Correlation between copy number variation genes (focal events) and molecular subtypes
Lung Adenocarcinoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1PR7V19
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/C1PR7V19
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 68 focal events and 12 molecular subtypes across 516 patients, 486 significant findings detected with P value < 0.05 and Q value < 0.25.

  • amp_1p22.3 cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_1q21.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

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

  • amp_5p15.33 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_6p21.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_7p11.2 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'.

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

  • amp_8p11.21 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 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

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

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

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

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

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

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

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

  • amp_22q11.22 cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • del_1p36.11 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

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

  • del_3q11.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

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

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

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

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

  • del_6q11.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • del_6q22.31 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • del_6q26 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

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

  • del_8p11.21 cnv correlated to 'CN_CNMF',  'RPPA_CHIERARCHICAL', and 'MRNASEQ_CNMF'.

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

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

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

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

  • del_10q26.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • del_11q23.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • del_11q25 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_12p13.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_12q12 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • del_13q12.11 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_13q12.13 cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_13q14.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_13q34 cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_14q32.12 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

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

  • del_15q15.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • del_17p13.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

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

  • del_19q11 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • del_20p13 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_20q13.12 cnv correlated to 'MRNA_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

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

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

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

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 68 focal events and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 486 significant findings detected.

Clinical
Features 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
del 8p23 2 257 (50%) 259 0.0233
(0.0441) 		0.0481
(0.0811) 		1e-05
(4.46e-05) 		0.0382
(0.0674) 		0.00924
(0.0195) 		8e-05
(0.000269) 		1e-05
(4.46e-05) 		1e-05
(4.46e-05) 		0.00035
(0.00102) 		0.0102
(0.0212) 		0.0212
(0.0409) 		0.00077
(0.00207)
del 13q14 2 282 (55%) 234 0.0119
(0.0244) 		0.0238
(0.0449) 		1e-05
(4.46e-05) 		0.00503
(0.0113) 		0.00868
(0.0185) 		0.00256
(0.00613) 		9e-05
(0.000299) 		1e-05
(4.46e-05) 		0.00195
(0.00479) 		0.00524
(0.0117) 		0.0497
(0.0834) 		7e-05
(0.00024)
del 13q12 11 294 (57%) 222 0.00077
(0.00207) 		0.0229
(0.0436) 		1e-05
(4.46e-05) 		0.00142
(0.00361) 		0.00693
(0.0152) 		0.00023
(0.000695) 		2e-05
(7.92e-05) 		1e-05
(4.46e-05) 		0.00338
(0.00786) 		0.0038
(0.00876) 		0.242
(0.311) 		0.00081
(0.00215)
amp 3q26 2 171 (33%) 345 0.00024
(0.000717) 		0.00178
(0.00439) 		1e-05
(4.46e-05) 		1e-05
(4.46e-05) 		0.43
(0.505) 		0.0117
(0.0241) 		1e-05
(4.46e-05) 		1e-05
(4.46e-05) 		1e-05
(4.46e-05) 		2e-05
(7.92e-05) 		0.459
(0.531) 		1e-05
(4.46e-05)
amp 7p11 2 272 (53%) 244 0.922
(0.942) 		0.815
(0.858) 		1e-05
(4.46e-05) 		0.0347
(0.0626) 		0.00316
(0.00743) 		0.0074
(0.0161) 		1e-05
(4.46e-05) 		1e-05
(4.46e-05) 		1e-05
(4.46e-05) 		2e-05
(7.92e-05) 		5e-05
(0.000175) 		1e-05
(4.46e-05)
amp 8q24 21 322 (62%) 194 0.0073
(0.0159) 		0.0264
(0.0486) 		1e-05
(4.46e-05) 		1e-05
(4.46e-05) 		0.738
(0.792) 		0.953
(0.969) 		1e-05
(4.46e-05) 		1e-05
(4.46e-05) 		1e-05
(4.46e-05) 		0.00016
(0.000502) 		0.0463
(0.0786) 		1e-05
(4.46e-05)
amp 11q13 3 170 (33%) 346 0.00116
(0.00302) 		0.00012
(0.000389) 		1e-05
(4.46e-05) 		5e-05
(0.000175) 		0.0461
(0.0784) 		0.92
(0.941) 		0.00015
(0.000474) 		1e-05
(4.46e-05) 		1e-05
(4.46e-05) 		1e-05
(4.46e-05) 		0.466
(0.539) 		0.00024
(0.000717)
amp 20q13 33 244 (47%) 272 0.00314
(0.00741) 		0.0149
(0.0299) 		1e-05
(4.46e-05) 		3e-05
(0.000112) 		0.0561
(0.0926) 		0.426
(0.503) 		0.00161
(0.00402) 		1e-05
(4.46e-05) 		2e-05
(7.92e-05) 		1e-05
(4.46e-05) 		0.0232
(0.044) 		1e-05
(4.46e-05)
del 4q34 3 188 (36%) 328 0.00455
(0.0103) 		0.00566
(0.0126) 		1e-05
(4.46e-05) 		1e-05
(4.46e-05) 		0.137
(0.199) 		0.255
(0.325) 		1e-05
(4.46e-05) 		1e-05
(4.46e-05) 		1e-05
(4.46e-05) 		1e-05
(4.46e-05) 		0.0236
(0.0446) 		1e-05
(4.46e-05)
del 13q12 13 293 (57%) 223 0.00891
(0.0189) 		0.0651
(0.103) 		1e-05
(4.46e-05) 		0.00158
(0.00397) 		0.0087
(0.0185) 		0.0006
(0.00168) 		5e-05
(0.000175) 		1e-05
(4.46e-05) 		0.00419
(0.00955) 		0.00585
(0.013) 		0.212
(0.283) 		0.00068
(0.00188)
del 13q34 243 (47%) 273 0.0241
(0.0452) 		0.0834
(0.129) 		1e-05
(4.46e-05) 		0.0394
(0.0691) 		0.00123
(0.00317) 		0.0208
(0.0402) 		0.0005
(0.00142) 		1e-05
(4.46e-05) 		0.00773
(0.0166) 		0.0201
(0.0391) 		0.224
(0.294) 		0.0217
(0.0415)
amp 5p15 33 328 (64%) 188 0.0576
(0.0943) 		0.225
(0.295) 		1e-05
(4.46e-05) 		0.00157
(0.00395) 		0.0403
(0.0706) 		0.0424
(0.0735) 		0.0231
(0.044) 		0.0002
(0.000614) 		0.00142
(0.00361) 		0.00081
(0.00215) 		0.361
(0.433) 		1e-05
(4.46e-05)
amp 12p12 1 179 (35%) 337 0.198
(0.266) 		0.0381
(0.0674) 		1e-05
(4.46e-05) 		0.00284
(0.00676) 		0.039
(0.0686) 		0.45
(0.523) 		1e-05
(4.46e-05) 		1e-05
(4.46e-05) 		2e-05
(7.92e-05) 		2e-05
(7.92e-05) 		0.676
(0.74) 		1e-05
(4.46e-05)
amp 17q12 226 (44%) 290 0.122
(0.18) 		0.0474
(0.08) 		1e-05
(4.46e-05) 		1e-05
(4.46e-05) 		0.307
(0.379) 		0.0171
(0.0339) 		1e-05
(4.46e-05) 		1e-05
(4.46e-05) 		1e-05
(4.46e-05) 		1e-05
(4.46e-05) 		0.543
(0.607) 		3e-05
(0.000112)
amp 19q12 137 (27%) 379 0.0938
(0.143) 		0.0416
(0.0725) 		1e-05
(4.46e-05) 		1e-05
(4.46e-05) 		0.787
(0.834) 		0.234
(0.304) 		1e-05
(4.46e-05) 		4e-05
(0.000145) 		1e-05
(4.46e-05) 		0.00019
(0.000585) 		0.0446
(0.0765) 		0.00014
(0.000446)
del 10q26 3 156 (30%) 360 0.275
(0.344) 		0.132
(0.193) 		0.00038
(0.0011) 		0.0384
(0.0677) 		8e-05
(0.000269) 		0.00023
(0.000695) 		0.00289
(0.00686) 		1e-05
(4.46e-05) 		0.0124
(0.0253) 		0.00137
(0.0035) 		0.0586
(0.095) 		0.00123
(0.00317)
del 17p13 3 281 (54%) 235 0.665
(0.728) 		0.558
(0.622) 		1e-05
(4.46e-05) 		2e-05
(7.92e-05) 		0.00072
(0.00196) 		0.00118
(0.00307) 		3e-05
(0.000112) 		1e-05
(4.46e-05) 		0.013
(0.0264) 		0.0249
(0.0465) 		0.921
(0.941) 		0.00208
(0.00508)
del 22q13 32 255 (49%) 261 0.025
(0.0466) 		0.081
(0.126) 		1e-05
(4.46e-05) 		1e-05
(4.46e-05) 		0.518
(0.587) 		0.351
(0.422) 		1e-05
(4.46e-05) 		1e-05
(4.46e-05) 		2e-05
(7.92e-05) 		2e-05
(7.92e-05) 		0.0152
(0.0305) 		4e-05
(0.000145)
amp 1q21 3 372 (72%) 144 0.856
(0.893) 		1
(1.00) 		1e-05
(4.46e-05) 		1e-05
(4.46e-05) 		0.0631
(0.101) 		0.0239
(0.045) 		1e-05
(4.46e-05) 		8e-05
(0.000269) 		0.00416
(0.00951) 		0.00101
(0.00265) 		0.00498
(0.0113) 		0.172
(0.238)
amp 8p11 21 173 (34%) 343 0.436
(0.51) 		0.636
(0.698) 		1e-05
(4.46e-05) 		1e-05
(4.46e-05) 		0.238
(0.306) 		0.868
(0.901) 		1e-05
(4.46e-05) 		1e-05
(4.46e-05) 		0.00042
(0.0012) 		0.00011
(0.00036) 		0.0131
(0.0264) 		0.00021
(0.000642)
amp 18q11 2 103 (20%) 413 0.196
(0.264) 		0.02
(0.0391) 		4e-05
(0.000145) 		1e-05
(4.46e-05) 		0.0581
(0.0945) 		0.374
(0.448) 		0.00013
(0.000416) 		6e-05
(0.000207) 		8e-05
(0.000269) 		2e-05
(7.92e-05) 		0.428
(0.504) 		3e-05
(0.000112)
del 3p21 31 246 (48%) 270 0.253
(0.324) 		0.143
(0.206) 		1e-05
(4.46e-05) 		1e-05
(4.46e-05) 		0.0323
(0.0584) 		0.179
(0.246) 		0.0017
(0.00422) 		1e-05
(4.46e-05) 		4e-05
(0.000145) 		1e-05
(4.46e-05) 		0.598
(0.663) 		5e-05
(0.000175)
del 5q12 1 177 (34%) 339 0.22
(0.29) 		0.182
(0.25) 		1e-05
(4.46e-05) 		1e-05
(4.46e-05) 		0.055
(0.0916) 		0.512
(0.584) 		2e-05
(7.92e-05) 		1e-05
(4.46e-05) 		1e-05
(4.46e-05) 		1e-05
(4.46e-05) 		0.0121
(0.0248) 		1e-05
(4.46e-05)
del 11p15 5 143 (28%) 373 0.266
(0.335) 		0.032
(0.058) 		1e-05
(4.46e-05) 		0.00089
(0.00235) 		0.625
(0.688) 		0.33
(0.401) 		4e-05
(0.000145) 		1e-05
(4.46e-05) 		0.00019
(0.000585) 		0.00025
(0.000745) 		0.0706
(0.11) 		0.00042
(0.0012)
del 15q11 2 262 (51%) 254 0.265
(0.334) 		0.142
(0.204) 		1e-05
(4.46e-05) 		0.00107
(0.0028) 		0.0541
(0.0903) 		0.0064
(0.0141) 		0.00087
(0.0023) 		1e-05
(4.46e-05) 		2e-05
(7.92e-05) 		0.00674
(0.0148) 		0.311
(0.383) 		8e-05
(0.000269)
del 15q15 1 274 (53%) 242 0.16
(0.225) 		0.0647
(0.103) 		1e-05
(4.46e-05) 		2e-05
(7.92e-05) 		0.0588
(0.0952) 		0.0158
(0.0317) 		0.00011
(0.00036) 		1e-05
(4.46e-05) 		3e-05
(0.000112) 		0.00031
(0.000907) 		0.231
(0.301) 		2e-05
(7.92e-05)
del 16q23 1 170 (33%) 346 0.086
(0.132) 		1
(1.00) 		2e-05
(7.92e-05) 		3e-05
(0.000112) 		0.198
(0.266) 		0.00168
(0.00418) 		1e-05
(4.46e-05) 		1e-05
(4.46e-05) 		0.0217
(0.0415) 		0.00331
(0.00774) 		0.862
(0.896) 		0.00053
(0.0015)
del 21q11 2 185 (36%) 331 0.227
(0.297) 		0.238
(0.306) 		1e-05
(4.46e-05) 		0.0272
(0.0501) 		0.00708
(0.0154) 		0.172
(0.238) 		1e-05
(4.46e-05) 		1e-05
(4.46e-05) 		1e-05
(4.46e-05) 		0.00018
(0.000563) 		0.439
(0.512) 		0.00028
(0.000825)
amp 12q14 1 168 (33%) 348 0.506
(0.579) 		0.137
(0.199) 		1e-05
(4.46e-05) 		0.00015
(0.000474) 		0.377
(0.449) 		0.583
(0.648) 		1e-05
(4.46e-05) 		1e-05
(4.46e-05) 		1e-05
(4.46e-05) 		1e-05
(4.46e-05) 		0.35
(0.422) 		1e-05
(4.46e-05)
amp 12q15 171 (33%) 345 0.36
(0.433) 		0.0633
(0.101) 		1e-05
(4.46e-05) 		5e-05
(0.000175) 		0.208
(0.278) 		0.096
(0.146) 		1e-05
(4.46e-05) 		1e-05
(4.46e-05) 		1e-05
(4.46e-05) 		1e-05
(4.46e-05) 		0.436
(0.51) 		1e-05
(4.46e-05)
amp 14q13 3 229 (44%) 287 0.484
(0.556) 		0.31
(0.382) 		1e-05
(4.46e-05) 		3e-05
(0.000112) 		0.0828
(0.128) 		0.851
(0.891) 		0.00072
(0.00196) 		1e-05
(4.46e-05) 		1e-05
(4.46e-05) 		1e-05
(4.46e-05) 		0.188
(0.257) 		0.00013
(0.000416)
amp 17q23 1 249 (48%) 267 0.0785
(0.122) 		0.3
(0.371) 		1e-05
(4.46e-05) 		1e-05
(4.46e-05) 		0.238
(0.306) 		0.0554
(0.0918) 		1e-05
(4.46e-05) 		1e-05
(4.46e-05) 		2e-05
(7.92e-05) 		1e-05
(4.46e-05) 		0.702
(0.759) 		2e-05
(7.92e-05)
del 1p36 11 125 (24%) 391 0.435
(0.509) 		0.125
(0.184) 		1e-05
(4.46e-05) 		1e-05
(4.46e-05) 		0.234
(0.304) 		0.129
(0.189) 		1e-05
(4.46e-05) 		1e-05
(4.46e-05) 		0.0248
(0.0463) 		0.0623
(0.1) 		0.0174
(0.0345) 		0.00854
(0.0183)
del 3p26 2 236 (46%) 280 0.168
(0.234) 		0.315
(0.385) 		3e-05
(0.000112) 		0.00012
(0.000389) 		0.0623
(0.1) 		0.302
(0.373) 		0.0357
(0.064) 		1e-05
(4.46e-05) 		3e-05
(0.000112) 		0.00022
(0.00067) 		0.796
(0.841) 		0.00044
(0.00125)
del 4p16 3 131 (25%) 385 0.803
(0.846) 		0.846
(0.886) 		0.00136
(0.00349) 		0.00039
(0.00113) 		0.905
(0.927) 		0.314
(0.384) 		0.0095
(0.02) 		1e-05
(4.46e-05) 		1e-05
(4.46e-05) 		1e-05
(4.46e-05) 		0.728
(0.783) 		0.00072
(0.00196)
del 5q31 1 208 (40%) 308 0.197
(0.266) 		0.145
(0.208) 		1e-05
(4.46e-05) 		1e-05
(4.46e-05) 		0.0615
(0.0989) 		0.251
(0.321) 		1e-05
(4.46e-05) 		1e-05
(4.46e-05) 		1e-05
(4.46e-05) 		1e-05
(4.46e-05) 		0.399
(0.475) 		1e-05
(4.46e-05)
del 9q21 11 256 (50%) 260 0.0643
(0.102) 		0.539
(0.606) 		1e-05
(4.46e-05) 		7e-05
(0.00024) 		0.274
(0.343) 		0.0578
(0.0944) 		0.00557
(0.0125) 		2e-05
(7.92e-05) 		2e-05
(7.92e-05) 		1e-05
(4.46e-05) 		0.19
(0.258) 		0.00019
(0.000585)
del 10p15 3 126 (24%) 390 1
(1.00) 		1
(1.00) 		0.00644
(0.0142) 		0.00982
(0.0205) 		0.136
(0.197) 		0.122
(0.18) 		0.134
(0.195) 		0.00202
(0.00495) 		0.00242
(0.00584) 		0.0188
(0.0369) 		0.032
(0.058) 		0.0122
(0.0248)
del 11q23 2 119 (23%) 397 0.453
(0.526) 		0.689
(0.749) 		1e-05
(4.46e-05) 		0.00024
(0.000717) 		0.0372
(0.0665) 		0.336
(0.407) 		3e-05
(0.000112) 		0.00067
(0.00186) 		0.00248
(0.00597) 		0.0553
(0.0918) 		0.0444
(0.0764) 		0.312
(0.383)
del 19p13 3 283 (55%) 233 0.255
(0.325) 		1
(1.00) 		1e-05
(4.46e-05) 		1e-05
(4.46e-05) 		0.52
(0.587) 		0.236
(0.305) 		1e-05
(4.46e-05) 		1e-05
(4.46e-05) 		1e-05
(4.46e-05) 		1e-05
(4.46e-05) 		0.104
(0.157) 		0.00078
(0.00209)
del 19p13 2 280 (54%) 236 0.745
(0.798) 		0.897
(0.922) 		1e-05
(4.46e-05) 		1e-05
(4.46e-05) 		0.698
(0.755) 		0.157
(0.222) 		1e-05
(4.46e-05) 		1e-05
(4.46e-05) 		1e-05
(4.46e-05) 		1e-05
(4.46e-05) 		0.0589
(0.0952) 		0.00078
(0.00209)
del 19p13 2 270 (52%) 246 0.693
(0.751) 		1
(1.00) 		1e-05
(4.46e-05) 		1e-05
(4.46e-05) 		0.893
(0.92) 		0.0677
(0.107) 		1e-05
(4.46e-05) 		1e-05
(4.46e-05) 		1e-05
(4.46e-05) 		1e-05
(4.46e-05) 		0.0534
(0.0895) 		9e-05
(0.000299)
del 19q11 134 (26%) 382 1
(1.00) 		0.881
(0.91) 		1e-05
(4.46e-05) 		0.00072
(0.00196) 		0.0903
(0.138) 		0.317
(0.387) 		0.00257
(0.00613) 		0.00221
(0.00538) 		0.00148
(0.00375) 		0.00028
(0.000825) 		0.413
(0.489) 		0.0443
(0.0764)
del 19q13 33 194 (38%) 322 0.52
(0.587) 		0.0959
(0.146) 		1e-05
(4.46e-05) 		1e-05
(4.46e-05) 		0.287
(0.356) 		0.174
(0.241) 		3e-05
(0.000112) 		2e-05
(7.92e-05) 		2e-05
(7.92e-05) 		1e-05
(4.46e-05) 		0.573
(0.638) 		0.0114
(0.0235)
del 20p13 131 (25%) 385 0.105
(0.158) 		0.224
(0.294) 		1e-05
(4.46e-05) 		0.00058
(0.00163) 		0.00344
(0.00797) 		0.00041
(0.00118) 		1e-05
(4.46e-05) 		1e-05
(4.46e-05) 		0.952
(0.969) 		0.709
(0.764) 		0.366
(0.439) 		0.0146
(0.0295)
amp 6p21 1 190 (37%) 326 0.637
(0.698) 		0.223
(0.294) 		1e-05
(4.46e-05) 		1e-05
(4.46e-05) 		0.0998
(0.151) 		0.467
(0.539) 		0.0539
(0.0901) 		0.00976
(0.0205) 		0.0352
(0.0633) 		0.00776
(0.0167) 		0.35
(0.422) 		0.0285
(0.0521)
amp 7q31 2 214 (41%) 302 0.956
(0.97) 		0.414
(0.49) 		1e-05
(4.46e-05) 		0.184
(0.252) 		0.157
(0.222) 		0.227
(0.297) 		1e-05
(4.46e-05) 		1e-05
(4.46e-05) 		0.00121
(0.00313) 		0.00161
(0.00402) 		0.114
(0.169) 		2e-05
(7.92e-05)
amp xq28 157 (30%) 359 0.191
(0.26) 		0.159
(0.224) 		1e-05
(4.46e-05) 		0.00077
(0.00207) 		0.286
(0.356) 		0.548
(0.611) 		3e-05
(0.000112) 		0.00013
(0.000416) 		0.0087
(0.0185) 		0.0846
(0.13) 		0.263
(0.333) 		0.0004
(0.00115)
del 6q22 31 252 (49%) 264 0.269
(0.338) 		0.146
(0.208) 		0.00012
(0.000389) 		1e-05
(4.46e-05) 		0.0495
(0.0834) 		0.00345
(0.00797) 		0.175
(0.241) 		0.00074
(0.00201) 		0.796
(0.841) 		0.00099
(0.00261) 		0.492
(0.564) 		0.344
(0.416)
del 9p21 3 291 (56%) 225 0.169
(0.234) 		0.313
(0.383) 		1e-05
(4.46e-05) 		0.0179
(0.0354) 		0.608
(0.671) 		0.0376
(0.067) 		0.114
(0.169) 		1e-05
(4.46e-05) 		0.19
(0.258) 		0.00178
(0.00439) 		0.0442
(0.0763) 		0.105
(0.158)
del 18q21 32 251 (49%) 265 0.406
(0.482) 		0.0914
(0.14) 		1e-05
(4.46e-05) 		0.949
(0.967) 		0.0472
(0.0799) 		0.00057
(0.0016) 		1e-05
(4.46e-05) 		1e-05
(4.46e-05) 		0.0202
(0.0393) 		0.113
(0.168) 		0.871
(0.902) 		0.063
(0.101)
del 1p13 1 149 (29%) 367 0.342
(0.415) 		0.54
(0.606) 		1e-05
(4.46e-05) 		0.00031
(0.000907) 		0.0859
(0.132) 		0.0562
(0.0926) 		2e-05
(7.92e-05) 		5e-05
(0.000175) 		0.192
(0.26) 		0.00501
(0.0113) 		0.839
(0.882) 		0.776
(0.825)
del 2q22 1 46 (9%) 470 0.869
(0.901) 		0.783
(0.832) 		0.00385
(0.00885) 		0.00242
(0.00584) 		0.157
(0.222) 		0.755
(0.806) 		0.0591
(0.0953) 		0.0163
(0.0325) 		0.0372
(0.0665) 		0.00769
(0.0166) 		0.856
(0.893) 		0.0884
(0.136)
del 3q29 135 (26%) 381 0.609
(0.671) 		0.683
(0.747) 		0.00322
(0.00755) 		0.00153
(0.00387) 		0.103
(0.155) 		0.0309
(0.0562) 		1e-05
(4.46e-05) 		1e-05
(4.46e-05) 		0.785
(0.833) 		0.0657
(0.104) 		0.146
(0.208) 		0.247
(0.317)
del 9p23 285 (55%) 231 0.167
(0.233) 		0.312
(0.383) 		1e-05
(4.46e-05) 		0.0408
(0.0712) 		0.877
(0.907) 		0.285
(0.356) 		0.0424
(0.0735) 		0.00026
(0.000771) 		0.168
(0.234) 		0.0257
(0.0476) 		0.287
(0.356) 		0.213
(0.283)
del 11q25 117 (23%) 399 0.108
(0.161) 		0.481
(0.554) 		6e-05
(0.000207) 		0.00019
(0.000585) 		0.00414
(0.00949) 		0.146
(0.208) 		6e-05
(0.000207) 		0.00302
(0.00714) 		0.0678
(0.107) 		0.14
(0.202) 		0.099
(0.15) 		0.424
(0.5)
del 12q12 98 (19%) 418 0.599
(0.663) 		0.75
(0.802) 		1e-05
(4.46e-05) 		0.0253
(0.0469) 		0.135
(0.197) 		0.0679
(0.107) 		0.0001
(0.00033) 		0.0447
(0.0766) 		0.0564
(0.0926) 		0.214
(0.283) 		0.9
(0.924) 		0.0261
(0.0481)
del 12q24 33 137 (27%) 379 0.213
(0.283) 		0.201
(0.27) 		9e-05
(0.000299) 		0.216
(0.286) 		0.0204
(0.0396) 		0.321
(0.391) 		4e-05
(0.000145) 		5e-05
(0.000175) 		0.203
(0.272) 		0.0119
(0.0244) 		0.506
(0.579) 		0.5
(0.573)
del 14q32 12 144 (28%) 372 0.704
(0.76) 		0.286
(0.356) 		1e-05
(4.46e-05) 		0.00337
(0.00786) 		0.377
(0.449) 		0.513
(0.585) 		0.257
(0.326) 		0.0117
(0.0241) 		0.00742
(0.0161) 		0.163
(0.228) 		0.046
(0.0784) 		0.0682
(0.107)
del xp22 2 143 (28%) 373 0.691
(0.749) 		0.892
(0.92) 		1e-05
(4.46e-05) 		0.0163
(0.0325) 		0.131
(0.191) 		0.01
(0.0209) 		0.0112
(0.0232) 		5e-05
(0.000175) 		0.272
(0.342) 		0.514
(0.585) 		0.99
(1.00) 		0.0684
(0.107)
amp 1p22 3 141 (27%) 375 1
(1.00) 		0.845
(0.886) 		1e-05
(4.46e-05) 		0.542
(0.607) 		0.0252
(0.0469) 		0.607
(0.671) 		0.0579
(0.0944) 		0.043
(0.0746) 		0.141
(0.203) 		0.0282
(0.0517) 		0.421
(0.498) 		0.179
(0.246)
amp 22q11 22 88 (17%) 428 0.195
(0.264) 		0.147
(0.21) 		1e-05
(4.46e-05) 		0.441
(0.513) 		0.0196
(0.0384) 		0.257
(0.326) 		0.107
(0.16) 		0.0563
(0.0926) 		0.0579
(0.0944) 		0.0283
(0.0518) 		0.596
(0.662) 		0.0214
(0.0412)
del 3q11 1 140 (27%) 376 0.608
(0.671) 		0.686
(0.748) 		0.0183
(0.0361) 		0.00631
(0.014) 		0.859
(0.895) 		0.771
(0.822) 		0.022
(0.042) 		0.0381
(0.0674) 		0.151
(0.214) 		0.741
(0.794) 		0.525
(0.591) 		0.841
(0.884)
del 6q26 257 (50%) 259 0.454
(0.527) 		0.23
(0.3) 		0.00065
(0.00181) 		4e-05
(0.000145) 		0.0766
(0.12) 		0.0556
(0.092) 		0.201
(0.27) 		0.00626
(0.0139) 		0.938
(0.957) 		0.0186
(0.0367) 		0.518
(0.587) 		0.286
(0.356)
del 12p13 2 138 (27%) 378 0.386
(0.46) 		1
(1.00) 		1e-05
(4.46e-05) 		0.0117
(0.0241) 		0.264
(0.333) 		0.114
(0.169) 		0.00016
(0.000502) 		0.00962
(0.0202) 		0.897
(0.922) 		0.979
(0.992) 		0.476
(0.549) 		0.112
(0.167)
del 8p11 21 123 (24%) 393 0.802
(0.846) 		0.256
(0.326) 		1e-05
(4.46e-05) 		0.346
(0.418) 		0.861
(0.896) 		0.0377
(0.067) 		0.00252
(0.00605) 		0.167
(0.233) 		0.205
(0.274) 		0.689
(0.749) 		0.541
(0.607) 		0.129
(0.19)
del 20q13 12 80 (16%) 436 0.0293
(0.0534) 		0.52
(0.587) 		0.517
(0.587) 		0.428
(0.504) 		0.166
(0.233) 		0.188
(0.257) 		0.128
(0.189) 		0.00426
(0.00968) 		0.157
(0.222) 		0.229
(0.299) 		0.0452
(0.0773) 		0.26
(0.329)
del 6q11 1 134 (26%) 382 0.54
(0.606) 		1
(1.00) 		0.0461
(0.0784) 		0.00222
(0.00539) 		0.236
(0.305) 		0.774
(0.825) 		0.433
(0.508) 		0.728
(0.783) 		0.0785
(0.122) 		0.149
(0.212) 		0.69
(0.749) 		0.111
(0.166)
'amp_1p22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S1.  Gene #1: 'amp_1p22.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
AMP PEAK 1(1P22.3) MUTATED 17 45 10 69
AMP PEAK 1(1P22.3) WILD-TYPE 52 183 69 71

