Correlation between copy number variation genes (focal events) and molecular subtypes
Colorectal Adenocarcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C1D21WTC
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/C1D21WTC
Overview
Introduction

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

Summary

Testing the association between copy number variation 73 focal events and 12 molecular subtypes across 615 patients, 383 significant findings detected with P value < 0.05 and Q value < 0.25.

  • amp_1q31.1 cnv correlated to 'CN_CNMF'.

  • amp_2q33.1 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_5p12 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • amp_5q22.3 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • amp_6p21.1 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_7p21.3 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

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

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

  • amp_8q12.1 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

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

  • amp_11p15.5 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_12p13.32 cnv correlated to 'CN_CNMF'.

  • amp_13q12.13 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • amp_13q12.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_13q22.1 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • amp_16p11.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

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

  • amp_17q24.1 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_19p13.2 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • amp_19q12 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • amp_20p12.1 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'RPPA_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • amp_20p11.21 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_20q11.21 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_20q12 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_20q13.31 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_1p36.11 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • del_1p33 cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_1p13.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_2p12 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • del_3p14.2 cnv correlated to 'RPPA_CNMF'.

  • del_4p16.2 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_4q22.1 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • del_4q35.1 cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_5q12.1 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_5q21.2 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_5q22.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

  • del_8p22 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • del_8q11.1 cnv correlated to 'CN_CNMF'.

  • del_9p24.2 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

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

  • del_10q21.1 cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

  • del_10q25.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_11q22.3 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • del_12p13.1 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_12q21.33 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_14q11.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_14q31.1 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

  • del_15q15.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_15q21.1 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_15q22.33 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_16q23.1 cnv correlated to 'MRNA_CNMF' and 'MRNA_CHIERARCHICAL'.

  • del_17p12 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • del_17q24.3 cnv correlated to 'CN_CNMF'.

  • del_18p11.31 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_18q12.2 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_18q21.2 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_18q22.1 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • del_20p12.1 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_21q11.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • del_22q13.32 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 73 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, 383 significant findings detected.

Clinical
Features 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
amp 20q11 21 469 (76%) 146 1e-05
(6.17e-05) 		1e-05
(6.17e-05) 		1e-05
(6.17e-05) 		1e-05
(6.17e-05) 		0.0323
(0.0805) 		0.642
(0.752) 		1e-05
(6.17e-05) 		1e-05
(6.17e-05) 		0.0164
(0.0457) 		0.00039
(0.00163) 		0.00331
(0.0111) 		0.0164
(0.0457)
amp 20q12 471 (77%) 144 1e-05
(6.17e-05) 		1e-05
(6.17e-05) 		1e-05
(6.17e-05) 		1e-05
(6.17e-05) 		0.0499
(0.114) 		0.621
(0.739) 		1e-05
(6.17e-05) 		1e-05
(6.17e-05) 		0.00724
(0.0225) 		0.00015
(0.000695) 		0.00163
(0.0059) 		0.0281
(0.0723)
amp 20q13 31 473 (77%) 142 1e-05
(6.17e-05) 		1e-05
(6.17e-05) 		1e-05
(6.17e-05) 		1e-05
(6.17e-05) 		0.0961
(0.197) 		0.48
(0.631) 		1e-05
(6.17e-05) 		1e-05
(6.17e-05) 		0.0151
(0.0426) 		0.00023
(0.00103) 		0.00402
(0.0131) 		0.0353
(0.086)
del 18p11 31 370 (60%) 245 1e-05
(6.17e-05) 		1e-05
(6.17e-05) 		1e-05
(6.17e-05) 		1e-05
(6.17e-05) 		0.533
(0.677) 		0.752
(0.832) 		1e-05
(6.17e-05) 		1e-05
(6.17e-05) 		0.00315
(0.0106) 		0.00712
(0.0222) 		2e-05
(0.000115) 		0.00053
(0.0021)
del 18q12 2 416 (68%) 199 1e-05
(6.17e-05) 		1e-05
(6.17e-05) 		1e-05
(6.17e-05) 		1e-05
(6.17e-05) 		0.319
(0.483) 		0.215
(0.361) 		1e-05
(6.17e-05) 		1e-05
(6.17e-05) 		0.00056
(0.0022) 		0.00755
(0.0234) 		4e-05
(0.00021) 		3e-05
(0.000167)
del 18q21 2 432 (70%) 183 1e-05
(6.17e-05) 		1e-05
(6.17e-05) 		1e-05
(6.17e-05) 		1e-05
(6.17e-05) 		0.455
(0.614) 		0.284
(0.441) 		1e-05
(6.17e-05) 		1e-05
(6.17e-05) 		2e-05
(0.000115) 		0.0314
(0.0791) 		1e-05
(6.17e-05) 		0.0001
(0.000481)
amp 7p21 3 363 (59%) 252 0.00107
(0.00402) 		1e-05
(6.17e-05) 		1e-05
(6.17e-05) 		1e-05
(6.17e-05) 		0.223
(0.367) 		0.0344
(0.0841) 		1e-05
(6.17e-05) 		1e-05
(6.17e-05) 		0.00866
(0.0262) 		0.169
(0.301) 		0.0248
(0.0652) 		0.0993
(0.2)
amp 13q12 2 396 (64%) 219 1e-05
(6.17e-05) 		1e-05
(6.17e-05) 		1e-05
(6.17e-05) 		1e-05
(6.17e-05) 		0.472
(0.626) 		0.144
(0.266) 		1e-05
(6.17e-05) 		1e-05
(6.17e-05) 		0.00058
(0.00227) 		0.708
(0.799) 		0.00357
(0.0119) 		0.0447
(0.104)
amp 17q12 160 (26%) 455 0.025
(0.0655) 		0.00806
(0.0246) 		1e-05
(6.17e-05) 		4e-05
(0.00021) 		0.709
(0.799) 		0.0449
(0.104) 		1e-05
(6.17e-05) 		1e-05
(6.17e-05) 		0.00576
(0.0182) 		0.0213
(0.0567) 		0.378
(0.545) 		0.333
(0.499)
del 14q11 2 212 (34%) 403 2e-05
(0.000115) 		1e-05
(6.17e-05) 		1e-05
(6.17e-05) 		1e-05
(6.17e-05) 		0.577
(0.714) 		0.00931
(0.0279) 		1e-05
(6.17e-05) 		1e-05
(6.17e-05) 		0.0578
(0.128) 		0.119
(0.23) 		0.0399
(0.0946) 		0.0455
(0.105)
del 17p12 370 (60%) 245 1e-05
(6.17e-05) 		1e-05
(6.17e-05) 		1e-05
(6.17e-05) 		1e-05
(6.17e-05) 		0.57
(0.71) 		0.732
(0.813) 		1e-05
(6.17e-05) 		1e-05
(6.17e-05) 		0.0129
(0.037) 		0.0128
(0.037) 		0.0357
(0.0867) 		0.162
(0.294)
del 18q22 1 427 (69%) 188 1e-05
(6.17e-05) 		1e-05
(6.17e-05) 		1e-05
(6.17e-05) 		1e-05
(6.17e-05) 		0.403
(0.565) 		0.279
(0.435) 		1e-05
(6.17e-05) 		1e-05
(6.17e-05) 		9e-05
(0.000443) 		0.0877
(0.183) 		2e-05
(0.000115) 		0.0009
(0.0034)
amp 8q12 1 331 (54%) 284 0.143
(0.264) 		0.0425
(0.1) 		1e-05
(6.17e-05) 		0.00175
(0.00613) 		0.616
(0.736) 		0.047
(0.108) 		0.00013
(0.000609) 		0.00112
(0.00417) 		0.11
(0.217) 		0.0151
(0.0426) 		0.0167
(0.0462) 		0.236
(0.384)
amp 13q12 13 401 (65%) 214 1e-05
(6.17e-05) 		1e-05
(6.17e-05) 		1e-05
(6.17e-05) 		1e-05
(6.17e-05) 		0.482
(0.631) 		0.107
(0.213) 		1e-05
(6.17e-05) 		1e-05
(6.17e-05) 		0.00031
(0.00134) 		0.481
(0.631) 		0.00174
(0.00613) 		0.0503
(0.114)
amp 13q22 1 397 (65%) 218 1e-05
(6.17e-05) 		1e-05
(6.17e-05) 		1e-05
(6.17e-05) 		1e-05
(6.17e-05) 		0.8
(0.869) 		0.223
(0.367) 		1e-05
(6.17e-05) 		1e-05
(6.17e-05) 		0.00127
(0.00469) 		0.343
(0.512) 		0.0394
(0.0939) 		0.177
(0.311)
amp 17q24 1 144 (23%) 471 0.00965
(0.0289) 		0.0084
(0.0255) 		1e-05
(6.17e-05) 		2e-05
(0.000115) 		0.65
(0.758) 		0.0913
(0.189) 		1e-05
(6.17e-05) 		1e-05
(6.17e-05) 		0.00019
(0.000867) 		0.032
(0.0799) 		0.466
(0.624) 		0.249
(0.397)
amp 20p11 21 363 (59%) 252 0.00022
(0.000988) 		2e-05
(0.000115) 		1e-05
(6.17e-05) 		1e-05
(6.17e-05) 		0.254
(0.403) 		0.0685
(0.148) 		1e-05
(6.17e-05) 		1e-05
(6.17e-05) 		0.0203
(0.0546) 		0.00776
(0.0239) 		0.127
(0.241) 		0.127
(0.241)
del 4q22 1 224 (36%) 391 0.0165
(0.0459) 		0.0306
(0.0775) 		1e-05
(6.17e-05) 		0.00166
(0.00598) 		0.481
(0.631) 		0.13
(0.245) 		0.00085
(0.00325) 		1e-05
(6.17e-05) 		0.018
(0.0492) 		0.132
(0.247) 		0.0376
(0.0902) 		0.211
(0.357)
del 8p23 2 290 (47%) 325 0.00045
(0.00185) 		0.0011
(0.00412) 		1e-05
(6.17e-05) 		1e-05
(6.17e-05) 		0.178
(0.312) 		0.891
(0.928) 		4e-05
(0.00021) 		1e-05
(6.17e-05) 		0.163
(0.294) 		0.0306
(0.0775) 		0.00387
(0.0128) 		0.515
(0.66)
amp 11p15 5 139 (23%) 476 0.00176
(0.00614) 		0.00173
(0.00613) 		5e-05
(0.000258) 		0.00059
(0.00229) 		0.283
(0.441) 		0.696
(0.79) 		3e-05
(0.000167) 		1e-05
(6.17e-05) 		0.429
(0.591) 		1e-05
(6.17e-05) 		0.888
(0.927) 		0.532
(0.677)
amp 16p11 2 173 (28%) 442 0.0184
(0.0501) 		0.0021
(0.00724) 		1e-05
(6.17e-05) 		9e-05
(0.000443) 		0.244
(0.392) 		0.303
(0.464) 		7e-05
(0.000354) 		8e-05
(4e-04) 		0.443
(0.601) 		0.719
(0.805) 		0.0336
(0.0828) 		0.0845
(0.177)
del 1p36 11 244 (40%) 371 0.0001
(0.000481) 		0.00045
(0.00185) 		1e-05
(6.17e-05) 		1e-05
(6.17e-05) 		0.317
(0.48) 		0.19
(0.33) 		1e-05
(6.17e-05) 		1e-05
(6.17e-05) 		0.402
(0.564) 		0.00995
(0.0295) 		0.226
(0.371) 		0.541
(0.684)
del 8p22 303 (49%) 312 0.00122
(0.00453) 		0.00037
(0.00157) 		1e-05
(6.17e-05) 		1e-05
(6.17e-05) 		0.523
(0.668) 		0.933
(0.958) 		0.00039
(0.00163) 		1e-05
(6.17e-05) 		0.317
(0.48) 		0.0607
(0.134) 		0.00535
(0.0169) 		0.615
(0.735)
del 12p13 1 92 (15%) 523 0.00505
(0.0162) 		0.00171
(0.00609) 		1e-05
(6.17e-05) 		0.0456
(0.105) 		0.526
(0.671) 		0.786
(0.859) 		0.0732
(0.158) 		0.00086
(0.00328) 		0.711
(0.8) 		0.756
(0.834) 		0.0281
(0.0723) 		0.0266
(0.0692)
del 14q31 1 218 (35%) 397 0.00052
(0.00208) 		0.00048
(0.00195) 		1e-05
(6.17e-05) 		0.00018
(0.00083) 		0.496
(0.642) 		0.0319
(0.0799) 		1e-05
(6.17e-05) 		1e-05
(6.17e-05) 		0.242
(0.391) 		0.1
(0.202) 		0.356
(0.523) 		0.0746
(0.161)
del 15q11 2 253 (41%) 362 0.00047
(0.00191) 		0.00392
(0.0129) 		1e-05
(6.17e-05) 		0.00025
(0.00111) 		0.353
(0.52) 		0.865
(0.915) 		1e-05
(6.17e-05) 		1e-05
(6.17e-05) 		0.437
(0.596) 		0.43
(0.591) 		0.046
(0.106) 		0.0677
(0.148)
del 20p12 1 135 (22%) 480 0.0569
(0.127) 		0.00056
(0.0022) 		1e-05
(6.17e-05) 		1e-05
(6.17e-05) 		0.105
(0.21) 		0.851
(0.906) 		6e-05
(0.000307) 		1e-05
(6.17e-05) 		0.0295
(0.0754) 		0.0129
(0.037) 		0.87
(0.916) 		0.128
(0.243)
del 21q11 2 214 (35%) 401 0.0199
(0.0541) 		0.00141
(0.00515) 		1e-05
(6.17e-05) 		0.00133
(0.0049) 		0.424
(0.585) 		0.509
(0.657) 		3e-05
(0.000167) 		0.00037
(0.00157) 		0.0379
(0.0907) 		0.313
(0.476) 		0.67
(0.771) 		0.344
(0.512)
amp 2q33 1 141 (23%) 474 0.0666
(0.145) 		0.00046
(0.00188) 		5e-05
(0.000258) 		0.0031
(0.0104) 		0.602
(0.728) 		0.286
(0.443) 		4e-05
(0.00021) 		7e-05
(0.000354) 		0.0555
(0.125) 		0.0437
(0.103) 		0.828
(0.891) 		0.793
(0.863)
amp 6p21 1 154 (25%) 461 0.0298
(0.0758) 		9e-05
(0.000443) 		1e-05
(6.17e-05) 		0.0403
(0.0954) 		0.301
(0.461) 		0.266
(0.42) 		0.191
(0.33) 		0.0002
(0.000908) 		0.183
(0.32) 		0.702
(0.795) 		0.0682
(0.148) 		0.0155
(0.0433)
del 2p12 21 (3%) 594 1
(1.00) 		0.962
(0.979) 		0.00022
(0.000988) 		0.00389
(0.0128) 		0.232
(0.378) 		0.00146
(0.00531) 		0.0124
(0.0358) 		0.0117
(0.0342) 		0.00606
(0.019) 		0.0923
(0.191) 		0.129
(0.245) 		0.0745
(0.161)
del 5q12 1 159 (26%) 456 0.00053
(0.0021) 		0.00026
(0.00114) 		1e-05
(6.17e-05) 		0.00237
(0.00808) 		0.628
(0.742) 		0.326
(0.489) 		0.0361
(0.0874) 		1e-05
(6.17e-05) 		0.699
(0.794) 		0.976
(0.987) 		0.149
(0.274) 		0.617
(0.737)
del 5q22 2 189 (31%) 426 0.00066
(0.00255) 		0.00067
(0.00257) 		1e-05
(6.17e-05) 		0.0255
(0.0666) 		0.894
(0.93) 		0.374
(0.542) 		0.0444
(0.104) 		0.00013
(0.000609) 		0.469
(0.624) 		0.351
(0.518) 		0.207
(0.351) 		0.784
(0.858)
del 10p15 3 115 (19%) 500 0.151
(0.276) 		0.195
(0.334) 		2e-05
(0.000115) 		0.00287
(0.00971) 		0.725
(0.808) 		0.729
(0.811) 		0.0252
(0.066) 		4e-05
(0.00021) 		0.636
(0.749) 		0.497
(0.642) 		0.0102
(0.0303) 		0.0448
(0.104)
del 15q15 2 251 (41%) 364 4e-05
(0.00021) 		0.00179
(0.00622) 		1e-05
(6.17e-05) 		0.0001
(0.000481) 		0.386
(0.55) 		0.549
(0.692) 		0.00015
(0.000695) 		1e-05
(6.17e-05) 		0.628
(0.742) 		0.415
(0.579) 		0.0574
(0.128) 		0.418
(0.581)
del 15q21 1 248 (40%) 367 0.0003
(0.0013) 		0.0237
(0.0626) 		1e-05
(6.17e-05) 		0.00019
(0.000867) 		0.222
(0.367) 		0.694
(0.79) 		0.00027
(0.00118) 		1e-05
(6.17e-05) 		0.671
(0.771) 		0.463
(0.623) 		0.0657
(0.144) 		0.423
(0.585)
del 15q22 33 238 (39%) 377 0.00011
(0.000521) 		0.00089
(0.00338) 		1e-05
(6.17e-05) 		2e-05
(0.000115) 		0.188
(0.327) 		0.468
(0.624) 		3e-05
(0.000167) 		1e-05
(6.17e-05) 		0.788
(0.859) 		0.898
(0.933) 		0.0831
(0.175) 		0.145
(0.268)
amp 8p11 23 211 (34%) 404 0.397
(0.561) 		0.212
(0.358) 		1e-05
(6.17e-05) 		0.0319
(0.0799) 		0.612
(0.735) 		0.595
(0.723) 		0.0173
(0.0477) 		0.0106
(0.0311) 		0.0133
(0.0378) 		0.0808
(0.171) 		0.694
(0.79) 		0.42
(0.583)
amp 8q24 21 368 (60%) 247 0.237
(0.385) 		0.0503
(0.114) 		1e-05
(6.17e-05) 		8e-05
(4e-04) 		0.493
(0.64) 		0.0862
(0.181) 		0.0001
(0.000481) 		0.00171
(0.00609) 		0.141
(0.262) 		0.033
(0.0819) 		0.0505
(0.114) 		0.514
(0.66)
amp 19p13 2 111 (18%) 504 0.107
(0.213) 		0.00785
(0.0241) 		1e-05
(6.17e-05) 		0.021
(0.0564) 		0.755
(0.834) 		0.228
(0.373) 		0.0371
(0.0895) 		1e-05
(6.17e-05) 		0.116
(0.227) 		0.672
(0.771) 		0.563
(0.704) 		0.0784
(0.168)
amp 20p12 1 278 (45%) 337 0.0178
(0.0489) 		0.00797
(0.0244) 		2e-05
(0.000115) 		0.108
(0.215) 		0.012
(0.0347) 		0.436
(0.596) 		0.0989
(0.2) 		0.00029
(0.00126) 		0.953
(0.973) 		0.672
(0.771) 		0.165
(0.297) 		0.17
(0.303)
del 1p33 176 (29%) 439 0.0202
(0.0545) 		0.0825
(0.174) 		1e-05
(6.17e-05) 		0.00025
(0.00111) 		0.256
(0.405) 		0.626
(0.742) 		0.00032
(0.00137) 		0.00051
(0.00206) 		0.456
(0.614) 		0.108
(0.214) 		0.778
(0.854) 		0.58
(0.714)
del 4p16 2 202 (33%) 413 0.0535
(0.121) 		0.035
(0.0854) 		1e-05
(6.17e-05) 		0.00874
(0.0264) 		0.851
(0.906) 		0.563
(0.704) 		0.0115
(0.0338) 		4e-05
(0.00021) 		0.379
(0.545) 		0.239
(0.387) 		0.0563
(0.126) 		0.922
(0.951)
del 4q35 1 233 (38%) 382 0.0212
(0.0566) 		0.0587
(0.13) 		1e-05
(6.17e-05) 		0.00235
(0.00804) 		0.58
(0.714) 		0.243
(0.391) 		0.00184
(0.00637) 		2e-05
(0.000115) 		0.194
(0.334) 		0.443
(0.601) 		0.215
(0.361) 		0.614
(0.735)
del 10q21 1 139 (23%) 476 0.034
(0.0837) 		0.119
(0.23) 		1e-05
(6.17e-05) 		0.00175
(0.00613) 		0.441
(0.601) 		0.815
(0.883) 		5e-05
(0.000258) 		0.00045
(0.00185) 		0.67
(0.771) 		0.0972
(0.199) 		0.352
(0.519) 		0.483
(0.632)
del 22q13 32 229 (37%) 386 0.0026
(0.00883) 		0.00011
(0.000521) 		1e-05
(6.17e-05) 		0.082
(0.173) 		0.0652
(0.143) 		0.221
(0.367) 		0.00409
(0.0133) 		4e-05
(0.00021) 		0.896
(0.931) 		0.274
(0.43) 		0.349
(0.517) 		0.479
(0.631)
amp 5p12 119 (19%) 496 0.131
(0.247) 		0.0204
(0.0548) 		1e-05
(6.17e-05) 		0.289
(0.447) 		0.973
(0.987) 		0.881
(0.923) 		0.00059
(0.00229) 		0.00509
(0.0163) 		0.915
(0.945) 		0.343
(0.512) 		0.0992
(0.2) 		0.183
(0.32)
amp 19q12 139 (23%) 476 0.0281
(0.0723) 		0.00134
(0.00491) 		1e-05
(6.17e-05) 		0.239
(0.388) 		0.591
(0.72) 		0.373
(0.541) 		0.0879
(0.183) 		0.00984
(0.0293) 		0.184
(0.321) 		0.88
(0.923) 		0.465
(0.624) 		0.669
(0.771)
del 1p13 2 176 (29%) 439 0.265
(0.419) 		0.401
(0.564) 		1e-05
(6.17e-05) 		0.00419
(0.0135) 		0.184
(0.321) 		0.845
(0.904) 		0.00052
(0.00208) 		0.00035
(0.0015) 		0.516
(0.66) 		0.117
(0.228) 		0.491
(0.639) 		0.221
(0.367)
del 5q21 2 187 (30%) 428 0.0547
(0.123) 		0.0143
(0.0406) 		1e-05
(6.17e-05) 		0.0119
(0.0346) 		0.735
(0.815) 		0.43
(0.591) 		0.192
(0.33) 		0.00168
(0.00603) 		0.629
(0.742) 		0.838
(0.897) 		0.154
(0.28) 		0.876
(0.921)
del 9p24 2 84 (14%) 531 0.221
(0.367) 		0.297
(0.456) 		0.00401
(0.0131) 		0.0655
(0.144) 		0.722
(0.807) 		0.315
(0.478) 		0.0276
(0.0715) 		0.015
(0.0425) 		0.213
(0.359) 		0.0237
(0.0626) 		0.681
(0.779) 		0.565
(0.705)
del 10q23 31 161 (26%) 454 0.114
(0.224) 		0.241
(0.389) 		1e-05
(6.17e-05) 		0.023
(0.0611) 		0.481
(0.631) 		0.868
(0.915) 		0.00898
(0.027) 		4e-05
(0.00021) 		0.523
(0.668) 		0.133
(0.249) 		0.122
(0.233) 		0.132
(0.247)
del 10q25 2 157 (26%) 458 0.223
(0.367) 		0.298
(0.458) 		1e-05
(6.17e-05) 		0.0115
(0.0338) 		0.819
(0.884) 		0.914
(0.945) 		0.00225
(0.00773) 		1e-05
(6.17e-05) 		0.992
(1) 		0.205
(0.349) 		0.167
(0.299) 		0.362
(0.53)
del 12q21 33 90 (15%) 525 0.0343
(0.0841) 		0.0335
(0.0828) 		1e-05
(6.17e-05) 		0.176
(0.311) 		0.98
(0.99) 		0.089
(0.185) 		0.0915
(0.189) 		0.00038
(0.0016) 		0.833
(0.893) 		0.774
(0.851) 		0.477
(0.631) 		0.197
(0.337)
amp 8p11 21 256 (42%) 359 0.174
(0.309) 		0.11
(0.217) 		1e-05
(6.17e-05) 		0.019
(0.0517) 		0.637
(0.749) 		0.321
(0.484) 		0.0389
(0.0928) 		0.0564
(0.126) 		0.0808
(0.171) 		0.249
(0.397) 		0.652
(0.759) 		0.78
(0.854)
del 19p13 3 97 (16%) 518 0.118
(0.229) 		0.467
(0.624) 		2e-05
(0.000115) 		0.857
(0.911) 		0.881
(0.923) 		0.866
(0.915) 		0.166
(0.298) 		0.116
(0.226) 		0.646
(0.755) 		0.00529
(0.0168) 		0.0373
(0.0898) 		0.193
(0.332)
amp 5q22 3 66 (11%) 549 0.603
(0.728) 		0.577
(0.714) 		0.00447
(0.0144) 		0.547
(0.691) 		0.779
(0.854) 		0.151
(0.276) 		0.527
(0.671) 		0.0155
(0.0433) 		0.621
(0.739) 		0.125
(0.24) 		0.89
(0.928) 		0.109
(0.216)
del 11q22 3 111 (18%) 504 0.384
(0.548) 		0.234
(0.381) 		0.00672
(0.021) 		0.393
(0.556) 		0.958
(0.977) 		0.948
(0.969) 		0.379
(0.545) 		0.0454
(0.105) 		0.817
(0.883) 		0.496
(0.642) 		0.369
(0.538) 		0.373
(0.541)
del 16q23 1 84 (14%) 531 0.0434
(0.102) 		0.00365
(0.0121) 		0.167
(0.299) 		0.41
(0.573) 		0.772
(0.849) 		0.934
(0.958) 		0.512
(0.658) 		0.557
(0.698) 		0.608
(0.733) 		0.272
(0.428) 		0.94
(0.963) 		0.4
(0.564)
amp 1q31 1 145 (24%) 470 0.583
(0.715) 		0.548
(0.692) 		0.00011
(0.000521) 		0.375
(0.542) 		0.272
(0.428) 		0.151
(0.276) 		0.888
(0.927) 		0.435
(0.596) 		0.347
(0.516) 		0.253
(0.402) 		0.39
(0.553) 		0.29
(0.447)
amp 12p13 32 150 (24%) 465 0.648
(0.757) 		0.591
(0.72) 		0.0311
(0.0786) 		0.0505
(0.114) 		0.579
(0.714) 		0.594
(0.723) 		0.407
(0.569) 		0.117
(0.228) 		0.719
(0.805) 		1
(1.00) 		0.51
(0.658) 		0.176
(0.311)
del 3p14 2 119 (19%) 496 0.622
(0.739) 		0.465
(0.624) 		0.455
(0.614) 		0.972
(0.987) 		0.0295
(0.0754) 		0.601
(0.728) 		0.216
(0.362) 		0.849
(0.906) 		0.383
(0.547) 		0.308
(0.469) 		0.994
(1.00) 		0.669
(0.771)
del 8q11 1 47 (8%) 568 0.579
(0.714) 		0.184
(0.321) 		4e-05
(0.00021) 		0.413
(0.576) 		0.28
(0.436) 		0.339
(0.508) 		0.43
(0.591) 		0.218
(0.364) 		0.163
(0.294) 		0.093
(0.192) 		0.602
(0.728) 		0.652
(0.759)
del 17q24 3 95 (15%) 520 0.975
(0.987) 		0.73
(0.812) 		0.00529
(0.0168) 		0.862
(0.913) 		0.249
(0.397) 		0.47
(0.625) 		0.903
(0.936) 		0.121
(0.232) 		0.641
(0.752) 		0.469
(0.624) 		0.309
(0.471) 		0.55
(0.692)
amp 10q22 3 40 (7%) 575 1
(1.00) 		0.858
(0.911) 		0.168
(0.301) 		0.133
(0.248) 		0.695
(0.79) 		0.442
(0.601) 		0.422
(0.585) 		0.486
(0.633) 		0.437
(0.596) 		0.974
(0.987) 		0.351
(0.518) 		0.484
(0.632)
amp 15q26 1 42 (7%) 573 0.71
(0.799) 		0.663
(0.769) 		0.0937
(0.192) 		0.551
(0.692) 		0.198
(0.338) 		0.807
(0.874) 		0.706
(0.798) 		0.831
(0.892) 		0.716
(0.804) 		0.826
(0.89) 		0.656
(0.761) 		0.741
(0.82)
del 2q22 1 35 (6%) 580 0.926
(0.953) 		0.614
(0.735) 		0.101
(0.202) 		0.572
(0.712) 		0.225
(0.369) 		0.297
(0.456) 		0.135
(0.252) 		0.0987
(0.2) 		0.582
(0.715) 		0.112
(0.219) 		0.706
(0.798) 		0.674
(0.772)
del 3p26 3 93 (15%) 522 0.359
(0.526) 		0.494
(0.641) 		0.139
(0.258) 		1
(1.00) 		0.172
(0.306) 		0.12
(0.232) 		0.199
(0.339) 		0.538
(0.682) 		0.478
(0.631) 		0.581
(0.715) 		0.388
(0.551) 		0.576
(0.714)
del 3q26 31 64 (10%) 551 0.639
(0.75) 		0.883
(0.924) 		0.382
(0.547) 		0.822
(0.887) 		0.244
(0.392) 		0.96
(0.978) 		0.555
(0.696) 		0.192
(0.33) 		0.72
(0.805) 		0.263
(0.416) 		0.158
(0.287) 		0.924
(0.952)
del 6p25 3 80 (13%) 535 0.906
(0.938) 		0.348
(0.517) 		0.372
(0.541) 		0.654
(0.76) 		0.361
(0.529) 		0.479
(0.631) 		0.613
(0.735) 		0.388
(0.551) 		0.586
(0.717) 		0.725
(0.808) 		0.626
(0.742) 		0.83
(0.892)
del 6q26 92 (15%) 523 0.8
(0.869) 		0.851
(0.906) 		0.771
(0.849) 		1
(1.00) 		0.382
(0.547) 		0.126
(0.241) 		0.0977
(0.199) 		0.0791
(0.169) 		0.379
(0.545) 		0.364
(0.531) 		0.214
(0.361) 		0.584
(0.716)
del 7q31 1 17 (3%) 598 0.292
(0.45) 		0.689
(0.786) 		0.636
(0.749) 		0.862
(0.913) 		0.599
(0.727) 		0.867
(0.915) 		0.452
(0.612) 		0.992
(1) 		0.107
(0.213) 		0.947
(0.969) 		0.252
(0.401) 		1
(1.00)
del 16p13 3 69 (11%) 546 0.0936
(0.192) 		0.0779
(0.167) 		0.222
(0.367) 		0.587
(0.717) 		0.401
(0.564) 		0.791
(0.862) 		0.325
(0.489) 		0.0797
(0.17) 		0.67
(0.771) 		0.136
(0.252) 		0.276
(0.432) 		0.929
(0.955)
'amp_1q31.1' versus 'CN_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00052

