED 49 35 21 19
DEL PEAK 36(15Q15.1) WILD-TYPE 106 100 168 24

Figure S354.  Get High-res Image Gene #65: 'del_15q15.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.1' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9e-05

Table S355.  Gene #66: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
DEL PEAK 37(16Q23.1) MUTATED 16 40 28 14
DEL PEAK 37(16Q23.1) WILD-TYPE 139 95 161 29

Figure S355.  Get High-res Image Gene #66: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S356.  Gene #66: 'del_16q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
DEL PEAK 37(16Q23.1) MUTATED 5 17 10 30 27 6 3
DEL PEAK 37(16Q23.1) WILD-TYPE 79 62 86 62 51 69 15

Figure S356.  Get High-res Image Gene #66: 'del_16q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16q23.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S357.  Gene #66: 'del_16q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
DEL PEAK 37(16Q23.1) MUTATED 19 65 14
DEL PEAK 37(16Q23.1) WILD-TYPE 122 147 147

Figure S357.  Get High-res Image Gene #66: 'del_16q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S358.  Gene #66: 'del_16q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 37(16Q23.1) MUTATED 24 31 17 26
DEL PEAK 37(16Q23.1) WILD-TYPE 152 72 153 39

Figure S358.  Get High-res Image Gene #66: 'del_16q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_CNMF'

P value = 0.008 (Fisher's exact test), Q value = 0.02

Table S359.  Gene #66: 'del_16q23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 221 152 145
DEL PEAK 37(16Q23.1) MUTATED 55 23 19
DEL PEAK 37(16Q23.1) WILD-TYPE 166 129 126

Figure S359.  Get High-res Image Gene #66: 'del_16q23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_16q23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0403 (Fisher's exact test), Q value = 0.076

Table S360.  Gene #66: 'del_16q23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
DEL PEAK 37(16Q23.1) MUTATED 25 30 42
DEL PEAK 37(16Q23.1) WILD-TYPE 165 112 144

Figure S360.  Get High-res Image Gene #66: 'del_16q23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9e-05

Table S361.  Gene #66: 'del_16q23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
DEL PEAK 37(16Q23.1) MUTATED 12 16 36 15 9
DEL PEAK 37(16Q23.1) WILD-TYPE 60 124 62 101 38

Figure S361.  Get High-res Image Gene #66: 'del_16q23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_16q23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00116 (Fisher's exact test), Q value = 0.0036

Table S362.  Gene #66: 'del_16q23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 244 89
DEL PEAK 37(16Q23.1) MUTATED 17 61 10
DEL PEAK 37(16Q23.1) WILD-TYPE 123 183 79

Figure S362.  Get High-res Image Gene #66: 'del_16q23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q23.3' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00016

Table S363.  Gene #67: 'del_16q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
DEL PEAK 38(16Q23.3) MUTATED 19 42 29 15
DEL PEAK 38(16Q23.3) WILD-TYPE 136 93 160 28

Figure S363.  Get High-res Image Gene #67: 'del_16q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S364.  Gene #67: 'del_16q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
DEL PEAK 38(16Q23.3) MUTATED 6 16 8 33 27 11 4
DEL PEAK 38(16Q23.3) WILD-TYPE 78 63 88 59 51 64 14

Figure S364.  Get High-res Image Gene #67: 'del_16q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16q23.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S365.  Gene #67: 'del_16q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
DEL PEAK 38(16Q23.3) MUTATED 23 64 17
DEL PEAK 38(16Q23.3) WILD-TYPE 118 148 144

Figure S365.  Get High-res Image Gene #67: 'del_16q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16q23.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S366.  Gene #67: 'del_16q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 38(16Q23.3) MUTATED 27 31 19 27
DEL PEAK 38(16Q23.3) WILD-TYPE 149 72 151 38

Figure S366.  Get High-res Image Gene #67: 'del_16q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_16q23.3' versus 'MIRSEQ_CNMF'