Figure S1.  Get High-res Image Gene #1: 'amp_1p22.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1p22.3' versus 'RPPA_CNMF'

P value = 0.0252 (Fisher's exact test), Q value = 0.047

Table S2.  Gene #1: 'amp_1p22.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 73 64
AMP PEAK 1(1P22.3) MUTATED 15 27 11
AMP PEAK 1(1P22.3) WILD-TYPE 29 46 53

Figure S2.  Get High-res Image Gene #1: 'amp_1p22.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_1p22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.043 (Fisher's exact test), Q value = 0.075

Table S3.  Gene #1: 'amp_1p22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
AMP PEAK 1(1P22.3) MUTATED 20 34 38 8 12 13 15
AMP PEAK 1(1P22.3) WILD-TYPE 58 76 59 40 41 36 62

Figure S3.  Get High-res Image Gene #1: 'amp_1p22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_1p22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0282 (Fisher's exact test), Q value = 0.052

Table S4.  Gene #1: 'amp_1p22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
AMP PEAK 1(1P22.3) MUTATED 15 52 33 39
AMP PEAK 1(1P22.3) WILD-TYPE 56 146 108 61

Figure S4.  Get High-res Image Gene #1: 'amp_1p22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_1q21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
AMP PEAK 2(1Q21.3) MUTATED 63 140 58 111
AMP PEAK 2(1Q21.3) WILD-TYPE 6 88 21 29

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

'amp_1q21.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S6.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
AMP PEAK 2(1Q21.3) MUTATED 80 124 127
AMP PEAK 2(1Q21.3) WILD-TYPE 64 25 35

Figure S6.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_1q21.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0239 (Fisher's exact test), Q value = 0.045

Table S7.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 40 33 45 31 32
AMP PEAK 2(1Q21.3) MUTATED 30 30 32 18 27
AMP PEAK 2(1Q21.3) WILD-TYPE 10 3 13 13 5

Figure S7.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_1q21.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S8.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
AMP PEAK 2(1Q21.3) MUTATED 106 134 129
AMP PEAK 2(1Q21.3) WILD-TYPE 60 61 22

Figure S8.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_1q21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00027

Table S9.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
AMP PEAK 2(1Q21.3) MUTATED 54 74 69 45 45 38 44
AMP PEAK 2(1Q21.3) WILD-TYPE 24 36 28 3 8 11 33

Figure S9.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_1q21.3' versus 'MIRSEQ_CNMF'

P value = 0.00416 (Fisher's exact test), Q value = 0.0095

Table S10.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
AMP PEAK 2(1Q21.3) MUTATED 122 180 65
AMP PEAK 2(1Q21.3) WILD-TYPE 67 48 28

Figure S10.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_1q21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00101 (Fisher's exact test), Q value = 0.0027

Table S11.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
AMP PEAK 2(1Q21.3) MUTATED 52 155 83 77
AMP PEAK 2(1Q21.3) WILD-TYPE 19 43 58 23

Figure S11.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_1q21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00498 (Fisher's exact test), Q value = 0.011

Table S12.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 198 91
AMP PEAK 2(1Q21.3) MUTATED 111 152 54
AMP PEAK 2(1Q21.3) WILD-TYPE 34 46 37

Figure S12.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_3q26.2' versus 'MRNA_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.00072

Table S13.  Gene #3: 'amp_3q26.2' versus Molecular Subtype #1: 'MRNA_CNMF'

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

Figure S13.  Get High-res Image Gene #3: 'amp_3q26.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_3q26.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00178 (Fisher's exact test), Q value = 0.0044

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 11 7
AMP PEAK 3(3Q26.2) MUTATED 0 6 4
AMP PEAK 3(3Q26.2) WILD-TYPE 14 5 3

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

'amp_3q26.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S15.  Gene #3: 'amp_3q26.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
AMP PEAK 3(3Q26.2) MUTATED 22 46 44 59
AMP PEAK 3(3Q26.2) WILD-TYPE 47 182 35 81

Figure S15.  Get High-res Image Gene #3: 'amp_3q26.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_3q26.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S16.  Gene #3: 'amp_3q26.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
AMP PEAK 3(3Q26.2) MUTATED 27 70 50
AMP PEAK 3(3Q26.2) WILD-TYPE 117 79 112

Figure S16.  Get High-res Image Gene #3: 'amp_3q26.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_3q26.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0117 (Fisher's exact test), Q value = 0.024

Table S17.  Gene #3: 'amp_3q26.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 40 33 45 31 32
AMP PEAK 3(3Q26.2) MUTATED 14 3 19 13 10
AMP PEAK 3(3Q26.2) WILD-TYPE 26 30 26 18 22

Figure S17.  Get High-res Image Gene #3: 'amp_3q26.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_3q26.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S18.  Gene #3: 'amp_3q26.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
AMP PEAK 3(3Q26.2) MUTATED 26 92 53
AMP PEAK 3(3Q26.2) WILD-TYPE 140 103 98

Figure S18.  Get High-res Image Gene #3: 'amp_3q26.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_3q26.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S19.  Gene #3: 'amp_3q26.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
AMP PEAK 3(3Q26.2) MUTATED 8 39 65 5 17 19 18
AMP PEAK 3(3Q26.2) WILD-TYPE 70 71 32 43 36 30 59

Figure S19.  Get High-res Image Gene #3: 'amp_3q26.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_3q26.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S20.  Gene #3: 'amp_3q26.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
AMP PEAK 3(3Q26.2) MUTATED 41 103 25
AMP PEAK 3(3Q26.2) WILD-TYPE 148 125 68

Figure S20.  Get High-res Image Gene #3: 'amp_3q26.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_3q26.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 7.9e-05

Table S21.  Gene #3: 'amp_3q26.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
AMP PEAK 3(3Q26.2) MUTATED 12 67 36 54
AMP PEAK 3(3Q26.2) WILD-TYPE 59 131 105 46

Figure S21.  Get High-res Image Gene #3: 'amp_3q26.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_3q26.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S22.  Gene #3: 'amp_3q26.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
AMP PEAK 3(3Q26.2) MUTATED 15 101 26
AMP PEAK 3(3Q26.2) WILD-TYPE 88 147 57

Figure S22.  Get High-res Image Gene #3: 'amp_3q26.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_5p15.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S23.  Gene #4: 'amp_5p15.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
AMP PEAK 4(5P15.33) MUTATED 47 109 48 124
AMP PEAK 4(5P15.33) WILD-TYPE 22 119 31 16

Figure S23.  Get High-res Image Gene #4: 'amp_5p15.33' versus Molecular Subtype #3: 'CN_CNMF'

'amp_5p15.33' versus 'METHLYATION_CNMF'

P value = 0.00157 (Fisher's exact test), Q value = 0.004

Table S24.  Gene #4: 'amp_5p15.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
AMP PEAK 4(5P15.33) MUTATED 76 108 108
AMP PEAK 4(5P15.33) WILD-TYPE 68 41 54

Figure S24.  Get High-res Image Gene #4: 'amp_5p15.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_5p15.33' versus 'RPPA_CNMF'

P value = 0.0403 (Fisher's exact test), Q value = 0.071

Table S25.  Gene #4: 'amp_5p15.33' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 73 64
AMP PEAK 4(5P15.33) MUTATED 26 57 39
AMP PEAK 4(5P15.33) WILD-TYPE 18 16 25

Figure S25.  Get High-res Image Gene #4: 'amp_5p15.33' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_5p15.33' versus 'RPPA_CHIERARCHICAL'

P value = 0.0424 (Fisher's exact test), Q value = 0.074

Table S26.  Gene #4: 'amp_5p15.33' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 40 33 45 31 32
AMP PEAK 4(5P15.33) MUTATED 30 19 35 15 23
AMP PEAK 4(5P15.33) WILD-TYPE 10 14 10 16 9

Figure S26.  Get High-res Image Gene #4: 'amp_5p15.33' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_5p15.33' versus 'MRNASEQ_CNMF'

P value = 0.0231 (Fisher's exact test), Q value = 0.044

Table S27.  Gene #4: 'amp_5p15.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
AMP PEAK 4(5P15.33) MUTATED 96 138 91
AMP PEAK 4(5P15.33) WILD-TYPE 70 57 60

Figure S27.  Get High-res Image Gene #4: 'amp_5p15.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_5p15.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.00061

Table S28.  Gene #4: 'amp_5p15.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
AMP PEAK 4(5P15.33) MUTATED 48 76 77 22 35 30 37
AMP PEAK 4(5P15.33) WILD-TYPE 30 34 20 26 18 19 40

Figure S28.  Get High-res Image Gene #4: 'amp_5p15.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'MIRSEQ_CNMF'

P value = 0.00142 (Fisher's exact test), Q value = 0.0036

Table S29.  Gene #4: 'amp_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
AMP PEAK 4(5P15.33) MUTATED 103 163 61
AMP PEAK 4(5P15.33) WILD-TYPE 86 65 32

Figure S29.  Get High-res Image Gene #4: 'amp_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_5p15.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00081 (Fisher's exact test), Q value = 0.0022

Table S30.  Gene #4: 'amp_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
AMP PEAK 4(5P15.33) MUTATED 44 134 73 76
AMP PEAK 4(5P15.33) WILD-TYPE 27 64 68 24

Figure S30.  Get High-res Image Gene #4: 'amp_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S31.  Gene #4: 'amp_5p15.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
AMP PEAK 4(5P15.33) MUTATED 42 187 56
AMP PEAK 4(5P15.33) WILD-TYPE 61 61 27

Figure S31.  Get High-res Image Gene #4: 'amp_5p15.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_6p21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S32.  Gene #5: 'amp_6p21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
AMP PEAK 5(6P21.1) MUTATED 43 61 28 58
AMP PEAK 5(6P21.1) WILD-TYPE 26 167 51 82

Figure S32.  Get High-res Image Gene #5: 'amp_6p21.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_6p21.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S33.  Gene #5: 'amp_6p21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
AMP PEAK 5(6P21.1) MUTATED 28 72 70
AMP PEAK 5(6P21.1) WILD-TYPE 116 77 92

Figure S33.  Get High-res Image Gene #5: 'amp_6p21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_6p21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00976 (Fisher's exact test), Q value = 0.02

Table S34.  Gene #5: 'amp_6p21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
AMP PEAK 5(6P21.1) MUTATED 26 35 44 24 25 17 18
AMP PEAK 5(6P21.1) WILD-TYPE 52 75 53 24 28 32 59

Figure S34.  Get High-res Image Gene #5: 'amp_6p21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_6p21.1' versus 'MIRSEQ_CNMF'

P value = 0.0352 (Fisher's exact test), Q value = 0.063

Table S35.  Gene #5: 'amp_6p21.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
AMP PEAK 5(6P21.1) MUTATED 58 97 31
AMP PEAK 5(6P21.1) WILD-TYPE 131 131 62

Figure S35.  Get High-res Image Gene #5: 'amp_6p21.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_6p21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00776 (Fisher's exact test), Q value = 0.017

Table S36.  Gene #5: 'amp_6p21.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
AMP PEAK 5(6P21.1) MUTATED 21 85 38 42
AMP PEAK 5(6P21.1) WILD-TYPE 50 113 103 58

Figure S36.  Get High-res Image Gene #5: 'amp_6p21.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_6p21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0285 (Fisher's exact test), Q value = 0.052

Table S37.  Gene #5: 'amp_6p21.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
AMP PEAK 5(6P21.1) MUTATED 27 97 36
AMP PEAK 5(6P21.1) WILD-TYPE 76 151 47

Figure S37.  Get High-res Image Gene #5: 'amp_6p21.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S38.  Gene #6: 'amp_7p11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
AMP PEAK 6(7P11.2) MUTATED 26 87 46 113
AMP PEAK 6(7P11.2) WILD-TYPE 43 141 33 27

Figure S38.  Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_7p11.2' versus 'METHLYATION_CNMF'

P value = 0.0347 (Fisher's exact test), Q value = 0.063

Table S39.  Gene #6: 'amp_7p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
AMP PEAK 6(7P11.2) MUTATED 64 79 96
AMP PEAK 6(7P11.2) WILD-TYPE 80 70 66

Figure S39.  Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_7p11.2' versus 'RPPA_CNMF'

P value = 0.00316 (Fisher's exact test), Q value = 0.0074

Table S40.  Gene #6: 'amp_7p11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 73 64
AMP PEAK 6(7P11.2) MUTATED 14 47 33
AMP PEAK 6(7P11.2) WILD-TYPE 30 26 31

Figure S40.  Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_7p11.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0074 (Fisher's exact test), Q value = 0.016

Table S41.  Gene #6: 'amp_7p11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 40 33 45 31 32
AMP PEAK 6(7P11.2) MUTATED 24 13 32 13 12
AMP PEAK 6(7P11.2) WILD-TYPE 16 20 13 18 20

Figure S41.  Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_7p11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S42.  Gene #6: 'amp_7p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
AMP PEAK 6(7P11.2) MUTATED 75 135 58
AMP PEAK 6(7P11.2) WILD-TYPE 91 60 93

Figure S42.  Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_7p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S43.  Gene #6: 'amp_7p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
AMP PEAK 6(7P11.2) MUTATED 31 81 57 9 24 32 34
AMP PEAK 6(7P11.2) WILD-TYPE 47 29 40 39 29 17 43

Figure S43.  Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_7p11.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S44.  Gene #6: 'amp_7p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
AMP PEAK 6(7P11.2) MUTATED 71 133 64
AMP PEAK 6(7P11.2) WILD-TYPE 118 95 29

Figure S44.  Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_7p11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 7.9e-05

Table S45.  Gene #6: 'amp_7p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
AMP PEAK 6(7P11.2) MUTATED 22 126 63 57
AMP PEAK 6(7P11.2) WILD-TYPE 49 72 78 43

Figure S45.  Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_7p11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00018

Table S46.  Gene #6: 'amp_7p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 198 91
AMP PEAK 6(7P11.2) MUTATED 61 107 65
AMP PEAK 6(7P11.2) WILD-TYPE 84 91 26

Figure S46.  Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_7p11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S47.  Gene #6: 'amp_7p11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
AMP PEAK 6(7P11.2) MUTATED 31 153 49
AMP PEAK 6(7P11.2) WILD-TYPE 72 95 34

Figure S47.  Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7q31.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S48.  Gene #7: 'amp_7q31.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
AMP PEAK 7(7Q31.2) MUTATED 19 67 30 98
AMP PEAK 7(7Q31.2) WILD-TYPE 50 161 49 42

Figure S48.  Get High-res Image Gene #7: 'amp_7q31.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_7q31.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S49.  Gene #7: 'amp_7q31.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
AMP PEAK 7(7Q31.2) MUTATED 55 106 49
AMP PEAK 7(7Q31.2) WILD-TYPE 111 89 102

Figure S49.  Get High-res Image Gene #7: 'amp_7q31.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_7q31.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S50.  Gene #7: 'amp_7q31.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
AMP PEAK 7(7Q31.2) MUTATED 22 71 46 5 16 22 28
AMP PEAK 7(7Q31.2) WILD-TYPE 56 39 51 43 37 27 49

Figure S50.  Get High-res Image Gene #7: 'amp_7q31.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_7q31.2' versus 'MIRSEQ_CNMF'

P value = 0.00121 (Fisher's exact test), Q value = 0.0031

Table S51.  Gene #7: 'amp_7q31.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
AMP PEAK 7(7Q31.2) MUTATED 59 103 48
AMP PEAK 7(7Q31.2) WILD-TYPE 130 125 45

Figure S51.  Get High-res Image Gene #7: 'amp_7q31.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_7q31.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00161 (Fisher's exact test), Q value = 0.004

Table S52.  Gene #7: 'amp_7q31.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
AMP PEAK 7(7Q31.2) MUTATED 18 97 50 45
AMP PEAK 7(7Q31.2) WILD-TYPE 53 101 91 55

Figure S52.  Get High-res Image Gene #7: 'amp_7q31.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_7q31.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 7.9e-05

Table S53.  Gene #7: 'amp_7q31.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
AMP PEAK 7(7Q31.2) MUTATED 22 123 37
AMP PEAK 7(7Q31.2) WILD-TYPE 81 125 46

Figure S53.  Get High-res Image Gene #7: 'amp_7q31.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8p11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S54.  Gene #8: 'amp_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
AMP PEAK 8(8P11.21) MUTATED 55 43 30 45
AMP PEAK 8(8P11.21) WILD-TYPE 14 185 49 95

Figure S54.  Get High-res Image Gene #8: 'amp_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8p11.21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S55.  Gene #8: 'amp_8p11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
AMP PEAK 8(8P11.21) MUTATED 27 69 57
AMP PEAK 8(8P11.21) WILD-TYPE 117 80 105

Figure S55.  Get High-res Image Gene #8: 'amp_8p11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8p11.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S56.  Gene #8: 'amp_8p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
AMP PEAK 8(8P11.21) MUTATED 32 67 71
AMP PEAK 8(8P11.21) WILD-TYPE 134 128 80

Figure S56.  Get High-res Image Gene #8: 'amp_8p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8p11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S57.  Gene #8: 'amp_8p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
AMP PEAK 8(8P11.21) MUTATED 17 37 39 15 32 18 12
AMP PEAK 8(8P11.21) WILD-TYPE 61 73 58 33 21 31 65

Figure S57.  Get High-res Image Gene #8: 'amp_8p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8p11.21' versus 'MIRSEQ_CNMF'

P value = 0.00042 (Fisher's exact test), Q value = 0.0012

Table S58.  Gene #8: 'amp_8p11.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
AMP PEAK 8(8P11.21) MUTATED 45 96 30
AMP PEAK 8(8P11.21) WILD-TYPE 144 132 63