Table S1.  Gene #1: 'amp_1q31.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
AMP PEAK 1(1Q31.1) MUTATED 39 67 39
AMP PEAK 1(1Q31.1) WILD-TYPE 214 142 114

Figure S1.  Get High-res Image Gene #1: 'amp_1q31.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_2q33.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00046 (Fisher's exact test), Q value = 0.0019

Table S2.  Gene #2: 'amp_2q33.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
AMP PEAK 2(2Q33.1) MUTATED 5 15 7 14
AMP PEAK 2(2Q33.1) WILD-TYPE 44 26 69 35

Figure S2.  Get High-res Image Gene #2: 'amp_2q33.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_2q33.1' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00026

Table S3.  Gene #2: 'amp_2q33.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
AMP PEAK 2(2Q33.1) MUTATED 36 64 41
AMP PEAK 2(2Q33.1) WILD-TYPE 217 145 112

Figure S3.  Get High-res Image Gene #2: 'amp_2q33.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_2q33.1' versus 'METHLYATION_CNMF'

P value = 0.0031 (Fisher's exact test), Q value = 0.01

Table S4.  Gene #2: 'amp_2q33.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
AMP PEAK 2(2Q33.1) MUTATED 20 54 24
AMP PEAK 2(2Q33.1) WILD-TYPE 82 103 106

Figure S4.  Get High-res Image Gene #2: 'amp_2q33.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_2q33.1' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00021

Table S5.  Gene #2: 'amp_2q33.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
AMP PEAK 2(2Q33.1) MUTATED 53 18 31 38
AMP PEAK 2(2Q33.1) WILD-TYPE 95 123 99 155

Figure S5.  Get High-res Image Gene #2: 'amp_2q33.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_2q33.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00035

Table S6.  Gene #2: 'amp_2q33.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
AMP PEAK 2(2Q33.1) MUTATED 27 17 7 13 32 34 10
AMP PEAK 2(2Q33.1) WILD-TYPE 53 69 57 44 58 104 87

Figure S6.  Get High-res Image Gene #2: 'amp_2q33.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_2q33.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0437 (Fisher's exact test), Q value = 0.1

Table S7.  Gene #2: 'amp_2q33.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 139 171
AMP PEAK 2(2Q33.1) MUTATED 50 40 29
AMP PEAK 2(2Q33.1) WILD-TYPE 178 99 142

Figure S7.  Get High-res Image Gene #2: 'amp_2q33.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_5p12' versus 'MRNA_CHIERARCHICAL'

P value = 0.0204 (Fisher's exact test), Q value = 0.055

Table S8.  Gene #3: 'amp_5p12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
AMP PEAK 3(5P12) MUTATED 8 16 11 11
AMP PEAK 3(5P12) WILD-TYPE 41 25 65 38

Figure S8.  Get High-res Image Gene #3: 'amp_5p12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_5p12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S9.  Gene #3: 'amp_5p12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
AMP PEAK 3(5P12) MUTATED 25 58 36
AMP PEAK 3(5P12) WILD-TYPE 228 151 117

Figure S9.  Get High-res Image Gene #3: 'amp_5p12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_5p12' versus 'MRNASEQ_CNMF'

P value = 0.00059 (Fisher's exact test), Q value = 0.0023

Table S10.  Gene #3: 'amp_5p12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
AMP PEAK 3(5P12) MUTATED 39 12 27 41
AMP PEAK 3(5P12) WILD-TYPE 109 129 103 152

Figure S10.  Get High-res Image Gene #3: 'amp_5p12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_5p12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00509 (Fisher's exact test), Q value = 0.016

Table S11.  Gene #3: 'amp_5p12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
AMP PEAK 3(5P12) MUTATED 17 10 6 10 26 36 14
AMP PEAK 3(5P12) WILD-TYPE 63 76 58 47 64 102 83

Figure S11.  Get High-res Image Gene #3: 'amp_5p12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_5q22.3' versus 'CN_CNMF'

P value = 0.00447 (Fisher's exact test), Q value = 0.014

Table S12.  Gene #4: 'amp_5q22.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
AMP PEAK 4(5Q22.3) MUTATED 16 33 17
AMP PEAK 4(5Q22.3) WILD-TYPE 237 176 136

Figure S12.  Get High-res Image Gene #4: 'amp_5q22.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_5q22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0155 (Fisher's exact test), Q value = 0.043

Table S13.  Gene #4: 'amp_5q22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
AMP PEAK 4(5Q22.3) MUTATED 12 9 1 6 12 21 5
AMP PEAK 4(5Q22.3) WILD-TYPE 68 77 63 51 78 117 92

Figure S13.  Get High-res Image Gene #4: 'amp_5q22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_6p21.1' versus 'MRNA_CNMF'

P value = 0.0298 (Fisher's exact test), Q value = 0.076

Table S14.  Gene #5: 'amp_6p21.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
AMP PEAK 5(6P21.1) MUTATED 8 16 23 4
AMP PEAK 5(6P21.1) WILD-TYPE 35 46 46 37

Figure S14.  Get High-res Image Gene #5: 'amp_6p21.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_6p21.1' versus 'MRNA_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00044

Table S15.  Gene #5: 'amp_6p21.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
AMP PEAK 5(6P21.1) MUTATED 4 12 13 22
AMP PEAK 5(6P21.1) WILD-TYPE 45 29 63 27

Figure S15.  Get High-res Image Gene #5: 'amp_6p21.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_6p21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S16.  Gene #5: 'amp_6p21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
AMP PEAK 5(6P21.1) MUTATED 23 82 49
AMP PEAK 5(6P21.1) WILD-TYPE 230 127 104

Figure S16.  Get High-res Image Gene #5: 'amp_6p21.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_6p21.1' versus 'METHLYATION_CNMF'

P value = 0.0403 (Fisher's exact test), Q value = 0.095

Table S17.  Gene #5: 'amp_6p21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
AMP PEAK 5(6P21.1) MUTATED 21 52 29
AMP PEAK 5(6P21.1) WILD-TYPE 81 105 101

Figure S17.  Get High-res Image Gene #5: 'amp_6p21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_6p21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.00091

Table S18.  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 80 86 64 57 90 138 97
AMP PEAK 5(6P21.1) MUTATED 19 20 7 20 31 44 13
AMP PEAK 5(6P21.1) WILD-TYPE 61 66 57 37 59 94 84

Figure S18.  Get High-res Image Gene #5: 'amp_6p21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_6p21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0155 (Fisher's exact test), Q value = 0.043

Table S19.  Gene #5: 'amp_6p21.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 15 34 31
AMP PEAK 5(6P21.1) MUTATED 10 7 11 15
AMP PEAK 5(6P21.1) WILD-TYPE 45 8 23 16

Figure S19.  Get High-res Image Gene #5: 'amp_6p21.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7p21.3' versus 'MRNA_CNMF'

P value = 0.00107 (Fisher's exact test), Q value = 0.004

Table S20.  Gene #6: 'amp_7p21.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
AMP PEAK 6(7P21.3) MUTATED 15 41 40 14
AMP PEAK 6(7P21.3) WILD-TYPE 28 21 29 27

Figure S20.  Get High-res Image Gene #6: 'amp_7p21.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_7p21.3' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S21.  Gene #6: 'amp_7p21.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
AMP PEAK 6(7P21.3) MUTATED 13 27 33 37
AMP PEAK 6(7P21.3) WILD-TYPE 36 14 43 12

Figure S21.  Get High-res Image Gene #6: 'amp_7p21.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_7p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S22.  Gene #6: 'amp_7p21.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
AMP PEAK 6(7P21.3) MUTATED 92 164 107
AMP PEAK 6(7P21.3) WILD-TYPE 161 45 46

Figure S22.  Get High-res Image Gene #6: 'amp_7p21.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_7p21.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S23.  Gene #6: 'amp_7p21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
AMP PEAK 6(7P21.3) MUTATED 55 127 65
AMP PEAK 6(7P21.3) WILD-TYPE 47 30 65

Figure S23.  Get High-res Image Gene #6: 'amp_7p21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_7p21.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0344 (Fisher's exact test), Q value = 0.084

Table S24.  Gene #6: 'amp_7p21.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 168 85
AMP PEAK 6(7P21.3) MUTATED 139 85 56
AMP PEAK 6(7P21.3) WILD-TYPE 89 83 29

Figure S24.  Get High-res Image Gene #6: 'amp_7p21.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_7p21.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S25.  Gene #6: 'amp_7p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
AMP PEAK 6(7P21.3) MUTATED 112 66 78 105
AMP PEAK 6(7P21.3) WILD-TYPE 36 75 52 88

Figure S25.  Get High-res Image Gene #6: 'amp_7p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_7p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S26.  Gene #6: 'amp_7p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
AMP PEAK 6(7P21.3) MUTATED 53 54 14 42 73 91 34
AMP PEAK 6(7P21.3) WILD-TYPE 27 32 50 15 17 47 63

Figure S26.  Get High-res Image Gene #6: 'amp_7p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_7p21.3' versus 'MIRSEQ_CNMF'

P value = 0.00866 (Fisher's exact test), Q value = 0.026

Table S27.  Gene #6: 'amp_7p21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 211 95 232
AMP PEAK 6(7P21.3) MUTATED 142 56 123
AMP PEAK 6(7P21.3) WILD-TYPE 69 39 109