P value = 0.0225 (Fisher's exact test), Q value = 0.047

Table S367.  Gene #67: 'del_16q23.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 221 152 145
DEL PEAK 38(16Q23.3) MUTATED 57 24 23
DEL PEAK 38(16Q23.3) WILD-TYPE 164 128 122

Figure S367.  Get High-res Image Gene #67: 'del_16q23.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_16q23.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00016

Table S368.  Gene #67: 'del_16q23.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
DEL PEAK 38(16Q23.3) MUTATED 14 17 37 17 9
DEL PEAK 38(16Q23.3) WILD-TYPE 58 123 61 99 38

Figure S368.  Get High-res Image Gene #67: 'del_16q23.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_16q23.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00366 (Fisher's exact test), Q value = 0.0098

Table S369.  Gene #67: 'del_16q23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 244 89
DEL PEAK 38(16Q23.3) MUTATED 23 62 9
DEL PEAK 38(16Q23.3) WILD-TYPE 117 182 80

Figure S369.  Get High-res Image Gene #67: 'del_16q23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S370.  Gene #68: 'del_17p11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
DEL PEAK 39(17P11.2) MUTATED 41 37 13 8
DEL PEAK 39(17P11.2) WILD-TYPE 114 98 176 35

Figure S370.  Get High-res Image Gene #68: 'del_17p11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_17p11.2' versus 'METHLYATION_CNMF'

P value = 0.0018 (Fisher's exact test), Q value = 0.0053

Table S371.  Gene #68: 'del_17p11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
DEL PEAK 39(17P11.2) MUTATED 9 23 18 25 13 6 5
DEL PEAK 39(17P11.2) WILD-TYPE 75 56 78 67 65 69 13

Figure S371.  Get High-res Image Gene #68: 'del_17p11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17p11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0239 (Fisher's exact test), Q value = 0.049

Table S372.  Gene #68: 'del_17p11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
DEL PEAK 39(17P11.2) MUTATED 19 24 28 16 6
DEL PEAK 39(17P11.2) WILD-TYPE 53 116 70 100 41

Figure S372.  Get High-res Image Gene #68: 'del_17p11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_17q25.3' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00013

Table S373.  Gene #69: 'del_17q25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
DEL PEAK 40(17Q25.3) MUTATED 3 8 10 22 19 4 5
DEL PEAK 40(17Q25.3) WILD-TYPE 81 71 86 70 59 71 13

Figure S373.  Get High-res Image Gene #69: 'del_17q25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17q25.3' versus 'MRNASEQ_CNMF'

P value = 0.0188 (Fisher's exact test), Q value = 0.04

Table S374.  Gene #69: 'del_17q25.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
DEL PEAK 40(17Q25.3) MUTATED 16 39 14
DEL PEAK 40(17Q25.3) WILD-TYPE 125 173 147

Figure S374.  Get High-res Image Gene #69: 'del_17q25.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_17q25.3' versus 'MIRSEQ_CNMF'

P value = 0.00856 (Fisher's exact test), Q value = 0.021

Table S375.  Gene #69: 'del_17q25.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 221 152 145
DEL PEAK 40(17Q25.3) MUTATED 42 15 13
DEL PEAK 40(17Q25.3) WILD-TYPE 179 137 132

Figure S375.  Get High-res Image Gene #69: 'del_17q25.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_17q25.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00371 (Fisher's exact test), Q value = 0.0099

Table S376.  Gene #69: 'del_17q25.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 244 89
DEL PEAK 40(17Q25.3) MUTATED 14 47 6
DEL PEAK 40(17Q25.3) WILD-TYPE 126 197 83

Figure S376.  Get High-res Image Gene #69: 'del_17q25.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18q21.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S377.  Gene #70: 'del_18q21.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
DEL PEAK 41(18Q21.2) MUTATED 122 80 44 22
DEL PEAK 41(18Q21.2) WILD-TYPE 33 55 145 21