Figure S58.  Get High-res Image Gene #8: 'amp_8p11.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_8p11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.00036

Table S59.  Gene #8: 'amp_8p11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
AMP PEAK 8(8P11.21) MUTATED 18 74 31 48
AMP PEAK 8(8P11.21) WILD-TYPE 53 124 110 52

Figure S59.  Get High-res Image Gene #8: 'amp_8p11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_8p11.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0131 (Fisher's exact test), Q value = 0.026

Table S60.  Gene #8: 'amp_8p11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 198 91
AMP PEAK 8(8P11.21) MUTATED 36 79 32
AMP PEAK 8(8P11.21) WILD-TYPE 109 119 59

Figure S60.  Get High-res Image Gene #8: 'amp_8p11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_8p11.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.00064

Table S61.  Gene #8: 'amp_8p11.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
AMP PEAK 8(8P11.21) MUTATED 19 101 27
AMP PEAK 8(8P11.21) WILD-TYPE 84 147 56

Figure S61.  Get High-res Image Gene #8: 'amp_8p11.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8q24.21' versus 'MRNA_CNMF'

P value = 0.0073 (Fisher's exact test), Q value = 0.016

Table S62.  Gene #9: 'amp_8q24.21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 5 9 12 6
AMP PEAK 9(8Q24.21) MUTATED 5 7 3 5
AMP PEAK 9(8Q24.21) WILD-TYPE 0 2 9 1

Figure S62.  Get High-res Image Gene #9: 'amp_8q24.21' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_8q24.21' versus 'MRNA_CHIERARCHICAL'

P value = 0.0264 (Fisher's exact test), Q value = 0.049

Table S63.  Gene #9: 'amp_8q24.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 11 7
AMP PEAK 9(8Q24.21) MUTATED 5 9 6
AMP PEAK 9(8Q24.21) WILD-TYPE 9 2 1

Figure S63.  Get High-res Image Gene #9: 'amp_8q24.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_8q24.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S64.  Gene #9: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
AMP PEAK 9(8Q24.21) MUTATED 66 94 53 109
AMP PEAK 9(8Q24.21) WILD-TYPE 3 134 26 31

Figure S64.  Get High-res Image Gene #9: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S65.  Gene #9: 'amp_8q24.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
AMP PEAK 9(8Q24.21) MUTATED 63 101 117
AMP PEAK 9(8Q24.21) WILD-TYPE 81 48 45

Figure S65.  Get High-res Image Gene #9: 'amp_8q24.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S66.  Gene #9: 'amp_8q24.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
AMP PEAK 9(8Q24.21) MUTATED 76 136 106
AMP PEAK 9(8Q24.21) WILD-TYPE 90 59 45

Figure S66.  Get High-res Image Gene #9: 'amp_8q24.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S67.  Gene #9: 'amp_8q24.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
AMP PEAK 9(8Q24.21) MUTATED 39 77 67 28 47 31 29
AMP PEAK 9(8Q24.21) WILD-TYPE 39 33 30 20 6 18 48

Figure S67.  Get High-res Image Gene #9: 'amp_8q24.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S68.  Gene #9: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
AMP PEAK 9(8Q24.21) MUTATED 89 167 62
AMP PEAK 9(8Q24.21) WILD-TYPE 100 61 31

Figure S68.  Get High-res Image Gene #9: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_8q24.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 5e-04

Table S69.  Gene #9: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
AMP PEAK 9(8Q24.21) MUTATED 36 139 72 71
AMP PEAK 9(8Q24.21) WILD-TYPE 35 59 69 29

Figure S69.  Get High-res Image Gene #9: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0463 (Fisher's exact test), Q value = 0.079

Table S70.  Gene #9: 'amp_8q24.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 198 91
AMP PEAK 9(8Q24.21) MUTATED 78 132 58
AMP PEAK 9(8Q24.21) WILD-TYPE 67 66 33

Figure S70.  Get High-res Image Gene #9: 'amp_8q24.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S71.  Gene #9: 'amp_8q24.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
AMP PEAK 9(8Q24.21) MUTATED 42 175 51
AMP PEAK 9(8Q24.21) WILD-TYPE 61 73 32

Figure S71.  Get High-res Image Gene #9: 'amp_8q24.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_11q13.3' versus 'MRNA_CNMF'

P value = 0.00116 (Fisher's exact test), Q value = 0.003

Table S72.  Gene #10: 'amp_11q13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 5 9 12 6
AMP PEAK 10(11Q13.3) MUTATED 2 1 2 6
AMP PEAK 10(11Q13.3) WILD-TYPE 3 8 10 0

Figure S72.  Get High-res Image Gene #10: 'amp_11q13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_11q13.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.00039

Table S73.  Gene #10: 'amp_11q13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 11 7
AMP PEAK 10(11Q13.3) MUTATED 3 1 7
AMP PEAK 10(11Q13.3) WILD-TYPE 11 10 0

Figure S73.  Get High-res Image Gene #10: 'amp_11q13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_11q13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S74.  Gene #10: 'amp_11q13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
AMP PEAK 10(11Q13.3) MUTATED 36 32 29 73
AMP PEAK 10(11Q13.3) WILD-TYPE 33 196 50 67

Figure S74.  Get High-res Image Gene #10: 'amp_11q13.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_11q13.3' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00018

Table S75.  Gene #10: 'amp_11q13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
AMP PEAK 10(11Q13.3) MUTATED 27 56 66
AMP PEAK 10(11Q13.3) WILD-TYPE 117 93 96

Figure S75.  Get High-res Image Gene #10: 'amp_11q13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_11q13.3' versus 'RPPA_CNMF'

P value = 0.0461 (Fisher's exact test), Q value = 0.078

Table S76.  Gene #10: 'amp_11q13.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 73 64
AMP PEAK 10(11Q13.3) MUTATED 8 27 25
AMP PEAK 10(11Q13.3) WILD-TYPE 36 46 39

Figure S76.  Get High-res Image Gene #10: 'amp_11q13.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_11q13.3' versus 'MRNASEQ_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.00047

Table S77.  Gene #10: 'amp_11q13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
AMP PEAK 10(11Q13.3) MUTATED 35 70 65
AMP PEAK 10(11Q13.3) WILD-TYPE 131 125 86

Figure S77.  Get High-res Image Gene #10: 'amp_11q13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_11q13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S78.  Gene #10: 'amp_11q13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
AMP PEAK 10(11Q13.3) MUTATED 20 43 38 4 35 16 14
AMP PEAK 10(11Q13.3) WILD-TYPE 58 67 59 44 18 33 63

Figure S78.  Get High-res Image Gene #10: 'amp_11q13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_11q13.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S79.  Gene #10: 'amp_11q13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
AMP PEAK 10(11Q13.3) MUTATED 35 102 30
AMP PEAK 10(11Q13.3) WILD-TYPE 154 126 63

Figure S79.  Get High-res Image Gene #10: 'amp_11q13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_11q13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S80.  Gene #10: 'amp_11q13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
AMP PEAK 10(11Q13.3) MUTATED 10 81 29 47
AMP PEAK 10(11Q13.3) WILD-TYPE 61 117 112 53

Figure S80.  Get High-res Image Gene #10: 'amp_11q13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_11q13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.00072

Table S81.  Gene #10: 'amp_11q13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
AMP PEAK 10(11Q13.3) MUTATED 18 98 29
AMP PEAK 10(11Q13.3) WILD-TYPE 85 150 54

Figure S81.  Get High-res Image Gene #10: 'amp_11q13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12p12.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.0381 (Fisher's exact test), Q value = 0.067

Table S82.  Gene #11: 'amp_12p12.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 11 7
AMP PEAK 11(12P12.1) MUTATED 2 3 5
AMP PEAK 11(12P12.1) WILD-TYPE 12 8 2

Figure S82.  Get High-res Image Gene #11: 'amp_12p12.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_12p12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S83.  Gene #11: 'amp_12p12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
AMP PEAK 11(12P12.1) MUTATED 26 45 62 46
AMP PEAK 11(12P12.1) WILD-TYPE 43 183 17 94

Figure S83.  Get High-res Image Gene #11: 'amp_12p12.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_12p12.1' versus 'METHLYATION_CNMF'

P value = 0.00284 (Fisher's exact test), Q value = 0.0068

Table S84.  Gene #11: 'amp_12p12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
AMP PEAK 11(12P12.1) MUTATED 33 61 59
AMP PEAK 11(12P12.1) WILD-TYPE 111 88 103

Figure S84.  Get High-res Image Gene #11: 'amp_12p12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_12p12.1' versus 'RPPA_CNMF'

P value = 0.039 (Fisher's exact test), Q value = 0.069

Table S85.  Gene #11: 'amp_12p12.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 73 64
AMP PEAK 11(12P12.1) MUTATED 7 27 22
AMP PEAK 11(12P12.1) WILD-TYPE 37 46 42

Figure S85.  Get High-res Image Gene #11: 'amp_12p12.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_12p12.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S86.  Gene #11: 'amp_12p12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
AMP PEAK 11(12P12.1) MUTATED 31 83 65
AMP PEAK 11(12P12.1) WILD-TYPE 135 112 86

Figure S86.  Get High-res Image Gene #11: 'amp_12p12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_12p12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S87.  Gene #11: 'amp_12p12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
AMP PEAK 11(12P12.1) MUTATED 12 43 35 5 33 30 21
AMP PEAK 11(12P12.1) WILD-TYPE 66 67 62 43 20 19 56

Figure S87.  Get High-res Image Gene #11: 'amp_12p12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_12p12.1' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 7.9e-05

Table S88.  Gene #11: 'amp_12p12.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
AMP PEAK 11(12P12.1) MUTATED 44 103 29
AMP PEAK 11(12P12.1) WILD-TYPE 145 125 64

Figure S88.  Get High-res Image Gene #11: 'amp_12p12.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_12p12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 7.9e-05

Table S89.  Gene #11: 'amp_12p12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
AMP PEAK 11(12P12.1) MUTATED 13 81 35 47
AMP PEAK 11(12P12.1) WILD-TYPE 58 117 106 53

Figure S89.  Get High-res Image Gene #11: 'amp_12p12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_12p12.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S90.  Gene #11: 'amp_12p12.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
AMP PEAK 11(12P12.1) MUTATED 17 107 25
AMP PEAK 11(12P12.1) WILD-TYPE 86 141 58

Figure S90.  Get High-res Image Gene #11: 'amp_12p12.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12q14.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S91.  Gene #12: 'amp_12q14.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
AMP PEAK 12(12Q14.1) MUTATED 30 42 64 32
AMP PEAK 12(12Q14.1) WILD-TYPE 39 186 15 108

Figure S91.  Get High-res Image Gene #12: 'amp_12q14.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_12q14.1' versus 'METHLYATION_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.00047

Table S92.  Gene #12: 'amp_12q14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
AMP PEAK 12(12Q14.1) MUTATED 32 67 48
AMP PEAK 12(12Q14.1) WILD-TYPE 112 82 114

Figure S92.  Get High-res Image Gene #12: 'amp_12q14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_12q14.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S93.  Gene #12: 'amp_12q14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
AMP PEAK 12(12Q14.1) MUTATED 24 72 72
AMP PEAK 12(12Q14.1) WILD-TYPE 142 123 79

Figure S93.  Get High-res Image Gene #12: 'amp_12q14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_12q14.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S94.  Gene #12: 'amp_12q14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
AMP PEAK 12(12Q14.1) MUTATED 13 31 37 6 37 31 13
AMP PEAK 12(12Q14.1) WILD-TYPE 65 79 60 42 16 18 64

Figure S94.  Get High-res Image Gene #12: 'amp_12q14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_12q14.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S95.  Gene #12: 'amp_12q14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
AMP PEAK 12(12Q14.1) MUTATED 34 105 27
AMP PEAK 12(12Q14.1) WILD-TYPE 155 123 66

Figure S95.  Get High-res Image Gene #12: 'amp_12q14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_12q14.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S96.  Gene #12: 'amp_12q14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
AMP PEAK 12(12Q14.1) MUTATED 12 78 25 51
AMP PEAK 12(12Q14.1) WILD-TYPE 59 120 116 49

Figure S96.  Get High-res Image Gene #12: 'amp_12q14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_12q14.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S97.  Gene #12: 'amp_12q14.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Figure S97.  Get High-res Image Gene #12: 'amp_12q14.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12q15' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S98.  Gene #13: 'amp_12q15' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
AMP PEAK 13(12Q15) MUTATED 30 44 63 34
AMP PEAK 13(12Q15) WILD-TYPE 39 184 16 106

Figure S98.  Get High-res Image Gene #13: 'amp_12q15' versus Molecular Subtype #3: 'CN_CNMF'

'amp_12q15' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00018

Table S99.  Gene #13: 'amp_12q15' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
AMP PEAK 13(12Q15) MUTATED 31 69 50
AMP PEAK 13(12Q15) WILD-TYPE 113 80 112

Figure S99.  Get High-res Image Gene #13: 'amp_12q15' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_12q15' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S100.  Gene #13: 'amp_12q15' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
AMP PEAK 13(12Q15) MUTATED 31 66 74
AMP PEAK 13(12Q15) WILD-TYPE 135 129 77

Figure S100.  Get High-res Image Gene #13: 'amp_12q15' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_12q15' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S101.  Gene #13: 'amp_12q15' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
AMP PEAK 13(12Q15) MUTATED 17 28 37 6 37 31 15
AMP PEAK 13(12Q15) WILD-TYPE 61 82 60 42 16 18 62

Figure S101.  Get High-res Image Gene #13: 'amp_12q15' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_12q15' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S102.  Gene #13: 'amp_12q15' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
AMP PEAK 13(12Q15) MUTATED 37 108 25
AMP PEAK 13(12Q15) WILD-TYPE 152 120 68

Figure S102.  Get High-res Image Gene #13: 'amp_12q15' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_12q15' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S103.  Gene #13: 'amp_12q15' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
AMP PEAK 13(12Q15) MUTATED 11 76 31 52
AMP PEAK 13(12Q15) WILD-TYPE 60 122 110 48

Figure S103.  Get High-res Image Gene #13: 'amp_12q15' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_12q15' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S104.  Gene #13: 'amp_12q15' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
AMP PEAK 13(12Q15) MUTATED 14 106 26
AMP PEAK 13(12Q15) WILD-TYPE 89 142 57

Figure S104.  Get High-res Image Gene #13: 'amp_12q15' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_14q13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S105.  Gene #14: 'amp_14q13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
AMP PEAK 14(14Q13.3) MUTATED 52 64 35 78
AMP PEAK 14(14Q13.3) WILD-TYPE 17 164 44 62

Figure S105.  Get High-res Image Gene #14: 'amp_14q13.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_14q13.3' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00011

Table S106.  Gene #14: 'amp_14q13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
AMP PEAK 14(14Q13.3) MUTATED 42 80 79
AMP PEAK 14(14Q13.3) WILD-TYPE 102 69 83

Figure S106.  Get High-res Image Gene #14: 'amp_14q13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_14q13.3' versus 'MRNASEQ_CNMF'

P value = 0.00072 (Fisher's exact test), Q value = 0.002

Table S107.  Gene #14: 'amp_14q13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
AMP PEAK 14(14Q13.3) MUTATED 54 100 74
AMP PEAK 14(14Q13.3) WILD-TYPE 112 95 77

Figure S107.  Get High-res Image Gene #14: 'amp_14q13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_14q13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S108.  Gene #14: 'amp_14q13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
AMP PEAK 14(14Q13.3) MUTATED 34 57 63 9 42 8 15
AMP PEAK 14(14Q13.3) WILD-TYPE 44 53 34 39 11 41 62

Figure S108.  Get High-res Image Gene #14: 'amp_14q13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_14q13.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S109.  Gene #14: 'amp_14q13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
AMP PEAK 14(14Q13.3) MUTATED 54 125 46
AMP PEAK 14(14Q13.3) WILD-TYPE 135 103 47

Figure S109.  Get High-res Image Gene #14: 'amp_14q13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_14q13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S110.  Gene #14: 'amp_14q13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
AMP PEAK 14(14Q13.3) MUTATED 27 111 34 53
AMP PEAK 14(14Q13.3) WILD-TYPE 44 87 107 47

Figure S110.  Get High-res Image Gene #14: 'amp_14q13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_14q13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.00042

Table S111.  Gene #14: 'amp_14q13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Figure S111.  Get High-res Image Gene #14: 'amp_14q13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17q12' versus 'MRNA_CHIERARCHICAL'

P value = 0.0474 (Fisher's exact test), Q value = 0.08

Table S112.  Gene #15: 'amp_17q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 11 7
AMP PEAK 15(17Q12) MUTATED 4 6 6
AMP PEAK 15(17Q12) WILD-TYPE 10 5 1

Figure S112.  Get High-res Image Gene #15: 'amp_17q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_17q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S113.  Gene #15: 'amp_17q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
AMP PEAK 15(17Q12) MUTATED 38 52 42 94
AMP PEAK 15(17Q12) WILD-TYPE 31 176 37 46

Figure S113.  Get High-res Image Gene #15: 'amp_17q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S114.  Gene #15: 'amp_17q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
AMP PEAK 15(17Q12) MUTATED 31 73 88
AMP PEAK 15(17Q12) WILD-TYPE 113 76 74

Figure S114.  Get High-res Image Gene #15: 'amp_17q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17q12' versus 'RPPA_CHIERARCHICAL'

P value = 0.0171 (Fisher's exact test), Q value = 0.034

Table S115.  Gene #15: 'amp_17q12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 40 33 45 31 32
AMP PEAK 15(17Q12) MUTATED 23 11 26 11 9
AMP PEAK 15(17Q12) WILD-TYPE 17 22 19 20 23

Figure S115.  Get High-res Image Gene #15: 'amp_17q12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_17q12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S116.  Gene #15: 'amp_17q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
AMP PEAK 15(17Q12) MUTATED 52 111 62
AMP PEAK 15(17Q12) WILD-TYPE 114 84 89

Figure S116.  Get High-res Image Gene #15: 'amp_17q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S117.  Gene #15: 'amp_17q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
AMP PEAK 15(17Q12) MUTATED 30 62 57 8 29 17 22
AMP PEAK 15(17Q12) WILD-TYPE 48 48 40 40 24 32 55

Figure S117.  Get High-res Image Gene #15: 'amp_17q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S118.  Gene #15: 'amp_17q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
AMP PEAK 15(17Q12) MUTATED 58 129 37
AMP PEAK 15(17Q12) WILD-TYPE 131 99 56

Figure S118.  Get High-res Image Gene #15: 'amp_17q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_17q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S119.  Gene #15: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
AMP PEAK 15(17Q12) MUTATED 21 102 40 61
AMP PEAK 15(17Q12) WILD-TYPE 50 96 101 39

Figure S119.  Get High-res Image Gene #15: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00011

Table S120.  Gene #15: 'amp_17q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
AMP PEAK 15(17Q12) MUTATED 24 125 38
AMP PEAK 15(17Q12) WILD-TYPE 79 123 45

Figure S120.  Get High-res Image Gene #15: 'amp_17q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17q23.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S121.  Gene #16: 'amp_17q23.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
AMP PEAK 16(17Q23.1) MUTATED 35 67 47 100
AMP PEAK 16(17Q23.1) WILD-TYPE 34 161 32 40

Figure S121.  Get High-res Image Gene #16: 'amp_17q23.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q23.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S122.  Gene #16: 'amp_17q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
AMP PEAK 16(17Q23.1) MUTATED 40 73 100
AMP PEAK 16(17Q23.1) WILD-TYPE 104 76 62

Figure S122.  Get High-res Image Gene #16: 'amp_17q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17q23.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S123.  Gene #16: 'amp_17q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
AMP PEAK 16(17Q23.1) MUTATED 62 127 59
AMP PEAK 16(17Q23.1) WILD-TYPE 104 68 92

Figure S123.  Get High-res Image Gene #16: 'amp_17q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S124.  Gene #16: 'amp_17q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
AMP PEAK 16(17Q23.1) MUTATED 36 74 55 7 29 22 25
AMP PEAK 16(17Q23.1) WILD-TYPE 42 36 42 41 24 27 52

Figure S124.  Get High-res Image Gene #16: 'amp_17q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_17q23.1' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 7.9e-05

Table S125.  Gene #16: 'amp_17q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
AMP PEAK 16(17Q23.1) MUTATED 68 136 43
AMP PEAK 16(17Q23.1) WILD-TYPE 121 92 50

Figure S125.  Get High-res Image Gene #16: 'amp_17q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_17q23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S126.  Gene #16: 'amp_17q23.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
AMP PEAK 16(17Q23.1) MUTATED 26 111 48 62
AMP PEAK 16(17Q23.1) WILD-TYPE 45 87 93 38

Figure S126.  Get High-res Image Gene #16: 'amp_17q23.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_17q23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 7.9e-05

Table S127.  Gene #16: 'amp_17q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
AMP PEAK 16(17Q23.1) MUTATED 28 134 43
AMP PEAK 16(17Q23.1) WILD-TYPE 75 114 40

Figure S127.  Get High-res Image Gene #16: 'amp_17q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_18q11.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.02 (Fisher's exact test), Q value = 0.039

Table S128.  Gene #17: 'amp_18q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 11 7
AMP PEAK 17(18Q11.2) MUTATED 1 1 4
AMP PEAK 17(18Q11.2) WILD-TYPE 13 10 3

Figure S128.  Get High-res Image Gene #17: 'amp_18q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_18q11.2' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00015

Table S129.  Gene #17: 'amp_18q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
AMP PEAK 17(18Q11.2) MUTATED 22 26 24 31
AMP PEAK 17(18Q11.2) WILD-TYPE 47 202 55 109

Figure S129.  Get High-res Image Gene #17: 'amp_18q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_18q11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S130.  Gene #17: 'amp_18q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
AMP PEAK 17(18Q11.2) MUTATED 11 51 31
AMP PEAK 17(18Q11.2) WILD-TYPE 133 98 131

Figure S130.  Get High-res Image Gene #17: 'amp_18q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_18q11.2' versus 'MRNASEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00042

Table S131.  Gene #17: 'amp_18q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
AMP PEAK 17(18Q11.2) MUTATED 17 41 44
AMP PEAK 17(18Q11.2) WILD-TYPE 149 154 107

Figure S131.  Get High-res Image Gene #17: 'amp_18q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_18q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00021

Table S132.  Gene #17: 'amp_18q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
AMP PEAK 17(18Q11.2) MUTATED 7 17 30 7 22 9 10
AMP PEAK 17(18Q11.2) WILD-TYPE 71 93 67 41 31 40 67

Figure S132.  Get High-res Image Gene #17: 'amp_18q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_18q11.2' versus 'MIRSEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00027

Table S133.  Gene #17: 'amp_18q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
AMP PEAK 17(18Q11.2) MUTATED 20 62 20
AMP PEAK 17(18Q11.2) WILD-TYPE 169 166 73

Figure S133.  Get High-res Image Gene #17: 'amp_18q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_18q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 7.9e-05

Table S134.  Gene #17: 'amp_18q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
AMP PEAK 17(18Q11.2) MUTATED 6 43 18 35
AMP PEAK 17(18Q11.2) WILD-TYPE 65 155 123 65

Figure S134.  Get High-res Image Gene #17: 'amp_18q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_18q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00011

Table S135.  Gene #17: 'amp_18q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
AMP PEAK 17(18Q11.2) MUTATED 9 70 12
AMP PEAK 17(18Q11.2) WILD-TYPE 94 178 71