Figure S27.  Get High-res Image Gene #6: 'amp_7p21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_7p21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0248 (Fisher's exact test), Q value = 0.065

Table S28.  Gene #6: 'amp_7p21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 20 28 28 18 17
AMP PEAK 6(7P21.3) MUTATED 16 11 23 22 15 7
AMP PEAK 6(7P21.3) WILD-TYPE 8 9 5 6 3 10

Figure S28.  Get High-res Image Gene #6: 'amp_7p21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_8p11.23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S29.  Gene #7: 'amp_8p11.23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
AMP PEAK 7(8P11.23) MUTATED 51 60 100
AMP PEAK 7(8P11.23) WILD-TYPE 202 149 53

Figure S29.  Get High-res Image Gene #7: 'amp_8p11.23' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8p11.23' versus 'METHLYATION_CNMF'

P value = 0.0319 (Fisher's exact test), Q value = 0.08

Table S30.  Gene #7: 'amp_8p11.23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
AMP PEAK 7(8P11.23) MUTATED 32 72 44
AMP PEAK 7(8P11.23) WILD-TYPE 70 85 86

Figure S30.  Get High-res Image Gene #7: 'amp_8p11.23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8p11.23' versus 'MRNASEQ_CNMF'

P value = 0.0173 (Fisher's exact test), Q value = 0.048

Table S31.  Gene #7: 'amp_8p11.23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
AMP PEAK 7(8P11.23) MUTATED 63 45 49 52
AMP PEAK 7(8P11.23) WILD-TYPE 85 96 81 141

Figure S31.  Get High-res Image Gene #7: 'amp_8p11.23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8p11.23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0106 (Fisher's exact test), Q value = 0.031

Table S32.  Gene #7: 'amp_8p11.23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
AMP PEAK 7(8P11.23) MUTATED 36 28 22 21 39 43 20
AMP PEAK 7(8P11.23) WILD-TYPE 44 58 42 36 51 95 77

Figure S32.  Get High-res Image Gene #7: 'amp_8p11.23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8p11.23' versus 'MIRSEQ_CNMF'

P value = 0.0133 (Fisher's exact test), Q value = 0.038

Table S33.  Gene #7: 'amp_8p11.23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 211 95 232
AMP PEAK 7(8P11.23) MUTATED 89 28 69
AMP PEAK 7(8P11.23) WILD-TYPE 122 67 163

Figure S33.  Get High-res Image Gene #7: 'amp_8p11.23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_8p11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S34.  Gene #8: 'amp_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
AMP PEAK 8(8P11.21) MUTATED 57 74 125
AMP PEAK 8(8P11.21) WILD-TYPE 196 135 28

Figure S34.  Get High-res Image Gene #8: 'amp_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8p11.21' versus 'METHLYATION_CNMF'

P value = 0.019 (Fisher's exact test), Q value = 0.052

Table S35.  Gene #8: 'amp_8p11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
AMP PEAK 8(8P11.21) MUTATED 42 84 49
AMP PEAK 8(8P11.21) WILD-TYPE 60 73 81

Figure S35.  Get High-res Image Gene #8: 'amp_8p11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8p11.21' versus 'MRNASEQ_CNMF'

P value = 0.0389 (Fisher's exact test), Q value = 0.093

Table S36.  Gene #8: 'amp_8p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
AMP PEAK 8(8P11.21) MUTATED 71 51 62 70
AMP PEAK 8(8P11.21) WILD-TYPE 77 90 68 123

Figure S36.  Get High-res Image Gene #8: 'amp_8p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8q12.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.0425 (Fisher's exact test), Q value = 0.1

Table S37.  Gene #9: 'amp_8q12.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
AMP PEAK 9(8Q12.1) MUTATED 17 26 36 27
AMP PEAK 9(8Q12.1) WILD-TYPE 32 15 40 22

Figure S37.  Get High-res Image Gene #9: 'amp_8q12.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_8q12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S38.  Gene #9: 'amp_8q12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
AMP PEAK 9(8Q12.1) MUTATED 78 104 149
AMP PEAK 9(8Q12.1) WILD-TYPE 175 105 4

Figure S38.  Get High-res Image Gene #9: 'amp_8q12.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8q12.1' versus 'METHLYATION_CNMF'

P value = 0.00175 (Fisher's exact test), Q value = 0.0061

Table S39.  Gene #9: 'amp_8q12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
AMP PEAK 9(8Q12.1) MUTATED 56 107 62
AMP PEAK 9(8Q12.1) WILD-TYPE 46 50 68

Figure S39.  Get High-res Image Gene #9: 'amp_8q12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8q12.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.047 (Fisher's exact test), Q value = 0.11

Table S40.  Gene #9: 'amp_8q12.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 168 85
AMP PEAK 9(8Q12.1) MUTATED 133 77 45
AMP PEAK 9(8Q12.1) WILD-TYPE 95 91 40

Figure S40.  Get High-res Image Gene #9: 'amp_8q12.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_8q12.1' versus 'MRNASEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00061

Table S41.  Gene #9: 'amp_8q12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
AMP PEAK 9(8Q12.1) MUTATED 95 56 79 98
AMP PEAK 9(8Q12.1) WILD-TYPE 53 85 51 95

Figure S41.  Get High-res Image Gene #9: 'amp_8q12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8q12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00112 (Fisher's exact test), Q value = 0.0042

Table S42.  Gene #9: 'amp_8q12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
AMP PEAK 9(8Q12.1) MUTATED 53 39 28 33 58 78 39
AMP PEAK 9(8Q12.1) WILD-TYPE 27 47 36 24 32 60 58

Figure S42.  Get High-res Image Gene #9: 'amp_8q12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8q12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0151 (Fisher's exact test), Q value = 0.043

Table S43.  Gene #9: 'amp_8q12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 139 171
AMP PEAK 9(8Q12.1) MUTATED 120 89 82
AMP PEAK 9(8Q12.1) WILD-TYPE 108 50 89

Figure S43.  Get High-res Image Gene #9: 'amp_8q12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_8q12.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0167 (Fisher's exact test), Q value = 0.046

Table S44.  Gene #9: 'amp_8q12.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 20 28 28 18 17
AMP PEAK 9(8Q12.1) MUTATED 16 13 22 18 15 5
AMP PEAK 9(8Q12.1) WILD-TYPE 8 7 6 10 3 12

Figure S44.  Get High-res Image Gene #9: 'amp_8q12.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_8q24.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S45.  Gene #10: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
AMP PEAK 10(8Q24.21) MUTATED 89 127 152
AMP PEAK 10(8Q24.21) WILD-TYPE 164 82 1

Figure S45.  Get High-res Image Gene #10: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 4e-04

Table S46.  Gene #10: 'amp_8q24.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
AMP PEAK 10(8Q24.21) MUTATED 58 119 68
AMP PEAK 10(8Q24.21) WILD-TYPE 44 38 62

Figure S46.  Get High-res Image Gene #10: 'amp_8q24.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00048

Table S47.  Gene #10: 'amp_8q24.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
AMP PEAK 10(8Q24.21) MUTATED 105 64 84 112
AMP PEAK 10(8Q24.21) WILD-TYPE 43 77 46 81

Figure S47.  Get High-res Image Gene #10: 'amp_8q24.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00171 (Fisher's exact test), Q value = 0.0061

Table S48.  Gene #10: '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 80 86 64 57 90 138 97
AMP PEAK 10(8Q24.21) MUTATED 54 44 30 37 66 86 48
AMP PEAK 10(8Q24.21) WILD-TYPE 26 42 34 20 24 52 49

Figure S48.  Get High-res Image Gene #10: 'amp_8q24.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.033 (Fisher's exact test), Q value = 0.082

Table S49.  Gene #10: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 139 171
AMP PEAK 10(8Q24.21) MUTATED 134 96 94
AMP PEAK 10(8Q24.21) WILD-TYPE 94 43 77

Figure S49.  Get High-res Image Gene #10: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_11p15.5' versus 'MRNA_CNMF'

P value = 0.00176 (Fisher's exact test), Q value = 0.0061

Table S50.  Gene #12: 'amp_11p15.5' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
AMP PEAK 12(11P15.5) MUTATED 4 20 24 5
AMP PEAK 12(11P15.5) WILD-TYPE 39 42 45 36

Figure S50.  Get High-res Image Gene #12: 'amp_11p15.5' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_11p15.5' versus 'MRNA_CHIERARCHICAL'

P value = 0.00173 (Fisher's exact test), Q value = 0.0061

Table S51.  Gene #12: 'amp_11p15.5' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
AMP PEAK 12(11P15.5) MUTATED 3 14 24 12
AMP PEAK 12(11P15.5) WILD-TYPE 46 27 52 37

Figure S51.  Get High-res Image Gene #12: 'amp_11p15.5' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_11p15.5' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00026

Table S52.  Gene #12: 'amp_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
AMP PEAK 12(11P15.5) MUTATED 36 58 45
AMP PEAK 12(11P15.5) WILD-TYPE 217 151 108

Figure S52.  Get High-res Image Gene #12: 'amp_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

'amp_11p15.5' versus 'METHLYATION_CNMF'

P value = 0.00059 (Fisher's exact test), Q value = 0.0023

Table S53.  Gene #12: 'amp_11p15.5' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
AMP PEAK 12(11P15.5) MUTATED 20 47 15
AMP PEAK 12(11P15.5) WILD-TYPE 82 110 115

Figure S53.  Get High-res Image Gene #12: 'amp_11p15.5' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_11p15.5' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00017

Table S54.  Gene #12: 'amp_11p15.5' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
AMP PEAK 12(11P15.5) MUTATED 52 13 24 48
AMP PEAK 12(11P15.5) WILD-TYPE 96 128 106 145

Figure S54.  Get High-res Image Gene #12: 'amp_11p15.5' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_11p15.5' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S55.  Gene #12: 'amp_11p15.5' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
AMP PEAK 12(11P15.5) MUTATED 30 15 2 10 21 44 15
AMP PEAK 12(11P15.5) WILD-TYPE 50 71 62 47 69 94 82

Figure S55.  Get High-res Image Gene #12: 'amp_11p15.5' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_11p15.5' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S56.  Gene #12: 'amp_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 139 171
AMP PEAK 12(11P15.5) MUTATED 35 67 22
AMP PEAK 12(11P15.5) WILD-TYPE 193 72 149

Figure S56.  Get High-res Image Gene #12: 'amp_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_12p13.32' versus 'CN_CNMF'

P value = 0.0311 (Fisher's exact test), Q value = 0.079

Table S57.  Gene #13: 'amp_12p13.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
AMP PEAK 13(12P13.32) MUTATED 68 38 44
AMP PEAK 13(12P13.32) WILD-TYPE 185 171 109

Figure S57.  Get High-res Image Gene #13: 'amp_12p13.32' versus Molecular Subtype #3: 'CN_CNMF'

'amp_13q12.13' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S58.  Gene #14: 'amp_13q12.13' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
AMP PEAK 14(13Q12.13) MUTATED 19 48 57 16
AMP PEAK 14(13Q12.13) WILD-TYPE 24 14 12 25

Figure S58.  Get High-res Image Gene #14: 'amp_13q12.13' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_13q12.13' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S59.  Gene #14: 'amp_13q12.13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
AMP PEAK 14(13Q12.13) MUTATED 15 30 51 44
AMP PEAK 14(13Q12.13) WILD-TYPE 34 11 25 5

Figure S59.  Get High-res Image Gene #14: 'amp_13q12.13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_13q12.13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S60.  Gene #14: 'amp_13q12.13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
AMP PEAK 14(13Q12.13) MUTATED 94 199 108
AMP PEAK 14(13Q12.13) WILD-TYPE 159 10 45

Figure S60.  Get High-res Image Gene #14: 'amp_13q12.13' versus Molecular Subtype #3: 'CN_CNMF'

'amp_13q12.13' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S61.  Gene #14: 'amp_13q12.13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
AMP PEAK 14(13Q12.13) MUTATED 56 138 64
AMP PEAK 14(13Q12.13) WILD-TYPE 46 19 66

Figure S61.  Get High-res Image Gene #14: 'amp_13q12.13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_13q12.13' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S62.  Gene #14: 'amp_13q12.13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
AMP PEAK 14(13Q12.13) MUTATED 118 65 82 133
AMP PEAK 14(13Q12.13) WILD-TYPE 30 76 48 60

Figure S62.  Get High-res Image Gene #14: 'amp_13q12.13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_13q12.13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S63.  Gene #14: 'amp_13q12.13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
AMP PEAK 14(13Q12.13) MUTATED 60 55 14 45 75 110 39
AMP PEAK 14(13Q12.13) WILD-TYPE 20 31 50 12 15 28 58

Figure S63.  Get High-res Image Gene #14: 'amp_13q12.13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_13q12.13' versus 'MIRSEQ_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.0013

Table S64.  Gene #14: 'amp_13q12.13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 211 95 232
AMP PEAK 14(13Q12.13) MUTATED 159 52 141
AMP PEAK 14(13Q12.13) WILD-TYPE 52 43 91

Figure S64.  Get High-res Image Gene #14: 'amp_13q12.13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_13q12.13' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00174 (Fisher's exact test), Q value = 0.0061

Table S65.  Gene #14: 'amp_13q12.13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 20 28 28 18 17
AMP PEAK 14(13Q12.13) MUTATED 22 11 26 19 15 9
AMP PEAK 14(13Q12.13) WILD-TYPE 2 9 2 9 3 8

Figure S65.  Get High-res Image Gene #14: 'amp_13q12.13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_13q12.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S66.  Gene #15: 'amp_13q12.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
AMP PEAK 15(13Q12.2) MUTATED 19 47 55 17
AMP PEAK 15(13Q12.2) WILD-TYPE 24 15 14 24

Figure S66.  Get High-res Image Gene #15: 'amp_13q12.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_13q12.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S67.  Gene #15: 'amp_13q12.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
AMP PEAK 15(13Q12.2) MUTATED 16 29 50 43
AMP PEAK 15(13Q12.2) WILD-TYPE 33 12 26 6

Figure S67.  Get High-res Image Gene #15: 'amp_13q12.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_13q12.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S68.  Gene #15: 'amp_13q12.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
AMP PEAK 15(13Q12.2) MUTATED 90 200 106
AMP PEAK 15(13Q12.2) WILD-TYPE 163 9 47

Figure S68.  Get High-res Image Gene #15: 'amp_13q12.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_13q12.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S69.  Gene #15: 'amp_13q12.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
AMP PEAK 15(13Q12.2) MUTATED 56 138 62
AMP PEAK 15(13Q12.2) WILD-TYPE 46 19 68

Figure S69.  Get High-res Image Gene #15: 'amp_13q12.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_13q12.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S70.  Gene #15: 'amp_13q12.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
AMP PEAK 15(13Q12.2) MUTATED 117 64 81 131
AMP PEAK 15(13Q12.2) WILD-TYPE 31 77 49 62

Figure S70.  Get High-res Image Gene #15: 'amp_13q12.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_13q12.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S71.  Gene #15: 'amp_13q12.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
AMP PEAK 15(13Q12.2) MUTATED 59 54 13 45 75 109 38
AMP PEAK 15(13Q12.2) WILD-TYPE 21 32 51 12 15 29 59

Figure S71.  Get High-res Image Gene #15: 'amp_13q12.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_13q12.2' versus 'MIRSEQ_CNMF'

P value = 0.00058 (Fisher's exact test), Q value = 0.0023

Table S72.  Gene #15: 'amp_13q12.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 211 95 232
AMP PEAK 15(13Q12.2) MUTATED 156 52 139
AMP PEAK 15(13Q12.2) WILD-TYPE 55 43 93

Figure S72.  Get High-res Image Gene #15: 'amp_13q12.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_13q12.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00357 (Fisher's exact test), Q value = 0.012

Table S73.  Gene #15: 'amp_13q12.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 20 28 28 18 17
AMP PEAK 15(13Q12.2) MUTATED 22 11 25 18 15 9
AMP PEAK 15(13Q12.2) WILD-TYPE 2 9 3 10 3 8

Figure S73.  Get High-res Image Gene #15: 'amp_13q12.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_13q12.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0447 (Fisher's exact test), Q value = 0.1

Table S74.  Gene #15: 'amp_13q12.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 15 34 31
AMP PEAK 15(13Q12.2) MUTATED 34 14 27 25
AMP PEAK 15(13Q12.2) WILD-TYPE 21 1 7 6

Figure S74.  Get High-res Image Gene #15: 'amp_13q12.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_13q22.1' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S75.  Gene #16: 'amp_13q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
AMP PEAK 16(13Q22.1) MUTATED 18 48 54 17
AMP PEAK 16(13Q22.1) WILD-TYPE 25 14 15 24

Figure S75.  Get High-res Image Gene #16: 'amp_13q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_13q22.1' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S76.  Gene #16: 'amp_13q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
AMP PEAK 16(13Q22.1) MUTATED 14 29 52 42
AMP PEAK 16(13Q22.1) WILD-TYPE 35 12 24 7

Figure S76.  Get High-res Image Gene #16: 'amp_13q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_13q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S77.  Gene #16: 'amp_13q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
AMP PEAK 16(13Q22.1) MUTATED 95 195 107
AMP PEAK 16(13Q22.1) WILD-TYPE 158 14 46

Figure S77.  Get High-res Image Gene #16: 'amp_13q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_13q22.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S78.  Gene #16: 'amp_13q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
AMP PEAK 16(13Q22.1) MUTATED 56 134 67
AMP PEAK 16(13Q22.1) WILD-TYPE 46 23 63

Figure S78.  Get High-res Image Gene #16: 'amp_13q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_13q22.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S79.  Gene #16: 'amp_13q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
AMP PEAK 16(13Q22.1) MUTATED 116 65 81 132
AMP PEAK 16(13Q22.1) WILD-TYPE 32 76 49 61

Figure S79.  Get High-res Image Gene #16: 'amp_13q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_13q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S80.  Gene #16: 'amp_13q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
AMP PEAK 16(13Q22.1) MUTATED 59 52 18 44 73 111 37
AMP PEAK 16(13Q22.1) WILD-TYPE 21 34 46 13 17 27 60

Figure S80.  Get High-res Image Gene #16: 'amp_13q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_13q22.1' versus 'MIRSEQ_CNMF'

P value = 0.00127 (Fisher's exact test), Q value = 0.0047

Table S81.  Gene #16: 'amp_13q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 211 95 232
AMP PEAK 16(13Q22.1) MUTATED 157 54 140
AMP PEAK 16(13Q22.1) WILD-TYPE 54 41 92

Figure S81.  Get High-res Image Gene #16: 'amp_13q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_13q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0394 (Fisher's exact test), Q value = 0.094

Table S82.  Gene #16: 'amp_13q22.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 20 28 28 18 17
AMP PEAK 16(13Q22.1) MUTATED 22 12 23 21 15 9
AMP PEAK 16(13Q22.1) WILD-TYPE 2 8 5 7 3 8

Figure S82.  Get High-res Image Gene #16: 'amp_13q22.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_16p11.2' versus 'MRNA_CNMF'

P value = 0.0184 (Fisher's exact test), Q value = 0.05

Table S83.  Gene #18: 'amp_16p11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
AMP PEAK 18(16P11.2) MUTATED 9 24 25 6
AMP PEAK 18(16P11.2) WILD-TYPE 34 38 44 35

Figure S83.  Get High-res Image Gene #18: 'amp_16p11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_16p11.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.0021 (Fisher's exact test), Q value = 0.0072

Table S84.  Gene #18: 'amp_16p11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
AMP PEAK 18(16P11.2) MUTATED 8 16 17 23
AMP PEAK 18(16P11.2) WILD-TYPE 41 25 59 26

Figure S84.  Get High-res Image Gene #18: 'amp_16p11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_16p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S85.  Gene #18: 'amp_16p11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
AMP PEAK 18(16P11.2) MUTATED 24 98 51
AMP PEAK 18(16P11.2) WILD-TYPE 229 111 102

Figure S85.  Get High-res Image Gene #18: 'amp_16p11.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_16p11.2' versus 'METHLYATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00044

Table S86.  Gene #18: 'amp_16p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
AMP PEAK 18(16P11.2) MUTATED 21 62 25
AMP PEAK 18(16P11.2) WILD-TYPE 81 95 105