Figure S377.  Get High-res Image Gene #70: 'del_18q21.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_18q21.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S378.  Gene #70: 'del_18q21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
DEL PEAK 41(18Q21.2) MUTATED 43 56 65 63 5 26 10
DEL PEAK 41(18Q21.2) WILD-TYPE 41 23 31 29 73 49 8

Figure S378.  Get High-res Image Gene #70: 'del_18q21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_18q21.2' versus 'MRNASEQ_CNMF'

P value = 0.0116 (Fisher's exact test), Q value = 0.027

Table S379.  Gene #70: 'del_18q21.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
DEL PEAK 41(18Q21.2) MUTATED 86 95 83
DEL PEAK 41(18Q21.2) WILD-TYPE 55 117 78

Figure S379.  Get High-res Image Gene #70: 'del_18q21.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_18q21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S380.  Gene #70: 'del_18q21.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 41(18Q21.2) MUTATED 103 68 86 7
DEL PEAK 41(18Q21.2) WILD-TYPE 73 35 84 58

Figure S380.  Get High-res Image Gene #70: 'del_18q21.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_18q21.2' versus 'MIRSEQ_CNMF'

P value = 0.0332 (Fisher's exact test), Q value = 0.064

Table S381.  Gene #70: 'del_18q21.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 221 152 145
DEL PEAK 41(18Q21.2) MUTATED 102 77 87
DEL PEAK 41(18Q21.2) WILD-TYPE 119 75 58

Figure S381.  Get High-res Image Gene #70: 'del_18q21.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_18q21.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S382.  Gene #70: 'del_18q21.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
DEL PEAK 41(18Q21.2) MUTATED 111 86 69
DEL PEAK 41(18Q21.2) WILD-TYPE 79 56 117

Figure S382.  Get High-res Image Gene #70: 'del_18q21.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_18q21.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00028

Table S383.  Gene #70: 'del_18q21.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
DEL PEAK 41(18Q21.2) MUTATED 39 76 53 69 9
DEL PEAK 41(18Q21.2) WILD-TYPE 33 64 45 47 38

Figure S383.  Get High-res Image Gene #70: 'del_18q21.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_18q23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S384.  Gene #71: 'del_18q23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
DEL PEAK 42(18Q23) MUTATED 128 89 48 23
DEL PEAK 42(18Q23) WILD-TYPE 27 46 141 20

Figure S384.  Get High-res Image Gene #71: 'del_18q23' versus Molecular Subtype #1: 'CN_CNMF'

'del_18q23' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S385.  Gene #71: 'del_18q23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
DEL PEAK 42(18Q23) MUTATED 45 57 71 70 9 25 11
DEL PEAK 42(18Q23) WILD-TYPE 39 22 25 22 69 50 7

Figure S385.  Get High-res Image Gene #71: 'del_18q23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_18q23' versus 'MRNASEQ_CNMF'

P value = 0.00635 (Fisher's exact test), Q value = 0.016

Table S386.  Gene #71: 'del_18q23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
DEL PEAK 42(18Q23) MUTATED 92 102 90
DEL PEAK 42(18Q23) WILD-TYPE 49 110 71

Figure S386.  Get High-res Image Gene #71: 'del_18q23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_18q23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S387.  Gene #71: 'del_18q23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 42(18Q23) MUTATED 110 70 95 9
DEL PEAK 42(18Q23) WILD-TYPE 66 33 75 56

Figure S387.  Get High-res Image Gene #71: 'del_18q23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_18q23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S388.  Gene #71: 'del_18q23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
DEL PEAK 42(18Q23) MUTATED 119 92 75
DEL PEAK 42(18Q23) WILD-TYPE 71 50 111

Figure S388.  Get High-res Image Gene #71: 'del_18q23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_18q23' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S389.  Gene #71: 'del_18q23' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
DEL PEAK 42(18Q23) MUTATED 45 84 57 68 9
DEL PEAK 42(18Q23) WILD-TYPE 27 56 41 48 38

Figure S389.  Get High-res Image Gene #71: 'del_18q23' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_18q23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0211 (Fisher's exact test), Q value = 0.045