Figure S135.  Get High-res Image Gene #17: 'amp_18q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19q12' versus 'MRNA_CHIERARCHICAL'

P value = 0.0416 (Fisher's exact test), Q value = 0.073

Table S136.  Gene #18: 'amp_19q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 11 7
AMP PEAK 18(19Q12) MUTATED 0 4 2
AMP PEAK 18(19Q12) WILD-TYPE 14 7 5

Figure S136.  Get High-res Image Gene #18: 'amp_19q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_19q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S137.  Gene #18: 'amp_19q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
AMP PEAK 18(19Q12) MUTATED 22 34 41 40
AMP PEAK 18(19Q12) WILD-TYPE 47 194 38 100

Figure S137.  Get High-res Image Gene #18: 'amp_19q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S138.  Gene #18: 'amp_19q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
AMP PEAK 18(19Q12) MUTATED 26 63 35
AMP PEAK 18(19Q12) WILD-TYPE 118 86 127

Figure S138.  Get High-res Image Gene #18: 'amp_19q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_19q12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S139.  Gene #18: 'amp_19q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
AMP PEAK 18(19Q12) MUTATED 19 62 54
AMP PEAK 18(19Q12) WILD-TYPE 147 133 97

Figure S139.  Get High-res Image Gene #18: 'amp_19q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_19q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00015

Table S140.  Gene #18: 'amp_19q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
AMP PEAK 18(19Q12) MUTATED 8 30 36 13 17 21 10
AMP PEAK 18(19Q12) WILD-TYPE 70 80 61 35 36 28 67

Figure S140.  Get High-res Image Gene #18: 'amp_19q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S141.  Gene #18: 'amp_19q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
AMP PEAK 18(19Q12) MUTATED 30 85 22
AMP PEAK 18(19Q12) WILD-TYPE 159 143 71

Figure S141.  Get High-res Image Gene #18: 'amp_19q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_19q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.00059

Table S142.  Gene #18: 'amp_19q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
AMP PEAK 18(19Q12) MUTATED 14 60 23 40
AMP PEAK 18(19Q12) WILD-TYPE 57 138 118 60

Figure S142.  Get High-res Image Gene #18: 'amp_19q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0446 (Fisher's exact test), Q value = 0.077

Table S143.  Gene #18: 'amp_19q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 198 91
AMP PEAK 18(19Q12) MUTATED 31 66 23
AMP PEAK 18(19Q12) WILD-TYPE 114 132 68

Figure S143.  Get High-res Image Gene #18: 'amp_19q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_19q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.00045

Table S144.  Gene #18: 'amp_19q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
AMP PEAK 18(19Q12) MUTATED 19 88 13
AMP PEAK 18(19Q12) WILD-TYPE 84 160 70

Figure S144.  Get High-res Image Gene #18: 'amp_19q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20q13.33' versus 'MRNA_CNMF'

P value = 0.00314 (Fisher's exact test), Q value = 0.0074

Table S145.  Gene #19: 'amp_20q13.33' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 5 9 12 6
AMP PEAK 19(20Q13.33) MUTATED 2 2 2 6
AMP PEAK 19(20Q13.33) WILD-TYPE 3 7 10 0

Figure S145.  Get High-res Image Gene #19: 'amp_20q13.33' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20q13.33' versus 'MRNA_CHIERARCHICAL'

P value = 0.0149 (Fisher's exact test), Q value = 0.03

Table S146.  Gene #19: 'amp_20q13.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 11 7
AMP PEAK 19(20Q13.33) MUTATED 3 3 6
AMP PEAK 19(20Q13.33) WILD-TYPE 11 8 1

Figure S146.  Get High-res Image Gene #19: 'amp_20q13.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20q13.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S147.  Gene #19: 'amp_20q13.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
AMP PEAK 19(20Q13.33) MUTATED 45 69 47 83
AMP PEAK 19(20Q13.33) WILD-TYPE 24 159 32 57

Figure S147.  Get High-res Image Gene #19: 'amp_20q13.33' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20q13.33' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00011

Table S148.  Gene #19: 'amp_20q13.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
AMP PEAK 19(20Q13.33) MUTATED 48 90 75
AMP PEAK 19(20Q13.33) WILD-TYPE 96 59 87

Figure S148.  Get High-res Image Gene #19: 'amp_20q13.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20q13.33' versus 'MRNASEQ_CNMF'

P value = 0.00161 (Fisher's exact test), Q value = 0.004

Table S149.  Gene #19: 'amp_20q13.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
AMP PEAK 19(20Q13.33) MUTATED 60 97 84
AMP PEAK 19(20Q13.33) WILD-TYPE 106 98 67

Figure S149.  Get High-res Image Gene #19: 'amp_20q13.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20q13.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S150.  Gene #19: 'amp_20q13.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
AMP PEAK 19(20Q13.33) MUTATED 27 48 67 22 38 18 21
AMP PEAK 19(20Q13.33) WILD-TYPE 51 62 30 26 15 31 56

Figure S150.  Get High-res Image Gene #19: 'amp_20q13.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20q13.33' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 7.9e-05

Table S151.  Gene #19: 'amp_20q13.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
AMP PEAK 19(20Q13.33) MUTATED 65 135 40
AMP PEAK 19(20Q13.33) WILD-TYPE 124 93 53

Figure S151.  Get High-res Image Gene #19: 'amp_20q13.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_20q13.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S152.  Gene #19: 'amp_20q13.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
AMP PEAK 19(20Q13.33) MUTATED 23 104 50 63
AMP PEAK 19(20Q13.33) WILD-TYPE 48 94 91 37

Figure S152.  Get High-res Image Gene #19: 'amp_20q13.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20q13.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0232 (Fisher's exact test), Q value = 0.044

Table S153.  Gene #19: 'amp_20q13.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 198 91
AMP PEAK 19(20Q13.33) MUTATED 56 106 42
AMP PEAK 19(20Q13.33) WILD-TYPE 89 92 49

Figure S153.  Get High-res Image Gene #19: 'amp_20q13.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_20q13.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S154.  Gene #19: 'amp_20q13.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
AMP PEAK 19(20Q13.33) MUTATED 29 139 36
AMP PEAK 19(20Q13.33) WILD-TYPE 74 109 47

Figure S154.  Get High-res Image Gene #19: 'amp_20q13.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_22q11.22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S155.  Gene #20: 'amp_22q11.22' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
AMP PEAK 20(22Q11.22) MUTATED 7 22 17 42
AMP PEAK 20(22Q11.22) WILD-TYPE 62 206 62 98

Figure S155.  Get High-res Image Gene #20: 'amp_22q11.22' versus Molecular Subtype #3: 'CN_CNMF'

'amp_22q11.22' versus 'RPPA_CNMF'

P value = 0.0196 (Fisher's exact test), Q value = 0.038

Table S156.  Gene #20: 'amp_22q11.22' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 73 64
AMP PEAK 20(22Q11.22) MUTATED 3 20 14
AMP PEAK 20(22Q11.22) WILD-TYPE 41 53 50

Figure S156.  Get High-res Image Gene #20: 'amp_22q11.22' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_22q11.22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0283 (Fisher's exact test), Q value = 0.052

Table S157.  Gene #20: 'amp_22q11.22' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
AMP PEAK 20(22Q11.22) MUTATED 11 33 17 27
AMP PEAK 20(22Q11.22) WILD-TYPE 60 165 124 73

Figure S157.  Get High-res Image Gene #20: 'amp_22q11.22' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_22q11.22' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0214 (Fisher's exact test), Q value = 0.041

Table S158.  Gene #20: 'amp_22q11.22' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
AMP PEAK 20(22Q11.22) MUTATED 10 54 13
AMP PEAK 20(22Q11.22) WILD-TYPE 93 194 70

Figure S158.  Get High-res Image Gene #20: 'amp_22q11.22' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_xq28' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S159.  Gene #21: 'amp_xq28' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
AMP PEAK 21(XQ28) MUTATED 24 37 26 70
AMP PEAK 21(XQ28) WILD-TYPE 45 191 53 70

Figure S159.  Get High-res Image Gene #21: 'amp_xq28' versus Molecular Subtype #3: 'CN_CNMF'

'amp_xq28' versus 'METHLYATION_CNMF'

P value = 0.00077 (Fisher's exact test), Q value = 0.0021

Table S160.  Gene #21: 'amp_xq28' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
AMP PEAK 21(XQ28) MUTATED 27 45 62
AMP PEAK 21(XQ28) WILD-TYPE 117 104 100

Figure S160.  Get High-res Image Gene #21: 'amp_xq28' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_xq28' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00011

Table S161.  Gene #21: 'amp_xq28' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
AMP PEAK 21(XQ28) MUTATED 37 83 36
AMP PEAK 21(XQ28) WILD-TYPE 129 112 115

Figure S161.  Get High-res Image Gene #21: 'amp_xq28' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_xq28' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.00042

Table S162.  Gene #21: 'amp_xq28' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
AMP PEAK 21(XQ28) MUTATED 20 49 38 6 14 14 15
AMP PEAK 21(XQ28) WILD-TYPE 58 61 59 42 39 35 62

Figure S162.  Get High-res Image Gene #21: 'amp_xq28' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_xq28' versus 'MIRSEQ_CNMF'

P value = 0.0087 (Fisher's exact test), Q value = 0.018

Table S163.  Gene #21: 'amp_xq28' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
AMP PEAK 21(XQ28) MUTATED 43 74 37
AMP PEAK 21(XQ28) WILD-TYPE 146 154 56

Figure S163.  Get High-res Image Gene #21: 'amp_xq28' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_xq28' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-04 (Fisher's exact test), Q value = 0.0012

Table S164.  Gene #21: 'amp_xq28' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
AMP PEAK 21(XQ28) MUTATED 15 85 30
AMP PEAK 21(XQ28) WILD-TYPE 88 163 53

Figure S164.  Get High-res Image Gene #21: 'amp_xq28' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p36.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S165.  Gene #22: 'del_1p36.11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
DEL PEAK 1(1P36.11) MUTATED 31 45 29 20
DEL PEAK 1(1P36.11) WILD-TYPE 38 183 50 120

Figure S165.  Get High-res Image Gene #22: 'del_1p36.11' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p36.11' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S166.  Gene #22: 'del_1p36.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
DEL PEAK 1(1P36.11) MUTATED 14 45 48
DEL PEAK 1(1P36.11) WILD-TYPE 130 104 114

Figure S166.  Get High-res Image Gene #22: 'del_1p36.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p36.11' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S167.  Gene #22: 'del_1p36.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
DEL PEAK 1(1P36.11) MUTATED 18 49 55
DEL PEAK 1(1P36.11) WILD-TYPE 148 146 96

Figure S167.  Get High-res Image Gene #22: 'del_1p36.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p36.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S168.  Gene #22: 'del_1p36.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 1(1P36.11) MUTATED 11 27 20 11 26 21 6
DEL PEAK 1(1P36.11) WILD-TYPE 67 83 77 37 27 28 71

Figure S168.  Get High-res Image Gene #22: 'del_1p36.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.11' versus 'MIRSEQ_CNMF'

P value = 0.0248 (Fisher's exact test), Q value = 0.046

Table S169.  Gene #22: 'del_1p36.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
DEL PEAK 1(1P36.11) MUTATED 38 67 16
DEL PEAK 1(1P36.11) WILD-TYPE 151 161 77

Figure S169.  Get High-res Image Gene #22: 'del_1p36.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_1p36.11' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0174 (Fisher's exact test), Q value = 0.035

Table S170.  Gene #22: 'del_1p36.11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 198 91
DEL PEAK 1(1P36.11) MUTATED 33 56 12
DEL PEAK 1(1P36.11) WILD-TYPE 112 142 79

Figure S170.  Get High-res Image Gene #22: 'del_1p36.11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_1p36.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00854 (Fisher's exact test), Q value = 0.018

Table S171.  Gene #22: 'del_1p36.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
DEL PEAK 1(1P36.11) MUTATED 18 71 12
DEL PEAK 1(1P36.11) WILD-TYPE 85 177 71

Figure S171.  Get High-res Image Gene #22: 'del_1p36.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S172.  Gene #23: 'del_1p13.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
DEL PEAK 2(1P13.1) MUTATED 35 46 36 32
DEL PEAK 2(1P13.1) WILD-TYPE 34 182 43 108

Figure S172.  Get High-res Image Gene #23: 'del_1p13.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p13.1' versus 'METHLYATION_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.00091

Table S173.  Gene #23: 'del_1p13.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
DEL PEAK 2(1P13.1) MUTATED 22 51 50
DEL PEAK 2(1P13.1) WILD-TYPE 122 98 112

Figure S173.  Get High-res Image Gene #23: 'del_1p13.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p13.1' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 7.9e-05

Table S174.  Gene #23: 'del_1p13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
DEL PEAK 2(1P13.1) MUTATED 34 47 66
DEL PEAK 2(1P13.1) WILD-TYPE 132 148 85

Figure S174.  Get High-res Image Gene #23: 'del_1p13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00018

Table S175.  Gene #23: 'del_1p13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 2(1P13.1) MUTATED 21 26 27 20 27 17 9
DEL PEAK 2(1P13.1) WILD-TYPE 57 84 70 28 26 32 68

Figure S175.  Get High-res Image Gene #23: 'del_1p13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00501 (Fisher's exact test), Q value = 0.011

Table S176.  Gene #23: 'del_1p13.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
DEL PEAK 2(1P13.1) MUTATED 15 73 29 29
DEL PEAK 2(1P13.1) WILD-TYPE 56 125 112 71

Figure S176.  Get High-res Image Gene #23: 'del_1p13.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_2q22.1' versus 'CN_CNMF'

P value = 0.00385 (Fisher's exact test), Q value = 0.0088

Table S177.  Gene #24: 'del_2q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
DEL PEAK 3(2Q22.1) MUTATED 10 10 12 14
DEL PEAK 3(2Q22.1) WILD-TYPE 59 218 67 126

Figure S177.  Get High-res Image Gene #24: 'del_2q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_2q22.1' versus 'METHLYATION_CNMF'

P value = 0.00242 (Fisher's exact test), Q value = 0.0058

Table S178.  Gene #24: 'del_2q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
DEL PEAK 3(2Q22.1) MUTATED 5 22 13
DEL PEAK 3(2Q22.1) WILD-TYPE 139 127 149

Figure S178.  Get High-res Image Gene #24: 'del_2q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_2q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0163 (Fisher's exact test), Q value = 0.032

Table S179.  Gene #24: 'del_2q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 3(2Q22.1) MUTATED 6 8 10 2 8 10 2
DEL PEAK 3(2Q22.1) WILD-TYPE 72 102 87 46 45 39 75

Figure S179.  Get High-res Image Gene #24: 'del_2q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_2q22.1' versus 'MIRSEQ_CNMF'

P value = 0.0372 (Fisher's exact test), Q value = 0.066

Table S180.  Gene #24: 'del_2q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
DEL PEAK 3(2Q22.1) MUTATED 9 26 10
DEL PEAK 3(2Q22.1) WILD-TYPE 180 202 83

Figure S180.  Get High-res Image Gene #24: 'del_2q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_2q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00769 (Fisher's exact test), Q value = 0.017

Table S181.  Gene #24: 'del_2q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
DEL PEAK 3(2Q22.1) MUTATED 3 18 7 17
DEL PEAK 3(2Q22.1) WILD-TYPE 68 180 134 83

Figure S181.  Get High-res Image Gene #24: 'del_2q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3p26.2' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00011

Table S182.  Gene #25: 'del_3p26.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
DEL PEAK 4(3P26.2) MUTATED 40 76 45 75
DEL PEAK 4(3P26.2) WILD-TYPE 29 152 34 65

Figure S182.  Get High-res Image Gene #25: 'del_3p26.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p26.2' versus 'METHLYATION_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00039

Table S183.  Gene #25: 'del_3p26.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
DEL PEAK 4(3P26.2) MUTATED 51 88 68
DEL PEAK 4(3P26.2) WILD-TYPE 93 61 94

Figure S183.  Get High-res Image Gene #25: 'del_3p26.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3p26.2' versus 'MRNASEQ_CNMF'

P value = 0.0357 (Fisher's exact test), Q value = 0.064

Table S184.  Gene #25: 'del_3p26.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
DEL PEAK 4(3P26.2) MUTATED 62 95 76
DEL PEAK 4(3P26.2) WILD-TYPE 104 100 75

Figure S184.  Get High-res Image Gene #25: 'del_3p26.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3p26.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S185.  Gene #25: 'del_3p26.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 4(3P26.2) MUTATED 31 40 66 15 35 26 20
DEL PEAK 4(3P26.2) WILD-TYPE 47 70 31 33 18 23 57

Figure S185.  Get High-res Image Gene #25: 'del_3p26.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p26.2' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00011

Table S186.  Gene #25: 'del_3p26.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
DEL PEAK 4(3P26.2) MUTATED 62 115 54
DEL PEAK 4(3P26.2) WILD-TYPE 127 113 39

Figure S186.  Get High-res Image Gene #25: 'del_3p26.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3p26.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.00067

Table S187.  Gene #25: 'del_3p26.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
DEL PEAK 4(3P26.2) MUTATED 29 86 52 64
DEL PEAK 4(3P26.2) WILD-TYPE 42 112 89 36

Figure S187.  Get High-res Image Gene #25: 'del_3p26.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3p26.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00044 (Fisher's exact test), Q value = 0.0013

Table S188.  Gene #25: 'del_3p26.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
DEL PEAK 4(3P26.2) MUTATED 31 131 38
DEL PEAK 4(3P26.2) WILD-TYPE 72 117 45

Figure S188.  Get High-res Image Gene #25: 'del_3p26.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p21.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S189.  Gene #26: 'del_3p21.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
DEL PEAK 5(3P21.31) MUTATED 42 74 50 80
DEL PEAK 5(3P21.31) WILD-TYPE 27 154 29 60

Figure S189.  Get High-res Image Gene #26: 'del_3p21.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p21.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S190.  Gene #26: 'del_3p21.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
DEL PEAK 5(3P21.31) MUTATED 44 101 71
DEL PEAK 5(3P21.31) WILD-TYPE 100 48 91

Figure S190.  Get High-res Image Gene #26: 'del_3p21.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3p21.31' versus 'RPPA_CNMF'

P value = 0.0323 (Fisher's exact test), Q value = 0.058

Table S191.  Gene #26: 'del_3p21.31' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 73 64
DEL PEAK 5(3P21.31) MUTATED 15 34 38
DEL PEAK 5(3P21.31) WILD-TYPE 29 39 26

Figure S191.  Get High-res Image Gene #26: 'del_3p21.31' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_3p21.31' versus 'MRNASEQ_CNMF'

P value = 0.0017 (Fisher's exact test), Q value = 0.0042

Table S192.  Gene #26: 'del_3p21.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
DEL PEAK 5(3P21.31) MUTATED 60 100 82
DEL PEAK 5(3P21.31) WILD-TYPE 106 95 69

Figure S192.  Get High-res Image Gene #26: 'del_3p21.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3p21.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S193.  Gene #26: 'del_3p21.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 5(3P21.31) MUTATED 28 44 70 15 37 29 19
DEL PEAK 5(3P21.31) WILD-TYPE 50 66 27 33 16 20 58

Figure S193.  Get High-res Image Gene #26: 'del_3p21.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p21.31' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00015

Table S194.  Gene #26: 'del_3p21.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
DEL PEAK 5(3P21.31) MUTATED 64 125 52
DEL PEAK 5(3P21.31) WILD-TYPE 125 103 41

Figure S194.  Get High-res Image Gene #26: 'del_3p21.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3p21.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S195.  Gene #26: 'del_3p21.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
DEL PEAK 5(3P21.31) MUTATED 31 93 48 69
DEL PEAK 5(3P21.31) WILD-TYPE 40 105 93 31

Figure S195.  Get High-res Image Gene #26: 'del_3p21.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3p21.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00018

Table S196.  Gene #26: 'del_3p21.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
DEL PEAK 5(3P21.31) MUTATED 31 140 39
DEL PEAK 5(3P21.31) WILD-TYPE 72 108 44

Figure S196.  Get High-res Image Gene #26: 'del_3p21.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3q11.1' versus 'CN_CNMF'

P value = 0.0183 (Fisher's exact test), Q value = 0.036

Table S197.  Gene #27: 'del_3q11.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
DEL PEAK 6(3Q11.1) MUTATED 29 54 17 40
DEL PEAK 6(3Q11.1) WILD-TYPE 40 174 62 100

Figure S197.  Get High-res Image Gene #27: 'del_3q11.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_3q11.1' versus 'METHLYATION_CNMF'

P value = 0.00631 (Fisher's exact test), Q value = 0.014

Table S198.  Gene #27: 'del_3q11.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
DEL PEAK 6(3Q11.1) MUTATED 29 55 47
DEL PEAK 6(3Q11.1) WILD-TYPE 115 94 115

Figure S198.  Get High-res Image Gene #27: 'del_3q11.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3q11.1' versus 'MRNASEQ_CNMF'

P value = 0.022 (Fisher's exact test), Q value = 0.042

Table S199.  Gene #27: 'del_3q11.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
DEL PEAK 6(3Q11.1) MUTATED 45 41 52
DEL PEAK 6(3Q11.1) WILD-TYPE 121 154 99

Figure S199.  Get High-res Image Gene #27: 'del_3q11.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3q11.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0381 (Fisher's exact test), Q value = 0.067

Table S200.  Gene #27: 'del_3q11.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 6(3Q11.1) MUTATED 20 25 23 17 22 17 14
DEL PEAK 6(3Q11.1) WILD-TYPE 58 85 74 31 31 32 63

Figure S200.  Get High-res Image Gene #27: 'del_3q11.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3q29' versus 'CN_CNMF'

P value = 0.00322 (Fisher's exact test), Q value = 0.0076

Table S201.  Gene #28: 'del_3q29' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
DEL PEAK 7(3Q29) MUTATED 31 50 20 34
DEL PEAK 7(3Q29) WILD-TYPE 38 178 59 106

Figure S201.  Get High-res Image Gene #28: 'del_3q29' versus Molecular Subtype #3: 'CN_CNMF'

'del_3q29' versus 'METHLYATION_CNMF'

P value = 0.00153 (Fisher's exact test), Q value = 0.0039

Table S202.  Gene #28: 'del_3q29' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
DEL PEAK 7(3Q29) MUTATED 24 51 49
DEL PEAK 7(3Q29) WILD-TYPE 120 98 113

Figure S202.  Get High-res Image Gene #28: 'del_3q29' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3q29' versus 'RPPA_CHIERARCHICAL'

P value = 0.0309 (Fisher's exact test), Q value = 0.056

Table S203.  Gene #28: 'del_3q29' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 40 33 45 31 32
DEL PEAK 7(3Q29) MUTATED 13 13 8 6 15
DEL PEAK 7(3Q29) WILD-TYPE 27 20 37 25 17

Figure S203.  Get High-res Image Gene #28: 'del_3q29' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_3q29' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S204.  Gene #28: 'del_3q29' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
DEL PEAK 7(3Q29) MUTATED 44 27 61
DEL PEAK 7(3Q29) WILD-TYPE 122 168 90

Figure S204.  Get High-res Image Gene #28: 'del_3q29' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3q29' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S205.  Gene #28: 'del_3q29' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 7(3Q29) MUTATED 24 19 13 23 29 13 11
DEL PEAK 7(3Q29) WILD-TYPE 54 91 84 25 24 36 66

Figure S205.  Get High-res Image Gene #28: 'del_3q29' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4p16.3' versus 'CN_CNMF'