Figure S86.  Get High-res Image Gene #18: 'amp_16p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_16p11.2' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00035

Table S87.  Gene #18: 'amp_16p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
AMP PEAK 18(16P11.2) MUTATED 57 21 33 61
AMP PEAK 18(16P11.2) WILD-TYPE 91 120 97 132

Figure S87.  Get High-res Image Gene #18: 'amp_16p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_16p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 4e-04

Table S88.  Gene #18: 'amp_16p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
AMP PEAK 18(16P11.2) MUTATED 20 24 6 15 35 54 18
AMP PEAK 18(16P11.2) WILD-TYPE 60 62 58 42 55 84 79

Figure S88.  Get High-res Image Gene #18: 'amp_16p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_16p11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0336 (Fisher's exact test), Q value = 0.083

Table S89.  Gene #18: 'amp_16p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 20 28 28 18 17
AMP PEAK 18(16P11.2) MUTATED 9 6 15 8 6 1
AMP PEAK 18(16P11.2) WILD-TYPE 15 14 13 20 12 16

Figure S89.  Get High-res Image Gene #18: 'amp_16p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_17q12' versus 'MRNA_CNMF'

P value = 0.025 (Fisher's exact test), Q value = 0.065

Table S90.  Gene #19: 'amp_17q12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
AMP PEAK 19(17Q12) MUTATED 7 23 21 6
AMP PEAK 19(17Q12) WILD-TYPE 36 39 48 35

Figure S90.  Get High-res Image Gene #19: 'amp_17q12' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_17q12' versus 'MRNA_CHIERARCHICAL'

P value = 0.00806 (Fisher's exact test), Q value = 0.025

Table S91.  Gene #19: 'amp_17q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
AMP PEAK 19(17Q12) MUTATED 6 15 17 19
AMP PEAK 19(17Q12) WILD-TYPE 43 26 59 30

Figure S91.  Get High-res Image Gene #19: 'amp_17q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_17q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S92.  Gene #19: 'amp_17q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
AMP PEAK 19(17Q12) MUTATED 32 67 61
AMP PEAK 19(17Q12) WILD-TYPE 221 142 92

Figure S92.  Get High-res Image Gene #19: 'amp_17q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q12' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00021

Table S93.  Gene #19: 'amp_17q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
AMP PEAK 19(17Q12) MUTATED 18 61 23
AMP PEAK 19(17Q12) WILD-TYPE 84 96 107

Figure S93.  Get High-res Image Gene #19: 'amp_17q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17q12' versus 'RPPA_CHIERARCHICAL'

P value = 0.0449 (Fisher's exact test), Q value = 0.1

Table S94.  Gene #19: 'amp_17q12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 168 85
AMP PEAK 19(17Q12) MUTATED 59 32 28
AMP PEAK 19(17Q12) WILD-TYPE 169 136 57

Figure S94.  Get High-res Image Gene #19: 'amp_17q12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_17q12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S95.  Gene #19: 'amp_17q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
AMP PEAK 19(17Q12) MUTATED 59 24 24 52
AMP PEAK 19(17Q12) WILD-TYPE 89 117 106 141

Figure S95.  Get High-res Image Gene #19: 'amp_17q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S96.  Gene #19: 'amp_17q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
AMP PEAK 19(17Q12) MUTATED 30 20 5 13 28 50 13
AMP PEAK 19(17Q12) WILD-TYPE 50 66 59 44 62 88 84

Figure S96.  Get High-res Image Gene #19: 'amp_17q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_CNMF'

P value = 0.00576 (Fisher's exact test), Q value = 0.018

Table S97.  Gene #19: 'amp_17q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 211 95 232
AMP PEAK 19(17Q12) MUTATED 64 13 61
AMP PEAK 19(17Q12) WILD-TYPE 147 82 171

Figure S97.  Get High-res Image Gene #19: 'amp_17q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_17q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0213 (Fisher's exact test), Q value = 0.057

Table S98.  Gene #19: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 139 171
AMP PEAK 19(17Q12) MUTATED 53 48 37
AMP PEAK 19(17Q12) WILD-TYPE 175 91 134

Figure S98.  Get High-res Image Gene #19: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_17q24.1' versus 'MRNA_CNMF'

P value = 0.00965 (Fisher's exact test), Q value = 0.029

Table S99.  Gene #20: 'amp_17q24.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
AMP PEAK 20(17Q24.1) MUTATED 4 19 22 6
AMP PEAK 20(17Q24.1) WILD-TYPE 39 43 47 35

Figure S99.  Get High-res Image Gene #20: 'amp_17q24.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_17q24.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.0084 (Fisher's exact test), Q value = 0.026

Table S100.  Gene #20: 'amp_17q24.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
AMP PEAK 20(17Q24.1) MUTATED 5 13 15 18
AMP PEAK 20(17Q24.1) WILD-TYPE 44 28 61 31

Figure S100.  Get High-res Image Gene #20: 'amp_17q24.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_17q24.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S101.  Gene #20: 'amp_17q24.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
AMP PEAK 20(17Q24.1) MUTATED 27 66 51
AMP PEAK 20(17Q24.1) WILD-TYPE 226 143 102

Figure S101.  Get High-res Image Gene #20: 'amp_17q24.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q24.1' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00011

Table S102.  Gene #20: 'amp_17q24.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
AMP PEAK 20(17Q24.1) MUTATED 13 59 21
AMP PEAK 20(17Q24.1) WILD-TYPE 89 98 109

Figure S102.  Get High-res Image Gene #20: 'amp_17q24.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17q24.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S103.  Gene #20: 'amp_17q24.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
AMP PEAK 20(17Q24.1) MUTATED 55 21 20 47
AMP PEAK 20(17Q24.1) WILD-TYPE 93 120 110 146

Figure S103.  Get High-res Image Gene #20: 'amp_17q24.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17q24.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S104.  Gene #20: 'amp_17q24.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
AMP PEAK 20(17Q24.1) MUTATED 29 20 4 11 24 43 12
AMP PEAK 20(17Q24.1) WILD-TYPE 51 66 60 46 66 95 85

Figure S104.  Get High-res Image Gene #20: 'amp_17q24.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_17q24.1' versus 'MIRSEQ_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.00087

Table S105.  Gene #20: 'amp_17q24.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 211 95 232
AMP PEAK 20(17Q24.1) MUTATED 61 8 53
AMP PEAK 20(17Q24.1) WILD-TYPE 150 87 179

Figure S105.  Get High-res Image Gene #20: 'amp_17q24.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_17q24.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.032 (Fisher's exact test), Q value = 0.08

Table S106.  Gene #20: 'amp_17q24.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 139 171
AMP PEAK 20(17Q24.1) MUTATED 45 43 34
AMP PEAK 20(17Q24.1) WILD-TYPE 183 96 137

Figure S106.  Get High-res Image Gene #20: 'amp_17q24.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_19p13.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00785 (Fisher's exact test), Q value = 0.024

Table S107.  Gene #21: 'amp_19p13.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
AMP PEAK 21(19P13.2) MUTATED 2 12 10 9
AMP PEAK 21(19P13.2) WILD-TYPE 47 29 66 40

Figure S107.  Get High-res Image Gene #21: 'amp_19p13.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_19p13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S108.  Gene #21: 'amp_19p13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
AMP PEAK 21(19P13.2) MUTATED 20 58 33
AMP PEAK 21(19P13.2) WILD-TYPE 233 151 120

Figure S108.  Get High-res Image Gene #21: 'amp_19p13.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19p13.2' versus 'METHLYATION_CNMF'

P value = 0.021 (Fisher's exact test), Q value = 0.056

Table S109.  Gene #21: 'amp_19p13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
AMP PEAK 21(19P13.2) MUTATED 13 42 24
AMP PEAK 21(19P13.2) WILD-TYPE 89 115 106

Figure S109.  Get High-res Image Gene #21: 'amp_19p13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_19p13.2' versus 'MRNASEQ_CNMF'

P value = 0.0371 (Fisher's exact test), Q value = 0.089

Table S110.  Gene #21: 'amp_19p13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
AMP PEAK 21(19P13.2) MUTATED 38 19 19 35
AMP PEAK 21(19P13.2) WILD-TYPE 110 122 111 158

Figure S110.  Get High-res Image Gene #21: 'amp_19p13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_19p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S111.  Gene #21: 'amp_19p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
AMP PEAK 21(19P13.2) MUTATED 13 20 2 11 27 31 7
AMP PEAK 21(19P13.2) WILD-TYPE 67 66 62 46 63 107 90

Figure S111.  Get High-res Image Gene #21: 'amp_19p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_19q12' versus 'MRNA_CNMF'

P value = 0.0281 (Fisher's exact test), Q value = 0.072

Table S112.  Gene #22: 'amp_19q12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
AMP PEAK 22(19Q12) MUTATED 5 21 13 6
AMP PEAK 22(19Q12) WILD-TYPE 38 41 56 35

Figure S112.  Get High-res Image Gene #22: 'amp_19q12' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_19q12' versus 'MRNA_CHIERARCHICAL'

P value = 0.00134 (Fisher's exact test), Q value = 0.0049

Table S113.  Gene #22: 'amp_19q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
AMP PEAK 22(19Q12) MUTATED 4 17 13 11
AMP PEAK 22(19Q12) WILD-TYPE 45 24 63 38

Figure S113.  Get High-res Image Gene #22: 'amp_19q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_19q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S114.  Gene #22: 'amp_19q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
AMP PEAK 22(19Q12) MUTATED 31 71 37
AMP PEAK 22(19Q12) WILD-TYPE 222 138 116

Figure S114.  Get High-res Image Gene #22: 'amp_19q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00984 (Fisher's exact test), Q value = 0.029

Table S115.  Gene #22: 'amp_19q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
AMP PEAK 22(19Q12) MUTATED 17 24 6 16 27 34 14
AMP PEAK 22(19Q12) WILD-TYPE 63 62 58 41 63 104 83

Figure S115.  Get High-res Image Gene #22: 'amp_19q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20p12.1' versus 'MRNA_CNMF'

P value = 0.0178 (Fisher's exact test), Q value = 0.049

Table S116.  Gene #23: 'amp_20p12.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
AMP PEAK 23(20P12.1) MUTATED 14 32 41 15
AMP PEAK 23(20P12.1) WILD-TYPE 29 30 28 26

Figure S116.  Get High-res Image Gene #23: 'amp_20p12.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20p12.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00797 (Fisher's exact test), Q value = 0.024

Table S117.  Gene #23: 'amp_20p12.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
AMP PEAK 23(20P12.1) MUTATED 13 20 42 27
AMP PEAK 23(20P12.1) WILD-TYPE 36 21 34 22

Figure S117.  Get High-res Image Gene #23: 'amp_20p12.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20p12.1' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00011

Table S118.  Gene #23: 'amp_20p12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
AMP PEAK 23(20P12.1) MUTATED 89 119 70
AMP PEAK 23(20P12.1) WILD-TYPE 164 90 83

Figure S118.  Get High-res Image Gene #23: 'amp_20p12.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20p12.1' versus 'RPPA_CNMF'

P value = 0.012 (Fisher's exact test), Q value = 0.035

Table S119.  Gene #23: 'amp_20p12.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 75 86 47 66 108 87 12
AMP PEAK 23(20P12.1) MUTATED 41 41 24 18 38 40 6
AMP PEAK 23(20P12.1) WILD-TYPE 34 45 23 48 70 47 6

Figure S119.  Get High-res Image Gene #23: 'amp_20p12.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_20p12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.0013

Table S120.  Gene #23: 'amp_20p12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
AMP PEAK 23(20P12.1) MUTATED 39 38 15 33 40 76 35
AMP PEAK 23(20P12.1) WILD-TYPE 41 48 49 24 50 62 62

Figure S120.  Get High-res Image Gene #23: 'amp_20p12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20p11.21' versus 'MRNA_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.00099

Table S121.  Gene #24: 'amp_20p11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
AMP PEAK 24(20P11.21) MUTATED 16 43 49 17
AMP PEAK 24(20P11.21) WILD-TYPE 27 19 20 24

Figure S121.  Get High-res Image Gene #24: 'amp_20p11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20p11.21' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00011

Table S122.  Gene #24: 'amp_20p11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
AMP PEAK 24(20P11.21) MUTATED 14 27 48 36
AMP PEAK 24(20P11.21) WILD-TYPE 35 14 28 13

Figure S122.  Get High-res Image Gene #24: 'amp_20p11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20p11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S123.  Gene #24: 'amp_20p11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
AMP PEAK 24(20P11.21) MUTATED 100 166 97
AMP PEAK 24(20P11.21) WILD-TYPE 153 43 56

Figure S123.  Get High-res Image Gene #24: 'amp_20p11.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20p11.21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S124.  Gene #24: 'amp_20p11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
AMP PEAK 24(20P11.21) MUTATED 51 118 64
AMP PEAK 24(20P11.21) WILD-TYPE 51 39 66

Figure S124.  Get High-res Image Gene #24: 'amp_20p11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20p11.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S125.  Gene #24: 'amp_20p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
AMP PEAK 24(20P11.21) MUTATED 113 62 70 115
AMP PEAK 24(20P11.21) WILD-TYPE 35 79 60 78

Figure S125.  Get High-res Image Gene #24: 'amp_20p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20p11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S126.  Gene #24: 'amp_20p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
AMP PEAK 24(20P11.21) MUTATED 56 51 17 40 61 99 36
AMP PEAK 24(20P11.21) WILD-TYPE 24 35 47 17 29 39 61

Figure S126.  Get High-res Image Gene #24: 'amp_20p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20p11.21' versus 'MIRSEQ_CNMF'

P value = 0.0203 (Fisher's exact test), Q value = 0.055

Table S127.  Gene #24: 'amp_20p11.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 211 95 232
AMP PEAK 24(20P11.21) MUTATED 139 50 126
AMP PEAK 24(20P11.21) WILD-TYPE 72 45 106

Figure S127.  Get High-res Image Gene #24: 'amp_20p11.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_20p11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00776 (Fisher's exact test), Q value = 0.024

Table S128.  Gene #24: 'amp_20p11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 139 171
AMP PEAK 24(20P11.21) MUTATED 130 96 89
AMP PEAK 24(20P11.21) WILD-TYPE 98 43 82

Figure S128.  Get High-res Image Gene #24: 'amp_20p11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20q11.21' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S129.  Gene #25: 'amp_20q11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
AMP PEAK 25(20Q11.21) MUTATED 18 60 63 23
AMP PEAK 25(20Q11.21) WILD-TYPE 25 2 6 18

Figure S129.  Get High-res Image Gene #25: 'amp_20q11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20q11.21' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S130.  Gene #25: 'amp_20q11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
AMP PEAK 25(20Q11.21) MUTATED 15 39 62 48
AMP PEAK 25(20Q11.21) WILD-TYPE 34 2 14 1

Figure S130.  Get High-res Image Gene #25: 'amp_20q11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20q11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S131.  Gene #25: 'amp_20q11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
AMP PEAK 25(20Q11.21) MUTATED 130 208 131
AMP PEAK 25(20Q11.21) WILD-TYPE 123 1 22

Figure S131.  Get High-res Image Gene #25: 'amp_20q11.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20q11.21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S132.  Gene #25: 'amp_20q11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
AMP PEAK 25(20Q11.21) MUTATED 68 155 76
AMP PEAK 25(20Q11.21) WILD-TYPE 34 2 54

Figure S132.  Get High-res Image Gene #25: 'amp_20q11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20q11.21' versus 'RPPA_CNMF'

P value = 0.0323 (Fisher's exact test), Q value = 0.081

Table S133.  Gene #25: 'amp_20q11.21' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 75 86 47 66 108 87 12
AMP PEAK 25(20Q11.21) MUTATED 64 70 39 49 71 62 10
AMP PEAK 25(20Q11.21) WILD-TYPE 11 16 8 17 37 25 2

Figure S133.  Get High-res Image Gene #25: 'amp_20q11.21' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_20q11.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S134.  Gene #25: 'amp_20q11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
AMP PEAK 25(20Q11.21) MUTATED 144 79 93 150
AMP PEAK 25(20Q11.21) WILD-TYPE 4 62 37 43

Figure S134.  Get High-res Image Gene #25: 'amp_20q11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20q11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S135.  Gene #25: 'amp_20q11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
AMP PEAK 25(20Q11.21) MUTATED 74 63 17 50 84 132 46
AMP PEAK 25(20Q11.21) WILD-TYPE 6 23 47 7 6 6 51

Figure S135.  Get High-res Image Gene #25: 'amp_20q11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20q11.21' versus 'MIRSEQ_CNMF'

P value = 0.0164 (Fisher's exact test), Q value = 0.046

Table S136.  Gene #25: 'amp_20q11.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 211 95 232
AMP PEAK 25(20Q11.21) MUTATED 174 68 167
AMP PEAK 25(20Q11.21) WILD-TYPE 37 27 65

Figure S136.  Get High-res Image Gene #25: 'amp_20q11.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_20q11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00039 (Fisher's exact test), Q value = 0.0016

Table S137.  Gene #25: 'amp_20q11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 139 171
AMP PEAK 25(20Q11.21) MUTATED 167 122 120
AMP PEAK 25(20Q11.21) WILD-TYPE 61 17 51

Figure S137.  Get High-res Image Gene #25: 'amp_20q11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20q11.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00331 (Fisher's exact test), Q value = 0.011

Table S138.  Gene #25: 'amp_20q11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 20 28 28 18 17
AMP PEAK 25(20Q11.21) MUTATED 23 15 26 22 17 9
AMP PEAK 25(20Q11.21) WILD-TYPE 1 5 2 6 1 8

Figure S138.  Get High-res Image Gene #25: 'amp_20q11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_20q11.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0164 (Fisher's exact test), Q value = 0.046

Table S139.  Gene #25: 'amp_20q11.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 15 34 31
AMP PEAK 25(20Q11.21) MUTATED 39 15 30 28
AMP PEAK 25(20Q11.21) WILD-TYPE 16 0 4 3

Figure S139.  Get High-res Image Gene #25: 'amp_20q11.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20q12' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S140.  Gene #26: 'amp_20q12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
AMP PEAK 26(20Q12) MUTATED 17 60 63 22
AMP PEAK 26(20Q12) WILD-TYPE 26 2 6 19

Figure S140.  Get High-res Image Gene #26: 'amp_20q12' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20q12' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S141.  Gene #26: 'amp_20q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
AMP PEAK 26(20Q12) MUTATED 14 39 61 48
AMP PEAK 26(20Q12) WILD-TYPE 35 2 15 1

Figure S141.  Get High-res Image Gene #26: 'amp_20q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S142.  Gene #26: 'amp_20q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
AMP PEAK 26(20Q12) MUTATED 130 208 133
AMP PEAK 26(20Q12) WILD-TYPE 123 1 20

Figure S142.  Get High-res Image Gene #26: 'amp_20q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S143.  Gene #26: 'amp_20q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
AMP PEAK 26(20Q12) MUTATED 69 155 79
AMP PEAK 26(20Q12) WILD-TYPE 33 2 51

Figure S143.  Get High-res Image Gene #26: 'amp_20q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20q12' versus 'RPPA_CNMF'

P value = 0.0499 (Fisher's exact test), Q value = 0.11

Table S144.  Gene #26: 'amp_20q12' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 75 86 47 66 108 87 12
AMP PEAK 26(20Q12) MUTATED 64 69 40 48 73 62 10
AMP PEAK 26(20Q12) WILD-TYPE 11 17 7 18 35 25 2

Figure S144.  Get High-res Image Gene #26: 'amp_20q12' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_20q12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S145.  Gene #26: 'amp_20q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
AMP PEAK 26(20Q12) MUTATED 144 80 95 149
AMP PEAK 26(20Q12) WILD-TYPE 4 61 35 44

Figure S145.  Get High-res Image Gene #26: 'amp_20q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S146.  Gene #26: 'amp_20q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
AMP PEAK 26(20Q12) MUTATED 74 64 19 50 85 132 44
AMP PEAK 26(20Q12) WILD-TYPE 6 22 45 7 5 6 53