Table S390.  Gene #71: 'del_18q23' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 244 89
DEL PEAK 42(18Q23) MUTATED 89 121 53
DEL PEAK 42(18Q23) WILD-TYPE 51 123 36

Figure S390.  Get High-res Image Gene #71: 'del_18q23' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S391.  Gene #72: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
DEL PEAK 43(19P13.3) MUTATED 77 55 27 16
DEL PEAK 43(19P13.3) WILD-TYPE 78 80 162 27

Figure S391.  Get High-res Image Gene #72: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_19p13.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S392.  Gene #72: 'del_19p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
DEL PEAK 43(19P13.3) MUTATED 17 28 49 41 14 21 5
DEL PEAK 43(19P13.3) WILD-TYPE 67 51 47 51 64 54 13

Figure S392.  Get High-res Image Gene #72: 'del_19p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19p13.3' versus 'MRNASEQ_CNMF'

P value = 0.0189 (Fisher's exact test), Q value = 0.041

Table S393.  Gene #72: 'del_19p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
DEL PEAK 43(19P13.3) MUTATED 61 63 49
DEL PEAK 43(19P13.3) WILD-TYPE 80 149 112

Figure S393.  Get High-res Image Gene #72: 'del_19p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_19p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-04 (Fisher's exact test), Q value = 0.002

Table S394.  Gene #72: 'del_19p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 43(19P13.3) MUTATED 71 39 54 9
DEL PEAK 43(19P13.3) WILD-TYPE 105 64 116 56

Figure S394.  Get High-res Image Gene #72: 'del_19p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.00046

Table S395.  Gene #72: 'del_19p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
DEL PEAK 43(19P13.3) MUTATED 72 59 41
DEL PEAK 43(19P13.3) WILD-TYPE 118 83 145

Figure S395.  Get High-res Image Gene #72: 'del_19p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9e-05

Table S396.  Gene #72: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
DEL PEAK 43(19P13.3) MUTATED 28 51 24 51 3
DEL PEAK 43(19P13.3) WILD-TYPE 44 89 74 65 44

Figure S396.  Get High-res Image Gene #72: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_19q13.43' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S397.  Gene #73: 'del_19q13.43' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
DEL PEAK 44(19Q13.43) MUTATED 45 38 9 5
DEL PEAK 44(19Q13.43) WILD-TYPE 110 97 180 38

Figure S397.  Get High-res Image Gene #73: 'del_19q13.43' versus Molecular Subtype #1: 'CN_CNMF'

'del_19q13.43' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S398.  Gene #73: 'del_19q13.43' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
DEL PEAK 44(19Q13.43) MUTATED 7 18 27 30 5 6 4
DEL PEAK 44(19Q13.43) WILD-TYPE 77 61 69 62 73 69 14

Figure S398.  Get High-res Image Gene #73: 'del_19q13.43' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19q13.43' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00016

Table S399.  Gene #73: 'del_19q13.43' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 44(19Q13.43) MUTATED 34 34 23 4
DEL PEAK 44(19Q13.43) WILD-TYPE 142 69 147 61

Figure S399.  Get High-res Image Gene #73: 'del_19q13.43' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_21q22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S400.  Gene #74: 'del_21q22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
DEL PEAK 45(21Q22.3) MUTATED 88 73 28 19
DEL PEAK 45(21Q22.3) WILD-TYPE 67 62 161 24

Figure S400.  Get High-res Image Gene #74: 'del_21q22.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_21q22.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S401.  Gene #74: 'del_21q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
DEL PEAK 45(21Q22.3) MUTATED 24 35 54 53 12 19 11
DEL PEAK 45(21Q22.3) WILD-TYPE 60 44 42 39 66 56 7

Figure S401.  Get High-res Image Gene #74: 'del_21q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_21q22.3' versus 'MRNASEQ_CNMF'