P value = 0.00136 (Fisher's exact test), Q value = 0.0035

Table S206.  Gene #29: 'del_4p16.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
DEL PEAK 8(4P16.3) MUTATED 23 39 26 43
DEL PEAK 8(4P16.3) WILD-TYPE 46 189 53 97

Figure S206.  Get High-res Image Gene #29: 'del_4p16.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_4p16.3' versus 'METHLYATION_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.0011

Table S207.  Gene #29: 'del_4p16.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
DEL PEAK 8(4P16.3) MUTATED 27 55 33
DEL PEAK 8(4P16.3) WILD-TYPE 117 94 129

Figure S207.  Get High-res Image Gene #29: 'del_4p16.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4p16.3' versus 'MRNASEQ_CNMF'

P value = 0.0095 (Fisher's exact test), Q value = 0.02

Table S208.  Gene #29: 'del_4p16.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
DEL PEAK 8(4P16.3) MUTATED 29 53 48
DEL PEAK 8(4P16.3) WILD-TYPE 137 142 103

Figure S208.  Get High-res Image Gene #29: 'del_4p16.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4p16.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S209.  Gene #29: 'del_4p16.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 8(4P16.3) MUTATED 14 21 43 5 23 11 13
DEL PEAK 8(4P16.3) WILD-TYPE 64 89 54 43 30 38 64

Figure S209.  Get High-res Image Gene #29: 'del_4p16.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4p16.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S210.  Gene #29: 'del_4p16.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
DEL PEAK 8(4P16.3) MUTATED 26 79 25
DEL PEAK 8(4P16.3) WILD-TYPE 163 149 68

Figure S210.  Get High-res Image Gene #29: 'del_4p16.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_4p16.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S211.  Gene #29: 'del_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
DEL PEAK 8(4P16.3) MUTATED 6 56 27 41
DEL PEAK 8(4P16.3) WILD-TYPE 65 142 114 59

Figure S211.  Get High-res Image Gene #29: 'del_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4p16.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00072 (Fisher's exact test), Q value = 0.002

Table S212.  Gene #29: 'del_4p16.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
DEL PEAK 8(4P16.3) MUTATED 14 80 18
DEL PEAK 8(4P16.3) WILD-TYPE 89 168 65

Figure S212.  Get High-res Image Gene #29: 'del_4p16.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q34.3' versus 'MRNA_CNMF'

P value = 0.00455 (Fisher's exact test), Q value = 0.01

Table S213.  Gene #30: 'del_4q34.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 5 9 12 6
DEL PEAK 9(4Q34.3) MUTATED 3 2 1 5
DEL PEAK 9(4Q34.3) WILD-TYPE 2 7 11 1

Figure S213.  Get High-res Image Gene #30: 'del_4q34.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_4q34.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.00566 (Fisher's exact test), Q value = 0.013

Table S214.  Gene #30: 'del_4q34.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 11 7
DEL PEAK 9(4Q34.3) MUTATED 2 3 6
DEL PEAK 9(4Q34.3) WILD-TYPE 12 8 1

Figure S214.  Get High-res Image Gene #30: 'del_4q34.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_4q34.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S215.  Gene #30: 'del_4q34.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
DEL PEAK 9(4Q34.3) MUTATED 40 49 42 57
DEL PEAK 9(4Q34.3) WILD-TYPE 29 179 37 83

Figure S215.  Get High-res Image Gene #30: 'del_4q34.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q34.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S216.  Gene #30: 'del_4q34.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
DEL PEAK 9(4Q34.3) MUTATED 27 87 49
DEL PEAK 9(4Q34.3) WILD-TYPE 117 62 113

Figure S216.  Get High-res Image Gene #30: 'del_4q34.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q34.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S217.  Gene #30: 'del_4q34.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
DEL PEAK 9(4Q34.3) MUTATED 35 73 78
DEL PEAK 9(4Q34.3) WILD-TYPE 131 122 73

Figure S217.  Get High-res Image Gene #30: 'del_4q34.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4q34.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S218.  Gene #30: 'del_4q34.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 9(4Q34.3) MUTATED 15 26 56 8 36 29 16
DEL PEAK 9(4Q34.3) WILD-TYPE 63 84 41 40 17 20 61

Figure S218.  Get High-res Image Gene #30: 'del_4q34.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S219.  Gene #30: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
DEL PEAK 9(4Q34.3) MUTATED 39 117 30
DEL PEAK 9(4Q34.3) WILD-TYPE 150 111 63

Figure S219.  Get High-res Image Gene #30: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_4q34.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S220.  Gene #30: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
DEL PEAK 9(4Q34.3) MUTATED 12 81 29 64
DEL PEAK 9(4Q34.3) WILD-TYPE 59 117 112 36

Figure S220.  Get High-res Image Gene #30: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0236 (Fisher's exact test), Q value = 0.045

Table S221.  Gene #30: 'del_4q34.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 198 91
DEL PEAK 9(4Q34.3) MUTATED 43 86 30
DEL PEAK 9(4Q34.3) WILD-TYPE 102 112 61

Figure S221.  Get High-res Image Gene #30: 'del_4q34.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_4q34.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S222.  Gene #30: 'del_4q34.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Figure S222.  Get High-res Image Gene #30: 'del_4q34.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S223.  Gene #31: 'del_5q12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
DEL PEAK 10(5Q12.1) MUTATED 27 38 38 74
DEL PEAK 10(5Q12.1) WILD-TYPE 42 190 41 66

Figure S223.  Get High-res Image Gene #31: 'del_5q12.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q12.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S224.  Gene #31: 'del_5q12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
DEL PEAK 10(5Q12.1) MUTATED 25 70 55
DEL PEAK 10(5Q12.1) WILD-TYPE 119 79 107

Figure S224.  Get High-res Image Gene #31: 'del_5q12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5q12.1' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 7.9e-05

Table S225.  Gene #31: 'del_5q12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
DEL PEAK 10(5Q12.1) MUTATED 33 80 62
DEL PEAK 10(5Q12.1) WILD-TYPE 133 115 89

Figure S225.  Get High-res Image Gene #31: 'del_5q12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_5q12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S226.  Gene #31: 'del_5q12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 10(5Q12.1) MUTATED 13 40 50 7 25 24 16
DEL PEAK 10(5Q12.1) WILD-TYPE 65 70 47 41 28 25 61

Figure S226.  Get High-res Image Gene #31: 'del_5q12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5q12.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S227.  Gene #31: 'del_5q12.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
DEL PEAK 10(5Q12.1) MUTATED 36 114 23
DEL PEAK 10(5Q12.1) WILD-TYPE 153 114 70

Figure S227.  Get High-res Image Gene #31: 'del_5q12.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_5q12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S228.  Gene #31: 'del_5q12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
DEL PEAK 10(5Q12.1) MUTATED 12 74 31 56
DEL PEAK 10(5Q12.1) WILD-TYPE 59 124 110 44

Figure S228.  Get High-res Image Gene #31: 'del_5q12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_5q12.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0121 (Fisher's exact test), Q value = 0.025

Table S229.  Gene #31: 'del_5q12.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 198 91
DEL PEAK 10(5Q12.1) MUTATED 38 81 27
DEL PEAK 10(5Q12.1) WILD-TYPE 107 117 64

Figure S229.  Get High-res Image Gene #31: 'del_5q12.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_5q12.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S230.  Gene #31: 'del_5q12.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
DEL PEAK 10(5Q12.1) MUTATED 14 112 20
DEL PEAK 10(5Q12.1) WILD-TYPE 89 136 63

Figure S230.  Get High-res Image Gene #31: 'del_5q12.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q31.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S231.  Gene #32: 'del_5q31.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
DEL PEAK 11(5Q31.1) MUTATED 34 49 46 79
DEL PEAK 11(5Q31.1) WILD-TYPE 35 179 33 61

Figure S231.  Get High-res Image Gene #32: 'del_5q31.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q31.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S232.  Gene #32: 'del_5q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
DEL PEAK 11(5Q31.1) MUTATED 31 81 72
DEL PEAK 11(5Q31.1) WILD-TYPE 113 68 90

Figure S232.  Get High-res Image Gene #32: 'del_5q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5q31.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S233.  Gene #32: 'del_5q31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
DEL PEAK 11(5Q31.1) MUTATED 36 97 73
DEL PEAK 11(5Q31.1) WILD-TYPE 130 98 78

Figure S233.  Get High-res Image Gene #32: 'del_5q31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_5q31.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S234.  Gene #32: 'del_5q31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 11(5Q31.1) MUTATED 13 51 54 11 30 27 20
DEL PEAK 11(5Q31.1) WILD-TYPE 65 59 43 37 23 22 57

Figure S234.  Get High-res Image Gene #32: 'del_5q31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5q31.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S235.  Gene #32: 'del_5q31.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
DEL PEAK 11(5Q31.1) MUTATED 44 127 33
DEL PEAK 11(5Q31.1) WILD-TYPE 145 101 60

Figure S235.  Get High-res Image Gene #32: 'del_5q31.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_5q31.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S236.  Gene #32: 'del_5q31.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
DEL PEAK 11(5Q31.1) MUTATED 16 87 36 65
DEL PEAK 11(5Q31.1) WILD-TYPE 55 111 105 35

Figure S236.  Get High-res Image Gene #32: 'del_5q31.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_5q31.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S237.  Gene #32: 'del_5q31.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
DEL PEAK 11(5Q31.1) MUTATED 21 131 28
DEL PEAK 11(5Q31.1) WILD-TYPE 82 117 55

Figure S237.  Get High-res Image Gene #32: 'del_5q31.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q11.1' versus 'CN_CNMF'

P value = 0.0461 (Fisher's exact test), Q value = 0.078

Table S238.  Gene #33: 'del_6q11.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
DEL PEAK 12(6Q11.1) MUTATED 25 50 26 33
DEL PEAK 12(6Q11.1) WILD-TYPE 44 178 53 107

Figure S238.  Get High-res Image Gene #33: 'del_6q11.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_6q11.1' versus 'METHLYATION_CNMF'

P value = 0.00222 (Fisher's exact test), Q value = 0.0054

Table S239.  Gene #33: 'del_6q11.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
DEL PEAK 12(6Q11.1) MUTATED 32 30 59
DEL PEAK 12(6Q11.1) WILD-TYPE 112 119 103

Figure S239.  Get High-res Image Gene #33: 'del_6q11.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_6q22.31' versus 'CN_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00039

Table S240.  Gene #34: 'del_6q22.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
DEL PEAK 13(6Q22.31) MUTATED 50 93 40 69
DEL PEAK 13(6Q22.31) WILD-TYPE 19 135 39 71

Figure S240.  Get High-res Image Gene #34: 'del_6q22.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_6q22.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S241.  Gene #34: 'del_6q22.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
DEL PEAK 13(6Q22.31) MUTATED 48 67 111
DEL PEAK 13(6Q22.31) WILD-TYPE 96 82 51

Figure S241.  Get High-res Image Gene #34: 'del_6q22.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_6q22.31' versus 'RPPA_CNMF'

P value = 0.0495 (Fisher's exact test), Q value = 0.083

Table S242.  Gene #34: 'del_6q22.31' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 73 64
DEL PEAK 13(6Q22.31) MUTATED 27 28 33
DEL PEAK 13(6Q22.31) WILD-TYPE 17 45 31

Figure S242.  Get High-res Image Gene #34: 'del_6q22.31' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_6q22.31' versus 'RPPA_CHIERARCHICAL'

P value = 0.00345 (Fisher's exact test), Q value = 0.008

Table S243.  Gene #34: 'del_6q22.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 40 33 45 31 32
DEL PEAK 13(6Q22.31) MUTATED 16 25 15 15 17
DEL PEAK 13(6Q22.31) WILD-TYPE 24 8 30 16 15

Figure S243.  Get High-res Image Gene #34: 'del_6q22.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_6q22.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00074 (Fisher's exact test), Q value = 0.002

Table S244.  Gene #34: 'del_6q22.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 13(6Q22.31) MUTATED 33 58 37 34 34 21 32
DEL PEAK 13(6Q22.31) WILD-TYPE 45 52 60 14 19 28 45

Figure S244.  Get High-res Image Gene #34: 'del_6q22.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_6q22.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00099 (Fisher's exact test), Q value = 0.0026

Table S245.  Gene #34: 'del_6q22.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
DEL PEAK 13(6Q22.31) MUTATED 35 118 58 39
DEL PEAK 13(6Q22.31) WILD-TYPE 36 80 83 61

Figure S245.  Get High-res Image Gene #34: 'del_6q22.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_6q26' versus 'CN_CNMF'

P value = 0.00065 (Fisher's exact test), Q value = 0.0018

Table S246.  Gene #35: 'del_6q26' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
DEL PEAK 14(6Q26) MUTATED 49 98 42 68
DEL PEAK 14(6Q26) WILD-TYPE 20 130 37 72

Figure S246.  Get High-res Image Gene #35: 'del_6q26' versus Molecular Subtype #3: 'CN_CNMF'

'del_6q26' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00015

Table S247.  Gene #35: 'del_6q26' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
DEL PEAK 14(6Q26) MUTATED 53 70 102
DEL PEAK 14(6Q26) WILD-TYPE 91 79 60

Figure S247.  Get High-res Image Gene #35: 'del_6q26' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_6q26' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00626 (Fisher's exact test), Q value = 0.014

Table S248.  Gene #35: 'del_6q26' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 14(6Q26) MUTATED 31 62 39 32 32 25 33
DEL PEAK 14(6Q26) WILD-TYPE 47 48 58 16 21 24 44

Figure S248.  Get High-res Image Gene #35: 'del_6q26' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_6q26' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0186 (Fisher's exact test), Q value = 0.037

Table S249.  Gene #35: 'del_6q26' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
DEL PEAK 14(6Q26) MUTATED 35 115 63 41
DEL PEAK 14(6Q26) WILD-TYPE 36 83 78 59

Figure S249.  Get High-res Image Gene #35: 'del_6q26' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MRNA_CNMF'

P value = 0.0233 (Fisher's exact test), Q value = 0.044

Table S250.  Gene #36: 'del_8p23.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 5 9 12 6
DEL PEAK 15(8P23.2) MUTATED 5 7 5 6
DEL PEAK 15(8P23.2) WILD-TYPE 0 2 7 0

Figure S250.  Get High-res Image Gene #36: 'del_8p23.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_8p23.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.0481 (Fisher's exact test), Q value = 0.081

Table S251.  Gene #36: 'del_8p23.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 11 7
DEL PEAK 15(8P23.2) MUTATED 7 9 7
DEL PEAK 15(8P23.2) WILD-TYPE 7 2 0

Figure S251.  Get High-res Image Gene #36: 'del_8p23.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_8p23.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S252.  Gene #36: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
DEL PEAK 15(8P23.2) MUTATED 32 78 47 100
DEL PEAK 15(8P23.2) WILD-TYPE 37 150 32 40

Figure S252.  Get High-res Image Gene #36: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_8p23.2' versus 'METHLYATION_CNMF'

P value = 0.0382 (Fisher's exact test), Q value = 0.067

Table S253.  Gene #36: 'del_8p23.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
DEL PEAK 15(8P23.2) MUTATED 59 75 90
DEL PEAK 15(8P23.2) WILD-TYPE 85 74 72

Figure S253.  Get High-res Image Gene #36: 'del_8p23.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_8p23.2' versus 'RPPA_CNMF'

P value = 0.00924 (Fisher's exact test), Q value = 0.02

Table S254.  Gene #36: 'del_8p23.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 73 64
DEL PEAK 15(8P23.2) MUTATED 13 42 34
DEL PEAK 15(8P23.2) WILD-TYPE 31 31 30

Figure S254.  Get High-res Image Gene #36: 'del_8p23.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_8p23.2' versus 'RPPA_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00027

Table S255.  Gene #36: 'del_8p23.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 40 33 45 31 32
DEL PEAK 15(8P23.2) MUTATED 20 9 35 14 11
DEL PEAK 15(8P23.2) WILD-TYPE 20 24 10 17 21

Figure S255.  Get High-res Image Gene #36: 'del_8p23.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_8p23.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S256.  Gene #36: 'del_8p23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
DEL PEAK 15(8P23.2) MUTATED 63 135 57
DEL PEAK 15(8P23.2) WILD-TYPE 103 60 94

Figure S256.  Get High-res Image Gene #36: 'del_8p23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_8p23.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S257.  Gene #36: 'del_8p23.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 15(8P23.2) MUTATED 34 72 64 11 20 24 30
DEL PEAK 15(8P23.2) WILD-TYPE 44 38 33 37 33 25 47

Figure S257.  Get High-res Image Gene #36: 'del_8p23.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.001

Table S258.  Gene #36: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
DEL PEAK 15(8P23.2) MUTATED 72 127 54
DEL PEAK 15(8P23.2) WILD-TYPE 117 101 39

Figure S258.  Get High-res Image Gene #36: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_8p23.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0102 (Fisher's exact test), Q value = 0.021

Table S259.  Gene #36: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
DEL PEAK 15(8P23.2) MUTATED 27 108 60 58
DEL PEAK 15(8P23.2) WILD-TYPE 44 90 81 42

Figure S259.  Get High-res Image Gene #36: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0212 (Fisher's exact test), Q value = 0.041

Table S260.  Gene #36: 'del_8p23.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 198 91
DEL PEAK 15(8P23.2) MUTATED 57 104 50
DEL PEAK 15(8P23.2) WILD-TYPE 88 94 41

Figure S260.  Get High-res Image Gene #36: 'del_8p23.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_8p23.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00077 (Fisher's exact test), Q value = 0.0021

Table S261.  Gene #36: 'del_8p23.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
DEL PEAK 15(8P23.2) MUTATED 34 136 41
DEL PEAK 15(8P23.2) WILD-TYPE 69 112 42

Figure S261.  Get High-res Image Gene #36: 'del_8p23.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S262.  Gene #37: 'del_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
DEL PEAK 16(8P11.21) MUTATED 5 34 24 60
DEL PEAK 16(8P11.21) WILD-TYPE 64 194 55 80

Figure S262.  Get High-res Image Gene #37: 'del_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

'del_8p11.21' versus 'RPPA_CHIERARCHICAL'

P value = 0.0377 (Fisher's exact test), Q value = 0.067

Table S263.  Gene #37: 'del_8p11.21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 40 33 45 31 32
DEL PEAK 16(8P11.21) MUTATED 10 3 17 5 9
DEL PEAK 16(8P11.21) WILD-TYPE 30 30 28 26 23

Figure S263.  Get High-res Image Gene #37: 'del_8p11.21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_8p11.21' versus 'MRNASEQ_CNMF'

P value = 0.00252 (Fisher's exact test), Q value = 0.006

Table S264.  Gene #37: 'del_8p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
DEL PEAK 16(8P11.21) MUTATED 35 62 25
DEL PEAK 16(8P11.21) WILD-TYPE 131 133 126

Figure S264.  Get High-res Image Gene #37: 'del_8p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9p23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S265.  Gene #38: 'del_9p23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
DEL PEAK 17(9P23) MUTATED 34 100 63 88
DEL PEAK 17(9P23) WILD-TYPE 35 128 16 52

Figure S265.  Get High-res Image Gene #38: 'del_9p23' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p23' versus 'METHLYATION_CNMF'

P value = 0.0408 (Fisher's exact test), Q value = 0.071

Table S266.  Gene #38: 'del_9p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
DEL PEAK 17(9P23) MUTATED 69 93 86
DEL PEAK 17(9P23) WILD-TYPE 75 56 76

Figure S266.  Get High-res Image Gene #38: 'del_9p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9p23' versus 'MRNASEQ_CNMF'

P value = 0.0424 (Fisher's exact test), Q value = 0.074

Table S267.  Gene #38: 'del_9p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
DEL PEAK 17(9P23) MUTATED 81 107 95
DEL PEAK 17(9P23) WILD-TYPE 85 88 56

Figure S267.  Get High-res Image Gene #38: 'del_9p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9p23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.00077

Table S268.  Gene #38: 'del_9p23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 17(9P23) MUTATED 42 51 63 24 27 40 36
DEL PEAK 17(9P23) WILD-TYPE 36 59 34 24 26 9 41

Figure S268.  Get High-res Image Gene #38: 'del_9p23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0257 (Fisher's exact test), Q value = 0.048

Table S269.  Gene #38: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
DEL PEAK 17(9P23) MUTATED 35 106 71 68
DEL PEAK 17(9P23) WILD-TYPE 36 92 70 32

Figure S269.  Get High-res Image Gene #38: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S270.  Gene #39: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
DEL PEAK 18(9P21.3) MUTATED 32 104 65 90
DEL PEAK 18(9P21.3) WILD-TYPE 37 124 14 50

Figure S270.  Get High-res Image Gene #39: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

P value = 0.0179 (Fisher's exact test), Q value = 0.035

Table S271.  Gene #39: 'del_9p21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
DEL PEAK 18(9P21.3) MUTATED 67 94 89
DEL PEAK 18(9P21.3) WILD-TYPE 77 55 73

Figure S271.  Get High-res Image Gene #39: 'del_9p21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9p21.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0376 (Fisher's exact test), Q value = 0.067

Table S272.  Gene #39: 'del_9p21.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 40 33 45 31 32
DEL PEAK 18(9P21.3) MUTATED 24 19 29 22 11
DEL PEAK 18(9P21.3) WILD-TYPE 16 14 16 9 21

Figure S272.  Get High-res Image Gene #39: 'del_9p21.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S273.  Gene #39: 'del_9p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 18(9P21.3) MUTATED 45 54 63 23 25 43 36
DEL PEAK 18(9P21.3) WILD-TYPE 33 56 34 25 28 6 41

Figure S273.  Get High-res Image Gene #39: 'del_9p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00178 (Fisher's exact test), Q value = 0.0044

Table S274.  Gene #39: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
DEL PEAK 18(9P21.3) MUTATED 35 104 75 73
DEL PEAK 18(9P21.3) WILD-TYPE 36 94 66 27

Figure S274.  Get High-res Image Gene #39: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0442 (Fisher's exact test), Q value = 0.076

Table S275.  Gene #39: 'del_9p21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 198 91
DEL PEAK 18(9P21.3) MUTATED 91 98 53
DEL PEAK 18(9P21.3) WILD-TYPE 54 100 38

Figure S275.  Get High-res Image Gene #39: 'del_9p21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_9q21.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S276.  Gene #40: 'del_9q21.11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
DEL PEAK 19(9Q21.11) MUTATED 39 81 58 78
DEL PEAK 19(9Q21.11) WILD-TYPE 30 147 21 62

Figure S276.  Get High-res Image Gene #40: 'del_9q21.11' versus Molecular Subtype #3: 'CN_CNMF'

'del_9q21.11' versus 'METHLYATION_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00024

Table S277.  Gene #40: 'del_9q21.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
DEL PEAK 19(9Q21.11) MUTATED 57 94 70
DEL PEAK 19(9Q21.11) WILD-TYPE 87 55 92

Figure S277.  Get High-res Image Gene #40: 'del_9q21.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9q21.11' versus 'MRNASEQ_CNMF'

P value = 0.00557 (Fisher's exact test), Q value = 0.012

Table S278.  Gene #40: 'del_9q21.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
DEL PEAK 19(9Q21.11) MUTATED 67 99 88
DEL PEAK 19(9Q21.11) WILD-TYPE 99 96 63

Figure S278.  Get High-res Image Gene #40: 'del_9q21.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9q21.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 7.9e-05