Figure S146.  Get High-res Image Gene #26: 'amp_20q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20q12' versus 'MIRSEQ_CNMF'

P value = 0.00724 (Fisher's exact test), Q value = 0.022

Table S147.  Gene #26: 'amp_20q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 211 95 232
AMP PEAK 26(20Q12) MUTATED 176 69 166
AMP PEAK 26(20Q12) WILD-TYPE 35 26 66

Figure S147.  Get High-res Image Gene #26: 'amp_20q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_20q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 7e-04

Table S148.  Gene #26: 'amp_20q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 139 171
AMP PEAK 26(20Q12) MUTATED 169 123 119
AMP PEAK 26(20Q12) WILD-TYPE 59 16 52

Figure S148.  Get High-res Image Gene #26: 'amp_20q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20q12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00163 (Fisher's exact test), Q value = 0.0059

Table S149.  Gene #26: 'amp_20q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 20 28 28 18 17
AMP PEAK 26(20Q12) MUTATED 23 16 27 23 17 9
AMP PEAK 26(20Q12) WILD-TYPE 1 4 1 5 1 8

Figure S149.  Get High-res Image Gene #26: 'amp_20q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_20q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0281 (Fisher's exact test), Q value = 0.072

Table S150.  Gene #26: 'amp_20q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 15 34 31
AMP PEAK 26(20Q12) MUTATED 41 15 30 29
AMP PEAK 26(20Q12) WILD-TYPE 14 0 4 2

Figure S150.  Get High-res Image Gene #26: 'amp_20q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20q13.31' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S151.  Gene #27: 'amp_20q13.31' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
AMP PEAK 27(20Q13.31) MUTATED 18 60 64 24
AMP PEAK 27(20Q13.31) WILD-TYPE 25 2 5 17

Figure S151.  Get High-res Image Gene #27: 'amp_20q13.31' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20q13.31' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S152.  Gene #27: 'amp_20q13.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
AMP PEAK 27(20Q13.31) MUTATED 15 39 64 48
AMP PEAK 27(20Q13.31) WILD-TYPE 34 2 12 1

Figure S152.  Get High-res Image Gene #27: 'amp_20q13.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20q13.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S153.  Gene #27: 'amp_20q13.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
AMP PEAK 27(20Q13.31) MUTATED 131 208 134
AMP PEAK 27(20Q13.31) WILD-TYPE 122 1 19

Figure S153.  Get High-res Image Gene #27: 'amp_20q13.31' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20q13.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S154.  Gene #27: 'amp_20q13.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
AMP PEAK 27(20Q13.31) MUTATED 69 154 78
AMP PEAK 27(20Q13.31) WILD-TYPE 33 3 52

Figure S154.  Get High-res Image Gene #27: 'amp_20q13.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20q13.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S155.  Gene #27: 'amp_20q13.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
AMP PEAK 27(20Q13.31) MUTATED 142 82 95 151
AMP PEAK 27(20Q13.31) WILD-TYPE 6 59 35 42

Figure S155.  Get High-res Image Gene #27: 'amp_20q13.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20q13.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S156.  Gene #27: 'amp_20q13.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
AMP PEAK 27(20Q13.31) MUTATED 73 64 18 50 85 132 48
AMP PEAK 27(20Q13.31) WILD-TYPE 7 22 46 7 5 6 49

Figure S156.  Get High-res Image Gene #27: 'amp_20q13.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20q13.31' versus 'MIRSEQ_CNMF'

P value = 0.0151 (Fisher's exact test), Q value = 0.043

Table S157.  Gene #27: 'amp_20q13.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 211 95 232
AMP PEAK 27(20Q13.31) MUTATED 176 69 169
AMP PEAK 27(20Q13.31) WILD-TYPE 35 26 63

Figure S157.  Get High-res Image Gene #27: 'amp_20q13.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_20q13.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.001

Table S158.  Gene #27: 'amp_20q13.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 139 171
AMP PEAK 27(20Q13.31) MUTATED 170 123 121
AMP PEAK 27(20Q13.31) WILD-TYPE 58 16 50

Figure S158.  Get High-res Image Gene #27: 'amp_20q13.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20q13.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00402 (Fisher's exact test), Q value = 0.013

Table S159.  Gene #27: 'amp_20q13.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 20 28 28 18 17
AMP PEAK 27(20Q13.31) MUTATED 22 16 27 23 17 9
AMP PEAK 27(20Q13.31) WILD-TYPE 2 4 1 5 1 8

Figure S159.  Get High-res Image Gene #27: 'amp_20q13.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_20q13.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0353 (Fisher's exact test), Q value = 0.086

Table S160.  Gene #27: 'amp_20q13.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 15 34 31
AMP PEAK 27(20Q13.31) MUTATED 41 15 29 29
AMP PEAK 27(20Q13.31) WILD-TYPE 14 0 5 2

Figure S160.  Get High-res Image Gene #27: 'amp_20q13.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p36.11' versus 'MRNA_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00048

Table S161.  Gene #28: 'del_1p36.11' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
DEL PEAK 1(1P36.11) MUTATED 14 36 36 7
DEL PEAK 1(1P36.11) WILD-TYPE 29 26 33 34

Figure S161.  Get High-res Image Gene #28: 'del_1p36.11' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_1p36.11' versus 'MRNA_CHIERARCHICAL'

P value = 0.00045 (Fisher's exact test), Q value = 0.0019

Table S162.  Gene #28: 'del_1p36.11' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
DEL PEAK 1(1P36.11) MUTATED 12 27 29 25
DEL PEAK 1(1P36.11) WILD-TYPE 37 14 47 24

Figure S162.  Get High-res Image Gene #28: 'del_1p36.11' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_1p36.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S163.  Gene #28: 'del_1p36.11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
DEL PEAK 1(1P36.11) MUTATED 61 121 62
DEL PEAK 1(1P36.11) WILD-TYPE 192 88 91

Figure S163.  Get High-res Image Gene #28: '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 = 6.2e-05

Table S164.  Gene #28: 'del_1p36.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
DEL PEAK 1(1P36.11) MUTATED 32 84 34
DEL PEAK 1(1P36.11) WILD-TYPE 70 73 96

Figure S164.  Get High-res Image Gene #28: '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 = 6.2e-05

Table S165.  Gene #28: 'del_1p36.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
DEL PEAK 1(1P36.11) MUTATED 75 29 53 86
DEL PEAK 1(1P36.11) WILD-TYPE 73 112 77 107

Figure S165.  Get High-res Image Gene #28: '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 = 6.2e-05

Table S166.  Gene #28: '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 80 86 64 57 90 138 97
DEL PEAK 1(1P36.11) MUTATED 36 30 6 22 48 72 29
DEL PEAK 1(1P36.11) WILD-TYPE 44 56 58 35 42 66 68

Figure S166.  Get High-res Image Gene #28: 'del_1p36.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00995 (Fisher's exact test), Q value = 0.03

Table S167.  Gene #28: 'del_1p36.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 139 171
DEL PEAK 1(1P36.11) MUTATED 79 70 65
DEL PEAK 1(1P36.11) WILD-TYPE 149 69 106

Figure S167.  Get High-res Image Gene #28: 'del_1p36.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_1p33' versus 'MRNA_CNMF'

P value = 0.0202 (Fisher's exact test), Q value = 0.055

Table S168.  Gene #29: 'del_1p33' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
DEL PEAK 2(1P33) MUTATED 12 21 23 4
DEL PEAK 2(1P33) WILD-TYPE 31 41 46 37

Figure S168.  Get High-res Image Gene #29: 'del_1p33' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_1p33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S169.  Gene #29: 'del_1p33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
DEL PEAK 2(1P33) MUTATED 44 95 37
DEL PEAK 2(1P33) WILD-TYPE 209 114 116

Figure S169.  Get High-res Image Gene #29: 'del_1p33' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p33' versus 'METHLYATION_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.0011

Table S170.  Gene #29: 'del_1p33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
DEL PEAK 2(1P33) MUTATED 26 64 25
DEL PEAK 2(1P33) WILD-TYPE 76 93 105

Figure S170.  Get High-res Image Gene #29: 'del_1p33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p33' versus 'MRNASEQ_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.0014

Table S171.  Gene #29: 'del_1p33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
DEL PEAK 2(1P33) MUTATED 58 23 38 56
DEL PEAK 2(1P33) WILD-TYPE 90 118 92 137

Figure S171.  Get High-res Image Gene #29: 'del_1p33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00051 (Fisher's exact test), Q value = 0.0021

Table S172.  Gene #29: 'del_1p33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
DEL PEAK 2(1P33) MUTATED 29 21 7 18 34 47 19
DEL PEAK 2(1P33) WILD-TYPE 51 65 57 39 56 91 78

Figure S172.  Get High-res Image Gene #29: 'del_1p33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S173.  Gene #30: 'del_1p13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
DEL PEAK 3(1P13.2) MUTATED 46 92 38
DEL PEAK 3(1P13.2) WILD-TYPE 207 117 115

Figure S173.  Get High-res Image Gene #30: 'del_1p13.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p13.2' versus 'METHLYATION_CNMF'

P value = 0.00419 (Fisher's exact test), Q value = 0.014

Table S174.  Gene #30: 'del_1p13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
DEL PEAK 3(1P13.2) MUTATED 25 62 30
DEL PEAK 3(1P13.2) WILD-TYPE 77 95 100

Figure S174.  Get High-res Image Gene #30: 'del_1p13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p13.2' versus 'MRNASEQ_CNMF'

P value = 0.00052 (Fisher's exact test), Q value = 0.0021

Table S175.  Gene #30: 'del_1p13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
DEL PEAK 3(1P13.2) MUTATED 53 22 42 58
DEL PEAK 3(1P13.2) WILD-TYPE 95 119 88 135

Figure S175.  Get High-res Image Gene #30: 'del_1p13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00035 (Fisher's exact test), Q value = 0.0015

Table S176.  Gene #30: 'del_1p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
DEL PEAK 3(1P13.2) MUTATED 30 20 8 15 37 46 19
DEL PEAK 3(1P13.2) WILD-TYPE 50 66 56 42 53 92 78

Figure S176.  Get High-res Image Gene #30: 'del_1p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_2p12' versus 'CN_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.00099

Table S177.  Gene #31: 'del_2p12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
DEL PEAK 4(2P12) MUTATED 1 14 6
DEL PEAK 4(2P12) WILD-TYPE 252 195 147

Figure S177.  Get High-res Image Gene #31: 'del_2p12' versus Molecular Subtype #3: 'CN_CNMF'

'del_2p12' versus 'METHLYATION_CNMF'

P value = 0.00389 (Fisher's exact test), Q value = 0.013

Table S178.  Gene #31: 'del_2p12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
DEL PEAK 4(2P12) MUTATED 0 7 0
DEL PEAK 4(2P12) WILD-TYPE 102 150 130

Figure S178.  Get High-res Image Gene #31: 'del_2p12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_2p12' versus 'RPPA_CHIERARCHICAL'

P value = 0.00146 (Fisher's exact test), Q value = 0.0053

Table S179.  Gene #31: 'del_2p12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 168 85
DEL PEAK 4(2P12) MUTATED 6 2 9
DEL PEAK 4(2P12) WILD-TYPE 222 166 76

Figure S179.  Get High-res Image Gene #31: 'del_2p12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_2p12' versus 'MRNASEQ_CNMF'

P value = 0.0124 (Fisher's exact test), Q value = 0.036

Table S180.  Gene #31: 'del_2p12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
DEL PEAK 4(2P12) MUTATED 3 2 2 14
DEL PEAK 4(2P12) WILD-TYPE 145 139 128 179

Figure S180.  Get High-res Image Gene #31: 'del_2p12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_2p12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0117 (Fisher's exact test), Q value = 0.034

Table S181.  Gene #31: 'del_2p12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
DEL PEAK 4(2P12) MUTATED 0 1 0 2 2 8 8
DEL PEAK 4(2P12) WILD-TYPE 80 85 64 55 88 130 89

Figure S181.  Get High-res Image Gene #31: 'del_2p12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_2p12' versus 'MIRSEQ_CNMF'

P value = 0.00606 (Fisher's exact test), Q value = 0.019

Table S182.  Gene #31: 'del_2p12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 211 95 232
DEL PEAK 4(2P12) MUTATED 5 0 15
DEL PEAK 4(2P12) WILD-TYPE 206 95 217

Figure S182.  Get High-res Image Gene #31: 'del_2p12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3p14.2' versus 'RPPA_CNMF'

P value = 0.0295 (Fisher's exact test), Q value = 0.075

Table S183.  Gene #34: 'del_3p14.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 75 86 47 66 108 87 12
DEL PEAK 7(3P14.2) MUTATED 20 8 7 16 14 20 2
DEL PEAK 7(3P14.2) WILD-TYPE 55 78 40 50 94 67 10

Figure S183.  Get High-res Image Gene #34: 'del_3p14.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_4p16.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.035 (Fisher's exact test), Q value = 0.085

Table S184.  Gene #36: 'del_4p16.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
DEL PEAK 9(4P16.2) MUTATED 11 16 23 24
DEL PEAK 9(4P16.2) WILD-TYPE 38 25 53 25

Figure S184.  Get High-res Image Gene #36: 'del_4p16.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_4p16.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S185.  Gene #36: 'del_4p16.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
DEL PEAK 9(4P16.2) MUTATED 47 108 47
DEL PEAK 9(4P16.2) WILD-TYPE 206 101 106

Figure S185.  Get High-res Image Gene #36: 'del_4p16.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_4p16.2' versus 'METHLYATION_CNMF'

P value = 0.00874 (Fisher's exact test), Q value = 0.026

Table S186.  Gene #36: 'del_4p16.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
DEL PEAK 9(4P16.2) MUTATED 29 64 32
DEL PEAK 9(4P16.2) WILD-TYPE 73 93 98

Figure S186.  Get High-res Image Gene #36: 'del_4p16.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4p16.2' versus 'MRNASEQ_CNMF'

P value = 0.0115 (Fisher's exact test), Q value = 0.034

Table S187.  Gene #36: 'del_4p16.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
DEL PEAK 9(4P16.2) MUTATED 58 31 45 67
DEL PEAK 9(4P16.2) WILD-TYPE 90 110 85 126

Figure S187.  Get High-res Image Gene #36: 'del_4p16.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4p16.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00021

Table S188.  Gene #36: 'del_4p16.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
DEL PEAK 9(4P16.2) MUTATED 29 25 6 19 40 57 25
DEL PEAK 9(4P16.2) WILD-TYPE 51 61 58 38 50 81 72

Figure S188.  Get High-res Image Gene #36: 'del_4p16.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4q22.1' versus 'MRNA_CNMF'

P value = 0.0165 (Fisher's exact test), Q value = 0.046

Table S189.  Gene #37: 'del_4q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
DEL PEAK 10(4Q22.1) MUTATED 14 27 30 7
DEL PEAK 10(4Q22.1) WILD-TYPE 29 35 39 34

Figure S189.  Get High-res Image Gene #37: 'del_4q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_4q22.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.0306 (Fisher's exact test), Q value = 0.077

Table S190.  Gene #37: 'del_4q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
DEL PEAK 10(4Q22.1) MUTATED 11 18 25 24
DEL PEAK 10(4Q22.1) WILD-TYPE 38 23 51 25

Figure S190.  Get High-res Image Gene #37: 'del_4q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_4q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S191.  Gene #37: 'del_4q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
DEL PEAK 10(4Q22.1) MUTATED 49 116 59
DEL PEAK 10(4Q22.1) WILD-TYPE 204 93 94

Figure S191.  Get High-res Image Gene #37: 'del_4q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q22.1' versus 'METHLYATION_CNMF'

P value = 0.00166 (Fisher's exact test), Q value = 0.006

Table S192.  Gene #37: 'del_4q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
DEL PEAK 10(4Q22.1) MUTATED 37 74 35
DEL PEAK 10(4Q22.1) WILD-TYPE 65 83 95

Figure S192.  Get High-res Image Gene #37: 'del_4q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q22.1' versus 'MRNASEQ_CNMF'

P value = 0.00085 (Fisher's exact test), Q value = 0.0033

Table S193.  Gene #37: 'del_4q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
DEL PEAK 10(4Q22.1) MUTATED 67 33 46 77
DEL PEAK 10(4Q22.1) WILD-TYPE 81 108 84 116

Figure S193.  Get High-res Image Gene #37: 'del_4q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S194.  Gene #37: 'del_4q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
DEL PEAK 10(4Q22.1) MUTATED 36 24 7 27 41 61 27
DEL PEAK 10(4Q22.1) WILD-TYPE 44 62 57 30 49 77 70

Figure S194.  Get High-res Image Gene #37: 'del_4q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4q22.1' versus 'MIRSEQ_CNMF'

P value = 0.018 (Fisher's exact test), Q value = 0.049

Table S195.  Gene #37: 'del_4q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 211 95 232
DEL PEAK 10(4Q22.1) MUTATED 86 23 85
DEL PEAK 10(4Q22.1) WILD-TYPE 125 72 147

Figure S195.  Get High-res Image Gene #37: 'del_4q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_4q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0376 (Fisher's exact test), Q value = 0.09

Table S196.  Gene #37: 'del_4q22.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 20 28 28 18 17
DEL PEAK 10(4Q22.1) MUTATED 15 6 15 12 10 3
DEL PEAK 10(4Q22.1) WILD-TYPE 9 14 13 16 8 14

Figure S196.  Get High-res Image Gene #37: 'del_4q22.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_4q35.1' versus 'MRNA_CNMF'

P value = 0.0212 (Fisher's exact test), Q value = 0.057

Table S197.  Gene #38: 'del_4q35.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
DEL PEAK 11(4Q35.1) MUTATED 13 29 29 8
DEL PEAK 11(4Q35.1) WILD-TYPE 30 33 40 33

Figure S197.  Get High-res Image Gene #38: 'del_4q35.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_4q35.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S198.  Gene #38: 'del_4q35.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
DEL PEAK 11(4Q35.1) MUTATED 52 120 61
DEL PEAK 11(4Q35.1) WILD-TYPE 201 89 92

Figure S198.  Get High-res Image Gene #38: 'del_4q35.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q35.1' versus 'METHLYATION_CNMF'

P value = 0.00235 (Fisher's exact test), Q value = 0.008

Table S199.  Gene #38: 'del_4q35.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
DEL PEAK 11(4Q35.1) MUTATED 39 75 36
DEL PEAK 11(4Q35.1) WILD-TYPE 63 82 94

Figure S199.  Get High-res Image Gene #38: 'del_4q35.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q35.1' versus 'MRNASEQ_CNMF'

P value = 0.00184 (Fisher's exact test), Q value = 0.0064

Table S200.  Gene #38: 'del_4q35.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
DEL PEAK 11(4Q35.1) MUTATED 67 35 54 76
DEL PEAK 11(4Q35.1) WILD-TYPE 81 106 76 117

Figure S200.  Get High-res Image Gene #38: 'del_4q35.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4q35.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00011

Table S201.  Gene #38: 'del_4q35.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
DEL PEAK 11(4Q35.1) MUTATED 38 26 8 26 44 61 29
DEL PEAK 11(4Q35.1) WILD-TYPE 42 60 56 31 46 77 68

Figure S201.  Get High-res Image Gene #38: 'del_4q35.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5q12.1' versus 'MRNA_CNMF'

P value = 0.00053 (Fisher's exact test), Q value = 0.0021

Table S202.  Gene #39: 'del_5q12.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
DEL PEAK 12(5Q12.1) MUTATED 10 21 19 1
DEL PEAK 12(5Q12.1) WILD-TYPE 33 41 50 40

Figure S202.  Get High-res Image Gene #39: 'del_5q12.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_5q12.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.0011

Table S203.  Gene #39: 'del_5q12.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
DEL PEAK 12(5Q12.1) MUTATED 9 18 8 16
DEL PEAK 12(5Q12.1) WILD-TYPE 40 23 68 33

Figure S203.  Get High-res Image Gene #39: 'del_5q12.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_5q12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S204.  Gene #39: 'del_5q12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
DEL PEAK 12(5Q12.1) MUTATED 27 72 60
DEL PEAK 12(5Q12.1) WILD-TYPE 226 137 93