P value = 0.00819 (Fisher's exact test), Q value = 0.02

Table S402.  Gene #74: 'del_21q22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
DEL PEAK 45(21Q22.3) MUTATED 71 72 62
DEL PEAK 45(21Q22.3) WILD-TYPE 70 140 99

Figure S402.  Get High-res Image Gene #74: 'del_21q22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_21q22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 9e-05

Table S403.  Gene #74: 'del_21q22.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 45(21Q22.3) MUTATED 89 46 59 11
DEL PEAK 45(21Q22.3) WILD-TYPE 87 57 111 54

Figure S403.  Get High-res Image Gene #74: 'del_21q22.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_21q22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00016

Table S404.  Gene #74: 'del_21q22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
DEL PEAK 45(21Q22.3) MUTATED 88 68 51
DEL PEAK 45(21Q22.3) WILD-TYPE 102 74 135

Figure S404.  Get High-res Image Gene #74: 'del_21q22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_21q22.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.00056

Table S405.  Gene #74: 'del_21q22.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
DEL PEAK 45(21Q22.3) MUTATED 39 60 39 49 6
DEL PEAK 45(21Q22.3) WILD-TYPE 33 80 59 67 41

Figure S405.  Get High-res Image Gene #74: 'del_21q22.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_xp22.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S406.  Gene #75: 'del_xp22.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
DEL PEAK 46(XP22.2) MUTATED 60 62 26 9
DEL PEAK 46(XP22.2) WILD-TYPE 95 73 163 34

Figure S406.  Get High-res Image Gene #75: 'del_xp22.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_xp22.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S407.  Gene #75: 'del_xp22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
DEL PEAK 46(XP22.2) MUTATED 14 25 35 50 17 9 7
DEL PEAK 46(XP22.2) WILD-TYPE 70 54 61 42 61 66 11

Figure S407.  Get High-res Image Gene #75: 'del_xp22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xp22.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00265 (Fisher's exact test), Q value = 0.0074

Table S408.  Gene #75: 'del_xp22.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 82 48
DEL PEAK 46(XP22.2) MUTATED 19 39 11
DEL PEAK 46(XP22.2) WILD-TYPE 57 43 37

Figure S408.  Get High-res Image Gene #75: 'del_xp22.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_xp22.2' versus 'MRNASEQ_CNMF'

P value = 0.0455 (Fisher's exact test), Q value = 0.084

Table S409.  Gene #75: 'del_xp22.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
DEL PEAK 46(XP22.2) MUTATED 48 71 37
DEL PEAK 46(XP22.2) WILD-TYPE 93 141 124

Figure S409.  Get High-res Image Gene #75: 'del_xp22.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_xp22.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0172 (Fisher's exact test), Q value = 0.038

Table S410.  Gene #75: 'del_xp22.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 46(XP22.2) MUTATED 60 40 38 18
DEL PEAK 46(XP22.2) WILD-TYPE 116 63 132 47

Figure S410.  Get High-res Image Gene #75: 'del_xp22.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_xp22.2' versus 'MIRSEQ_CNMF'

P value = 0.0054 (Fisher's exact test), Q value = 0.014

Table S411.  Gene #75: 'del_xp22.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 221 152 145
DEL PEAK 46(XP22.2) MUTATED 79 31 44
DEL PEAK 46(XP22.2) WILD-TYPE 142 121 101

Figure S411.  Get High-res Image Gene #75: 'del_xp22.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_xp22.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0044 (Fisher's exact test), Q value = 0.012

Table S412.  Gene #75: 'del_xp22.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
DEL PEAK 46(XP22.2) MUTATED 23 38 41 30 6
DEL PEAK 46(XP22.2) WILD-TYPE 49 102 57 86 41

Figure S412.  Get High-res Image Gene #75: 'del_xp22.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_xp21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S413.  Gene #76: 'del_xp21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
DEL PEAK 47(XP21.3) MUTATED 66 59 27 7
DEL PEAK 47(XP21.3) WILD-TYPE 89 76 162 36