Table S279.  Gene #40: 'del_9q21.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 19(9Q21.11) MUTATED 35 47 59 16 38 31 28
DEL PEAK 19(9Q21.11) WILD-TYPE 43 63 38 32 15 18 49

Figure S279.  Get High-res Image Gene #40: 'del_9q21.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9q21.11' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 7.9e-05

Table S280.  Gene #40: 'del_9q21.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
DEL PEAK 19(9Q21.11) MUTATED 70 125 57
DEL PEAK 19(9Q21.11) WILD-TYPE 119 103 36

Figure S280.  Get High-res Image Gene #40: 'del_9q21.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_9q21.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S281.  Gene #40: 'del_9q21.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
DEL PEAK 19(9Q21.11) MUTATED 26 101 54 71
DEL PEAK 19(9Q21.11) WILD-TYPE 45 97 87 29

Figure S281.  Get High-res Image Gene #40: 'del_9q21.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9q21.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.00059

Table S282.  Gene #40: 'del_9q21.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
DEL PEAK 19(9Q21.11) MUTATED 34 141 40
DEL PEAK 19(9Q21.11) WILD-TYPE 69 107 43

Figure S282.  Get High-res Image Gene #40: 'del_9q21.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10p15.3' versus 'CN_CNMF'

P value = 0.00644 (Fisher's exact test), Q value = 0.014

Table S283.  Gene #41: 'del_10p15.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
DEL PEAK 20(10P15.3) MUTATED 15 41 25 45
DEL PEAK 20(10P15.3) WILD-TYPE 54 187 54 95

Figure S283.  Get High-res Image Gene #41: 'del_10p15.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_10p15.3' versus 'METHLYATION_CNMF'

P value = 0.00982 (Fisher's exact test), Q value = 0.021

Table S284.  Gene #41: 'del_10p15.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
DEL PEAK 20(10P15.3) MUTATED 23 46 41
DEL PEAK 20(10P15.3) WILD-TYPE 121 103 121

Figure S284.  Get High-res Image Gene #41: 'del_10p15.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10p15.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00202 (Fisher's exact test), Q value = 0.0049

Table S285.  Gene #41: 'del_10p15.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 20(10P15.3) MUTATED 16 26 39 6 16 8 14
DEL PEAK 20(10P15.3) WILD-TYPE 62 84 58 42 37 41 63

Figure S285.  Get High-res Image Gene #41: 'del_10p15.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10p15.3' versus 'MIRSEQ_CNMF'

P value = 0.00242 (Fisher's exact test), Q value = 0.0058

Table S286.  Gene #41: 'del_10p15.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
DEL PEAK 20(10P15.3) MUTATED 33 58 34
DEL PEAK 20(10P15.3) WILD-TYPE 156 170 59

Figure S286.  Get High-res Image Gene #41: 'del_10p15.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_10p15.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0188 (Fisher's exact test), Q value = 0.037

Table S287.  Gene #41: 'del_10p15.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
DEL PEAK 20(10P15.3) MUTATED 9 51 32 33
DEL PEAK 20(10P15.3) WILD-TYPE 62 147 109 67

Figure S287.  Get High-res Image Gene #41: 'del_10p15.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_10p15.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.032 (Fisher's exact test), Q value = 0.058

Table S288.  Gene #41: 'del_10p15.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 198 91
DEL PEAK 20(10P15.3) MUTATED 26 54 29
DEL PEAK 20(10P15.3) WILD-TYPE 119 144 62

Figure S288.  Get High-res Image Gene #41: 'del_10p15.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_10p15.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0122 (Fisher's exact test), Q value = 0.025

Table S289.  Gene #41: 'del_10p15.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
DEL PEAK 20(10P15.3) MUTATED 15 69 25
DEL PEAK 20(10P15.3) WILD-TYPE 88 179 58

Figure S289.  Get High-res Image Gene #41: 'del_10p15.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q26.3' versus 'CN_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.0011

Table S290.  Gene #42: 'del_10q26.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
DEL PEAK 21(10Q26.3) MUTATED 18 53 23 62
DEL PEAK 21(10Q26.3) WILD-TYPE 51 175 56 78

Figure S290.  Get High-res Image Gene #42: 'del_10q26.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q26.3' versus 'METHLYATION_CNMF'

P value = 0.0384 (Fisher's exact test), Q value = 0.068

Table S291.  Gene #42: 'del_10q26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
DEL PEAK 21(10Q26.3) MUTATED 32 53 50
DEL PEAK 21(10Q26.3) WILD-TYPE 112 96 112

Figure S291.  Get High-res Image Gene #42: 'del_10q26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10q26.3' versus 'RPPA_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00027

Table S292.  Gene #42: 'del_10q26.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 73 64
DEL PEAK 21(10Q26.3) MUTATED 5 36 20
DEL PEAK 21(10Q26.3) WILD-TYPE 39 37 44

Figure S292.  Get High-res Image Gene #42: 'del_10q26.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_10q26.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 7e-04

Table S293.  Gene #42: 'del_10q26.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 40 33 45 31 32
DEL PEAK 21(10Q26.3) MUTATED 21 4 21 10 5
DEL PEAK 21(10Q26.3) WILD-TYPE 19 29 24 21 27

Figure S293.  Get High-res Image Gene #42: 'del_10q26.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_10q26.3' versus 'MRNASEQ_CNMF'

P value = 0.00289 (Fisher's exact test), Q value = 0.0069

Table S294.  Gene #42: 'del_10q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
DEL PEAK 21(10Q26.3) MUTATED 42 76 36
DEL PEAK 21(10Q26.3) WILD-TYPE 124 119 115

Figure S294.  Get High-res Image Gene #42: 'del_10q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10q26.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S295.  Gene #42: 'del_10q26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 21(10Q26.3) MUTATED 23 44 48 1 11 9 18
DEL PEAK 21(10Q26.3) WILD-TYPE 55 66 49 47 42 40 59

Figure S295.  Get High-res Image Gene #42: 'del_10q26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10q26.3' versus 'MIRSEQ_CNMF'

P value = 0.0124 (Fisher's exact test), Q value = 0.025

Table S296.  Gene #42: 'del_10q26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
DEL PEAK 21(10Q26.3) MUTATED 43 74 36
DEL PEAK 21(10Q26.3) WILD-TYPE 146 154 57

Figure S296.  Get High-res Image Gene #42: 'del_10q26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_10q26.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00137 (Fisher's exact test), Q value = 0.0035

Table S297.  Gene #42: 'del_10q26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
DEL PEAK 21(10Q26.3) MUTATED 12 62 36 43
DEL PEAK 21(10Q26.3) WILD-TYPE 59 136 105 57

Figure S297.  Get High-res Image Gene #42: 'del_10q26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_10q26.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00123 (Fisher's exact test), Q value = 0.0032

Table S298.  Gene #42: 'del_10q26.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
DEL PEAK 21(10Q26.3) MUTATED 16 85 26
DEL PEAK 21(10Q26.3) WILD-TYPE 87 163 57

Figure S298.  Get High-res Image Gene #42: 'del_10q26.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11p15.5' versus 'MRNA_CHIERARCHICAL'

P value = 0.032 (Fisher's exact test), Q value = 0.058

Table S299.  Gene #43: 'del_11p15.5' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 11 7
DEL PEAK 22(11P15.5) MUTATED 1 2 4
DEL PEAK 22(11P15.5) WILD-TYPE 13 9 3

Figure S299.  Get High-res Image Gene #43: 'del_11p15.5' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_11p15.5' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S300.  Gene #43: 'del_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
DEL PEAK 22(11P15.5) MUTATED 20 31 30 62
DEL PEAK 22(11P15.5) WILD-TYPE 49 197 49 78

Figure S300.  Get High-res Image Gene #43: 'del_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

'del_11p15.5' versus 'METHLYATION_CNMF'

P value = 0.00089 (Fisher's exact test), Q value = 0.0024

Table S301.  Gene #43: 'del_11p15.5' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
DEL PEAK 22(11P15.5) MUTATED 27 57 42
DEL PEAK 22(11P15.5) WILD-TYPE 117 92 120

Figure S301.  Get High-res Image Gene #43: 'del_11p15.5' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_11p15.5' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00015

Table S302.  Gene #43: 'del_11p15.5' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
DEL PEAK 22(11P15.5) MUTATED 26 72 42
DEL PEAK 22(11P15.5) WILD-TYPE 140 123 109

Figure S302.  Get High-res Image Gene #43: 'del_11p15.5' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_11p15.5' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S303.  Gene #43: 'del_11p15.5' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 22(11P15.5) MUTATED 8 36 38 8 14 23 13
DEL PEAK 22(11P15.5) WILD-TYPE 70 74 59 40 39 26 64

Figure S303.  Get High-res Image Gene #43: 'del_11p15.5' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.00059

Table S304.  Gene #43: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
DEL PEAK 22(11P15.5) MUTATED 35 82 23
DEL PEAK 22(11P15.5) WILD-TYPE 154 146 70

Figure S304.  Get High-res Image Gene #43: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_11p15.5' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00025 (Fisher's exact test), Q value = 0.00074

Table S305.  Gene #43: 'del_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
DEL PEAK 22(11P15.5) MUTATED 14 63 24 39
DEL PEAK 22(11P15.5) WILD-TYPE 57 135 117 61

Figure S305.  Get High-res Image Gene #43: 'del_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00042 (Fisher's exact test), Q value = 0.0012

Table S306.  Gene #43: 'del_11p15.5' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
DEL PEAK 22(11P15.5) MUTATED 17 87 17
DEL PEAK 22(11P15.5) WILD-TYPE 86 161 66

Figure S306.  Get High-res Image Gene #43: 'del_11p15.5' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11q23.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S307.  Gene #44: 'del_11q23.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
DEL PEAK 23(11Q23.2) MUTATED 31 34 30 24
DEL PEAK 23(11Q23.2) WILD-TYPE 38 194 49 116

Figure S307.  Get High-res Image Gene #44: 'del_11q23.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_11q23.2' versus 'METHLYATION_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.00072

Table S308.  Gene #44: 'del_11q23.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
DEL PEAK 23(11Q23.2) MUTATED 21 51 32
DEL PEAK 23(11Q23.2) WILD-TYPE 123 98 130

Figure S308.  Get High-res Image Gene #44: 'del_11q23.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_11q23.2' versus 'RPPA_CNMF'

P value = 0.0372 (Fisher's exact test), Q value = 0.066

Table S309.  Gene #44: 'del_11q23.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 73 64
DEL PEAK 23(11Q23.2) MUTATED 8 11 21
DEL PEAK 23(11Q23.2) WILD-TYPE 36 62 43

Figure S309.  Get High-res Image Gene #44: 'del_11q23.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_11q23.2' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00011

Table S310.  Gene #44: 'del_11q23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
DEL PEAK 23(11Q23.2) MUTATED 20 44 53
DEL PEAK 23(11Q23.2) WILD-TYPE 146 151 98

Figure S310.  Get High-res Image Gene #44: 'del_11q23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_11q23.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00067 (Fisher's exact test), Q value = 0.0019

Table S311.  Gene #44: 'del_11q23.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 23(11Q23.2) MUTATED 10 26 22 15 20 16 8
DEL PEAK 23(11Q23.2) WILD-TYPE 68 84 75 33 33 33 69

Figure S311.  Get High-res Image Gene #44: 'del_11q23.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_11q23.2' versus 'MIRSEQ_CNMF'

P value = 0.00248 (Fisher's exact test), Q value = 0.006

Table S312.  Gene #44: 'del_11q23.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
DEL PEAK 23(11Q23.2) MUTATED 35 69 14
DEL PEAK 23(11Q23.2) WILD-TYPE 154 159 79

Figure S312.  Get High-res Image Gene #44: 'del_11q23.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_11q23.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0444 (Fisher's exact test), Q value = 0.076

Table S313.  Gene #44: 'del_11q23.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 198 91
DEL PEAK 23(11Q23.2) MUTATED 29 55 14
DEL PEAK 23(11Q23.2) WILD-TYPE 116 143 77

Figure S313.  Get High-res Image Gene #44: 'del_11q23.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_11q25' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00021

Table S314.  Gene #45: 'del_11q25' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
DEL PEAK 24(11Q25) MUTATED 27 34 26 30
DEL PEAK 24(11Q25) WILD-TYPE 42 194 53 110

Figure S314.  Get High-res Image Gene #45: 'del_11q25' versus Molecular Subtype #3: 'CN_CNMF'

'del_11q25' versus 'METHLYATION_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.00059

Table S315.  Gene #45: 'del_11q25' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
DEL PEAK 24(11Q25) MUTATED 19 50 36
DEL PEAK 24(11Q25) WILD-TYPE 125 99 126

Figure S315.  Get High-res Image Gene #45: 'del_11q25' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_11q25' versus 'RPPA_CNMF'

P value = 0.00414 (Fisher's exact test), Q value = 0.0095

Table S316.  Gene #45: 'del_11q25' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 73 64
DEL PEAK 24(11Q25) MUTATED 9 8 22
DEL PEAK 24(11Q25) WILD-TYPE 35 65 42

Figure S316.  Get High-res Image Gene #45: 'del_11q25' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_11q25' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00021

Table S317.  Gene #45: 'del_11q25' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
DEL PEAK 24(11Q25) MUTATED 19 47 49
DEL PEAK 24(11Q25) WILD-TYPE 147 148 102

Figure S317.  Get High-res Image Gene #45: 'del_11q25' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_11q25' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00302 (Fisher's exact test), Q value = 0.0071

Table S318.  Gene #45: 'del_11q25' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 24(11Q25) MUTATED 11 25 22 14 19 16 8
DEL PEAK 24(11Q25) WILD-TYPE 67 85 75 34 34 33 69

Figure S318.  Get High-res Image Gene #45: 'del_11q25' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_12p13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S319.  Gene #46: 'del_12p13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
DEL PEAK 25(12P13.2) MUTATED 18 50 9 61
DEL PEAK 25(12P13.2) WILD-TYPE 51 178 70 79

Figure S319.  Get High-res Image Gene #46: 'del_12p13.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_12p13.2' versus 'METHLYATION_CNMF'

P value = 0.0117 (Fisher's exact test), Q value = 0.024

Table S320.  Gene #46: 'del_12p13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
DEL PEAK 25(12P13.2) MUTATED 26 41 53
DEL PEAK 25(12P13.2) WILD-TYPE 118 108 109

Figure S320.  Get High-res Image Gene #46: 'del_12p13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_12p13.2' versus 'MRNASEQ_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 5e-04

Table S321.  Gene #46: 'del_12p13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
DEL PEAK 25(12P13.2) MUTATED 54 60 22
DEL PEAK 25(12P13.2) WILD-TYPE 112 135 129

Figure S321.  Get High-res Image Gene #46: 'del_12p13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_12p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00962 (Fisher's exact test), Q value = 0.02

Table S322.  Gene #46: 'del_12p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 25(12P13.2) MUTATED 23 35 34 11 8 5 20
DEL PEAK 25(12P13.2) WILD-TYPE 55 75 63 37 45 44 57

Figure S322.  Get High-res Image Gene #46: 'del_12p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_12q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S323.  Gene #47: 'del_12q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
DEL PEAK 26(12Q12) MUTATED 8 37 5 48
DEL PEAK 26(12Q12) WILD-TYPE 61 191 74 92

Figure S323.  Get High-res Image Gene #47: 'del_12q12' versus Molecular Subtype #3: 'CN_CNMF'

'del_12q12' versus 'METHLYATION_CNMF'

P value = 0.0253 (Fisher's exact test), Q value = 0.047

Table S324.  Gene #47: 'del_12q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
DEL PEAK 26(12Q12) MUTATED 25 21 42
DEL PEAK 26(12Q12) WILD-TYPE 119 128 120

Figure S324.  Get High-res Image Gene #47: 'del_12q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_12q12' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00033

Table S325.  Gene #47: 'del_12q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
DEL PEAK 26(12Q12) MUTATED 42 43 12
DEL PEAK 26(12Q12) WILD-TYPE 124 152 139

Figure S325.  Get High-res Image Gene #47: 'del_12q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_12q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0447 (Fisher's exact test), Q value = 0.077

Table S326.  Gene #47: 'del_12q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 26(12Q12) MUTATED 16 26 20 10 2 7 16
DEL PEAK 26(12Q12) WILD-TYPE 62 84 77 38 51 42 61

Figure S326.  Get High-res Image Gene #47: 'del_12q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_12q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0261 (Fisher's exact test), Q value = 0.048

Table S327.  Gene #47: 'del_12q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
DEL PEAK 26(12Q12) MUTATED 16 43 25
DEL PEAK 26(12Q12) WILD-TYPE 87 205 58

Figure S327.  Get High-res Image Gene #47: 'del_12q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_12q24.33' versus 'CN_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 3e-04

Table S328.  Gene #48: 'del_12q24.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
DEL PEAK 27(12Q24.33) MUTATED 10 60 12 55
DEL PEAK 27(12Q24.33) WILD-TYPE 59 168 67 85

Figure S328.  Get High-res Image Gene #48: 'del_12q24.33' versus Molecular Subtype #3: 'CN_CNMF'

'del_12q24.33' versus 'RPPA_CNMF'

P value = 0.0204 (Fisher's exact test), Q value = 0.04

Table S329.  Gene #48: 'del_12q24.33' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 73 64
DEL PEAK 27(12Q24.33) MUTATED 17 28 12
DEL PEAK 27(12Q24.33) WILD-TYPE 27 45 52

Figure S329.  Get High-res Image Gene #48: 'del_12q24.33' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_12q24.33' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00015

Table S330.  Gene #48: 'del_12q24.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
DEL PEAK 27(12Q24.33) MUTATED 55 60 21
DEL PEAK 27(12Q24.33) WILD-TYPE 111 135 130

Figure S330.  Get High-res Image Gene #48: 'del_12q24.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_12q24.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00018

Table S331.  Gene #48: 'del_12q24.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 27(12Q24.33) MUTATED 22 34 31 16 2 6 25
DEL PEAK 27(12Q24.33) WILD-TYPE 56 76 66 32 51 43 52

Figure S331.  Get High-res Image Gene #48: 'del_12q24.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_12q24.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0119 (Fisher's exact test), Q value = 0.024

Table S332.  Gene #48: 'del_12q24.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
DEL PEAK 27(12Q24.33) MUTATED 20 50 49 16
DEL PEAK 27(12Q24.33) WILD-TYPE 51 148 92 84

Figure S332.  Get High-res Image Gene #48: 'del_12q24.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_13q12.11' versus 'MRNA_CNMF'

P value = 0.00077 (Fisher's exact test), Q value = 0.0021

Table S333.  Gene #49: 'del_13q12.11' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 5 9 12 6
DEL PEAK 28(13Q12.11) MUTATED 5 6 1 4
DEL PEAK 28(13Q12.11) WILD-TYPE 0 3 11 2

Figure S333.  Get High-res Image Gene #49: 'del_13q12.11' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_13q12.11' versus 'MRNA_CHIERARCHICAL'

P value = 0.0229 (Fisher's exact test), Q value = 0.044

Table S334.  Gene #49: 'del_13q12.11' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 11 7
DEL PEAK 28(13Q12.11) MUTATED 3 8 5
DEL PEAK 28(13Q12.11) WILD-TYPE 11 3 2

Figure S334.  Get High-res Image Gene #49: 'del_13q12.11' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_13q12.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S335.  Gene #49: 'del_13q12.11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
DEL PEAK 28(13Q12.11) MUTATED 49 86 48 111
DEL PEAK 28(13Q12.11) WILD-TYPE 20 142 31 29

Figure S335.  Get High-res Image Gene #49: 'del_13q12.11' versus Molecular Subtype #3: 'CN_CNMF'

'del_13q12.11' versus 'METHLYATION_CNMF'

P value = 0.00142 (Fisher's exact test), Q value = 0.0036

Table S336.  Gene #49: 'del_13q12.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
DEL PEAK 28(13Q12.11) MUTATED 65 94 103
DEL PEAK 28(13Q12.11) WILD-TYPE 79 55 59

Figure S336.  Get High-res Image Gene #49: 'del_13q12.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_13q12.11' versus 'RPPA_CNMF'

P value = 0.00693 (Fisher's exact test), Q value = 0.015

Table S337.  Gene #49: 'del_13q12.11' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 73 64
DEL PEAK 28(13Q12.11) MUTATED 18 49 29
DEL PEAK 28(13Q12.11) WILD-TYPE 26 24 35

Figure S337.  Get High-res Image Gene #49: 'del_13q12.11' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_13q12.11' versus 'RPPA_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 7e-04

Table S338.  Gene #49: 'del_13q12.11' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 40 33 45 31 32
DEL PEAK 28(13Q12.11) MUTATED 27 11 33 13 12
DEL PEAK 28(13Q12.11) WILD-TYPE 13 22 12 18 20

Figure S338.  Get High-res Image Gene #49: 'del_13q12.11' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_13q12.11' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 7.9e-05

Table S339.  Gene #49: 'del_13q12.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
DEL PEAK 28(13Q12.11) MUTATED 73 133 85
DEL PEAK 28(13Q12.11) WILD-TYPE 93 62 66

Figure S339.  Get High-res Image Gene #49: 'del_13q12.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_13q12.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S340.  Gene #49: 'del_13q12.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 28(13Q12.11) MUTATED 38 80 67 15 39 22 30
DEL PEAK 28(13Q12.11) WILD-TYPE 40 30 30 33 14 27 47

Figure S340.  Get High-res Image Gene #49: 'del_13q12.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_13q12.11' versus 'MIRSEQ_CNMF'

P value = 0.00338 (Fisher's exact test), Q value = 0.0079

Table S341.  Gene #49: 'del_13q12.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
DEL PEAK 28(13Q12.11) MUTATED 90 143 59
DEL PEAK 28(13Q12.11) WILD-TYPE 99 85 34

Figure S341.  Get High-res Image Gene #49: 'del_13q12.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_13q12.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0038 (Fisher's exact test), Q value = 0.0088

Table S342.  Gene #49: 'del_13q12.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
DEL PEAK 28(13Q12.11) MUTATED 37 124 65 66
DEL PEAK 28(13Q12.11) WILD-TYPE 34 74 76 34

Figure S342.  Get High-res Image Gene #49: 'del_13q12.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_13q12.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00081 (Fisher's exact test), Q value = 0.0022

Table S343.  Gene #49: 'del_13q12.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
DEL PEAK 28(13Q12.11) MUTATED 44 160 48
DEL PEAK 28(13Q12.11) WILD-TYPE 59 88 35

Figure S343.  Get High-res Image Gene #49: 'del_13q12.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_13q12.13' versus 'MRNA_CNMF'

P value = 0.00891 (Fisher's exact test), Q value = 0.019

Table S344.  Gene #50: 'del_13q12.13' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 5 9 12 6
DEL PEAK 29(13Q12.13) MUTATED 4 5 1 4
DEL PEAK 29(13Q12.13) WILD-TYPE 1 4 11 2

Figure S344.  Get High-res Image Gene #50: 'del_13q12.13' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_13q12.13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S345.  Gene #50: 'del_13q12.13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
DEL PEAK 29(13Q12.13) MUTATED 51 85 46 111
DEL PEAK 29(13Q12.13) WILD-TYPE 18 143 33 29

Figure S345.  Get High-res Image Gene #50: 'del_13q12.13' versus Molecular Subtype #3: 'CN_CNMF'

'del_13q12.13' versus 'METHLYATION_CNMF'

P value = 0.00158 (Fisher's exact test), Q value = 0.004

Table S346.  Gene #50: 'del_13q12.13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
DEL PEAK 29(13Q12.13) MUTATED 65 93 103
DEL PEAK 29(13Q12.13) WILD-TYPE 79 56 59

Figure S346.  Get High-res Image Gene #50: 'del_13q12.13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_13q12.13' versus 'RPPA_CNMF'

P value = 0.0087 (Fisher's exact test), Q value = 0.018

Table S347.  Gene #50: 'del_13q12.13' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 73 64
DEL PEAK 29(13Q12.13) MUTATED 18 49 30
DEL PEAK 29(13Q12.13) WILD-TYPE 26 24 34

Figure S347.  Get High-res Image Gene #50: 'del_13q12.13' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_13q12.13' versus 'RPPA_CHIERARCHICAL'

P value = 6e-04 (Fisher's exact test), Q value = 0.0017

Table S348.  Gene #50: 'del_13q12.13' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 40 33 45 31 32
DEL PEAK 29(13Q12.13) MUTATED 27 12 33 13 12
DEL PEAK 29(13Q12.13) WILD-TYPE 13 21 12 18 20

Figure S348.  Get High-res Image Gene #50: 'del_13q12.13' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_13q12.13' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00018

Table S349.  Gene #50: 'del_13q12.13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
DEL PEAK 29(13Q12.13) MUTATED 74 131 85
DEL PEAK 29(13Q12.13) WILD-TYPE 92 64 66

Figure S349.  Get High-res Image Gene #50: 'del_13q12.13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_13q12.13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S350.  Gene #50: 'del_13q12.13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 29(13Q12.13) MUTATED 40 79 63 15 41 23 29
DEL PEAK 29(13Q12.13) WILD-TYPE 38 31 34 33 12 26 48

Figure S350.  Get High-res Image Gene #50: 'del_13q12.13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_13q12.13' versus 'MIRSEQ_CNMF'

P value = 0.00419 (Fisher's exact test), Q value = 0.0096

Table S351.  Gene #50: 'del_13q12.13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
DEL PEAK 29(13Q12.13) MUTATED 90 142 59
DEL PEAK 29(13Q12.13) WILD-TYPE 99 86 34

Figure S351.  Get High-res Image Gene #50: 'del_13q12.13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_13q12.13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00585 (Fisher's exact test), Q value = 0.013

Table S352.  Gene #50: 'del_13q12.13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
DEL PEAK 29(13Q12.13) MUTATED 36 123 66 66
DEL PEAK 29(13Q12.13) WILD-TYPE 35 75 75 34

Figure S352.  Get High-res Image Gene #50: 'del_13q12.13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_13q12.13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00068 (Fisher's exact test), Q value = 0.0019

Table S353.  Gene #50: 'del_13q12.13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
DEL PEAK 29(13Q12.13) MUTATED 44 161 49
DEL PEAK 29(13Q12.13) WILD-TYPE 59 87 34

Figure S353.  Get High-res Image Gene #50: 'del_13q12.13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_13q14.2' versus 'MRNA_CNMF'

P value = 0.0119 (Fisher's exact test), Q value = 0.024

Table S354.  Gene #51: 'del_13q14.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 5 9 12 6
DEL PEAK 30(13Q14.2) MUTATED 4 4 1 4
DEL PEAK 30(13Q14.2) WILD-TYPE 1 5 11 2

Figure S354.  Get High-res Image Gene #51: 'del_13q14.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_13q14.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.0238 (Fisher's exact test), Q value = 0.045

Table S355.  Gene #51: 'del_13q14.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 11 7
DEL PEAK 30(13Q14.2) MUTATED 2 6 5
DEL PEAK 30(13Q14.2) WILD-TYPE 12 5 2

Figure S355.  Get High-res Image Gene #51: 'del_13q14.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_13q14.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S356.  Gene #51: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
DEL PEAK 30(13Q14.2) MUTATED 51 77 43 111
DEL PEAK 30(13Q14.2) WILD-TYPE 18 151 36 29

Figure S356.  Get High-res Image Gene #51: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_13q14.2' versus 'METHLYATION_CNMF'

P value = 0.00503 (Fisher's exact test), Q value = 0.011

Table S357.  Gene #51: 'del_13q14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
DEL PEAK 30(13Q14.2) MUTATED 62 89 96
DEL PEAK 30(13Q14.2) WILD-TYPE 82 60 66

Figure S357.  Get High-res Image Gene #51: 'del_13q14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_13q14.2' versus 'RPPA_CNMF'

P value = 0.00868 (Fisher's exact test), Q value = 0.018

Table S358.  Gene #51: 'del_13q14.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 73 64
DEL PEAK 30(13Q14.2) MUTATED 15 46 30
DEL PEAK 30(13Q14.2) WILD-TYPE 29 27 34

Figure S358.  Get High-res Image Gene #51: 'del_13q14.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_13q14.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00256 (Fisher's exact test), Q value = 0.0061

Table S359.  Gene #51: 'del_13q14.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 40 33 45 31 32
DEL PEAK 30(13Q14.2) MUTATED 26 11 30 13 11
DEL PEAK 30(13Q14.2) WILD-TYPE 14 22 15 18 21

Figure S359.  Get High-res Image Gene #51: 'del_13q14.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_13q14.2' versus 'MRNASEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 3e-04

Table S360.  Gene #51: 'del_13q14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
DEL PEAK 30(13Q14.2) MUTATED 70 126 83
DEL PEAK 30(13Q14.2) WILD-TYPE 96 69 68

Figure S360.  Get High-res Image Gene #51: 'del_13q14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_13q14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S361.  Gene #51: 'del_13q14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 30(13Q14.2) MUTATED 38 78 61 12 41 21 28
DEL PEAK 30(13Q14.2) WILD-TYPE 40 32 36 36 12 28 49

Figure S361.  Get High-res Image Gene #51: 'del_13q14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_CNMF'

P value = 0.00195 (Fisher's exact test), Q value = 0.0048

Table S362.  Gene #51: 'del_13q14.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
DEL PEAK 30(13Q14.2) MUTATED 84 139 55
DEL PEAK 30(13Q14.2) WILD-TYPE 105 89 38

Figure S362.  Get High-res Image Gene #51: 'del_13q14.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_13q14.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00524 (Fisher's exact test), Q value = 0.012

Table S363.  Gene #51: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
DEL PEAK 30(13Q14.2) MUTATED 33 123 63 59
DEL PEAK 30(13Q14.2) WILD-TYPE 38 75 78 41

Figure S363.  Get High-res Image Gene #51: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0497 (Fisher's exact test), Q value = 0.083

Table S364.  Gene #51: 'del_13q14.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 198 91
DEL PEAK 30(13Q14.2) MUTATED 71 122 47
DEL PEAK 30(13Q14.2) WILD-TYPE 74 76 44

Figure S364.  Get High-res Image Gene #51: 'del_13q14.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_13q14.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00024

Table S365.  Gene #51: 'del_13q14.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
DEL PEAK 30(13Q14.2) MUTATED 39 156 45
DEL PEAK 30(13Q14.2) WILD-TYPE 64 92 38

Figure S365.  Get High-res Image Gene #51: 'del_13q14.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_13q34' versus 'MRNA_CNMF'

P value = 0.0241 (Fisher's exact test), Q value = 0.045

Table S366.  Gene #52: 'del_13q34' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 5 9 12 6
DEL PEAK 31(13Q34) MUTATED 3 5 1 4
DEL PEAK 31(13Q34) WILD-TYPE 2 4 11 2

Figure S366.  Get High-res Image Gene #52: 'del_13q34' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_13q34' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S367.  Gene #52: 'del_13q34' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
DEL PEAK 31(13Q34) MUTATED 49 67 37 90
DEL PEAK 31(13Q34) WILD-TYPE 20 161 42 50

Figure S367.  Get High-res Image Gene #52: 'del_13q34' versus Molecular Subtype #3: 'CN_CNMF'

'del_13q34' versus 'METHLYATION_CNMF'

P value = 0.0394 (Fisher's exact test), Q value = 0.069

Table S368.  Gene #52: 'del_13q34' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
DEL PEAK 31(13Q34) MUTATED 55 74 84
DEL PEAK 31(13Q34) WILD-TYPE 89 75 78

Figure S368.  Get High-res Image Gene #52: 'del_13q34' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_13q34' versus 'RPPA_CNMF'

P value = 0.00123 (Fisher's exact test), Q value = 0.0032

Table S369.  Gene #52: 'del_13q34' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 73 64
DEL PEAK 31(13Q34) MUTATED 10 41 24
DEL PEAK 31(13Q34) WILD-TYPE 34 32 40

Figure S369.  Get High-res Image Gene #52: 'del_13q34' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_13q34' versus 'RPPA_CHIERARCHICAL'

P value = 0.0208 (Fisher's exact test), Q value = 0.04

Table S370.  Gene #52: 'del_13q34' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 40 33 45 31 32
DEL PEAK 31(13Q34) MUTATED 23 10 23 11 8
DEL PEAK 31(13Q34) WILD-TYPE 17 23 22 20 24

Figure S370.  Get High-res Image Gene #52: 'del_13q34' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_13q34' versus 'MRNASEQ_CNMF'

P value = 5e-04 (Fisher's exact test), Q value = 0.0014

Table S371.  Gene #52: 'del_13q34' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
DEL PEAK 31(13Q34) MUTATED 58 108 74
DEL PEAK 31(13Q34) WILD-TYPE 108 87 77

Figure S371.  Get High-res Image Gene #52: 'del_13q34' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_13q34' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S372.  Gene #52: 'del_13q34' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 31(13Q34) MUTATED 31 70 49 14 34 19 23
DEL PEAK 31(13Q34) WILD-TYPE 47 40 48 34 19 30 54

Figure S372.  Get High-res Image Gene #52: 'del_13q34' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_13q34' versus 'MIRSEQ_CNMF'

P value = 0.00773 (Fisher's exact test), Q value = 0.017

Table S373.  Gene #52: 'del_13q34' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
DEL PEAK 31(13Q34) MUTATED 73 113 53
DEL PEAK 31(13Q34) WILD-TYPE 116 115 40

Figure S373.  Get High-res Image Gene #52: 'del_13q34' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_13q34' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0201 (Fisher's exact test), Q value = 0.039

Table S374.  Gene #52: 'del_13q34' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
DEL PEAK 31(13Q34) MUTATED 31 108 53 47
DEL PEAK 31(13Q34) WILD-TYPE 40 90 88 53

Figure S374.  Get High-res Image Gene #52: 'del_13q34' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_13q34' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0217 (Fisher's exact test), Q value = 0.042

Table S375.  Gene #52: 'del_13q34' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
DEL PEAK 31(13Q34) MUTATED 37 129 39
DEL PEAK 31(13Q34) WILD-TYPE 66 119 44

Figure S375.  Get High-res Image Gene #52: 'del_13q34' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_14q32.12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S376.  Gene #53: 'del_14q32.12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
DEL PEAK 32(14Q32.12) MUTATED 15 44 41 44
DEL PEAK 32(14Q32.12) WILD-TYPE 54 184 38 96

Figure S376.  Get High-res Image Gene #53: 'del_14q32.12' versus Molecular Subtype #3: 'CN_CNMF'

'del_14q32.12' versus 'METHLYATION_CNMF'

P value = 0.00337 (Fisher's exact test), Q value = 0.0079

Table S377.  Gene #53: 'del_14q32.12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
DEL PEAK 32(14Q32.12) MUTATED 27 54 44
DEL PEAK 32(14Q32.12) WILD-TYPE 117 95 118

Figure S377.  Get High-res Image Gene #53: 'del_14q32.12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_14q32.12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0117 (Fisher's exact test), Q value = 0.024

Table S378.  Gene #53: 'del_14q32.12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 32(14Q32.12) MUTATED 17 31 27 12 16 25 15
DEL PEAK 32(14Q32.12) WILD-TYPE 61 79 70 36 37 24 62

Figure S378.  Get High-res Image Gene #53: 'del_14q32.12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_14q32.12' versus 'MIRSEQ_CNMF'

P value = 0.00742 (Fisher's exact test), Q value = 0.016

Table S379.  Gene #53: 'del_14q32.12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
DEL PEAK 32(14Q32.12) MUTATED 48 79 17
DEL PEAK 32(14Q32.12) WILD-TYPE 141 149 76

Figure S379.  Get High-res Image Gene #53: 'del_14q32.12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_14q32.12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.046 (Fisher's exact test), Q value = 0.078

Table S380.  Gene #53: 'del_14q32.12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 198 91
DEL PEAK 32(14Q32.12) MUTATED 48 58 17
DEL PEAK 32(14Q32.12) WILD-TYPE 97 140 74

Figure S380.  Get High-res Image Gene #53: 'del_14q32.12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_15q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S381.  Gene #54: 'del_15q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
DEL PEAK 33(15Q11.2) MUTATED 46 77 37 102
DEL PEAK 33(15Q11.2) WILD-TYPE 23 151 42 38

Figure S381.  Get High-res Image Gene #54: 'del_15q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q11.2' versus 'METHLYATION_CNMF'

P value = 0.00107 (Fisher's exact test), Q value = 0.0028

Table S382.  Gene #54: 'del_15q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
DEL PEAK 33(15Q11.2) MUTATED 54 79 94
DEL PEAK 33(15Q11.2) WILD-TYPE 90 70 68

Figure S382.  Get High-res Image Gene #54: 'del_15q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_15q11.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0064 (Fisher's exact test), Q value = 0.014

Table S383.  Gene #54: 'del_15q11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 40 33 45 31 32
DEL PEAK 33(15Q11.2) MUTATED 23 9 29 11 17
DEL PEAK 33(15Q11.2) WILD-TYPE 17 24 16 20 15

Figure S383.  Get High-res Image Gene #54: 'del_15q11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_15q11.2' versus 'MRNASEQ_CNMF'

P value = 0.00087 (Fisher's exact test), Q value = 0.0023

Table S384.  Gene #54: 'del_15q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
DEL PEAK 33(15Q11.2) MUTATED 72 119 67
DEL PEAK 33(15Q11.2) WILD-TYPE 94 76 84

Figure S384.  Get High-res Image Gene #54: 'del_15q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_15q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S385.  Gene #54: 'del_15q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 33(15Q11.2) MUTATED 39 73 62 11 36 9 28
DEL PEAK 33(15Q11.2) WILD-TYPE 39 37 35 37 17 40 49

Figure S385.  Get High-res Image Gene #54: 'del_15q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_15q11.2' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 7.9e-05

Table S386.  Gene #54: 'del_15q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
DEL PEAK 33(15Q11.2) MUTATED 71 133 55
DEL PEAK 33(15Q11.2) WILD-TYPE 118 95 38

Figure S386.  Get High-res Image Gene #54: 'del_15q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_15q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00674 (Fisher's exact test), Q value = 0.015

Table S387.  Gene #54: 'del_15q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
DEL PEAK 33(15Q11.2) MUTATED 28 116 61 54
DEL PEAK 33(15Q11.2) WILD-TYPE 43 82 80 46

Figure S387.  Get High-res Image Gene #54: 'del_15q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_15q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00027

Table S388.  Gene #54: 'del_15q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
DEL PEAK 33(15Q11.2) MUTATED 33 136 51
DEL PEAK 33(15Q11.2) WILD-TYPE 70 112 32

Figure S388.  Get High-res Image Gene #54: 'del_15q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_15q15.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S389.  Gene #55: 'del_15q15.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
DEL PEAK 34(15Q15.1) MUTATED 51 79 36 108
DEL PEAK 34(15Q15.1) WILD-TYPE 18 149 43 32

Figure S389.  Get High-res Image Gene #55: 'del_15q15.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q15.1' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 7.9e-05

Table S390.  Gene #55: 'del_15q15.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
DEL PEAK 34(15Q15.1) MUTATED 52 82 101
DEL PEAK 34(15Q15.1) WILD-TYPE 92 67 61

Figure S390.  Get High-res Image Gene #55: 'del_15q15.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_15q15.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0158 (Fisher's exact test), Q value = 0.032

Table S391.  Gene #55: 'del_15q15.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 40 33 45 31 32
DEL PEAK 34(15Q15.1) MUTATED 23 11 30 11 17
DEL PEAK 34(15Q15.1) WILD-TYPE 17 22 15 20 15

Figure S391.  Get High-res Image Gene #55: 'del_15q15.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_15q15.1' versus 'MRNASEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00036

Table S392.  Gene #55: 'del_15q15.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
DEL PEAK 34(15Q15.1) MUTATED 73 126 71
DEL PEAK 34(15Q15.1) WILD-TYPE 93 69 80

Figure S392.  Get High-res Image Gene #55: 'del_15q15.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_15q15.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S393.  Gene #55: 'del_15q15.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 34(15Q15.1) MUTATED 39 76 64 12 39 11 29
DEL PEAK 34(15Q15.1) WILD-TYPE 39 34 33 36 14 38 48

Figure S393.  Get High-res Image Gene #55: 'del_15q15.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_15q15.1' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00011

Table S394.  Gene #55: 'del_15q15.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
DEL PEAK 34(15Q15.1) MUTATED 73 141 57
DEL PEAK 34(15Q15.1) WILD-TYPE 116 87 36

Figure S394.  Get High-res Image Gene #55: 'del_15q15.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_15q15.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.00091

Table S395.  Gene #55: 'del_15q15.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
DEL PEAK 34(15Q15.1) MUTATED 30 125 59 57
DEL PEAK 34(15Q15.1) WILD-TYPE 41 73 82 43

Figure S395.  Get High-res Image Gene #55: 'del_15q15.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_15q15.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 7.9e-05

Table S396.  Gene #55: 'del_15q15.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
DEL PEAK 34(15Q15.1) MUTATED 33 146 49
DEL PEAK 34(15Q15.1) WILD-TYPE 70 102 34

Figure S396.  Get High-res Image Gene #55: 'del_15q15.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q23.1' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 7.9e-05

Table S397.  Gene #56: 'del_16q23.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
DEL PEAK 35(16Q23.1) MUTATED 30 48 34 58
DEL PEAK 35(16Q23.1) WILD-TYPE 39 180 45 82

Figure S397.  Get High-res Image Gene #56: 'del_16q23.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_16q23.1' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00011

Table S398.  Gene #56: 'del_16q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
DEL PEAK 35(16Q23.1) MUTATED 26 55 66
DEL PEAK 35(16Q23.1) WILD-TYPE 118 94 96

Figure S398.  Get High-res Image Gene #56: 'del_16q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_16q23.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.00168 (Fisher's exact test), Q value = 0.0042

Table S399.  Gene #56: 'del_16q23.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 40 33 45 31 32
DEL PEAK 35(16Q23.1) MUTATED 8 10 26 7 8
DEL PEAK 35(16Q23.1) WILD-TYPE 32 23 19 24 24

Figure S399.  Get High-res Image Gene #56: 'del_16q23.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_16q23.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S400.  Gene #56: 'del_16q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
DEL PEAK 35(16Q23.1) MUTATED 36 92 42
DEL PEAK 35(16Q23.1) WILD-TYPE 130 103 109

Figure S400.  Get High-res Image Gene #56: 'del_16q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_16q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S401.  Gene #56: 'del_16q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 35(16Q23.1) MUTATED 20 60 37 9 17 17 10
DEL PEAK 35(16Q23.1) WILD-TYPE 58 50 60 39 36 32 67

Figure S401.  Get High-res Image Gene #56: 'del_16q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_CNMF'

P value = 0.0217 (Fisher's exact test), Q value = 0.042

Table S402.  Gene #56: 'del_16q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
DEL PEAK 35(16Q23.1) MUTATED 49 87 34
DEL PEAK 35(16Q23.1) WILD-TYPE 140 141 59

Figure S402.  Get High-res Image Gene #56: 'del_16q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_16q23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00331 (Fisher's exact test), Q value = 0.0077

Table S403.  Gene #56: 'del_16q23.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
DEL PEAK 35(16Q23.1) MUTATED 20 77 32 41
DEL PEAK 35(16Q23.1) WILD-TYPE 51 121 109 59

Figure S403.  Get High-res Image Gene #56: 'del_16q23.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00053 (Fisher's exact test), Q value = 0.0015

Table S404.  Gene #56: 'del_16q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
DEL PEAK 35(16Q23.1) MUTATED 18 94 29
DEL PEAK 35(16Q23.1) WILD-TYPE 85 154 54

Figure S404.  Get High-res Image Gene #56: 'del_16q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S405.  Gene #57: 'del_17p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
DEL PEAK 36(17P13.3) MUTATED 39 84 45 113
DEL PEAK 36(17P13.3) WILD-TYPE 30 144 34 27

Figure S405.  Get High-res Image Gene #57: 'del_17p13.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_17p13.3' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 7.9e-05

Table S406.  Gene #57: 'del_17p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
DEL PEAK 36(17P13.3) MUTATED 54 82 108
DEL PEAK 36(17P13.3) WILD-TYPE 90 67 54

Figure S406.  Get High-res Image Gene #57: 'del_17p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_17p13.3' versus 'RPPA_CNMF'

P value = 0.00072 (Fisher's exact test), Q value = 0.002

Table S407.  Gene #57: 'del_17p13.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 73 64
DEL PEAK 36(17P13.3) MUTATED 19 55 33
DEL PEAK 36(17P13.3) WILD-TYPE 25 18 31

Figure S407.  Get High-res Image Gene #57: 'del_17p13.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_17p13.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00118 (Fisher's exact test), Q value = 0.0031

Table S408.  Gene #57: 'del_17p13.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 40 33 45 31 32
DEL PEAK 36(17P13.3) MUTATED 29 10 33 17 18
DEL PEAK 36(17P13.3) WILD-TYPE 11 23 12 14 14

Figure S408.  Get High-res Image Gene #57: 'del_17p13.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_17p13.3' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00011

Table S409.  Gene #57: 'del_17p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
DEL PEAK 36(17P13.3) MUTATED 78 132 69
DEL PEAK 36(17P13.3) WILD-TYPE 88 63 82

Figure S409.  Get High-res Image Gene #57: 'del_17p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_17p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S410.  Gene #57: 'del_17p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 36(17P13.3) MUTATED 39 75 62 10 33 24 36
DEL PEAK 36(17P13.3) WILD-TYPE 39 35 35 38 20 25 41

Figure S410.  Get High-res Image Gene #57: 'del_17p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_17p13.3' versus 'MIRSEQ_CNMF'

P value = 0.013 (Fisher's exact test), Q value = 0.026

Table S411.  Gene #57: 'del_17p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
DEL PEAK 36(17P13.3) MUTATED 90 140 47
DEL PEAK 36(17P13.3) WILD-TYPE 99 88 46

Figure S411.  Get High-res Image Gene #57: 'del_17p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_17p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0249 (Fisher's exact test), Q value = 0.046

Table S412.  Gene #57: 'del_17p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
DEL PEAK 36(17P13.3) MUTATED 30 118 69 60
DEL PEAK 36(17P13.3) WILD-TYPE 41 80 72 40

Figure S412.  Get High-res Image Gene #57: 'del_17p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_17p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00208 (Fisher's exact test), Q value = 0.0051

Table S413.  Gene #57: 'del_17p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
DEL PEAK 36(17P13.3) MUTATED 40 147 47
DEL PEAK 36(17P13.3) WILD-TYPE 63 101 36

Figure S413.  Get High-res Image Gene #57: 'del_17p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18q21.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S414.  Gene #58: 'del_18q21.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
DEL PEAK 37(18Q21.32) MUTATED 21 88 44 98
DEL PEAK 37(18Q21.32) WILD-TYPE 48 140 35 42

Figure S414.  Get High-res Image Gene #58: 'del_18q21.32' versus Molecular Subtype #3: 'CN_CNMF'

'del_18q21.32' versus 'RPPA_CNMF'

P value = 0.0472 (Fisher's exact test), Q value = 0.08

Table S415.  Gene #58: 'del_18q21.32' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 73 64
DEL PEAK 37(18Q21.32) MUTATED 17 45 31
DEL PEAK 37(18Q21.32) WILD-TYPE 27 28 33

Figure S415.  Get High-res Image Gene #58: 'del_18q21.32' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_18q21.32' versus 'RPPA_CHIERARCHICAL'

P value = 0.00057 (Fisher's exact test), Q value = 0.0016

Table S416.  Gene #58: 'del_18q21.32' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 40 33 45 31 32
DEL PEAK 37(18Q21.32) MUTATED 18 10 35 16 14
DEL PEAK 37(18Q21.32) WILD-TYPE 22 23 10 15 18

Figure S416.  Get High-res Image Gene #58: 'del_18q21.32' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_18q21.32' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S417.  Gene #58: 'del_18q21.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
DEL PEAK 37(18Q21.32) MUTATED 69 121 59
DEL PEAK 37(18Q21.32) WILD-TYPE 97 74 92

Figure S417.  Get High-res Image Gene #58: 'del_18q21.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_18q21.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S418.  Gene #58: 'del_18q21.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 37(18Q21.32) MUTATED 39 63 57 10 17 29 34
DEL PEAK 37(18Q21.32) WILD-TYPE 39 47 40 38 36 20 43

Figure S418.  Get High-res Image Gene #58: 'del_18q21.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_18q21.32' versus 'MIRSEQ_CNMF'

P value = 0.0202 (Fisher's exact test), Q value = 0.039

Table S419.  Gene #58: 'del_18q21.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
DEL PEAK 37(18Q21.32) MUTATED 78 116 54
DEL PEAK 37(18Q21.32) WILD-TYPE 111 112 39

Figure S419.  Get High-res Image Gene #58: 'del_18q21.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_19p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S420.  Gene #59: 'del_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
DEL PEAK 38(19P13.3) MUTATED 48 85 67 83
DEL PEAK 38(19P13.3) WILD-TYPE 21 143 12 57

Figure S420.  Get High-res Image Gene #59: 'del_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_19p13.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S421.  Gene #59: 'del_19p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
DEL PEAK 38(19P13.3) MUTATED 54 118 76
DEL PEAK 38(19P13.3) WILD-TYPE 90 31 86

Figure S421.  Get High-res Image Gene #59: 'del_19p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_19p13.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S422.  Gene #59: 'del_19p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
DEL PEAK 38(19P13.3) MUTATED 56 113 111
DEL PEAK 38(19P13.3) WILD-TYPE 110 82 40

Figure S422.  Get High-res Image Gene #59: 'del_19p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_19p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S423.  Gene #59: 'del_19p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 38(19P13.3) MUTATED 26 53 64 39 34 42 22
DEL PEAK 38(19P13.3) WILD-TYPE 52 57 33 9 19 7 55

Figure S423.  Get High-res Image Gene #59: 'del_19p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S424.  Gene #59: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
DEL PEAK 38(19P13.3) MUTATED 81 153 43
DEL PEAK 38(19P13.3) WILD-TYPE 108 75 50

Figure S424.  Get High-res Image Gene #59: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_19p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S425.  Gene #59: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
DEL PEAK 38(19P13.3) MUTATED 36 116 52 73
DEL PEAK 38(19P13.3) WILD-TYPE 35 82 89 27

Figure S425.  Get High-res Image Gene #59: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00078 (Fisher's exact test), Q value = 0.0021

Table S426.  Gene #59: 'del_19p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
DEL PEAK 38(19P13.3) MUTATED 47 153 34
DEL PEAK 38(19P13.3) WILD-TYPE 56 95 49

Figure S426.  Get High-res Image Gene #59: 'del_19p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19p13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S427.  Gene #60: 'del_19p13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
DEL PEAK 39(19P13.2) MUTATED 49 82 66 83
DEL PEAK 39(19P13.2) WILD-TYPE 20 146 13 57

Figure S427.  Get High-res Image Gene #60: 'del_19p13.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_19p13.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S428.  Gene #60: 'del_19p13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
DEL PEAK 39(19P13.2) MUTATED 50 118 78
DEL PEAK 39(19P13.2) WILD-TYPE 94 31 84

Figure S428.  Get High-res Image Gene #60: 'del_19p13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_19p13.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S429.  Gene #60: 'del_19p13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
DEL PEAK 39(19P13.2) MUTATED 54 110 113
DEL PEAK 39(19P13.2) WILD-TYPE 112 85 38

Figure S429.  Get High-res Image Gene #60: 'del_19p13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_19p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S430.  Gene #60: 'del_19p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 39(19P13.2) MUTATED 25 55 61 39 37 38 22
DEL PEAK 39(19P13.2) WILD-TYPE 53 55 36 9 16 11 55

Figure S430.  Get High-res Image Gene #60: 'del_19p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S431.  Gene #60: 'del_19p13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
DEL PEAK 39(19P13.2) MUTATED 79 151 44
DEL PEAK 39(19P13.2) WILD-TYPE 110 77 49

Figure S431.  Get High-res Image Gene #60: 'del_19p13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_19p13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S432.  Gene #60: 'del_19p13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
DEL PEAK 39(19P13.2) MUTATED 37 114 50 73
DEL PEAK 39(19P13.2) WILD-TYPE 34 84 91 27

Figure S432.  Get High-res Image Gene #60: 'del_19p13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_19p13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00078 (Fisher's exact test), Q value = 0.0021

Table S433.  Gene #60: 'del_19p13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
DEL PEAK 39(19P13.2) MUTATED 46 153 35
DEL PEAK 39(19P13.2) WILD-TYPE 57 95 48

Figure S433.  Get High-res Image Gene #60: 'del_19p13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19p13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S434.  Gene #61: 'del_19p13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
DEL PEAK 40(19P13.2) MUTATED 50 76 64 80
DEL PEAK 40(19P13.2) WILD-TYPE 19 152 15 60

Figure S434.  Get High-res Image Gene #61: 'del_19p13.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_19p13.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S435.  Gene #61: 'del_19p13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
DEL PEAK 40(19P13.2) MUTATED 45 115 77
DEL PEAK 40(19P13.2) WILD-TYPE 99 34 85

Figure S435.  Get High-res Image Gene #61: 'del_19p13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_19p13.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S436.  Gene #61: 'del_19p13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
DEL PEAK 40(19P13.2) MUTATED 51 103 113
DEL PEAK 40(19P13.2) WILD-TYPE 115 92 38

Figure S436.  Get High-res Image Gene #61: 'del_19p13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_19p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S437.  Gene #61: 'del_19p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 40(19P13.2) MUTATED 22 52 55 38 40 38 22
DEL PEAK 40(19P13.2) WILD-TYPE 56 58 42 10 13 11 55

Figure S437.  Get High-res Image Gene #61: 'del_19p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S438.  Gene #61: 'del_19p13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
DEL PEAK 40(19P13.2) MUTATED 76 148 40
DEL PEAK 40(19P13.2) WILD-TYPE 113 80 53

Figure S438.  Get High-res Image Gene #61: 'del_19p13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_19p13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S439.  Gene #61: 'del_19p13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
DEL PEAK 40(19P13.2) MUTATED 36 108 48 72
DEL PEAK 40(19P13.2) WILD-TYPE 35 90 93 28

Figure S439.  Get High-res Image Gene #61: 'del_19p13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_19p13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 3e-04

Table S440.  Gene #61: 'del_19p13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
DEL PEAK 40(19P13.2) MUTATED 43 152 33
DEL PEAK 40(19P13.2) WILD-TYPE 60 96 50

Figure S440.  Get High-res Image Gene #61: 'del_19p13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19q11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S441.  Gene #62: 'del_19q11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
DEL PEAK 41(19Q11) MUTATED 24 37 19 54
DEL PEAK 41(19Q11) WILD-TYPE 45 191 60 86

Figure S441.  Get High-res Image Gene #62: 'del_19q11' versus Molecular Subtype #3: 'CN_CNMF'

'del_19q11' versus 'METHLYATION_CNMF'

P value = 0.00072 (Fisher's exact test), Q value = 0.002

Table S442.  Gene #62: 'del_19q11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
DEL PEAK 41(19Q11) MUTATED 21 44 51
DEL PEAK 41(19Q11) WILD-TYPE 123 105 111

Figure S442.  Get High-res Image Gene #62: 'del_19q11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_19q11' versus 'MRNASEQ_CNMF'

P value = 0.00257 (Fisher's exact test), Q value = 0.0061

Table S443.  Gene #62: 'del_19q11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
DEL PEAK 41(19Q11) MUTATED 29 65 39
DEL PEAK 41(19Q11) WILD-TYPE 137 130 112

Figure S443.  Get High-res Image Gene #62: 'del_19q11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_19q11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00221 (Fisher's exact test), Q value = 0.0054

Table S444.  Gene #62: 'del_19q11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 41(19Q11) MUTATED 15 39 31 11 15 14 8
DEL PEAK 41(19Q11) WILD-TYPE 63 71 66 37 38 35 69

Figure S444.  Get High-res Image Gene #62: 'del_19q11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_19q11' versus 'MIRSEQ_CNMF'

P value = 0.00148 (Fisher's exact test), Q value = 0.0038

Table S445.  Gene #62: 'del_19q11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
DEL PEAK 41(19Q11) MUTATED 31 67 30
DEL PEAK 41(19Q11) WILD-TYPE 158 161 63

Figure S445.  Get High-res Image Gene #62: 'del_19q11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_19q11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 0.00082

Table S446.  Gene #62: 'del_19q11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
DEL PEAK 41(19Q11) MUTATED 13 61 20 34
DEL PEAK 41(19Q11) WILD-TYPE 58 137 121 66

Figure S446.  Get High-res Image Gene #62: 'del_19q11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_19q11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0443 (Fisher's exact test), Q value = 0.076

Table S447.  Gene #62: 'del_19q11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
DEL PEAK 41(19Q11) MUTATED 18 74 19
DEL PEAK 41(19Q11) WILD-TYPE 85 174 64

Figure S447.  Get High-res Image Gene #62: 'del_19q11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19q13.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S448.  Gene #63: 'del_19q13.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
DEL PEAK 42(19Q13.33) MUTATED 30 52 38 74
DEL PEAK 42(19Q13.33) WILD-TYPE 39 176 41 66

Figure S448.  Get High-res Image Gene #63: 'del_19q13.33' versus Molecular Subtype #3: 'CN_CNMF'

'del_19q13.33' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S449.  Gene #63: 'del_19q13.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
DEL PEAK 42(19Q13.33) MUTATED 25 72 66
DEL PEAK 42(19Q13.33) WILD-TYPE 119 77 96

Figure S449.  Get High-res Image Gene #63: 'del_19q13.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_19q13.33' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00011

Table S450.  Gene #63: 'del_19q13.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
DEL PEAK 42(19Q13.33) MUTATED 38 85 68
DEL PEAK 42(19Q13.33) WILD-TYPE 128 110 83

Figure S450.  Get High-res Image Gene #63: 'del_19q13.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_19q13.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 7.9e-05

Table S451.  Gene #63: 'del_19q13.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 42(19Q13.33) MUTATED 19 46 45 23 24 23 11
DEL PEAK 42(19Q13.33) WILD-TYPE 59 64 52 25 29 26 66

Figure S451.  Get High-res Image Gene #63: 'del_19q13.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_19q13.33' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 7.9e-05

Table S452.  Gene #63: 'del_19q13.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
DEL PEAK 42(19Q13.33) MUTATED 47 107 35
DEL PEAK 42(19Q13.33) WILD-TYPE 142 121 58

Figure S452.  Get High-res Image Gene #63: 'del_19q13.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_19q13.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S453.  Gene #63: 'del_19q13.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
DEL PEAK 42(19Q13.33) MUTATED 22 87 28 52
DEL PEAK 42(19Q13.33) WILD-TYPE 49 111 113 48

Figure S453.  Get High-res Image Gene #63: 'del_19q13.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_19q13.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0114 (Fisher's exact test), Q value = 0.024

Table S454.  Gene #63: 'del_19q13.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
DEL PEAK 42(19Q13.33) MUTATED 27 103 25
DEL PEAK 42(19Q13.33) WILD-TYPE 76 145 58

Figure S454.  Get High-res Image Gene #63: 'del_19q13.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_20p13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S455.  Gene #64: 'del_20p13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
DEL PEAK 43(20P13) MUTATED 10 40 24 57
DEL PEAK 43(20P13) WILD-TYPE 59 188 55 83

Figure S455.  Get High-res Image Gene #64: 'del_20p13' versus Molecular Subtype #3: 'CN_CNMF'

'del_20p13' versus 'METHLYATION_CNMF'

P value = 0.00058 (Fisher's exact test), Q value = 0.0016

Table S456.  Gene #64: 'del_20p13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
DEL PEAK 43(20P13) MUTATED 32 26 58
DEL PEAK 43(20P13) WILD-TYPE 112 123 104

Figure S456.  Get High-res Image Gene #64: 'del_20p13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_20p13' versus 'RPPA_CNMF'

P value = 0.00344 (Fisher's exact test), Q value = 0.008

Table S457.  Gene #64: 'del_20p13' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 73 64
DEL PEAK 43(20P13) MUTATED 6 30 15
DEL PEAK 43(20P13) WILD-TYPE 38 43 49

Figure S457.  Get High-res Image Gene #64: 'del_20p13' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_20p13' versus 'RPPA_CHIERARCHICAL'

P value = 0.00041 (Fisher's exact test), Q value = 0.0012

Table S458.  Gene #64: 'del_20p13' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 40 33 45 31 32
DEL PEAK 43(20P13) MUTATED 15 2 21 7 6
DEL PEAK 43(20P13) WILD-TYPE 25 31 24 24 26

Figure S458.  Get High-res Image Gene #64: 'del_20p13' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_20p13' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S459.  Gene #64: 'del_20p13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
DEL PEAK 43(20P13) MUTATED 39 72 19
DEL PEAK 43(20P13) WILD-TYPE 127 123 132

Figure S459.  Get High-res Image Gene #64: 'del_20p13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_20p13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S460.  Gene #64: 'del_20p13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 43(20P13) MUTATED 23 44 20 0 10 16 17
DEL PEAK 43(20P13) WILD-TYPE 55 66 77 48 43 33 60

Figure S460.  Get High-res Image Gene #64: 'del_20p13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_20p13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0146 (Fisher's exact test), Q value = 0.029

Table S461.  Gene #64: 'del_20p13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
DEL PEAK 43(20P13) MUTATED 15 65 26
DEL PEAK 43(20P13) WILD-TYPE 88 183 57

Figure S461.  Get High-res Image Gene #64: 'del_20p13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_20q13.12' versus 'MRNA_CNMF'

P value = 0.0293 (Fisher's exact test), Q value = 0.053

Table S462.  Gene #65: 'del_20q13.12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 5 9 12 6
DEL PEAK 44(20Q13.12) MUTATED 3 0 3 0
DEL PEAK 44(20Q13.12) WILD-TYPE 2 9 9 6

Figure S462.  Get High-res Image Gene #65: 'del_20q13.12' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_20q13.12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00426 (Fisher's exact test), Q value = 0.0097

Table S463.  Gene #65: 'del_20q13.12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 44(20Q13.12) MUTATED 18 15 6 12 9 12 8
DEL PEAK 44(20Q13.12) WILD-TYPE 60 95 91 36 44 37 69

Figure S463.  Get High-res Image Gene #65: 'del_20q13.12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_20q13.12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0452 (Fisher's exact test), Q value = 0.077

Table S464.  Gene #65: 'del_20q13.12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 198 91
DEL PEAK 44(20Q13.12) MUTATED 28 30 7
DEL PEAK 44(20Q13.12) WILD-TYPE 117 168 84

Figure S464.  Get High-res Image Gene #65: 'del_20q13.12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_21q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S465.  Gene #66: 'del_21q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
DEL PEAK 45(21Q11.2) MUTATED 38 60 45 42
DEL PEAK 45(21Q11.2) WILD-TYPE 31 168 34 98

Figure S465.  Get High-res Image Gene #66: 'del_21q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_21q11.2' versus 'METHLYATION_CNMF'

P value = 0.0272 (Fisher's exact test), Q value = 0.05

Table S466.  Gene #66: 'del_21q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
DEL PEAK 45(21Q11.2) MUTATED 38 61 59
DEL PEAK 45(21Q11.2) WILD-TYPE 106 88 103

Figure S466.  Get High-res Image Gene #66: 'del_21q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_21q11.2' versus 'RPPA_CNMF'

P value = 0.00708 (Fisher's exact test), Q value = 0.015

Table S467.  Gene #66: 'del_21q11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 73 64
DEL PEAK 45(21Q11.2) MUTATED 8 31 29
DEL PEAK 45(21Q11.2) WILD-TYPE 36 42 35

Figure S467.  Get High-res Image Gene #66: 'del_21q11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_21q11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S468.  Gene #66: 'del_21q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
DEL PEAK 45(21Q11.2) MUTATED 28 77 77
DEL PEAK 45(21Q11.2) WILD-TYPE 138 118 74

Figure S468.  Get High-res Image Gene #66: 'del_21q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_21q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S469.  Gene #66: 'del_21q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 45(21Q11.2) MUTATED 11 39 41 12 35 22 22
DEL PEAK 45(21Q11.2) WILD-TYPE 67 71 56 36 18 27 55

Figure S469.  Get High-res Image Gene #66: 'del_21q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_21q11.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S470.  Gene #66: 'del_21q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
DEL PEAK 45(21Q11.2) MUTATED 46 109 26
DEL PEAK 45(21Q11.2) WILD-TYPE 143 119 67

Figure S470.  Get High-res Image Gene #66: 'del_21q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_21q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.00056

Table S471.  Gene #66: 'del_21q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
DEL PEAK 45(21Q11.2) MUTATED 17 76 37 51
DEL PEAK 45(21Q11.2) WILD-TYPE 54 122 104 49

Figure S471.  Get High-res Image Gene #66: 'del_21q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_21q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 0.00082

Table S472.  Gene #66: 'del_21q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
DEL PEAK 45(21Q11.2) MUTATED 22 106 23
DEL PEAK 45(21Q11.2) WILD-TYPE 81 142 60

Figure S472.  Get High-res Image Gene #66: 'del_21q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_22q13.32' versus 'MRNA_CNMF'

P value = 0.025 (Fisher's exact test), Q value = 0.047

Table S473.  Gene #67: 'del_22q13.32' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 5 9 12 6
DEL PEAK 46(22Q13.32) MUTATED 3 7 2 4
DEL PEAK 46(22Q13.32) WILD-TYPE 2 2 10 2

Figure S473.  Get High-res Image Gene #67: 'del_22q13.32' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_22q13.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S474.  Gene #67: 'del_22q13.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
DEL PEAK 46(22Q13.32) MUTATED 52 72 45 86
DEL PEAK 46(22Q13.32) WILD-TYPE 17 156 34 54

Figure S474.  Get High-res Image Gene #67: 'del_22q13.32' versus Molecular Subtype #3: 'CN_CNMF'

'del_22q13.32' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S475.  Gene #67: 'del_22q13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
DEL PEAK 46(22Q13.32) MUTATED 41 94 90
DEL PEAK 46(22Q13.32) WILD-TYPE 103 55 72

Figure S475.  Get High-res Image Gene #67: 'del_22q13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_22q13.32' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S476.  Gene #67: 'del_22q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
DEL PEAK 46(22Q13.32) MUTATED 53 113 86
DEL PEAK 46(22Q13.32) WILD-TYPE 113 82 65

Figure S476.  Get High-res Image Gene #67: 'del_22q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_22q13.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S477.  Gene #67: 'del_22q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 46(22Q13.32) MUTATED 26 67 54 15 42 28 20
DEL PEAK 46(22Q13.32) WILD-TYPE 52 43 43 33 11 21 57

Figure S477.  Get High-res Image Gene #67: 'del_22q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.32' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 7.9e-05

Table S478.  Gene #67: 'del_22q13.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
DEL PEAK 46(22Q13.32) MUTATED 67 139 45
DEL PEAK 46(22Q13.32) WILD-TYPE 122 89 48

Figure S478.  Get High-res Image Gene #67: 'del_22q13.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_22q13.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 7.9e-05

Table S479.  Gene #67: 'del_22q13.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
DEL PEAK 46(22Q13.32) MUTATED 24 116 49 62
DEL PEAK 46(22Q13.32) WILD-TYPE 47 82 92 38

Figure S479.  Get High-res Image Gene #67: 'del_22q13.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_22q13.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0152 (Fisher's exact test), Q value = 0.031

Table S480.  Gene #67: 'del_22q13.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 198 91
DEL PEAK 46(22Q13.32) MUTATED 70 110 34
DEL PEAK 46(22Q13.32) WILD-TYPE 75 88 57

Figure S480.  Get High-res Image Gene #67: 'del_22q13.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_22q13.32' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00015

Table S481.  Gene #67: 'del_22q13.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
DEL PEAK 46(22Q13.32) MUTATED 34 145 35
DEL PEAK 46(22Q13.32) WILD-TYPE 69 103 48

Figure S481.  Get High-res Image Gene #67: 'del_22q13.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xp22.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S482.  Gene #68: 'del_xp22.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 228 79 140
DEL PEAK 47(XP22.2) MUTATED 18 37 21 67
DEL PEAK 47(XP22.2) WILD-TYPE 51 191 58 73

Figure S482.  Get High-res Image Gene #68: 'del_xp22.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_xp22.2' versus 'METHLYATION_CNMF'

P value = 0.0163 (Fisher's exact test), Q value = 0.032

Table S483.  Gene #68: 'del_xp22.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 149 162
DEL PEAK 47(XP22.2) MUTATED 28 41 55
DEL PEAK 47(XP22.2) WILD-TYPE 116 108 107

Figure S483.  Get High-res Image Gene #68: 'del_xp22.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_xp22.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.01 (Fisher's exact test), Q value = 0.021

Table S484.  Gene #68: 'del_xp22.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 40 33 45 31 32
DEL PEAK 47(XP22.2) MUTATED 7 3 19 6 9
DEL PEAK 47(XP22.2) WILD-TYPE 33 30 26 25 23

Figure S484.  Get High-res Image Gene #68: 'del_xp22.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_xp22.2' versus 'MRNASEQ_CNMF'

P value = 0.0112 (Fisher's exact test), Q value = 0.023

Table S485.  Gene #68: 'del_xp22.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 195 151
DEL PEAK 47(XP22.2) MUTATED 39 69 34
DEL PEAK 47(XP22.2) WILD-TYPE 127 126 117

Figure S485.  Get High-res Image Gene #68: 'del_xp22.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_xp22.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00018

Table S486.  Gene #68: 'del_xp22.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 47(XP22.2) MUTATED 23 48 33 9 8 8 13
DEL PEAK 47(XP22.2) WILD-TYPE 55 62 64 39 45 41 64

Figure S486.  Get High-res Image Gene #68: 'del_xp22.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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/LUAD-TP/15092520/transformed.cor.cli.txt

  • Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LUAD-TP/15111023/LUAD-TP.transferedmergedcluster.txt

  • Number of patients = 516

  • Number of significantly focal cnvs = 68

  • Number of molecular subtypes = 12

  • Exclude genes that fewer than K tumors have alterations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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