Figure S204.  Get High-res Image Gene #39: 'del_5q12.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q12.1' versus 'METHLYATION_CNMF'

P value = 0.00237 (Fisher's exact test), Q value = 0.0081

Table S205.  Gene #39: 'del_5q12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
DEL PEAK 12(5Q12.1) MUTATED 24 59 26
DEL PEAK 12(5Q12.1) WILD-TYPE 78 98 104

Figure S205.  Get High-res Image Gene #39: 'del_5q12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5q12.1' versus 'MRNASEQ_CNMF'

P value = 0.0361 (Fisher's exact test), Q value = 0.087

Table S206.  Gene #39: 'del_5q12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
DEL PEAK 12(5Q12.1) MUTATED 47 25 38 49
DEL PEAK 12(5Q12.1) WILD-TYPE 101 116 92 144

Figure S206.  Get High-res Image Gene #39: 'del_5q12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_5q12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S207.  Gene #39: 'del_5q12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
DEL PEAK 12(5Q12.1) MUTATED 25 19 4 21 32 43 15
DEL PEAK 12(5Q12.1) WILD-TYPE 55 67 60 36 58 95 82

Figure S207.  Get High-res Image Gene #39: 'del_5q12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5q21.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.0143 (Fisher's exact test), Q value = 0.041

Table S208.  Gene #40: 'del_5q21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
DEL PEAK 13(5Q21.2) MUTATED 10 19 16 17
DEL PEAK 13(5Q21.2) WILD-TYPE 39 22 60 32

Figure S208.  Get High-res Image Gene #40: 'del_5q21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_5q21.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S209.  Gene #40: 'del_5q21.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
DEL PEAK 13(5Q21.2) MUTATED 37 81 69
DEL PEAK 13(5Q21.2) WILD-TYPE 216 128 84

Figure S209.  Get High-res Image Gene #40: 'del_5q21.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q21.2' versus 'METHLYATION_CNMF'

P value = 0.0119 (Fisher's exact test), Q value = 0.035

Table S210.  Gene #40: 'del_5q21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
DEL PEAK 13(5Q21.2) MUTATED 28 64 33
DEL PEAK 13(5Q21.2) WILD-TYPE 74 93 97

Figure S210.  Get High-res Image Gene #40: 'del_5q21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5q21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00168 (Fisher's exact test), Q value = 0.006

Table S211.  Gene #40: 'del_5q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
DEL PEAK 13(5Q21.2) MUTATED 28 24 8 20 34 51 21
DEL PEAK 13(5Q21.2) WILD-TYPE 52 62 56 37 56 87 76

Figure S211.  Get High-res Image Gene #40: 'del_5q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5q22.2' versus 'MRNA_CNMF'

P value = 0.00066 (Fisher's exact test), Q value = 0.0025

Table S212.  Gene #41: 'del_5q22.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
DEL PEAK 14(5Q22.2) MUTATED 9 23 26 3
DEL PEAK 14(5Q22.2) WILD-TYPE 34 39 43 38

Figure S212.  Get High-res Image Gene #41: 'del_5q22.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_5q22.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00067 (Fisher's exact test), Q value = 0.0026

Table S213.  Gene #41: 'del_5q22.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
DEL PEAK 14(5Q22.2) MUTATED 9 21 14 17
DEL PEAK 14(5Q22.2) WILD-TYPE 40 20 62 32

Figure S213.  Get High-res Image Gene #41: 'del_5q22.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_5q22.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S214.  Gene #41: 'del_5q22.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
DEL PEAK 14(5Q22.2) MUTATED 41 81 67
DEL PEAK 14(5Q22.2) WILD-TYPE 212 128 86

Figure S214.  Get High-res Image Gene #41: 'del_5q22.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q22.2' versus 'METHLYATION_CNMF'

P value = 0.0255 (Fisher's exact test), Q value = 0.067

Table S215.  Gene #41: 'del_5q22.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
DEL PEAK 14(5Q22.2) MUTATED 29 64 35
DEL PEAK 14(5Q22.2) WILD-TYPE 73 93 95

Figure S215.  Get High-res Image Gene #41: 'del_5q22.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5q22.2' versus 'MRNASEQ_CNMF'

P value = 0.0444 (Fisher's exact test), Q value = 0.1

Table S216.  Gene #41: 'del_5q22.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
DEL PEAK 14(5Q22.2) MUTATED 58 34 37 59
DEL PEAK 14(5Q22.2) WILD-TYPE 90 107 93 134

Figure S216.  Get High-res Image Gene #41: 'del_5q22.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_5q22.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.00061

Table S217.  Gene #41: 'del_5q22.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
DEL PEAK 14(5Q22.2) MUTATED 32 25 8 22 30 53 18
DEL PEAK 14(5Q22.2) WILD-TYPE 48 61 56 35 60 85 79

Figure S217.  Get High-res Image Gene #41: 'del_5q22.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MRNA_CNMF'

P value = 0.00045 (Fisher's exact test), Q value = 0.0019

Table S218.  Gene #45: 'del_8p23.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
DEL PEAK 18(8P23.2) MUTATED 17 42 37 11
DEL PEAK 18(8P23.2) WILD-TYPE 26 20 32 30

Figure S218.  Get High-res Image Gene #45: 'del_8p23.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_8p23.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.0011 (Fisher's exact test), Q value = 0.0041

Table S219.  Gene #45: 'del_8p23.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
DEL PEAK 18(8P23.2) MUTATED 14 28 36 29
DEL PEAK 18(8P23.2) WILD-TYPE 35 13 40 20

Figure S219.  Get High-res Image Gene #45: '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 = 6.2e-05

Table S220.  Gene #45: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
DEL PEAK 18(8P23.2) MUTATED 45 124 121
DEL PEAK 18(8P23.2) WILD-TYPE 208 85 32

Figure S220.  Get High-res Image Gene #45: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_8p23.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S221.  Gene #45: 'del_8p23.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
DEL PEAK 18(8P23.2) MUTATED 39 99 44
DEL PEAK 18(8P23.2) WILD-TYPE 63 58 86

Figure S221.  Get High-res Image Gene #45: 'del_8p23.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_8p23.2' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00021

Table S222.  Gene #45: 'del_8p23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
DEL PEAK 18(8P23.2) MUTATED 82 42 65 100
DEL PEAK 18(8P23.2) WILD-TYPE 66 99 65 93

Figure S222.  Get High-res Image Gene #45: '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 = 6.2e-05

Table S223.  Gene #45: '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 80 86 64 57 90 138 97
DEL PEAK 18(8P23.2) MUTATED 38 33 10 31 59 83 35
DEL PEAK 18(8P23.2) WILD-TYPE 42 53 54 26 31 55 62

Figure S223.  Get High-res Image Gene #45: 'del_8p23.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0306 (Fisher's exact test), Q value = 0.077

Table S224.  Gene #45: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 139 171
DEL PEAK 18(8P23.2) MUTATED 98 79 78
DEL PEAK 18(8P23.2) WILD-TYPE 130 60 93

Figure S224.  Get High-res Image Gene #45: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00387 (Fisher's exact test), Q value = 0.013

Table S225.  Gene #45: 'del_8p23.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 20 28 28 18 17
DEL PEAK 18(8P23.2) MUTATED 16 8 15 17 12 2
DEL PEAK 18(8P23.2) WILD-TYPE 8 12 13 11 6 15

Figure S225.  Get High-res Image Gene #45: 'del_8p23.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_8p22' versus 'MRNA_CNMF'

P value = 0.00122 (Fisher's exact test), Q value = 0.0045

Table S226.  Gene #46: 'del_8p22' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
DEL PEAK 19(8P22) MUTATED 16 41 39 13
DEL PEAK 19(8P22) WILD-TYPE 27 21 30 28

Figure S226.  Get High-res Image Gene #46: 'del_8p22' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_8p22' versus 'MRNA_CHIERARCHICAL'

P value = 0.00037 (Fisher's exact test), Q value = 0.0016

Table S227.  Gene #46: 'del_8p22' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
DEL PEAK 19(8P22) MUTATED 13 28 39 29
DEL PEAK 19(8P22) WILD-TYPE 36 13 37 20

Figure S227.  Get High-res Image Gene #46: 'del_8p22' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_8p22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S228.  Gene #46: 'del_8p22' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
DEL PEAK 19(8P22) MUTATED 50 128 125
DEL PEAK 19(8P22) WILD-TYPE 203 81 28

Figure S228.  Get High-res Image Gene #46: 'del_8p22' versus Molecular Subtype #3: 'CN_CNMF'

'del_8p22' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S229.  Gene #46: 'del_8p22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
DEL PEAK 19(8P22) MUTATED 40 104 49
DEL PEAK 19(8P22) WILD-TYPE 62 53 81

Figure S229.  Get High-res Image Gene #46: 'del_8p22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_8p22' versus 'MRNASEQ_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.0016

Table S230.  Gene #46: 'del_8p22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
DEL PEAK 19(8P22) MUTATED 85 48 69 100
DEL PEAK 19(8P22) WILD-TYPE 63 93 61 93

Figure S230.  Get High-res Image Gene #46: 'del_8p22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_8p22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S231.  Gene #46: 'del_8p22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
DEL PEAK 19(8P22) MUTATED 38 39 10 32 62 85 36
DEL PEAK 19(8P22) WILD-TYPE 42 47 54 25 28 53 61

Figure S231.  Get High-res Image Gene #46: 'del_8p22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_8p22' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00535 (Fisher's exact test), Q value = 0.017

Table S232.  Gene #46: 'del_8p22' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 20 28 28 18 17
DEL PEAK 19(8P22) MUTATED 16 9 15 17 12 2
DEL PEAK 19(8P22) WILD-TYPE 8 11 13 11 6 15

Figure S232.  Get High-res Image Gene #46: 'del_8p22' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_8q11.1' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00021

Table S233.  Gene #47: 'del_8q11.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
DEL PEAK 20(8Q11.1) MUTATED 14 30 3
DEL PEAK 20(8Q11.1) WILD-TYPE 239 179 150

Figure S233.  Get High-res Image Gene #47: 'del_8q11.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p24.2' versus 'CN_CNMF'

P value = 0.00401 (Fisher's exact test), Q value = 0.013

Table S234.  Gene #48: 'del_9p24.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
DEL PEAK 21(9P24.2) MUTATED 21 36 27
DEL PEAK 21(9P24.2) WILD-TYPE 232 173 126

Figure S234.  Get High-res Image Gene #48: 'del_9p24.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p24.2' versus 'MRNASEQ_CNMF'

P value = 0.0276 (Fisher's exact test), Q value = 0.072

Table S235.  Gene #48: 'del_9p24.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
DEL PEAK 21(9P24.2) MUTATED 29 11 20 24
DEL PEAK 21(9P24.2) WILD-TYPE 119 130 110 169

Figure S235.  Get High-res Image Gene #48: 'del_9p24.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9p24.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.015 (Fisher's exact test), Q value = 0.042

Table S236.  Gene #48: 'del_9p24.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
DEL PEAK 21(9P24.2) MUTATED 12 9 4 12 18 23 6
DEL PEAK 21(9P24.2) WILD-TYPE 68 77 60 45 72 115 91

Figure S236.  Get High-res Image Gene #48: 'del_9p24.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9p24.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0237 (Fisher's exact test), Q value = 0.063

Table S237.  Gene #48: 'del_9p24.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 139 171
DEL PEAK 21(9P24.2) MUTATED 30 29 17
DEL PEAK 21(9P24.2) WILD-TYPE 198 110 154

Figure S237.  Get High-res Image Gene #48: 'del_9p24.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_10p15.3' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00011

Table S238.  Gene #49: 'del_10p15.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
DEL PEAK 22(10P15.3) MUTATED 24 52 39
DEL PEAK 22(10P15.3) WILD-TYPE 229 157 114

Figure S238.  Get High-res Image Gene #49: 'del_10p15.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_10p15.3' versus 'METHLYATION_CNMF'

P value = 0.00287 (Fisher's exact test), Q value = 0.0097

Table S239.  Gene #49: 'del_10p15.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
DEL PEAK 22(10P15.3) MUTATED 17 44 16
DEL PEAK 22(10P15.3) WILD-TYPE 85 113 114

Figure S239.  Get High-res Image Gene #49: 'del_10p15.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10p15.3' versus 'MRNASEQ_CNMF'

P value = 0.0252 (Fisher's exact test), Q value = 0.066

Table S240.  Gene #49: 'del_10p15.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
DEL PEAK 22(10P15.3) MUTATED 37 16 26 35
DEL PEAK 22(10P15.3) WILD-TYPE 111 125 104 158

Figure S240.  Get High-res Image Gene #49: 'del_10p15.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10p15.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00021

Table S241.  Gene #49: '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 80 86 64 57 90 138 97
DEL PEAK 22(10P15.3) MUTATED 14 12 3 11 33 29 12
DEL PEAK 22(10P15.3) WILD-TYPE 66 74 61 46 57 109 85

Figure S241.  Get High-res Image Gene #49: 'del_10p15.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10p15.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0102 (Fisher's exact test), Q value = 0.03

Table S242.  Gene #49: 'del_10p15.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 20 28 28 18 17
DEL PEAK 22(10P15.3) MUTATED 3 7 11 5 6 0
DEL PEAK 22(10P15.3) WILD-TYPE 21 13 17 23 12 17

Figure S242.  Get High-res Image Gene #49: 'del_10p15.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_10p15.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0448 (Fisher's exact test), Q value = 0.1

Table S243.  Gene #49: 'del_10p15.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 15 34 31
DEL PEAK 22(10P15.3) MUTATED 12 8 5 7
DEL PEAK 22(10P15.3) WILD-TYPE 43 7 29 24

Figure S243.  Get High-res Image Gene #49: 'del_10p15.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q21.1' versus 'MRNA_CNMF'

P value = 0.034 (Fisher's exact test), Q value = 0.084

Table S244.  Gene #50: 'del_10q21.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
DEL PEAK 23(10Q21.1) MUTATED 6 14 23 5
DEL PEAK 23(10Q21.1) WILD-TYPE 37 48 46 36

Figure S244.  Get High-res Image Gene #50: 'del_10q21.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_10q21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S245.  Gene #50: 'del_10q21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
DEL PEAK 23(10Q21.1) MUTATED 25 67 47
DEL PEAK 23(10Q21.1) WILD-TYPE 228 142 106

Figure S245.  Get High-res Image Gene #50: 'del_10q21.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q21.1' versus 'METHLYATION_CNMF'

P value = 0.00175 (Fisher's exact test), Q value = 0.0061

Table S246.  Gene #50: 'del_10q21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
DEL PEAK 23(10Q21.1) MUTATED 17 51 22
DEL PEAK 23(10Q21.1) WILD-TYPE 85 106 108

Figure S246.  Get High-res Image Gene #50: 'del_10q21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10q21.1' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00026

Table S247.  Gene #50: 'del_10q21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
DEL PEAK 23(10Q21.1) MUTATED 51 17 25 45
DEL PEAK 23(10Q21.1) WILD-TYPE 97 124 105 148

Figure S247.  Get High-res Image Gene #50: 'del_10q21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10q21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00045 (Fisher's exact test), Q value = 0.0019

Table S248.  Gene #50: 'del_10q21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
DEL PEAK 23(10Q21.1) MUTATED 20 18 3 13 30 38 16
DEL PEAK 23(10Q21.1) WILD-TYPE 60 68 61 44 60 100 81

Figure S248.  Get High-res Image Gene #50: 'del_10q21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S249.  Gene #51: 'del_10q23.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
DEL PEAK 24(10Q23.31) MUTATED 38 68 55
DEL PEAK 24(10Q23.31) WILD-TYPE 215 141 98

Figure S249.  Get High-res Image Gene #51: 'del_10q23.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q23.31' versus 'METHLYATION_CNMF'

P value = 0.023 (Fisher's exact test), Q value = 0.061

Table S250.  Gene #51: 'del_10q23.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
DEL PEAK 24(10Q23.31) MUTATED 22 56 31
DEL PEAK 24(10Q23.31) WILD-TYPE 80 101 99

Figure S250.  Get High-res Image Gene #51: 'del_10q23.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10q23.31' versus 'MRNASEQ_CNMF'

P value = 0.00898 (Fisher's exact test), Q value = 0.027

Table S251.  Gene #51: 'del_10q23.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
DEL PEAK 24(10Q23.31) MUTATED 54 28 32 45
DEL PEAK 24(10Q23.31) WILD-TYPE 94 113 98 148

Figure S251.  Get High-res Image Gene #51: 'del_10q23.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00021

Table S252.  Gene #51: 'del_10q23.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
DEL PEAK 24(10Q23.31) MUTATED 27 21 4 13 38 33 23
DEL PEAK 24(10Q23.31) WILD-TYPE 53 65 60 44 52 105 74

Figure S252.  Get High-res Image Gene #51: 'del_10q23.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10q25.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S253.  Gene #52: 'del_10q25.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
DEL PEAK 25(10Q25.2) MUTATED 37 69 51
DEL PEAK 25(10Q25.2) WILD-TYPE 216 140 102

Figure S253.  Get High-res Image Gene #52: 'del_10q25.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q25.2' versus 'METHLYATION_CNMF'

P value = 0.0115 (Fisher's exact test), Q value = 0.034

Table S254.  Gene #52: 'del_10q25.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
DEL PEAK 25(10Q25.2) MUTATED 21 54 27
DEL PEAK 25(10Q25.2) WILD-TYPE 81 103 103

Figure S254.  Get High-res Image Gene #52: 'del_10q25.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10q25.2' versus 'MRNASEQ_CNMF'

P value = 0.00225 (Fisher's exact test), Q value = 0.0077

Table S255.  Gene #52: 'del_10q25.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
DEL PEAK 25(10Q25.2) MUTATED 50 21 32 52
DEL PEAK 25(10Q25.2) WILD-TYPE 98 120 98 141

Figure S255.  Get High-res Image Gene #52: 'del_10q25.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10q25.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S256.  Gene #52: 'del_10q25.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
DEL PEAK 25(10Q25.2) MUTATED 26 15 2 11 39 35 27
DEL PEAK 25(10Q25.2) WILD-TYPE 54 71 62 46 51 103 70

Figure S256.  Get High-res Image Gene #52: 'del_10q25.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_11q22.3' versus 'CN_CNMF'

P value = 0.00672 (Fisher's exact test), Q value = 0.021

Table S257.  Gene #53: 'del_11q22.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
DEL PEAK 26(11Q22.3) MUTATED 32 50 29
DEL PEAK 26(11Q22.3) WILD-TYPE 221 159 124

Figure S257.  Get High-res Image Gene #53: 'del_11q22.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_11q22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0454 (Fisher's exact test), Q value = 0.11

Table S258.  Gene #53: 'del_11q22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
DEL PEAK 26(11Q22.3) MUTATED 15 17 3 13 13 29 20
DEL PEAK 26(11Q22.3) WILD-TYPE 65 69 61 44 77 109 77

Figure S258.  Get High-res Image Gene #53: 'del_11q22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_12p13.1' versus 'MRNA_CNMF'

P value = 0.00505 (Fisher's exact test), Q value = 0.016

Table S259.  Gene #54: 'del_12p13.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
DEL PEAK 27(12P13.1) MUTATED 2 14 11 1
DEL PEAK 27(12P13.1) WILD-TYPE 41 48 58 40

Figure S259.  Get High-res Image Gene #54: 'del_12p13.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_12p13.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00171 (Fisher's exact test), Q value = 0.0061

Table S260.  Gene #54: 'del_12p13.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
DEL PEAK 27(12P13.1) MUTATED 0 9 10 9
DEL PEAK 27(12P13.1) WILD-TYPE 49 32 66 40

Figure S260.  Get High-res Image Gene #54: 'del_12p13.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_12p13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S261.  Gene #54: 'del_12p13.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
DEL PEAK 27(12P13.1) MUTATED 11 53 28
DEL PEAK 27(12P13.1) WILD-TYPE 242 156 125

Figure S261.  Get High-res Image Gene #54: 'del_12p13.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_12p13.1' versus 'METHLYATION_CNMF'