Figure S413.  Get High-res Image Gene #76: 'del_xp21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_xp21.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S414.  Gene #76: 'del_xp21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
DEL PEAK 47(XP21.3) MUTATED 16 26 38 45 15 12 7
DEL PEAK 47(XP21.3) WILD-TYPE 68 53 58 47 63 63 11

Figure S414.  Get High-res Image Gene #76: 'del_xp21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xp21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0238 (Fisher's exact test), Q value = 0.049

Table S415.  Gene #76: 'del_xp21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 47(XP21.3) MUTATED 62 39 40 16
DEL PEAK 47(XP21.3) WILD-TYPE 114 64 130 49

Figure S415.  Get High-res Image Gene #76: 'del_xp21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_xp21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0136 (Fisher's exact test), Q value = 0.031

Table S416.  Gene #76: 'del_xp21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
DEL PEAK 47(XP21.3) MUTATED 23 42 37 33 5
DEL PEAK 47(XP21.3) WILD-TYPE 49 98 61 83 42

Figure S416.  Get High-res Image Gene #76: 'del_xp21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_xq21.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S417.  Gene #77: 'del_xq21.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
DEL PEAK 48(XQ21.33) MUTATED 34 34 10 2
DEL PEAK 48(XQ21.33) WILD-TYPE 121 101 179 41

Figure S417.  Get High-res Image Gene #77: 'del_xq21.33' versus Molecular Subtype #1: 'CN_CNMF'

'del_xq21.33' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S418.  Gene #77: 'del_xq21.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
DEL PEAK 48(XQ21.33) MUTATED 4 16 15 31 11 0 3
DEL PEAK 48(XQ21.33) WILD-TYPE 80 63 81 61 67 75 15

Figure S418.  Get High-res Image Gene #77: 'del_xq21.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xq21.33' versus 'MRNASEQ_CNMF'

P value = 0.00066 (Fisher's exact test), Q value = 0.0022

Table S419.  Gene #77: 'del_xq21.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
DEL PEAK 48(XQ21.33) MUTATED 12 48 19
DEL PEAK 48(XQ21.33) WILD-TYPE 129 164 142

Figure S419.  Get High-res Image Gene #77: 'del_xq21.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_xq21.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00349 (Fisher's exact test), Q value = 0.0094

Table S420.  Gene #77: 'del_xq21.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 48(XQ21.33) MUTATED 17 26 23 13
DEL PEAK 48(XQ21.33) WILD-TYPE 159 77 147 52

Figure S420.  Get High-res Image Gene #77: 'del_xq21.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_xq21.33' versus 'MIRSEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00053

Table S421.  Gene #77: 'del_xq21.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 221 152 145
DEL PEAK 48(XQ21.33) MUTATED 51 15 13
DEL PEAK 48(XQ21.33) WILD-TYPE 170 137 132

Figure S421.  Get High-res Image Gene #77: 'del_xq21.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_xq21.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0124 (Fisher's exact test), Q value = 0.029

Table S422.  Gene #77: 'del_xq21.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
DEL PEAK 48(XQ21.33) MUTATED 18 29 32
DEL PEAK 48(XQ21.33) WILD-TYPE 172 113 154

Figure S422.  Get High-res Image Gene #77: 'del_xq21.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_xq21.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0414 (Fisher's exact test), Q value = 0.078

Table S423.  Gene #77: 'del_xq21.33' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
DEL PEAK 48(XQ21.33) MUTATED 7 18 23 18 3
DEL PEAK 48(XQ21.33) WILD-TYPE 65 122 75 98 44

Figure S423.  Get High-res Image Gene #77: 'del_xq21.33' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

Methods & Data
Input

  • Copy number data file = all_lesions.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/HNSC-TP/15085744/transformed.cor.cli.txt

  • Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/HNSC-TP/15111022/HNSC-TP.transferedmergedcluster.txt

  • Number of patients = 522

  • Number of significantly focal cnvs = 77

  • Number of molecular subtypes = 10

  • Exclude genes that fewer than K tumors have alterations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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