P value = 0.0456 (Fisher's exact test), Q value = 0.11

Table S262.  Gene #54: 'del_12p13.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
DEL PEAK 27(12P13.1) MUTATED 11 35 20
DEL PEAK 27(12P13.1) WILD-TYPE 91 122 110

Figure S262.  Get High-res Image Gene #54: 'del_12p13.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_12p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00086 (Fisher's exact test), Q value = 0.0033

Table S263.  Gene #54: 'del_12p13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
DEL PEAK 27(12P13.1) MUTATED 18 12 1 12 16 25 8
DEL PEAK 27(12P13.1) WILD-TYPE 62 74 63 45 74 113 89

Figure S263.  Get High-res Image Gene #54: 'del_12p13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_12p13.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0281 (Fisher's exact test), Q value = 0.072

Table S264.  Gene #54: 'del_12p13.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 20 28 28 18 17
DEL PEAK 27(12P13.1) MUTATED 2 1 10 7 2 1
DEL PEAK 27(12P13.1) WILD-TYPE 22 19 18 21 16 16

Figure S264.  Get High-res Image Gene #54: 'del_12p13.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_12p13.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0266 (Fisher's exact test), Q value = 0.069

Table S265.  Gene #54: 'del_12p13.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 15 34 31
DEL PEAK 27(12P13.1) MUTATED 6 4 3 10
DEL PEAK 27(12P13.1) WILD-TYPE 49 11 31 21

Figure S265.  Get High-res Image Gene #54: 'del_12p13.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_12q21.33' versus 'MRNA_CNMF'

P value = 0.0343 (Fisher's exact test), Q value = 0.084

Table S266.  Gene #55: 'del_12q21.33' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
DEL PEAK 28(12Q21.33) MUTATED 4 15 12 2
DEL PEAK 28(12Q21.33) WILD-TYPE 39 47 57 39

Figure S266.  Get High-res Image Gene #55: 'del_12q21.33' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_12q21.33' versus 'MRNA_CHIERARCHICAL'

P value = 0.0335 (Fisher's exact test), Q value = 0.083

Table S267.  Gene #55: 'del_12q21.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
DEL PEAK 28(12Q21.33) MUTATED 3 10 9 11
DEL PEAK 28(12Q21.33) WILD-TYPE 46 31 67 38

Figure S267.  Get High-res Image Gene #55: 'del_12q21.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_12q21.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S268.  Gene #55: 'del_12q21.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
DEL PEAK 28(12Q21.33) MUTATED 13 48 29
DEL PEAK 28(12Q21.33) WILD-TYPE 240 161 124

Figure S268.  Get High-res Image Gene #55: 'del_12q21.33' versus Molecular Subtype #3: 'CN_CNMF'

'del_12q21.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00038 (Fisher's exact test), Q value = 0.0016

Table S269.  Gene #55: 'del_12q21.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
DEL PEAK 28(12Q21.33) MUTATED 16 4 3 10 21 26 10
DEL PEAK 28(12Q21.33) WILD-TYPE 64 82 61 47 69 112 87

Figure S269.  Get High-res Image Gene #55: 'del_12q21.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_14q11.2' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00011

Table S270.  Gene #56: 'del_14q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
DEL PEAK 29(14Q11.2) MUTATED 8 31 34 6
DEL PEAK 29(14Q11.2) WILD-TYPE 35 31 35 35

Figure S270.  Get High-res Image Gene #56: 'del_14q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_14q11.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S271.  Gene #56: 'del_14q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
DEL PEAK 29(14Q11.2) MUTATED 5 21 28 25
DEL PEAK 29(14Q11.2) WILD-TYPE 44 20 48 24

Figure S271.  Get High-res Image Gene #56: 'del_14q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_14q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S272.  Gene #56: 'del_14q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
DEL PEAK 29(14Q11.2) MUTATED 35 144 33
DEL PEAK 29(14Q11.2) WILD-TYPE 218 65 120

Figure S272.  Get High-res Image Gene #56: 'del_14q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_14q11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S273.  Gene #56: 'del_14q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
DEL PEAK 29(14Q11.2) MUTATED 30 73 29
DEL PEAK 29(14Q11.2) WILD-TYPE 72 84 101

Figure S273.  Get High-res Image Gene #56: 'del_14q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_14q11.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00931 (Fisher's exact test), Q value = 0.028

Table S274.  Gene #56: 'del_14q11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 168 85
DEL PEAK 29(14Q11.2) MUTATED 72 54 42
DEL PEAK 29(14Q11.2) WILD-TYPE 156 114 43

Figure S274.  Get High-res Image Gene #56: 'del_14q11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_14q11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S275.  Gene #56: 'del_14q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
DEL PEAK 29(14Q11.2) MUTATED 79 27 28 77
DEL PEAK 29(14Q11.2) WILD-TYPE 69 114 102 116

Figure S275.  Get High-res Image Gene #56: 'del_14q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_14q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S276.  Gene #56: 'del_14q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
DEL PEAK 29(14Q11.2) MUTATED 37 25 3 23 38 67 18
DEL PEAK 29(14Q11.2) WILD-TYPE 43 61 61 34 52 71 79

Figure S276.  Get High-res Image Gene #56: 'del_14q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_14q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0399 (Fisher's exact test), Q value = 0.095

Table S277.  Gene #56: 'del_14q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 20 28 28 18 17
DEL PEAK 29(14Q11.2) MUTATED 13 6 12 14 10 2
DEL PEAK 29(14Q11.2) WILD-TYPE 11 14 16 14 8 15

Figure S277.  Get High-res Image Gene #56: 'del_14q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_14q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0455 (Fisher's exact test), Q value = 0.11

Table S278.  Gene #56: 'del_14q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 15 34 31
DEL PEAK 29(14Q11.2) MUTATED 16 6 17 18
DEL PEAK 29(14Q11.2) WILD-TYPE 39 9 17 13

Figure S278.  Get High-res Image Gene #56: 'del_14q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_14q31.1' versus 'MRNA_CNMF'

P value = 0.00052 (Fisher's exact test), Q value = 0.0021

Table S279.  Gene #57: 'del_14q31.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
DEL PEAK 30(14Q31.1) MUTATED 11 30 34 7
DEL PEAK 30(14Q31.1) WILD-TYPE 32 32 35 34

Figure S279.  Get High-res Image Gene #57: 'del_14q31.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_14q31.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00048 (Fisher's exact test), Q value = 0.0019

Table S280.  Gene #57: 'del_14q31.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
DEL PEAK 30(14Q31.1) MUTATED 8 20 28 26
DEL PEAK 30(14Q31.1) WILD-TYPE 41 21 48 23

Figure S280.  Get High-res Image Gene #57: 'del_14q31.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_14q31.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S281.  Gene #57: 'del_14q31.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
DEL PEAK 30(14Q31.1) MUTATED 40 144 34
DEL PEAK 30(14Q31.1) WILD-TYPE 213 65 119

Figure S281.  Get High-res Image Gene #57: 'del_14q31.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_14q31.1' versus 'METHLYATION_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.00083

Table S282.  Gene #57: 'del_14q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
DEL PEAK 30(14Q31.1) MUTATED 29 74 32
DEL PEAK 30(14Q31.1) WILD-TYPE 73 83 98

Figure S282.  Get High-res Image Gene #57: 'del_14q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_14q31.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0319 (Fisher's exact test), Q value = 0.08

Table S283.  Gene #57: 'del_14q31.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 168 85
DEL PEAK 30(14Q31.1) MUTATED 73 59 41
DEL PEAK 30(14Q31.1) WILD-TYPE 155 109 44

Figure S283.  Get High-res Image Gene #57: 'del_14q31.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_14q31.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S284.  Gene #57: 'del_14q31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
DEL PEAK 30(14Q31.1) MUTATED 79 28 30 80
DEL PEAK 30(14Q31.1) WILD-TYPE 69 113 100 113

Figure S284.  Get High-res Image Gene #57: 'del_14q31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_14q31.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S285.  Gene #57: 'del_14q31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
DEL PEAK 30(14Q31.1) MUTATED 36 26 6 24 36 68 21
DEL PEAK 30(14Q31.1) WILD-TYPE 44 60 58 33 54 70 76

Figure S285.  Get High-res Image Gene #57: 'del_14q31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_15q11.2' versus 'MRNA_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.0019

Table S286.  Gene #58: 'del_15q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
DEL PEAK 31(15Q11.2) MUTATED 12 33 37 9
DEL PEAK 31(15Q11.2) WILD-TYPE 31 29 32 32

Figure S286.  Get High-res Image Gene #58: 'del_15q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_15q11.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00392 (Fisher's exact test), Q value = 0.013

Table S287.  Gene #58: 'del_15q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
DEL PEAK 31(15Q11.2) MUTATED 12 23 29 27
DEL PEAK 31(15Q11.2) WILD-TYPE 37 18 47 22

Figure S287.  Get High-res Image Gene #58: 'del_15q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_15q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S288.  Gene #58: 'del_15q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
DEL PEAK 31(15Q11.2) MUTATED 47 136 70
DEL PEAK 31(15Q11.2) WILD-TYPE 206 73 83

Figure S288.  Get High-res Image Gene #58: 'del_15q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q11.2' versus 'METHLYATION_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.0011

Table S289.  Gene #58: 'del_15q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
DEL PEAK 31(15Q11.2) MUTATED 36 84 41
DEL PEAK 31(15Q11.2) WILD-TYPE 66 73 89

Figure S289.  Get High-res Image Gene #58: 'del_15q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_15q11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S290.  Gene #58: 'del_15q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
DEL PEAK 31(15Q11.2) MUTATED 77 36 52 87
DEL PEAK 31(15Q11.2) WILD-TYPE 71 105 78 106

Figure S290.  Get High-res Image Gene #58: '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 = 6.2e-05

Table S291.  Gene #58: '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 80 86 64 57 90 138 97
DEL PEAK 31(15Q11.2) MUTATED 39 32 5 23 52 66 35
DEL PEAK 31(15Q11.2) WILD-TYPE 41 54 59 34 38 72 62

Figure S291.  Get High-res Image Gene #58: 'del_15q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_15q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.046 (Fisher's exact test), Q value = 0.11

Table S292.  Gene #58: 'del_15q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 20 28 28 18 17
DEL PEAK 31(15Q11.2) MUTATED 13 9 17 18 10 3
DEL PEAK 31(15Q11.2) WILD-TYPE 11 11 11 10 8 14

Figure S292.  Get High-res Image Gene #58: 'del_15q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_15q15.2' versus 'MRNA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00021

Table S293.  Gene #59: 'del_15q15.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
DEL PEAK 32(15Q15.2) MUTATED 11 34 39 8
DEL PEAK 32(15Q15.2) WILD-TYPE 32 28 30 33

Figure S293.  Get High-res Image Gene #59: 'del_15q15.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_15q15.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00179 (Fisher's exact test), Q value = 0.0062

Table S294.  Gene #59: 'del_15q15.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
DEL PEAK 32(15Q15.2) MUTATED 11 24 31 26
DEL PEAK 32(15Q15.2) WILD-TYPE 38 17 45 23

Figure S294.  Get High-res Image Gene #59: 'del_15q15.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_15q15.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S295.  Gene #59: 'del_15q15.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
DEL PEAK 32(15Q15.2) MUTATED 48 134 69
DEL PEAK 32(15Q15.2) WILD-TYPE 205 75 84

Figure S295.  Get High-res Image Gene #59: 'del_15q15.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q15.2' versus 'METHLYATION_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00048

Table S296.  Gene #59: 'del_15q15.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
DEL PEAK 32(15Q15.2) MUTATED 36 84 38
DEL PEAK 32(15Q15.2) WILD-TYPE 66 73 92

Figure S296.  Get High-res Image Gene #59: 'del_15q15.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_15q15.2' versus 'MRNASEQ_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 7e-04

Table S297.  Gene #59: 'del_15q15.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
DEL PEAK 32(15Q15.2) MUTATED 78 39 48 85
DEL PEAK 32(15Q15.2) WILD-TYPE 70 102 82 108

Figure S297.  Get High-res Image Gene #59: 'del_15q15.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_15q15.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S298.  Gene #59: 'del_15q15.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
DEL PEAK 32(15Q15.2) MUTATED 41 32 5 23 47 66 36
DEL PEAK 32(15Q15.2) WILD-TYPE 39 54 59 34 43 72 61

Figure S298.  Get High-res Image Gene #59: 'del_15q15.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_15q21.1' versus 'MRNA_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.0013

Table S299.  Gene #60: 'del_15q21.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
DEL PEAK 33(15Q21.1) MUTATED 14 33 38 8
DEL PEAK 33(15Q21.1) WILD-TYPE 29 29 31 33

Figure S299.  Get High-res Image Gene #60: 'del_15q21.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_15q21.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.0237 (Fisher's exact test), Q value = 0.063

Table S300.  Gene #60: 'del_15q21.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
DEL PEAK 33(15Q21.1) MUTATED 14 23 30 26
DEL PEAK 33(15Q21.1) WILD-TYPE 35 18 46 23

Figure S300.  Get High-res Image Gene #60: 'del_15q21.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_15q21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S301.  Gene #60: 'del_15q21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
DEL PEAK 33(15Q21.1) MUTATED 48 131 69
DEL PEAK 33(15Q21.1) WILD-TYPE 205 78 84

Figure S301.  Get High-res Image Gene #60: 'del_15q21.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q21.1' versus 'METHLYATION_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.00087

Table S302.  Gene #60: 'del_15q21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
DEL PEAK 33(15Q21.1) MUTATED 35 82 37
DEL PEAK 33(15Q21.1) WILD-TYPE 67 75 93

Figure S302.  Get High-res Image Gene #60: 'del_15q21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_15q21.1' versus 'MRNASEQ_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.0012

Table S303.  Gene #60: 'del_15q21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
DEL PEAK 33(15Q21.1) MUTATED 76 39 47 85
DEL PEAK 33(15Q21.1) WILD-TYPE 72 102 83 108

Figure S303.  Get High-res Image Gene #60: 'del_15q21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_15q21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S304.  Gene #60: 'del_15q21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
DEL PEAK 33(15Q21.1) MUTATED 39 31 5 23 46 65 38
DEL PEAK 33(15Q21.1) WILD-TYPE 41 55 59 34 44 73 59

Figure S304.  Get High-res Image Gene #60: 'del_15q21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_15q22.33' versus 'MRNA_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00052

Table S305.  Gene #61: 'del_15q22.33' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
DEL PEAK 34(15Q22.33) MUTATED 12 31 36 6
DEL PEAK 34(15Q22.33) WILD-TYPE 31 31 33 35

Figure S305.  Get High-res Image Gene #61: 'del_15q22.33' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_15q22.33' versus 'MRNA_CHIERARCHICAL'

P value = 0.00089 (Fisher's exact test), Q value = 0.0034

Table S306.  Gene #61: 'del_15q22.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
DEL PEAK 34(15Q22.33) MUTATED 11 21 25 28
DEL PEAK 34(15Q22.33) WILD-TYPE 38 20 51 21

Figure S306.  Get High-res Image Gene #61: 'del_15q22.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_15q22.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S307.  Gene #61: 'del_15q22.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
DEL PEAK 34(15Q22.33) MUTATED 41 129 68
DEL PEAK 34(15Q22.33) WILD-TYPE 212 80 85

Figure S307.  Get High-res Image Gene #61: 'del_15q22.33' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q22.33' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00011

Table S308.  Gene #61: 'del_15q22.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
DEL PEAK 34(15Q22.33) MUTATED 34 83 35
DEL PEAK 34(15Q22.33) WILD-TYPE 68 74 95

Figure S308.  Get High-res Image Gene #61: 'del_15q22.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_15q22.33' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00017

Table S309.  Gene #61: 'del_15q22.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
DEL PEAK 34(15Q22.33) MUTATED 74 32 49 82
DEL PEAK 34(15Q22.33) WILD-TYPE 74 109 81 111

Figure S309.  Get High-res Image Gene #61: 'del_15q22.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_15q22.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S310.  Gene #61: 'del_15q22.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
DEL PEAK 34(15Q22.33) MUTATED 37 29 3 23 50 64 31
DEL PEAK 34(15Q22.33) WILD-TYPE 43 57 61 34 40 74 66

Figure S310.  Get High-res Image Gene #61: 'del_15q22.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MRNA_CNMF'

P value = 0.0434 (Fisher's exact test), Q value = 0.1

Table S311.  Gene #63: 'del_16q23.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
DEL PEAK 36(16Q23.1) MUTATED 12 7 6 5
DEL PEAK 36(16Q23.1) WILD-TYPE 31 55 63 36

Figure S311.  Get High-res Image Gene #63: 'del_16q23.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_16q23.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00365 (Fisher's exact test), Q value = 0.012

Table S312.  Gene #63: 'del_16q23.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
DEL PEAK 36(16Q23.1) MUTATED 15 3 6 6
DEL PEAK 36(16Q23.1) WILD-TYPE 34 38 70 43

Figure S312.  Get High-res Image Gene #63: 'del_16q23.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_17p12' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S313.  Gene #64: 'del_17p12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
DEL PEAK 37(17P12) MUTATED 16 50 52 15
DEL PEAK 37(17P12) WILD-TYPE 27 12 17 26

Figure S313.  Get High-res Image Gene #64: 'del_17p12' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_17p12' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S314.  Gene #64: 'del_17p12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
DEL PEAK 37(17P12) MUTATED 14 32 49 38
DEL PEAK 37(17P12) WILD-TYPE 35 9 27 11

Figure S314.  Get High-res Image Gene #64: 'del_17p12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_17p12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S315.  Gene #64: 'del_17p12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
DEL PEAK 37(17P12) MUTATED 77 171 122
DEL PEAK 37(17P12) WILD-TYPE 176 38 31

Figure S315.  Get High-res Image Gene #64: 'del_17p12' versus Molecular Subtype #3: 'CN_CNMF'

'del_17p12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S316.  Gene #64: 'del_17p12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
DEL PEAK 37(17P12) MUTATED 45 128 61
DEL PEAK 37(17P12) WILD-TYPE 57 29 69

Figure S316.  Get High-res Image Gene #64: 'del_17p12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_17p12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S317.  Gene #64: 'del_17p12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
DEL PEAK 37(17P12) MUTATED 116 57 72 123
DEL PEAK 37(17P12) WILD-TYPE 32 84 58 70

Figure S317.  Get High-res Image Gene #64: 'del_17p12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_17p12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S318.  Gene #64: 'del_17p12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
DEL PEAK 37(17P12) MUTATED 58 49 8 39 68 106 40
DEL PEAK 37(17P12) WILD-TYPE 22 37 56 18 22 32 57

Figure S318.  Get High-res Image Gene #64: 'del_17p12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_17p12' versus 'MIRSEQ_CNMF'

P value = 0.0129 (Fisher's exact test), Q value = 0.037

Table S319.  Gene #64: 'del_17p12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 211 95 232
DEL PEAK 37(17P12) MUTATED 141 47 135
DEL PEAK 37(17P12) WILD-TYPE 70 48 97

Figure S319.  Get High-res Image Gene #64: 'del_17p12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_17p12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0128 (Fisher's exact test), Q value = 0.037

Table S320.  Gene #64: 'del_17p12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 139 171
DEL PEAK 37(17P12) MUTATED 128 98 97
DEL PEAK 37(17P12) WILD-TYPE 100 41 74

Figure S320.  Get High-res Image Gene #64: 'del_17p12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_17p12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0357 (Fisher's exact test), Q value = 0.087

Table S321.  Gene #64: 'del_17p12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 20 28 28 18 17
DEL PEAK 37(17P12) MUTATED 18 14 21 16 12 5
DEL PEAK 37(17P12) WILD-TYPE 6 6 7 12 6 12

Figure S321.  Get High-res Image Gene #64: 'del_17p12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_17q24.3' versus 'CN_CNMF'

P value = 0.00529 (Fisher's exact test), Q value = 0.017

Table S322.  Gene #65: 'del_17q24.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
DEL PEAK 38(17Q24.3) MUTATED 26 44 25
DEL PEAK 38(17Q24.3) WILD-TYPE 227 165 128

Figure S322.  Get High-res Image Gene #65: 'del_17q24.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_18p11.31' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S323.  Gene #66: 'del_18p11.31' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
DEL PEAK 39(18P11.31) MUTATED 11 51 52 13
DEL PEAK 39(18P11.31) WILD-TYPE 32 11 17 28

Figure S323.  Get High-res Image Gene #66: 'del_18p11.31' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_18p11.31' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S324.  Gene #66: 'del_18p11.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
DEL PEAK 39(18P11.31) MUTATED 9 34 43 41
DEL PEAK 39(18P11.31) WILD-TYPE 40 7 33 8

Figure S324.  Get High-res Image Gene #66: 'del_18p11.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_18p11.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S325.  Gene #66: 'del_18p11.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
DEL PEAK 39(18P11.31) MUTATED 72 189 109
DEL PEAK 39(18P11.31) WILD-TYPE 181 20 44

Figure S325.  Get High-res Image Gene #66: 'del_18p11.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_18p11.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S326.  Gene #66: 'del_18p11.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
DEL PEAK 39(18P11.31) MUTATED 50 141 50
DEL PEAK 39(18P11.31) WILD-TYPE 52 16 80

Figure S326.  Get High-res Image Gene #66: 'del_18p11.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_18p11.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S327.  Gene #66: 'del_18p11.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
DEL PEAK 39(18P11.31) MUTATED 134 45 71 118
DEL PEAK 39(18P11.31) WILD-TYPE 14 96 59 75

Figure S327.  Get High-res Image Gene #66: 'del_18p11.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_18p11.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S328.  Gene #66: 'del_18p11.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
DEL PEAK 39(18P11.31) MUTATED 66 46 6 40 70 106 34
DEL PEAK 39(18P11.31) WILD-TYPE 14 40 58 17 20 32 63

Figure S328.  Get High-res Image Gene #66: 'del_18p11.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_18p11.31' versus 'MIRSEQ_CNMF'

P value = 0.00315 (Fisher's exact test), Q value = 0.011

Table S329.  Gene #66: 'del_18p11.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 211 95 232
DEL PEAK 39(18P11.31) MUTATED 143 47 129
DEL PEAK 39(18P11.31) WILD-TYPE 68 48 103

Figure S329.  Get High-res Image Gene #66: 'del_18p11.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_18p11.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00712 (Fisher's exact test), Q value = 0.022

Table S330.  Gene #66: 'del_18p11.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 139 171
DEL PEAK 39(18P11.31) MUTATED 126 98 95
DEL PEAK 39(18P11.31) WILD-TYPE 102 41 76

Figure S330.  Get High-res Image Gene #66: 'del_18p11.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_18p11.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00011

Table S331.  Gene #66: 'del_18p11.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 20 28 28 18 17
DEL PEAK 39(18P11.31) MUTATED 21 9 24 21 13 4
DEL PEAK 39(18P11.31) WILD-TYPE 3 11 4 7 5 13

Figure S331.  Get High-res Image Gene #66: 'del_18p11.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_18p11.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00053 (Fisher's exact test), Q value = 0.0021

Table S332.  Gene #66: 'del_18p11.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 15 34 31
DEL PEAK 39(18P11.31) MUTATED 28 13 23 28
DEL PEAK 39(18P11.31) WILD-TYPE 27 2 11 3

Figure S332.  Get High-res Image Gene #66: 'del_18p11.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18q12.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S333.  Gene #67: 'del_18q12.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
DEL PEAK 40(18Q12.2) MUTATED 17 54 56 17
DEL PEAK 40(18Q12.2) WILD-TYPE 26 8 13 24

Figure S333.  Get High-res Image Gene #67: 'del_18q12.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_18q12.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S334.  Gene #67: 'del_18q12.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
DEL PEAK 40(18Q12.2) MUTATED 14 36 52 42
DEL PEAK 40(18Q12.2) WILD-TYPE 35 5 24 7

Figure S334.  Get High-res Image Gene #67: 'del_18q12.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_18q12.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S335.  Gene #67: 'del_18q12.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
DEL PEAK 40(18Q12.2) MUTATED 83 196 137
DEL PEAK 40(18Q12.2) WILD-TYPE 170 13 16

Figure S335.  Get High-res Image Gene #67: 'del_18q12.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_18q12.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S336.  Gene #67: 'del_18q12.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
DEL PEAK 40(18Q12.2) MUTATED 57 149 62
DEL PEAK 40(18Q12.2) WILD-TYPE 45 8 68

Figure S336.  Get High-res Image Gene #67: 'del_18q12.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_18q12.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S337.  Gene #67: 'del_18q12.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
DEL PEAK 40(18Q12.2) MUTATED 135 61 83 135
DEL PEAK 40(18Q12.2) WILD-TYPE 13 80 47 58

Figure S337.  Get High-res Image Gene #67: 'del_18q12.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_18q12.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S338.  Gene #67: 'del_18q12.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
DEL PEAK 40(18Q12.2) MUTATED 67 58 8 45 77 114 45
DEL PEAK 40(18Q12.2) WILD-TYPE 13 28 56 12 13 24 52

Figure S338.  Get High-res Image Gene #67: 'del_18q12.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_18q12.2' versus 'MIRSEQ_CNMF'

P value = 0.00056 (Fisher's exact test), Q value = 0.0022

Table S339.  Gene #67: 'del_18q12.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 211 95 232
DEL PEAK 40(18Q12.2) MUTATED 161 53 148
DEL PEAK 40(18Q12.2) WILD-TYPE 50 42 84

Figure S339.  Get High-res Image Gene #67: 'del_18q12.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_18q12.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00755 (Fisher's exact test), Q value = 0.023

Table S340.  Gene #67: 'del_18q12.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 139 171
DEL PEAK 40(18Q12.2) MUTATED 147 108 107
DEL PEAK 40(18Q12.2) WILD-TYPE 81 31 64

Figure S340.  Get High-res Image Gene #67: 'del_18q12.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_18q12.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00021

Table S341.  Gene #67: 'del_18q12.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 20 28 28 18 17
DEL PEAK 40(18Q12.2) MUTATED 22 13 27 23 14 5
DEL PEAK 40(18Q12.2) WILD-TYPE 2 7 1 5 4 12

Figure S341.  Get High-res Image Gene #67: 'del_18q12.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_18q12.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00017

Table S342.  Gene #67: 'del_18q12.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 15 34 31
DEL PEAK 40(18Q12.2) MUTATED 33 15 26 30
DEL PEAK 40(18Q12.2) WILD-TYPE 22 0 8 1

Figure S342.  Get High-res Image Gene #67: 'del_18q12.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18q21.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S343.  Gene #68: 'del_18q21.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
DEL PEAK 41(18Q21.2) MUTATED 17 55 57 18
DEL PEAK 41(18Q21.2) WILD-TYPE 26 7 12 23

Figure S343.  Get High-res Image Gene #68: 'del_18q21.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_18q21.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S344.  Gene #68: 'del_18q21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
DEL PEAK 41(18Q21.2) MUTATED 14 36 55 42
DEL PEAK 41(18Q21.2) WILD-TYPE 35 5 21 7

Figure S344.  Get High-res Image Gene #68: 'del_18q21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_18q21.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S345.  Gene #68: 'del_18q21.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
DEL PEAK 41(18Q21.2) MUTATED 91 199 142
DEL PEAK 41(18Q21.2) WILD-TYPE 162 10 11

Figure S345.  Get High-res Image Gene #68: 'del_18q21.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_18q21.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S346.  Gene #68: 'del_18q21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
DEL PEAK 41(18Q21.2) MUTATED 57 151 73
DEL PEAK 41(18Q21.2) WILD-TYPE 45 6 57

Figure S346.  Get High-res Image Gene #68: 'del_18q21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_18q21.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S347.  Gene #68: 'del_18q21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
DEL PEAK 41(18Q21.2) MUTATED 136 69 88 137
DEL PEAK 41(18Q21.2) WILD-TYPE 12 72 42 56

Figure S347.  Get High-res Image Gene #68: 'del_18q21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_18q21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S348.  Gene #68: 'del_18q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
DEL PEAK 41(18Q21.2) MUTATED 68 62 13 45 80 116 46
DEL PEAK 41(18Q21.2) WILD-TYPE 12 24 51 12 10 22 51

Figure S348.  Get High-res Image Gene #68: 'del_18q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_18q21.2' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00011

Table S349.  Gene #68: 'del_18q21.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 211 95 232
DEL PEAK 41(18Q21.2) MUTATED 170 55 153
DEL PEAK 41(18Q21.2) WILD-TYPE 41 40 79

Figure S349.  Get High-res Image Gene #68: 'del_18q21.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_18q21.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0314 (Fisher's exact test), Q value = 0.079

Table S350.  Gene #68: 'del_18q21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 139 171
DEL PEAK 41(18Q21.2) MUTATED 158 109 111
DEL PEAK 41(18Q21.2) WILD-TYPE 70 30 60

Figure S350.  Get High-res Image Gene #68: 'del_18q21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_18q21.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S351.  Gene #68: 'del_18q21.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 20 28 28 18 17
DEL PEAK 41(18Q21.2) MUTATED 24 14 27 23 14 6
DEL PEAK 41(18Q21.2) WILD-TYPE 0 6 1 5 4 11

Figure S351.  Get High-res Image Gene #68: 'del_18q21.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_18q21.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00048

Table S352.  Gene #68: 'del_18q21.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 15 34 31
DEL PEAK 41(18Q21.2) MUTATED 34 15 29 30
DEL PEAK 41(18Q21.2) WILD-TYPE 21 0 5 1

Figure S352.  Get High-res Image Gene #68: 'del_18q21.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18q22.1' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S353.  Gene #69: 'del_18q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
DEL PEAK 42(18Q22.1) MUTATED 17 55 56 19
DEL PEAK 42(18Q22.1) WILD-TYPE 26 7 13 22

Figure S353.  Get High-res Image Gene #69: 'del_18q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_18q22.1' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S354.  Gene #69: 'del_18q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
DEL PEAK 42(18Q22.1) MUTATED 15 36 54 42
DEL PEAK 42(18Q22.1) WILD-TYPE 34 5 22 7

Figure S354.  Get High-res Image Gene #69: 'del_18q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_18q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S355.  Gene #69: 'del_18q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
DEL PEAK 42(18Q22.1) MUTATED 87 199 141
DEL PEAK 42(18Q22.1) WILD-TYPE 166 10 12

Figure S355.  Get High-res Image Gene #69: 'del_18q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_18q22.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S356.  Gene #69: 'del_18q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
DEL PEAK 42(18Q22.1) MUTATED 55 151 70
DEL PEAK 42(18Q22.1) WILD-TYPE 47 6 60

Figure S356.  Get High-res Image Gene #69: 'del_18q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_18q22.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S357.  Gene #69: 'del_18q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
DEL PEAK 42(18Q22.1) MUTATED 135 69 85 136
DEL PEAK 42(18Q22.1) WILD-TYPE 13 72 45 57

Figure S357.  Get High-res Image Gene #69: 'del_18q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_18q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S358.  Gene #69: 'del_18q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
DEL PEAK 42(18Q22.1) MUTATED 67 61 13 43 79 115 47
DEL PEAK 42(18Q22.1) WILD-TYPE 13 25 51 14 11 23 50

Figure S358.  Get High-res Image Gene #69: 'del_18q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_18q22.1' versus 'MIRSEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00044

Table S359.  Gene #69: 'del_18q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 211 95 232
DEL PEAK 42(18Q22.1) MUTATED 167 53 153
DEL PEAK 42(18Q22.1) WILD-TYPE 44 42 79

Figure S359.  Get High-res Image Gene #69: 'del_18q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_18q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00011

Table S360.  Gene #69: 'del_18q22.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 20 28 28 18 17
DEL PEAK 42(18Q22.1) MUTATED 24 14 26 22 14 6
DEL PEAK 42(18Q22.1) WILD-TYPE 0 6 2 6 4 11

Figure S360.  Get High-res Image Gene #69: 'del_18q22.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_18q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9e-04 (Fisher's exact test), Q value = 0.0034

Table S361.  Gene #69: 'del_18q22.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 15 34 31
DEL PEAK 42(18Q22.1) MUTATED 34 15 29 28
DEL PEAK 42(18Q22.1) WILD-TYPE 21 0 5 3

Figure S361.  Get High-res Image Gene #69: 'del_18q22.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19p13.3' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00011

Table S362.  Gene #70: 'del_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
DEL PEAK 43(19P13.3) MUTATED 19 42 36
DEL PEAK 43(19P13.3) WILD-TYPE 234 167 117

Figure S362.  Get High-res Image Gene #70: 'del_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_19p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00529 (Fisher's exact test), Q value = 0.017

Table S363.  Gene #70: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 139 171
DEL PEAK 43(19P13.3) MUTATED 28 35 25
DEL PEAK 43(19P13.3) WILD-TYPE 200 104 146

Figure S363.  Get High-res Image Gene #70: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0373 (Fisher's exact test), Q value = 0.09

Table S364.  Gene #70: 'del_19p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 20 28 28 18 17
DEL PEAK 43(19P13.3) MUTATED 9 3 10 2 3 2
DEL PEAK 43(19P13.3) WILD-TYPE 15 17 18 26 15 15

Figure S364.  Get High-res Image Gene #70: 'del_19p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_20p12.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00056 (Fisher's exact test), Q value = 0.0022

Table S365.  Gene #71: 'del_20p12.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
DEL PEAK 44(20P12.1) MUTATED 4 16 10 14
DEL PEAK 44(20P12.1) WILD-TYPE 45 25 66 35

Figure S365.  Get High-res Image Gene #71: 'del_20p12.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_20p12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S366.  Gene #71: 'del_20p12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
DEL PEAK 44(20P12.1) MUTATED 30 57 48
DEL PEAK 44(20P12.1) WILD-TYPE 223 152 105

Figure S366.  Get High-res Image Gene #71: 'del_20p12.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_20p12.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S367.  Gene #71: 'del_20p12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
DEL PEAK 44(20P12.1) MUTATED 18 57 16
DEL PEAK 44(20P12.1) WILD-TYPE 84 100 114

Figure S367.  Get High-res Image Gene #71: 'del_20p12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_20p12.1' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00031

Table S368.  Gene #71: 'del_20p12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
DEL PEAK 44(20P12.1) MUTATED 53 20 27 34
DEL PEAK 44(20P12.1) WILD-TYPE 95 121 103 159

Figure S368.  Get High-res Image Gene #71: 'del_20p12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_20p12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S369.  Gene #71: 'del_20p12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
DEL PEAK 44(20P12.1) MUTATED 25 20 0 14 29 36 10
DEL PEAK 44(20P12.1) WILD-TYPE 55 66 64 43 61 102 87

Figure S369.  Get High-res Image Gene #71: 'del_20p12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_20p12.1' versus 'MIRSEQ_CNMF'

P value = 0.0295 (Fisher's exact test), Q value = 0.075

Table S370.  Gene #71: 'del_20p12.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 211 95 232
DEL PEAK 44(20P12.1) MUTATED 57 15 42
DEL PEAK 44(20P12.1) WILD-TYPE 154 80 190

Figure S370.  Get High-res Image Gene #71: 'del_20p12.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_20p12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0129 (Fisher's exact test), Q value = 0.037

Table S371.  Gene #71: 'del_20p12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 139 171
DEL PEAK 44(20P12.1) MUTATED 46 41 27
DEL PEAK 44(20P12.1) WILD-TYPE 182 98 144

Figure S371.  Get High-res Image Gene #71: 'del_20p12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_21q11.2' versus 'MRNA_CNMF'

P value = 0.0199 (Fisher's exact test), Q value = 0.054

Table S372.  Gene #72: 'del_21q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
DEL PEAK 45(21Q11.2) MUTATED 11 29 25 8
DEL PEAK 45(21Q11.2) WILD-TYPE 32 33 44 33

Figure S372.  Get High-res Image Gene #72: 'del_21q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_21q11.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00141 (Fisher's exact test), Q value = 0.0051

Table S373.  Gene #72: 'del_21q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
DEL PEAK 45(21Q11.2) MUTATED 11 23 19 20
DEL PEAK 45(21Q11.2) WILD-TYPE 38 18 57 29

Figure S373.  Get High-res Image Gene #72: 'del_21q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_21q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S374.  Gene #72: 'del_21q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
DEL PEAK 45(21Q11.2) MUTATED 59 105 50
DEL PEAK 45(21Q11.2) WILD-TYPE 194 104 103

Figure S374.  Get High-res Image Gene #72: 'del_21q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_21q11.2' versus 'METHLYATION_CNMF'

P value = 0.00133 (Fisher's exact test), Q value = 0.0049

Table S375.  Gene #72: 'del_21q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
DEL PEAK 45(21Q11.2) MUTATED 29 73 37
DEL PEAK 45(21Q11.2) WILD-TYPE 73 84 93

Figure S375.  Get High-res Image Gene #72: 'del_21q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_21q11.2' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00017

Table S376.  Gene #72: 'del_21q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
DEL PEAK 45(21Q11.2) MUTATED 75 33 40 64
DEL PEAK 45(21Q11.2) WILD-TYPE 73 108 90 129

Figure S376.  Get High-res Image Gene #72: 'del_21q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_21q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00037 (Fisher's exact test), Q value = 0.0016

Table S377.  Gene #72: 'del_21q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
DEL PEAK 45(21Q11.2) MUTATED 35 27 9 23 38 55 25
DEL PEAK 45(21Q11.2) WILD-TYPE 45 59 55 34 52 83 72

Figure S377.  Get High-res Image Gene #72: 'del_21q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_21q11.2' versus 'MIRSEQ_CNMF'

P value = 0.0379 (Fisher's exact test), Q value = 0.091

Table S378.  Gene #72: 'del_21q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 211 95 232
DEL PEAK 45(21Q11.2) MUTATED 86 25 77
DEL PEAK 45(21Q11.2) WILD-TYPE 125 70 155

Figure S378.  Get High-res Image Gene #72: 'del_21q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_22q13.32' versus 'MRNA_CNMF'

P value = 0.0026 (Fisher's exact test), Q value = 0.0088

Table S379.  Gene #73: 'del_22q13.32' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
DEL PEAK 46(22Q13.32) MUTATED 13 31 34 8
DEL PEAK 46(22Q13.32) WILD-TYPE 30 31 35 33

Figure S379.  Get High-res Image Gene #73: 'del_22q13.32' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_22q13.32' versus 'MRNA_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.00052

Table S380.  Gene #73: 'del_22q13.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
DEL PEAK 46(22Q13.32) MUTATED 7 19 33 27
DEL PEAK 46(22Q13.32) WILD-TYPE 42 22 43 22

Figure S380.  Get High-res Image Gene #73: 'del_22q13.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_22q13.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.2e-05

Table S381.  Gene #73: 'del_22q13.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
DEL PEAK 46(22Q13.32) MUTATED 53 117 59
DEL PEAK 46(22Q13.32) WILD-TYPE 200 92 94

Figure S381.  Get High-res Image Gene #73: 'del_22q13.32' versus Molecular Subtype #3: 'CN_CNMF'

'del_22q13.32' versus 'MRNASEQ_CNMF'

P value = 0.00409 (Fisher's exact test), Q value = 0.013

Table S382.  Gene #73: 'del_22q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
DEL PEAK 46(22Q13.32) MUTATED 66 37 44 81
DEL PEAK 46(22Q13.32) WILD-TYPE 82 104 86 112

Figure S382.  Get High-res Image Gene #73: 'del_22q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_22q13.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00021

Table S383.  Gene #73: 'del_22q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
DEL PEAK 46(22Q13.32) MUTATED 34 30 8 24 38 67 27
DEL PEAK 46(22Q13.32) WILD-TYPE 46 56 56 33 52 71 70

Figure S383.  Get High-res Image Gene #73: 'del_22q13.32' 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/COADREAD-TP/19781253/transformed.cor.cli.txt

  • Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/COADREAD-TP/20147373/COADREAD-TP.transferedmergedcluster.txt

  • Number of patients = 615

  • Number of significantly focal cnvs = 73

  • Number of molecular subtypes = 12

  • Exclude genes that fewer than K tumors have alterations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
Copyright © 2015 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle