Correlation between copy number variation genes (focal events) and molecular subtypes
Colon Adenocarcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C16Q1WF4
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/C16Q1WF4
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 69 focal events and 12 molecular subtypes across 450 patients, 366 significant findings detected with P value < 0.05 and Q value < 0.25.

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

  • amp_5p13.2 cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

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

  • amp_7p21.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_8p11.23 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

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

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

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

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

  • amp_12p13.33 cnv correlated to 'CN_CNMF'.

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

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

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

  • amp_16q12.1 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_17p11.2 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF', and 'METHLYATION_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', and 'MIRSEQ_CNMF'.

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

  • amp_19q13.11 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

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

  • amp_20q13.12 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_1p36.11 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

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

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

  • del_1q43 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • del_3p26.2 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_3p14.2 cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

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

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

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

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

  • del_5q21.1 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

  • del_6p25.3 cnv correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_6q26 cnv correlated to 'RPPA_CNMF'.

  • del_8p23.3 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_8p22 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_8q11.1 cnv correlated to 'CN_CNMF'.

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

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

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

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

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

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

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

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

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

  • del_17q24.3 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • del_18p11.31 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_18q12.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_18q21.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

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

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 69 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, 366 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 21 323 (72%) 127 1e-05
(6.13e-05) 		1e-05
(6.13e-05) 		1e-05
(6.13e-05) 		1e-05
(6.13e-05) 		0.00948
(0.0278) 		4e-05
(0.000211) 		1e-05
(6.13e-05) 		1e-05
(6.13e-05) 		0.823
(0.905) 		0.00166
(0.00592) 		1
(1.00) 		0.00405
(0.0134)
amp 20q12 324 (72%) 126 1e-05
(6.13e-05) 		1e-05
(6.13e-05) 		1e-05
(6.13e-05) 		1e-05
(6.13e-05) 		0.0187
(0.0489) 		9e-05
(0.000421) 		1e-05
(6.13e-05) 		1e-05
(6.13e-05) 		0.775
(0.88) 		0.00129
(0.00471) 		1
(1.00) 		0.00559
(0.0176)
amp 20q13 12 326 (72%) 124 1e-05
(6.13e-05) 		1e-05
(6.13e-05) 		1e-05
(6.13e-05) 		1e-05
(6.13e-05) 		0.0112
(0.0322) 		6e-05
(0.000297) 		1e-05
(6.13e-05) 		1e-05
(6.13e-05) 		0.791
(0.889) 		0.00268
(0.00925) 		1
(1.00) 		0.00589
(0.0184)
amp 17q12 114 (25%) 336 0.025
(0.0622) 		0.0142
(0.039) 		1e-05
(6.13e-05) 		5e-05
(0.000254) 		0.669
(0.802) 		0.0188
(0.0491) 		5e-05
(0.000254) 		0.00108
(0.00405) 		0.0365
(0.0866) 		0.0139
(0.0383) 		0.532
(0.688) 		0.559
(0.704)
del 8p22 203 (45%) 247 0.00436
(0.0142) 		0.00017
(0.000753) 		1e-05
(6.13e-05) 		3e-05
(0.000167) 		0.42
(0.583) 		0.0174
(0.0463) 		1e-05
(6.13e-05) 		1e-05
(6.13e-05) 		0.453
(0.611) 		0.0145
(0.0396) 		0.762
(0.87) 		0.0477
(0.108)
del 14q31 1 150 (33%) 300 1e-05
(6.13e-05) 		0.00012
(0.000552) 		1e-05
(6.13e-05) 		1e-05
(6.13e-05) 		0.019
(0.0492) 		0.218
(0.369) 		1e-05
(6.13e-05) 		1e-05
(6.13e-05) 		0.279
(0.432) 		0.0219
(0.0553) 		0.27
(0.428) 		0.014
(0.0386)
del 17p12 254 (56%) 196 1e-05
(6.13e-05) 		1e-05
(6.13e-05) 		1e-05
(6.13e-05) 		1e-05
(6.13e-05) 		0.0517
(0.116) 		0.00076
(0.00294) 		1e-05
(6.13e-05) 		1e-05
(6.13e-05) 		0.669
(0.802) 		0.0217
(0.0552) 		0.608
(0.749) 		0.00131
(0.00474)
del 18p11 31 246 (55%) 204 1e-05
(6.13e-05) 		1e-05
(6.13e-05) 		1e-05
(6.13e-05) 		1e-05
(6.13e-05) 		0.223
(0.372) 		0.0045
(0.0144) 		1e-05
(6.13e-05) 		1e-05
(6.13e-05) 		0.838
(0.917) 		0.0111
(0.0321) 		0.162
(0.289) 		0.0036
(0.0122)
del 18q12 2 274 (61%) 176 1e-05
(6.13e-05) 		1e-05
(6.13e-05) 		1e-05
(6.13e-05) 		1e-05
(6.13e-05) 		0.361
(0.525) 		0.00444
(0.0142) 		1e-05
(6.13e-05) 		1e-05
(6.13e-05) 		0.914
(0.962) 		0.02
(0.0511) 		0.151
(0.274) 		0.00523
(0.0167)
del 18q21 2 287 (64%) 163 1e-05
(6.13e-05) 		1e-05
(6.13e-05) 		1e-05
(6.13e-05) 		1e-05
(6.13e-05) 		0.177
(0.308) 		0.00707
(0.0217) 		1e-05
(6.13e-05) 		1e-05
(6.13e-05) 		0.377
(0.543) 		0.0345
(0.0824) 		0.0939
(0.189) 		0.00818
(0.0245)
del 20p12 1 86 (19%) 364 0.048
(0.109) 		0.0285
(0.0698) 		2e-05
(0.000117) 		8e-05
(0.000385) 		0.0835
(0.172) 		0.0166
(0.0444) 		1e-05
(6.13e-05) 		3e-05
(0.000167) 		0.105
(0.207) 		0.0104
(0.0302) 		0.802
(0.891) 		0.0477
(0.108)
amp 7p21 2 255 (57%) 195 0.00989
(0.0289) 		3e-05
(0.000167) 		1e-05
(6.13e-05) 		1e-05
(6.13e-05) 		0.0804
(0.168) 		0.0005
(0.002) 		4e-05
(0.000211) 		1e-05
(6.13e-05) 		0.544
(0.696) 		0.455
(0.611) 		0.843
(0.921) 		0.0342
(0.0819)
amp 8q12 1 236 (52%) 214 0.488
(0.646) 		0.00581
(0.0182) 		1e-05
(6.13e-05) 		0.00387
(0.013) 		0.268
(0.428) 		0.0192
(0.0493) 		8e-05
(0.000385) 		4e-05
(0.000211) 		0.384
(0.551) 		0.0378
(0.0888) 		0.272
(0.43) 		0.0134
(0.0374)
amp 20p11 21 252 (56%) 198 0.00211
(0.00737) 		3e-05
(0.000167) 		1e-05
(6.13e-05) 		1e-05
(6.13e-05) 		0.00639
(0.0197) 		0.07
(0.149) 		1e-05
(6.13e-05) 		1e-05
(6.13e-05) 		0.166
(0.293) 		0.0375
(0.0888) 		0.921
(0.964) 		0.0504
(0.113)
del 1p36 11 168 (37%) 282 7e-05
(0.000341) 		0.00785
(0.0236) 		1e-05
(6.13e-05) 		1e-05
(6.13e-05) 		0.0947
(0.19) 		0.028
(0.0689) 		1e-05
(6.13e-05) 		1e-05
(6.13e-05) 		0.664
(0.799) 		0.0203
(0.0517) 		0.92
(0.964) 		0.257
(0.416)
amp 8q24 21 260 (58%) 190 0.561
(0.705) 		0.0294
(0.0713) 		1e-05
(6.13e-05) 		0.00014
(0.00063) 		0.184
(0.318) 		0.0919
(0.187) 		0.00021
(0.000915) 		5e-05
(0.000254) 		0.713
(0.833) 		0.0378
(0.0888) 		0.264
(0.424) 		0.0152
(0.0412)
amp 11p15 5 94 (21%) 356 5e-05
(0.000254) 		0.0059
(0.0184) 		3e-05
(0.000167) 		7e-05
(0.000341) 		0.129
(0.243) 		0.19
(0.326) 		1e-05
(6.13e-05) 		1e-05
(6.13e-05) 		0.107
(0.21) 		1e-05
(6.13e-05) 		0.942
(0.977) 		0.276
(0.43)
amp 13q12 13 275 (61%) 175 1e-05
(6.13e-05) 		1e-05
(6.13e-05) 		1e-05
(6.13e-05) 		1e-05
(6.13e-05) 		0.0789
(0.165) 		0.0897
(0.184) 		1e-05
(6.13e-05) 		1e-05
(6.13e-05) 		0.573
(0.717) 		0.81
(0.896) 		0.395
(0.561) 		0.0161
(0.0435)
amp 16p11 2 126 (28%) 324 0.00041
(0.00166) 		1e-05
(6.13e-05) 		1e-05
(6.13e-05) 		0.00945
(0.0278) 		0.106
(0.208) 		0.0276
(0.0683) 		0.00116
(0.00433) 		1e-05
(6.13e-05) 		0.893
(0.948) 		0.143
(0.261) 		0.959
(0.985) 		0.0625
(0.136)
amp 16q12 1 111 (25%) 339 4e-05
(0.000211) 		1e-05
(6.13e-05) 		1e-05
(6.13e-05) 		0.0298
(0.0719) 		0.05
(0.113) 		0.0789
(0.165) 		0.00102
(0.00384) 		1e-05
(6.13e-05) 		0.975
(0.994) 		0.083
(0.172) 		0.556
(0.704) 		0.0229
(0.0573)
amp 17q24 1 106 (24%) 344 0.0177
(0.0466) 		0.00749
(0.0227) 		1e-05
(6.13e-05) 		2e-05
(0.000117) 		0.327
(0.492) 		0.0541
(0.12) 		2e-05
(0.000117) 		1e-05
(6.13e-05) 		0.0122
(0.0345) 		0.0546
(0.121) 		0.209
(0.355) 		0.535
(0.689)
del 4p16 2 139 (31%) 311 0.00073
(0.00286) 		0.00159
(0.0057) 		1e-05
(6.13e-05) 		0.00413
(0.0136) 		0.796
(0.889) 		0.00437
(0.0142) 		1e-05
(6.13e-05) 		1e-05
(6.13e-05) 		0.356
(0.522) 		0.446
(0.608) 		0.145
(0.263) 		0.236
(0.388)
del 5q12 1 106 (24%) 344 0.0012
(0.00444) 		0.0031
(0.0107) 		1e-05
(6.13e-05) 		0.0138
(0.0382) 		0.0254
(0.0633) 		0.194
(0.332) 		5e-05
(0.000254) 		7e-05
(0.000341) 		0.705
(0.826) 		0.566
(0.71) 		1
(1.00) 		0.14
(0.257)
del 8p23 3 189 (42%) 261 0.0122
(0.0345) 		0.00016
(0.000716) 		1e-05
(6.13e-05) 		1e-05
(6.13e-05) 		0.402
(0.566) 		0.0549
(0.121) 		1e-05
(6.13e-05) 		1e-05
(6.13e-05) 		0.22
(0.37) 		0.0527
(0.118) 		0.892
(0.948) 		0.0436
(0.101)
del 12p13 2 60 (13%) 390 0.0104
(0.0302) 		0.00321
(0.0109) 		1e-05
(6.13e-05) 		0.00444
(0.0142) 		0.773
(0.88) 		0.839
(0.918) 		0.00039
(0.00159) 		1e-05
(6.13e-05) 		0.794
(0.889) 		0.356
(0.522) 		0.225
(0.375) 		0.00195
(0.0069)
del 15q15 2 172 (38%) 278 0.00143
(0.00515) 		0.00062
(0.00244) 		1e-05
(6.13e-05) 		6e-05
(0.000297) 		0.012
(0.0342) 		0.156
(0.279) 		1e-05
(6.13e-05) 		1e-05
(6.13e-05) 		0.923
(0.964) 		0.559
(0.704) 		0.155
(0.279) 		0.169
(0.297)
del 15q21 1 169 (38%) 281 0.0192
(0.0493) 		0.0147
(0.04) 		1e-05
(6.13e-05) 		0.00014
(0.00063) 		0.0477
(0.108) 		0.144
(0.262) 		1e-05
(6.13e-05) 		1e-05
(6.13e-05) 		0.884
(0.946) 		0.677
(0.808) 		0.134
(0.25) 		0.13
(0.245)
del 22q13 32 160 (36%) 290 0.00054
(0.00215) 		0.00026
(0.0011) 		1e-05
(6.13e-05) 		0.00557
(0.0176) 		0.143
(0.261) 		0.0116
(0.0331) 		1e-05
(6.13e-05) 		1e-05
(6.13e-05) 		0.421
(0.583) 		0.792
(0.889) 		0.731
(0.845) 		0.546
(0.696)
amp 13q22 1 277 (62%) 173 9e-05
(0.000421) 		1e-05
(6.13e-05) 		1e-05
(6.13e-05) 		1e-05
(6.13e-05) 		0.125
(0.239) 		0.132
(0.247) 		1e-05
(6.13e-05) 		1e-05
(6.13e-05) 		0.452
(0.611) 		0.996
(1.00) 		0.397
(0.563) 		0.0765
(0.161)
amp 19q13 11 95 (21%) 355 0.182
(0.316) 		0.0311
(0.075) 		0.00013
(0.000595) 		0.221
(0.371) 		0.0168
(0.0447) 		0.778
(0.881) 		0.373
(0.541) 		0.00019
(0.000832) 		0.46
(0.616) 		0.557
(0.704) 		0.0177
(0.0466) 		0.00196
(0.00691)
amp 20p12 1 208 (46%) 242 0.0464
(0.106) 		0.00087
(0.00332) 		1e-05
(6.13e-05) 		0.0806
(0.168) 		0.0379
(0.0888) 		0.475
(0.632) 		0.0221
(0.0555) 		1e-05
(6.13e-05) 		0.261
(0.421) 		0.339
(0.506) 		0.276
(0.43) 		0.527
(0.684)
del 1q43 54 (12%) 396 0.0608
(0.133) 		0.502
(0.659) 		2e-05
(0.000117) 		0.00254
(0.0088) 		0.487
(0.645) 		0.392
(0.558) 		9e-05
(0.000421) 		0.00025
(0.00107) 		0.142
(0.26) 		0.00062
(0.00244) 		0.0275
(0.0682) 		0.961
(0.986)
del 4q22 1 151 (34%) 299 0.00037
(0.00152) 		0.004
(0.0133) 		1e-05
(6.13e-05) 		0.00079
(0.00303) 		0.691
(0.818) 		0.416
(0.58) 		1e-05
(6.13e-05) 		1e-05
(6.13e-05) 		0.391
(0.558) 		0.171
(0.3) 		0.318
(0.482) 		0.204
(0.348)
del 4q35 1 159 (35%) 291 0.00093
(0.00353) 		0.00767
(0.0232) 		1e-05
(6.13e-05) 		3e-05
(0.000167) 		0.889
(0.948) 		0.285
(0.44) 		1e-05
(6.13e-05) 		1e-05
(6.13e-05) 		0.367
(0.533) 		0.417
(0.58) 		0.547
(0.696) 		0.914
(0.962)
del 5q21 1 127 (28%) 323 0.277
(0.43) 		0.0439
(0.101) 		1e-05
(6.13e-05) 		0.00443
(0.0142) 		0.0475
(0.108) 		0.325
(0.49) 		0.00703
(0.0216) 		0.00029
(0.00121) 		0.944
(0.977) 		0.892
(0.948) 		0.868
(0.932) 		0.495
(0.651)
del 5q22 2 130 (29%) 320 0.0136
(0.038) 		0.00916
(0.0272) 		1e-05
(6.13e-05) 		0.0289
(0.0704) 		0.0639
(0.138) 		0.144
(0.262) 		0.00027
(0.00113) 		6e-05
(0.000297) 		0.913
(0.962) 		0.273
(0.43) 		0.616
(0.757) 		0.455
(0.611)
del 10q21 1 98 (22%) 352 0.00312
(0.0107) 		0.0279
(0.0688) 		1e-05
(6.13e-05) 		4e-05
(0.000211) 		0.591
(0.732) 		0.14
(0.258) 		1e-05
(6.13e-05) 		1e-05
(6.13e-05) 		0.752
(0.862) 		0.493
(0.649) 		0.755
(0.864) 		0.728
(0.844)
del 15q11 2 177 (39%) 273 0.00039
(0.00159) 		0.00078
(0.003) 		1e-05
(6.13e-05) 		0.00012
(0.000552) 		0.116
(0.223) 		0.353
(0.521) 		1e-05
(6.13e-05) 		1e-05
(6.13e-05) 		0.981
(0.999) 		0.777
(0.881) 		0.257
(0.416) 		0.274
(0.43)
del 15q22 33 161 (36%) 289 0.00035
(0.00145) 		0.00042
(0.00169) 		1e-05
(6.13e-05) 		0.0001
(0.000465) 		0.27
(0.429) 		0.219
(0.369) 		1e-05
(6.13e-05) 		1e-05
(6.13e-05) 		0.789
(0.889) 		0.851
(0.921) 		0.104
(0.206) 		0.0778
(0.163)
amp 6p21 1 96 (21%) 354 0.262
(0.422) 		5e-05
(0.000254) 		1e-05
(6.13e-05) 		0.00923
(0.0273) 		0.392
(0.558) 		0.222
(0.372) 		0.0189
(0.0492) 		9e-05
(0.000421) 		0.706
(0.826) 		0.775
(0.88) 		0.309
(0.469) 		0.4
(0.564)
del 1p33 123 (27%) 327 0.0159
(0.0429) 		0.559
(0.704) 		1e-05
(6.13e-05) 		6e-05
(0.000297) 		0.358
(0.524) 		0.244
(0.399) 		0.00027
(0.00113) 		2e-05
(0.000117) 		0.718
(0.837) 		0.152
(0.274) 		1
(1.00) 		0.351
(0.518)
del 10p15 3 80 (18%) 370 0.116
(0.223) 		0.106
(0.208) 		2e-05
(0.000117) 		4e-05
(0.000211) 		0.736
(0.85) 		0.233
(0.385) 		0.00031
(0.00129) 		0.00014
(0.00063) 		0.455
(0.611) 		0.178
(0.31) 		0.52
(0.678) 		0.0218
(0.0552)
del 10q25 2 109 (24%) 341 0.125
(0.239) 		0.018
(0.0473) 		1e-05
(6.13e-05) 		2e-05
(0.000117) 		0.116
(0.223) 		0.149
(0.271) 		1e-05
(6.13e-05) 		1e-05
(6.13e-05) 		0.963
(0.987) 		0.489
(0.646) 		0.531
(0.687) 		0.741
(0.853)
del 21q11 2 141 (31%) 309 0.0163
(0.0438) 		0.0698
(0.149) 		1e-05
(6.13e-05) 		0.00608
(0.0189) 		0.865
(0.931) 		0.3
(0.458) 		4e-05
(0.000211) 		0.0004
(0.00162) 		0.937
(0.976) 		0.126
(0.239) 		0.672
(0.804) 		0.346
(0.514)
amp 2q33 1 92 (20%) 358 0.168
(0.296) 		0.112
(0.218) 		0.00076
(0.00294) 		0.00865
(0.0259) 		0.235
(0.388) 		0.375
(0.541) 		0.00017
(0.000753) 		0.00209
(0.00733) 		0.295
(0.451) 		0.106
(0.208) 		0.951
(0.98) 		0.675
(0.806)
amp 5p13 2 88 (20%) 362 0.381
(0.547) 		0.189
(0.325) 		0.00023
(0.000992) 		0.861
(0.929) 		0.011
(0.032) 		0.82
(0.903) 		0.013
(0.0366) 		0.00229
(0.00797) 		0.729
(0.844) 		0.664
(0.799) 		0.757
(0.866) 		0.586
(0.73)
amp 8p11 21 188 (42%) 262 0.446
(0.608) 		0.0189
(0.0492) 		1e-05
(6.13e-05) 		0.0899
(0.184) 		0.551
(0.701) 		0.19
(0.326) 		0.0388
(0.0904) 		0.00169
(0.00601) 		0.72
(0.839) 		0.322
(0.487) 		0.541
(0.695) 		0.103
(0.204)
amp 19p13 2 75 (17%) 375 0.0675
(0.145) 		0.0551
(0.121) 		4e-05
(0.000211) 		0.0137
(0.038) 		0.37
(0.537) 		0.169
(0.297) 		0.462
(0.617) 		0.00025
(0.00107) 		0.351
(0.518) 		0.438
(0.601) 		0.102
(0.203) 		0.0223
(0.0561)
del 1p13 1 119 (26%) 331 0.0876
(0.18) 		0.544
(0.696) 		1e-05
(6.13e-05) 		0.00131
(0.00474) 		0.291
(0.447) 		0.29
(0.446) 		0.00022
(0.000954) 		9e-05
(0.000421) 		0.8
(0.89) 		0.167
(0.295) 		0.954
(0.983) 		0.644
(0.784)
del 10q23 31 109 (24%) 341 0.0992
(0.198) 		0.0645
(0.139) 		1e-05
(6.13e-05) 		0.00019
(0.000832) 		0.973
(0.994) 		0.134
(0.25) 		0.00123
(0.00451) 		3e-05
(0.000167) 		0.579
(0.723) 		0.137
(0.254) 		0.348
(0.517) 		0.4
(0.564)
del 19p13 3 63 (14%) 387 0.13
(0.245) 		0.124
(0.237) 		0.00076
(0.00294) 		0.459
(0.615) 		0.59
(0.732) 		0.651
(0.79) 		0.004
(0.0133) 		0.00102
(0.00384) 		0.652
(0.791) 		0.0087
(0.0259) 		0.484
(0.643) 		0.285
(0.44)
amp 17p11 2 44 (10%) 406 0.266
(0.424) 		0.00422
(0.0138) 		0.0121
(0.0344) 		0.0294
(0.0713) 		0.875
(0.938) 		0.272
(0.43) 		0.0759
(0.16) 		0.225
(0.375) 		0.543
(0.696) 		0.803
(0.891) 		0.174
(0.305) 		0.0655
(0.141)
del 3p26 2 72 (16%) 378 0.219
(0.369) 		0.236
(0.388) 		0.0012
(0.00444) 		0.0734
(0.156) 		0.946
(0.978) 		0.636
(0.777) 		0.00718
(0.0219) 		0.00327
(0.0111) 		0.741
(0.853) 		0.789
(0.889) 		0.534
(0.689) 		0.411
(0.576)
del 9p21 3 62 (14%) 388 0.453
(0.611) 		0.0902
(0.184) 		0.00399
(0.0133) 		0.115
(0.222) 		0.658
(0.796) 		0.277
(0.43) 		0.0192
(0.0493) 		0.00123
(0.00451) 		0.623
(0.763) 		0.257
(0.416) 		0.203
(0.346) 		0.583
(0.727)
amp 5q22 3 46 (10%) 404 0.925
(0.965) 		1
(1.00) 		0.00724
(0.022) 		0.335
(0.502) 		0.339
(0.506) 		0.392
(0.558) 		0.179
(0.311) 		0.0358
(0.0851) 		0.95
(0.98) 		0.701
(0.825) 		0.356
(0.522) 		0.329
(0.494)
amp 8p11 23 158 (35%) 292 0.303
(0.461) 		0.108
(0.212) 		1e-05
(6.13e-05) 		0.0809
(0.168) 		0.295
(0.451) 		0.276
(0.43) 		0.112
(0.218) 		0.038
(0.089) 		0.36
(0.525) 		0.264
(0.424) 		0.503
(0.66) 		0.126
(0.239)
del 16q23 1 61 (14%) 389 0.269
(0.428) 		0.00543
(0.0172) 		0.417
(0.58) 		0.704
(0.826) 		0.902
(0.954) 		0.554
(0.703) 		0.277
(0.43) 		0.0126
(0.0354) 		0.526
(0.684) 		0.465
(0.62) 		0.722
(0.839) 		0.477
(0.634)
del 17q24 3 69 (15%) 381 0.0968
(0.194) 		0.516
(0.675) 		0.00407
(0.0134) 		0.226
(0.376) 		0.414
(0.578) 		0.422
(0.584) 		0.044
(0.101) 		0.138
(0.256) 		0.723
(0.839) 		0.97
(0.993) 		0.81
(0.896) 		0.432
(0.594)
amp 12p13 33 111 (25%) 339 0.657
(0.796) 		0.792
(0.889) 		0.0319
(0.0766) 		0.0613
(0.134) 		0.807
(0.895) 		0.576
(0.72) 		0.751
(0.862) 		0.848
(0.921) 		0.511
(0.669) 		0.795
(0.889) 		0.63
(0.771) 		0.851
(0.921)
del 3p14 2 88 (20%) 362 0.555
(0.704) 		0.837
(0.917) 		0.156
(0.279) 		0.255
(0.414) 		0.437
(0.6) 		0.622
(0.763) 		0.126
(0.239) 		0.0411
(0.0957) 		0.651
(0.79) 		0.698
(0.824) 		0.129
(0.243) 		0.702
(0.825)
del 6p25 3 56 (12%) 394 0.853
(0.922) 		0.739
(0.852) 		0.109
(0.212) 		0.399
(0.564) 		0.431
(0.593) 		0.445
(0.608) 		0.527
(0.684) 		0.895
(0.948) 		0.67
(0.802) 		0.941
(0.977) 		0.0549
(0.121) 		0.0435
(0.101)
del 6q26 62 (14%) 388 0.587
(0.73) 		0.401
(0.565) 		0.919
(0.964) 		0.815
(0.9) 		0.0286
(0.0698) 		0.767
(0.874) 		0.381
(0.547) 		0.686
(0.815) 		0.697
(0.824) 		0.939
(0.977) 		0.44
(0.603) 		0.0578
(0.127)
del 8q11 1 30 (7%) 420 0.261
(0.421) 		0.0975
(0.195) 		0.0164
(0.0439) 		0.906
(0.957) 		0.158
(0.281) 		0.679
(0.809) 		0.375
(0.541) 		0.0752
(0.159) 		0.2
(0.342) 		0.296
(0.451) 		0.662
(0.799) 		0.893
(0.948)
del 2p21 17 (4%) 433 0.595
(0.737) 		0.865
(0.931) 		0.895
(0.948) 		0.848
(0.921) 		0.526
(0.684) 		0.782
(0.884) 		0.35
(0.518) 		0.282
(0.437) 		0.0914
(0.186) 		0.346
(0.514)
del 2q22 1 24 (5%) 426 0.973
(0.994) 		0.537
(0.69) 		0.412
(0.577) 		0.68
(0.809) 		1
(1.00) 		0.421
(0.583) 		0.228
(0.378) 		0.324
(0.489) 		0.25
(0.407) 		0.164
(0.291) 		1
(1.00) 		0.848
(0.921)
del 3q26 31 46 (10%) 404 0.64
(0.781) 		0.537
(0.69) 		0.214
(0.363) 		0.447
(0.608) 		0.452
(0.611) 		0.932
(0.972) 		0.0931
(0.189) 		0.139
(0.256) 		0.156
(0.279) 		0.816
(0.9) 		0.0926
(0.188) 		0.701
(0.825)
del 7q31 1 13 (3%) 437 1
(1.00) 		0.599
(0.74) 		0.0505
(0.113) 		0.159
(0.282) 		0.427
(0.589) 		0.848
(0.921) 		0.36
(0.525) 		0.603
(0.744) 		0.795
(0.889) 		0.829
(0.911)
del 13q14 13 19 (4%) 431 0.273
(0.43) 		0.864
(0.931) 		0.244
(0.399) 		0.243
(0.398) 		0.885
(0.946) 		0.797
(0.889) 		0.922
(0.964) 		0.882
(0.944) 		0.688
(0.816) 		0.944
(0.977) 		0.45
(0.611) 		0.311
(0.471)
del 16p13 3 56 (12%) 394 0.231
(0.383) 		0.0631
(0.137) 		0.0937
(0.189) 		0.133
(0.248) 		0.956
(0.983) 		0.798
(0.889) 		0.0617
(0.134) 		0.0687
(0.147) 		0.851
(0.921) 		0.701
(0.825) 		0.615
(0.757) 		1
(1.00)
'amp_2q33.1' versus 'CN_CNMF'

P value = 0.00076 (Fisher's exact test), Q value = 0.0029

Table S1.  Gene #1: 'amp_2q33.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
AMP PEAK 1(2Q33.1) MUTATED 27 50 15
AMP PEAK 1(2Q33.1) WILD-TYPE 175 120 63

Figure S1.  Get High-res Image Gene #1: 'amp_2q33.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_2q33.1' versus 'METHLYATION_CNMF'

P value = 0.00865 (Fisher's exact test), Q value = 0.026

Table S2.  Gene #1: 'amp_2q33.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
AMP PEAK 1(2Q33.1) MUTATED 38 15 13
AMP PEAK 1(2Q33.1) WILD-TYPE 82 82 63

Figure S2.  Get High-res Image Gene #1: 'amp_2q33.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_2q33.1' versus 'MRNASEQ_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.00075

Table S3.  Gene #1: 'amp_2q33.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
AMP PEAK 1(2Q33.1) MUTATED 41 12 19 20
AMP PEAK 1(2Q33.1) WILD-TYPE 80 95 71 110

Figure S3.  Get High-res Image Gene #1: 'amp_2q33.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_2q33.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00209 (Fisher's exact test), Q value = 0.0073

Table S4.  Gene #1: 'amp_2q33.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
AMP PEAK 1(2Q33.1) MUTATED 19 33 12 26 2
AMP PEAK 1(2Q33.1) WILD-TYPE 60 75 84 103 34

Figure S4.  Get High-res Image Gene #1: 'amp_2q33.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_5p13.2' versus 'CN_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.00099

Table S5.  Gene #2: 'amp_5p13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
AMP PEAK 2(5P13.2) MUTATED 23 48 17
AMP PEAK 2(5P13.2) WILD-TYPE 179 122 61

Figure S5.  Get High-res Image Gene #2: 'amp_5p13.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_5p13.2' versus 'RPPA_CNMF'

P value = 0.011 (Fisher's exact test), Q value = 0.032

Table S6.  Gene #2: 'amp_5p13.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 144 125
AMP PEAK 2(5P13.2) MUTATED 26 22 19
AMP PEAK 2(5P13.2) WILD-TYPE 59 122 106

Figure S6.  Get High-res Image Gene #2: 'amp_5p13.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_5p13.2' versus 'MRNASEQ_CNMF'

P value = 0.013 (Fisher's exact test), Q value = 0.037

Table S7.  Gene #2: 'amp_5p13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
AMP PEAK 2(5P13.2) MUTATED 29 10 19 30
AMP PEAK 2(5P13.2) WILD-TYPE 92 97 71 100

Figure S7.  Get High-res Image Gene #2: 'amp_5p13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_5p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00229 (Fisher's exact test), Q value = 0.008

Table S8.  Gene #2: 'amp_5p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
AMP PEAK 2(5P13.2) MUTATED 25 16 10 32 5
AMP PEAK 2(5P13.2) WILD-TYPE 54 92 86 97 31

Figure S8.  Get High-res Image Gene #2: 'amp_5p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_5q22.3' versus 'CN_CNMF'

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

Table S9.  Gene #3: 'amp_5q22.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
AMP PEAK 3(5Q22.3) MUTATED 12 27 7
AMP PEAK 3(5Q22.3) WILD-TYPE 190 143 71

Figure S9.  Get High-res Image Gene #3: 'amp_5q22.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_5q22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0358 (Fisher's exact test), Q value = 0.085

Table S10.  Gene #3: 'amp_5q22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
AMP PEAK 3(5Q22.3) MUTATED 13 13 3 14 3
AMP PEAK 3(5Q22.3) WILD-TYPE 66 95 93 115 33

Figure S10.  Get High-res Image Gene #3: 'amp_5q22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_6p21.1' versus 'MRNA_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00025

Table S11.  Gene #4: 'amp_6p21.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
AMP PEAK 4(6P21.1) MUTATED 3 10 16
AMP PEAK 4(6P21.1) WILD-TYPE 39 62 16

Figure S11.  Get High-res Image Gene #4: '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 = 6.1e-05

Table S12.  Gene #4: 'amp_6p21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
AMP PEAK 4(6P21.1) MUTATED 17 62 17
AMP PEAK 4(6P21.1) WILD-TYPE 185 108 61

Figure S12.  Get High-res Image Gene #4: 'amp_6p21.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_6p21.1' versus 'METHLYATION_CNMF'

P value = 0.00923 (Fisher's exact test), Q value = 0.027

Table S13.  Gene #4: 'amp_6p21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
AMP PEAK 4(6P21.1) MUTATED 38 16 12
AMP PEAK 4(6P21.1) WILD-TYPE 82 81 64

Figure S13.  Get High-res Image Gene #4: 'amp_6p21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_6p21.1' versus 'MRNASEQ_CNMF'

P value = 0.0189 (Fisher's exact test), Q value = 0.049

Table S14.  Gene #4: 'amp_6p21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
AMP PEAK 4(6P21.1) MUTATED 30 12 24 30
AMP PEAK 4(6P21.1) WILD-TYPE 91 95 66 100

Figure S14.  Get High-res Image Gene #4: 'amp_6p21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_6p21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00042

Table S15.  Gene #4: 'amp_6p21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
AMP PEAK 4(6P21.1) MUTATED 26 25 9 34 2
AMP PEAK 4(6P21.1) WILD-TYPE 53 83 87 95 34

Figure S15.  Get High-res Image Gene #4: 'amp_6p21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_7p21.2' versus 'MRNA_CNMF'

P value = 0.00989 (Fisher's exact test), Q value = 0.029

Table S16.  Gene #5: 'amp_7p21.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
AMP PEAK 5(7P21.2) MUTATED 11 39 11 9
AMP PEAK 5(7P21.2) WILD-TYPE 24 22 18 12

Figure S16.  Get High-res Image Gene #5: 'amp_7p21.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_7p21.2' versus 'MRNA_CHIERARCHICAL'

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

Table S17.  Gene #5: 'amp_7p21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
AMP PEAK 5(7P21.2) MUTATED 10 34 26
AMP PEAK 5(7P21.2) WILD-TYPE 32 38 6

Figure S17.  Get High-res Image Gene #5: 'amp_7p21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_7p21.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S18.  Gene #5: 'amp_7p21.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
AMP PEAK 5(7P21.2) MUTATED 70 129 56
AMP PEAK 5(7P21.2) WILD-TYPE 132 41 22

Figure S18.  Get High-res Image Gene #5: 'amp_7p21.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_7p21.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S19.  Gene #5: 'amp_7p21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
AMP PEAK 5(7P21.2) MUTATED 94 46 38
AMP PEAK 5(7P21.2) WILD-TYPE 26 51 38

Figure S19.  Get High-res Image Gene #5: 'amp_7p21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_7p21.2' versus 'RPPA_CHIERARCHICAL'

P value = 5e-04 (Fisher's exact test), Q value = 0.002

Table S20.  Gene #5: 'amp_7p21.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 51 33 35 39 42 86 22 20 26
AMP PEAK 5(7P21.2) MUTATED 38 11 24 17 27 38 10 11 18
AMP PEAK 5(7P21.2) WILD-TYPE 13 22 11 22 15 48 12 9 8

Figure S20.  Get High-res Image Gene #5: 'amp_7p21.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_7p21.2' versus 'MRNASEQ_CNMF'

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

Table S21.  Gene #5: 'amp_7p21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
AMP PEAK 5(7P21.2) MUTATED 89 46 51 68
AMP PEAK 5(7P21.2) WILD-TYPE 32 61 39 62

Figure S21.  Get High-res Image Gene #5: 'amp_7p21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_7p21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S22.  Gene #5: 'amp_7p21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
AMP PEAK 5(7P21.2) MUTATED 60 75 34 76 9
AMP PEAK 5(7P21.2) WILD-TYPE 19 33 62 53 27

Figure S22.  Get High-res Image Gene #5: 'amp_7p21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_7p21.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0342 (Fisher's exact test), Q value = 0.082

Table S23.  Gene #5: 'amp_7p21.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 22 17 24 10
AMP PEAK 5(7P21.2) MUTATED 12 15 11 12 7
AMP PEAK 5(7P21.2) WILD-TYPE 0 7 6 12 3

Figure S23.  Get High-res Image Gene #5: 'amp_7p21.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8p11.23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S24.  Gene #6: 'amp_8p11.23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
AMP PEAK 6(8P11.23) MUTATED 44 56 58
AMP PEAK 6(8P11.23) WILD-TYPE 158 114 20

Figure S24.  Get High-res Image Gene #6: 'amp_8p11.23' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8p11.23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.038 (Fisher's exact test), Q value = 0.089

Table S25.  Gene #6: 'amp_8p11.23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
AMP PEAK 6(8P11.23) MUTATED 33 45 31 41 6
AMP PEAK 6(8P11.23) WILD-TYPE 46 63 65 88 30

Figure S25.  Get High-res Image Gene #6: 'amp_8p11.23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8p11.21' versus 'MRNA_CHIERARCHICAL'

P value = 0.0189 (Fisher's exact test), Q value = 0.049

Table S26.  Gene #7: 'amp_8p11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
AMP PEAK 7(8P11.21) MUTATED 10 26 18
AMP PEAK 7(8P11.21) WILD-TYPE 32 46 14

Figure S26.  Get High-res Image Gene #7: 'amp_8p11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_8p11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S27.  Gene #7: 'amp_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
AMP PEAK 7(8P11.21) MUTATED 50 72 66
AMP PEAK 7(8P11.21) WILD-TYPE 152 98 12

Figure S27.  Get High-res Image Gene #7: 'amp_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8p11.21' versus 'MRNASEQ_CNMF'

P value = 0.0388 (Fisher's exact test), Q value = 0.09

Table S28.  Gene #7: 'amp_8p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
AMP PEAK 7(8P11.21) MUTATED 56 36 46 48
AMP PEAK 7(8P11.21) WILD-TYPE 65 71 44 82

Figure S28.  Get High-res Image Gene #7: 'amp_8p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8p11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00169 (Fisher's exact test), Q value = 0.006

Table S29.  Gene #7: 'amp_8p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
AMP PEAK 7(8P11.21) MUTATED 44 49 32 54 7
AMP PEAK 7(8P11.21) WILD-TYPE 35 59 64 75 29

Figure S29.  Get High-res Image Gene #7: 'amp_8p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8q12.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00581 (Fisher's exact test), Q value = 0.018

Table S30.  Gene #8: 'amp_8q12.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
AMP PEAK 8(8Q12.1) MUTATED 13 34 22
AMP PEAK 8(8Q12.1) WILD-TYPE 29 38 10

Figure S30.  Get High-res Image Gene #8: '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 = 6.1e-05

Table S31.  Gene #8: 'amp_8q12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
AMP PEAK 8(8Q12.1) MUTATED 63 98 75
AMP PEAK 8(8Q12.1) WILD-TYPE 139 72 3

Figure S31.  Get High-res Image Gene #8: 'amp_8q12.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8q12.1' versus 'METHLYATION_CNMF'

P value = 0.00387 (Fisher's exact test), Q value = 0.013

Table S32.  Gene #8: 'amp_8q12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
AMP PEAK 8(8Q12.1) MUTATED 81 44 41
AMP PEAK 8(8Q12.1) WILD-TYPE 39 53 35

Figure S32.  Get High-res Image Gene #8: 'amp_8q12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8q12.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0192 (Fisher's exact test), Q value = 0.049

Table S33.  Gene #8: 'amp_8q12.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 51 33 35 39 42 86 22 20 26
AMP PEAK 8(8Q12.1) MUTATED 35 13 15 19 20 41 7 9 19
AMP PEAK 8(8Q12.1) WILD-TYPE 16 20 20 20 22 45 15 11 7

Figure S33.  Get High-res Image Gene #8: 'amp_8q12.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_8q12.1' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00039

Table S34.  Gene #8: 'amp_8q12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
AMP PEAK 8(8Q12.1) MUTATED 78 40 55 61
AMP PEAK 8(8Q12.1) WILD-TYPE 43 67 35 69

Figure S34.  Get High-res Image Gene #8: 'amp_8q12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8q12.1' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S35.  Gene #8: 'amp_8q12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
AMP PEAK 8(8Q12.1) MUTATED 51 65 39 71 8
AMP PEAK 8(8Q12.1) WILD-TYPE 28 43 57 58 28

Figure S35.  Get High-res Image Gene #8: 'amp_8q12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8q12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0378 (Fisher's exact test), Q value = 0.089

Table S36.  Gene #8: 'amp_8q12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 50 77 135
AMP PEAK 8(8Q12.1) MUTATED 66 30 50 63
AMP PEAK 8(8Q12.1) WILD-TYPE 69 20 27 72

Figure S36.  Get High-res Image Gene #8: 'amp_8q12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_8q12.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0134 (Fisher's exact test), Q value = 0.037

Table S37.  Gene #8: 'amp_8q12.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 22 17 24 10
AMP PEAK 8(8Q12.1) MUTATED 10 18 9 9 6
AMP PEAK 8(8Q12.1) WILD-TYPE 2 4 8 15 4

Figure S37.  Get High-res Image Gene #8: 'amp_8q12.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8q24.21' versus 'MRNA_CHIERARCHICAL'

P value = 0.0294 (Fisher's exact test), Q value = 0.071

Table S38.  Gene #9: 'amp_8q24.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
AMP PEAK 9(8Q24.21) MUTATED 17 38 23
AMP PEAK 9(8Q24.21) WILD-TYPE 25 34 9

Figure S38.  Get High-res Image Gene #9: 'amp_8q24.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_8q24.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S39.  Gene #9: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
AMP PEAK 9(8Q24.21) MUTATED 72 111 77
AMP PEAK 9(8Q24.21) WILD-TYPE 130 59 1

Figure S39.  Get High-res Image Gene #9: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00063

Table S40.  Gene #9: 'amp_8q24.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
AMP PEAK 9(8Q24.21) MUTATED 90 46 44
AMP PEAK 9(8Q24.21) WILD-TYPE 30 51 32

Figure S40.  Get High-res Image Gene #9: 'amp_8q24.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.00092

Table S41.  Gene #9: 'amp_8q24.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
AMP PEAK 9(8Q24.21) MUTATED 84 46 59 69
AMP PEAK 9(8Q24.21) WILD-TYPE 37 61 31 61

Figure S41.  Get High-res Image Gene #9: 'amp_8q24.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00025

Table S42.  Gene #9: 'amp_8q24.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
AMP PEAK 9(8Q24.21) MUTATED 56 69 44 78 11
AMP PEAK 9(8Q24.21) WILD-TYPE 23 39 52 51 25

Figure S42.  Get High-res Image Gene #9: 'amp_8q24.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0378 (Fisher's exact test), Q value = 0.089

Table S43.  Gene #9: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 50 77 135
AMP PEAK 9(8Q24.21) MUTATED 73 33 54 71
AMP PEAK 9(8Q24.21) WILD-TYPE 62 17 23 64

Figure S43.  Get High-res Image Gene #9: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0152 (Fisher's exact test), Q value = 0.041

Table S44.  Gene #9: 'amp_8q24.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 22 17 24 10
AMP PEAK 9(8Q24.21) MUTATED 10 19 11 10 6
AMP PEAK 9(8Q24.21) WILD-TYPE 2 3 6 14 4

Figure S44.  Get High-res Image Gene #9: 'amp_8q24.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_11p15.5' versus 'MRNA_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00025

Table S45.  Gene #10: 'amp_11p15.5' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
AMP PEAK 10(11P15.5) MUTATED 2 18 3 12
AMP PEAK 10(11P15.5) WILD-TYPE 33 43 26 9

Figure S45.  Get High-res Image Gene #10: 'amp_11p15.5' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_11p15.5' versus 'MRNA_CHIERARCHICAL'

P value = 0.0059 (Fisher's exact test), Q value = 0.018

Table S46.  Gene #10: 'amp_11p15.5' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
AMP PEAK 10(11P15.5) MUTATED 3 21 11
AMP PEAK 10(11P15.5) WILD-TYPE 39 51 21

Figure S46.  Get High-res Image Gene #10: 'amp_11p15.5' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_11p15.5' versus 'CN_CNMF'

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

Table S47.  Gene #10: 'amp_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
AMP PEAK 10(11P15.5) MUTATED 23 50 21
AMP PEAK 10(11P15.5) WILD-TYPE 179 120 57

Figure S47.  Get High-res Image Gene #10: 'amp_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

'amp_11p15.5' versus 'METHLYATION_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00034

Table S48.  Gene #10: 'amp_11p15.5' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
AMP PEAK 10(11P15.5) MUTATED 35 6 15
AMP PEAK 10(11P15.5) WILD-TYPE 85 91 61

Figure S48.  Get High-res Image Gene #10: 'amp_11p15.5' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_11p15.5' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S49.  Gene #10: 'amp_11p15.5' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
AMP PEAK 10(11P15.5) MUTATED 40 6 17 30
AMP PEAK 10(11P15.5) WILD-TYPE 81 101 73 100

Figure S49.  Get High-res Image Gene #10: '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 = 6.1e-05

Table S50.  Gene #10: 'amp_11p15.5' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
AMP PEAK 10(11P15.5) MUTATED 21 27 3 41 1
AMP PEAK 10(11P15.5) WILD-TYPE 58 81 93 88 35

Figure S50.  Get High-res Image Gene #10: '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 = 6.1e-05

Table S51.  Gene #10: 'amp_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 50 77 135
AMP PEAK 10(11P15.5) MUTATED 8 12 46 18
AMP PEAK 10(11P15.5) WILD-TYPE 127 38 31 117

Figure S51.  Get High-res Image Gene #10: 'amp_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_12p13.33' versus 'CN_CNMF'

P value = 0.0319 (Fisher's exact test), Q value = 0.077

Table S52.  Gene #11: 'amp_12p13.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
AMP PEAK 11(12P13.33) MUTATED 55 31 25
AMP PEAK 11(12P13.33) WILD-TYPE 147 139 53

Figure S52.  Get High-res Image Gene #11: 'amp_12p13.33' versus Molecular Subtype #3: 'CN_CNMF'

'amp_13q12.13' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S53.  Gene #12: 'amp_13q12.13' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
AMP PEAK 12(13Q12.13) MUTATED 15 51 10 16
AMP PEAK 12(13Q12.13) WILD-TYPE 20 10 19 5

Figure S53.  Get High-res Image Gene #12: '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 = 6.1e-05

Table S54.  Gene #12: 'amp_13q12.13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
AMP PEAK 12(13Q12.13) MUTATED 13 49 30
AMP PEAK 12(13Q12.13) WILD-TYPE 29 23 2

Figure S54.  Get High-res Image Gene #12: '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 = 6.1e-05

Table S55.  Gene #12: 'amp_13q12.13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
AMP PEAK 12(13Q12.13) MUTATED 66 159 50
AMP PEAK 12(13Q12.13) WILD-TYPE 136 11 28

Figure S55.  Get High-res Image Gene #12: '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 = 6.1e-05

Table S56.  Gene #12: 'amp_13q12.13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
AMP PEAK 12(13Q12.13) MUTATED 101 43 36
AMP PEAK 12(13Q12.13) WILD-TYPE 19 54 40

Figure S56.  Get High-res Image Gene #12: '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 = 6.1e-05

Table S57.  Gene #12: 'amp_13q12.13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
AMP PEAK 12(13Q12.13) MUTATED 92 37 55 89
AMP PEAK 12(13Q12.13) WILD-TYPE 29 70 35 41

Figure S57.  Get High-res Image Gene #12: '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 = 6.1e-05

Table S58.  Gene #12: 'amp_13q12.13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
AMP PEAK 12(13Q12.13) MUTATED 68 76 26 95 8
AMP PEAK 12(13Q12.13) WILD-TYPE 11 32 70 34 28

Figure S58.  Get High-res Image Gene #12: 'amp_13q12.13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_13q12.13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0161 (Fisher's exact test), Q value = 0.044

Table S59.  Gene #12: 'amp_13q12.13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 22 17 24 10
AMP PEAK 12(13Q12.13) MUTATED 10 19 13 11 5
AMP PEAK 12(13Q12.13) WILD-TYPE 2 3 4 13 5

Figure S59.  Get High-res Image Gene #12: 'amp_13q12.13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_13q22.1' versus 'MRNA_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00042

Table S60.  Gene #13: 'amp_13q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
AMP PEAK 13(13Q22.1) MUTATED 15 49 12 15
AMP PEAK 13(13Q22.1) WILD-TYPE 20 12 17 6

Figure S60.  Get High-res Image Gene #13: '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 = 6.1e-05

Table S61.  Gene #13: 'amp_13q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
AMP PEAK 13(13Q22.1) MUTATED 13 48 30
AMP PEAK 13(13Q22.1) WILD-TYPE 29 24 2

Figure S61.  Get High-res Image Gene #13: '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 = 6.1e-05

Table S62.  Gene #13: 'amp_13q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
AMP PEAK 13(13Q22.1) MUTATED 71 155 51
AMP PEAK 13(13Q22.1) WILD-TYPE 131 15 27

Figure S62.  Get High-res Image Gene #13: '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 = 6.1e-05

Table S63.  Gene #13: 'amp_13q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
AMP PEAK 13(13Q22.1) MUTATED 99 47 36
AMP PEAK 13(13Q22.1) WILD-TYPE 21 50 40

Figure S63.  Get High-res Image Gene #13: '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 = 6.1e-05

Table S64.  Gene #13: 'amp_13q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
AMP PEAK 13(13Q22.1) MUTATED 92 40 56 87
AMP PEAK 13(13Q22.1) WILD-TYPE 29 67 34 43

Figure S64.  Get High-res Image Gene #13: '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 = 6.1e-05

Table S65.  Gene #13: 'amp_13q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
AMP PEAK 13(13Q22.1) MUTATED 67 76 30 93 9
AMP PEAK 13(13Q22.1) WILD-TYPE 12 32 66 36 27

Figure S65.  Get High-res Image Gene #13: 'amp_13q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_16p11.2' versus 'MRNA_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.0017

Table S66.  Gene #14: 'amp_16p11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
AMP PEAK 14(16P11.2) MUTATED 6 24 3 12
AMP PEAK 14(16P11.2) WILD-TYPE 29 37 26 9

Figure S66.  Get High-res Image Gene #14: 'amp_16p11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_16p11.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S67.  Gene #14: 'amp_16p11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
AMP PEAK 14(16P11.2) MUTATED 6 16 23
AMP PEAK 14(16P11.2) WILD-TYPE 36 56 9

Figure S67.  Get High-res Image Gene #14: '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 = 6.1e-05

Table S68.  Gene #14: 'amp_16p11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
AMP PEAK 14(16P11.2) MUTATED 20 89 17
AMP PEAK 14(16P11.2) WILD-TYPE 182 81 61

Figure S68.  Get High-res Image Gene #14: 'amp_16p11.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_16p11.2' versus 'METHLYATION_CNMF'

P value = 0.00945 (Fisher's exact test), Q value = 0.028

Table S69.  Gene #14: 'amp_16p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
AMP PEAK 14(16P11.2) MUTATED 43 17 20
AMP PEAK 14(16P11.2) WILD-TYPE 77 80 56

Figure S69.  Get High-res Image Gene #14: 'amp_16p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_16p11.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0276 (Fisher's exact test), Q value = 0.068

Table S70.  Gene #14: 'amp_16p11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 51 33 35 39 42 86 22 20 26
AMP PEAK 14(16P11.2) MUTATED 20 3 14 12 12 22 2 6 6
AMP PEAK 14(16P11.2) WILD-TYPE 31 30 21 27 30 64 20 14 20

Figure S70.  Get High-res Image Gene #14: 'amp_16p11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_16p11.2' versus 'MRNASEQ_CNMF'

P value = 0.00116 (Fisher's exact test), Q value = 0.0043

Table S71.  Gene #14: 'amp_16p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
AMP PEAK 14(16P11.2) MUTATED 43 16 23 44
AMP PEAK 14(16P11.2) WILD-TYPE 78 91 67 86

Figure S71.  Get High-res Image Gene #14: 'amp_16p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_16p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S72.  Gene #14: 'amp_16p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
AMP PEAK 14(16P11.2) MUTATED 30 30 12 53 1
AMP PEAK 14(16P11.2) WILD-TYPE 49 78 84 76 35

Figure S72.  Get High-res Image Gene #14: 'amp_16p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_16q12.1' versus 'MRNA_CNMF'

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

Table S73.  Gene #15: 'amp_16q12.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
AMP PEAK 15(16Q12.1) MUTATED 4 22 2 12
AMP PEAK 15(16Q12.1) WILD-TYPE 31 39 27 9

Figure S73.  Get High-res Image Gene #15: 'amp_16q12.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_16q12.1' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S74.  Gene #15: 'amp_16q12.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
AMP PEAK 15(16Q12.1) MUTATED 3 17 20
AMP PEAK 15(16Q12.1) WILD-TYPE 39 55 12

Figure S74.  Get High-res Image Gene #15: 'amp_16q12.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_16q12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S75.  Gene #15: 'amp_16q12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
AMP PEAK 15(16Q12.1) MUTATED 16 82 13
AMP PEAK 15(16Q12.1) WILD-TYPE 186 88 65

Figure S75.  Get High-res Image Gene #15: 'amp_16q12.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_16q12.1' versus 'METHLYATION_CNMF'

P value = 0.0298 (Fisher's exact test), Q value = 0.072

Table S76.  Gene #15: 'amp_16q12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
AMP PEAK 15(16Q12.1) MUTATED 37 15 18
AMP PEAK 15(16Q12.1) WILD-TYPE 83 82 58

Figure S76.  Get High-res Image Gene #15: 'amp_16q12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_16q12.1' versus 'MRNASEQ_CNMF'

P value = 0.00102 (Fisher's exact test), Q value = 0.0038

Table S77.  Gene #15: 'amp_16q12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
AMP PEAK 15(16Q12.1) MUTATED 39 13 20 39
AMP PEAK 15(16Q12.1) WILD-TYPE 82 94 70 91

Figure S77.  Get High-res Image Gene #15: 'amp_16q12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_16q12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S78.  Gene #15: 'amp_16q12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
AMP PEAK 15(16Q12.1) MUTATED 29 25 10 47 0
AMP PEAK 15(16Q12.1) WILD-TYPE 50 83 86 82 36

Figure S78.  Get High-res Image Gene #15: 'amp_16q12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_16q12.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0229 (Fisher's exact test), Q value = 0.057

Table S79.  Gene #15: 'amp_16q12.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 22 17 24 10
AMP PEAK 15(16Q12.1) MUTATED 7 10 4 3 2
AMP PEAK 15(16Q12.1) WILD-TYPE 5 12 13 21 8

Figure S79.  Get High-res Image Gene #15: 'amp_16q12.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17p11.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00422 (Fisher's exact test), Q value = 0.014

Table S80.  Gene #16: 'amp_17p11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
AMP PEAK 16(17P11.2) MUTATED 2 3 8
AMP PEAK 16(17P11.2) WILD-TYPE 40 69 24

Figure S80.  Get High-res Image Gene #16: 'amp_17p11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_17p11.2' versus 'CN_CNMF'

P value = 0.0121 (Fisher's exact test), Q value = 0.034

Table S81.  Gene #16: 'amp_17p11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
AMP PEAK 16(17P11.2) MUTATED 13 26 5
AMP PEAK 16(17P11.2) WILD-TYPE 189 144 73

Figure S81.  Get High-res Image Gene #16: 'amp_17p11.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17p11.2' versus 'METHLYATION_CNMF'

P value = 0.0294 (Fisher's exact test), Q value = 0.071

Table S82.  Gene #16: 'amp_17p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
AMP PEAK 16(17P11.2) MUTATED 20 8 4
AMP PEAK 16(17P11.2) WILD-TYPE 100 89 72

Figure S82.  Get High-res Image Gene #16: 'amp_17p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17q12' versus 'MRNA_CNMF'

P value = 0.025 (Fisher's exact test), Q value = 0.062

Table S83.  Gene #17: 'amp_17q12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
AMP PEAK 17(17Q12) MUTATED 4 21 4 7
AMP PEAK 17(17Q12) WILD-TYPE 31 40 25 14

Figure S83.  Get High-res Image Gene #17: 'amp_17q12' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_17q12' versus 'MRNA_CHIERARCHICAL'

P value = 0.0142 (Fisher's exact test), Q value = 0.039

Table S84.  Gene #17: 'amp_17q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
AMP PEAK 17(17Q12) MUTATED 6 16 14
AMP PEAK 17(17Q12) WILD-TYPE 36 56 18

Figure S84.  Get High-res Image Gene #17: 'amp_17q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_17q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S85.  Gene #17: 'amp_17q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
AMP PEAK 17(17Q12) MUTATED 25 63 26
AMP PEAK 17(17Q12) WILD-TYPE 177 107 52

Figure S85.  Get High-res Image Gene #17: 'amp_17q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q12' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00025

Table S86.  Gene #17: 'amp_17q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
AMP PEAK 17(17Q12) MUTATED 48 18 11
AMP PEAK 17(17Q12) WILD-TYPE 72 79 65

Figure S86.  Get High-res Image Gene #17: 'amp_17q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17q12' versus 'RPPA_CHIERARCHICAL'

P value = 0.0188 (Fisher's exact test), Q value = 0.049

Table S87.  Gene #17: 'amp_17q12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 51 33 35 39 42 86 22 20 26
AMP PEAK 17(17Q12) MUTATED 17 5 6 8 13 19 0 5 10
AMP PEAK 17(17Q12) WILD-TYPE 34 28 29 31 29 67 22 15 16

Figure S87.  Get High-res Image Gene #17: 'amp_17q12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_17q12' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00025

Table S88.  Gene #17: 'amp_17q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
AMP PEAK 17(17Q12) MUTATED 50 15 16 32
AMP PEAK 17(17Q12) WILD-TYPE 71 92 74 98

Figure S88.  Get High-res Image Gene #17: 'amp_17q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00108 (Fisher's exact test), Q value = 0.004

Table S89.  Gene #17: 'amp_17q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
AMP PEAK 17(17Q12) MUTATED 21 38 12 37 5
AMP PEAK 17(17Q12) WILD-TYPE 58 70 84 92 31

Figure S89.  Get High-res Image Gene #17: 'amp_17q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_CNMF'

P value = 0.0365 (Fisher's exact test), Q value = 0.087

Table S90.  Gene #17: 'amp_17q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 65 172
AMP PEAK 17(17Q12) MUTATED 48 9 44
AMP PEAK 17(17Q12) WILD-TYPE 112 56 128

Figure S90.  Get High-res Image Gene #17: 'amp_17q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_17q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0139 (Fisher's exact test), Q value = 0.038

Table S91.  Gene #17: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 50 77 135
AMP PEAK 17(17Q12) MUTATED 30 12 31 28
AMP PEAK 17(17Q12) WILD-TYPE 105 38 46 107

Figure S91.  Get High-res Image Gene #17: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_17q24.1' versus 'MRNA_CNMF'

P value = 0.0177 (Fisher's exact test), Q value = 0.047

Table S92.  Gene #18: 'amp_17q24.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
AMP PEAK 18(17Q24.1) MUTATED 2 19 5 6
AMP PEAK 18(17Q24.1) WILD-TYPE 33 42 24 15

Figure S92.  Get High-res Image Gene #18: 'amp_17q24.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_17q24.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00749 (Fisher's exact test), Q value = 0.023

Table S93.  Gene #18: 'amp_17q24.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
AMP PEAK 18(17Q24.1) MUTATED 4 15 13
AMP PEAK 18(17Q24.1) WILD-TYPE 38 57 19

Figure S93.  Get High-res Image Gene #18: '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 = 6.1e-05

Table S94.  Gene #18: 'amp_17q24.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
AMP PEAK 18(17Q24.1) MUTATED 20 59 27
AMP PEAK 18(17Q24.1) WILD-TYPE 182 111 51

Figure S94.  Get High-res Image Gene #18: '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 = 0.00012

Table S95.  Gene #18: 'amp_17q24.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
AMP PEAK 18(17Q24.1) MUTATED 47 18 8
AMP PEAK 18(17Q24.1) WILD-TYPE 73 79 68

Figure S95.  Get High-res Image Gene #18: 'amp_17q24.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17q24.1' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

Table S96.  Gene #18: 'amp_17q24.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
AMP PEAK 18(17Q24.1) MUTATED 49 15 14 28
AMP PEAK 18(17Q24.1) WILD-TYPE 72 92 76 102

Figure S96.  Get High-res Image Gene #18: '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 = 6.1e-05

Table S97.  Gene #18: 'amp_17q24.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
AMP PEAK 18(17Q24.1) MUTATED 21 39 8 34 4
AMP PEAK 18(17Q24.1) WILD-TYPE 58 69 88 95 32

Figure S97.  Get High-res Image Gene #18: 'amp_17q24.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_17q24.1' versus 'MIRSEQ_CNMF'

P value = 0.0122 (Fisher's exact test), Q value = 0.035

Table S98.  Gene #18: 'amp_17q24.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 65 172
AMP PEAK 18(17Q24.1) MUTATED 46 7 39
AMP PEAK 18(17Q24.1) WILD-TYPE 114 58 133

Figure S98.  Get High-res Image Gene #18: 'amp_17q24.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_19p13.2' versus 'CN_CNMF'

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

Table S99.  Gene #19: 'amp_19p13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
AMP PEAK 19(19P13.2) MUTATED 17 44 14
AMP PEAK 19(19P13.2) WILD-TYPE 185 126 64

Figure S99.  Get High-res Image Gene #19: 'amp_19p13.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19p13.2' versus 'METHLYATION_CNMF'

P value = 0.0137 (Fisher's exact test), Q value = 0.038

Table S100.  Gene #19: 'amp_19p13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
AMP PEAK 19(19P13.2) MUTATED 33 15 9
AMP PEAK 19(19P13.2) WILD-TYPE 87 82 67

Figure S100.  Get High-res Image Gene #19: 'amp_19p13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_19p13.2' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S101.  Gene #19: 'amp_19p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
AMP PEAK 19(19P13.2) MUTATED 25 18 9 22 1
AMP PEAK 19(19P13.2) WILD-TYPE 54 90 87 107 35

Figure S101.  Get High-res Image Gene #19: 'amp_19p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_19p13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0223 (Fisher's exact test), Q value = 0.056

Table S102.  Gene #19: 'amp_19p13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 22 17 24 10
AMP PEAK 19(19P13.2) MUTATED 3 8 1 1 1
AMP PEAK 19(19P13.2) WILD-TYPE 9 14 16 23 9

Figure S102.  Get High-res Image Gene #19: 'amp_19p13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19q13.11' versus 'MRNA_CHIERARCHICAL'

P value = 0.0311 (Fisher's exact test), Q value = 0.075

Table S103.  Gene #20: 'amp_19q13.11' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
AMP PEAK 20(19Q13.11) MUTATED 2 16 7
AMP PEAK 20(19Q13.11) WILD-TYPE 40 56 25

Figure S103.  Get High-res Image Gene #20: 'amp_19q13.11' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_19q13.11' versus 'CN_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00059

Table S104.  Gene #20: 'amp_19q13.11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
AMP PEAK 20(19Q13.11) MUTATED 27 54 14
AMP PEAK 20(19Q13.11) WILD-TYPE 175 116 64

Figure S104.  Get High-res Image Gene #20: 'amp_19q13.11' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19q13.11' versus 'RPPA_CNMF'

P value = 0.0168 (Fisher's exact test), Q value = 0.045

Table S105.  Gene #20: 'amp_19q13.11' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 144 125
AMP PEAK 20(19Q13.11) MUTATED 25 33 17
AMP PEAK 20(19Q13.11) WILD-TYPE 60 111 108

Figure S105.  Get High-res Image Gene #20: 'amp_19q13.11' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_19q13.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.00083

Table S106.  Gene #20: 'amp_19q13.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
AMP PEAK 20(19Q13.11) MUTATED 28 24 13 29 1
AMP PEAK 20(19Q13.11) WILD-TYPE 51 84 83 100 35

Figure S106.  Get High-res Image Gene #20: 'amp_19q13.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_19q13.11' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0177 (Fisher's exact test), Q value = 0.047

Table S107.  Gene #20: 'amp_19q13.11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 32 24
AMP PEAK 20(19Q13.11) MUTATED 5 11 1
AMP PEAK 20(19Q13.11) WILD-TYPE 24 21 23

Figure S107.  Get High-res Image Gene #20: 'amp_19q13.11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_19q13.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00196 (Fisher's exact test), Q value = 0.0069

Table S108.  Gene #20: 'amp_19q13.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 22 17 24 10
AMP PEAK 20(19Q13.11) MUTATED 4 10 1 1 1
AMP PEAK 20(19Q13.11) WILD-TYPE 8 12 16 23 9

Figure S108.  Get High-res Image Gene #20: 'amp_19q13.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20p12.1' versus 'MRNA_CNMF'

P value = 0.0464 (Fisher's exact test), Q value = 0.11

Table S109.  Gene #21: 'amp_20p12.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
AMP PEAK 21(20P12.1) MUTATED 12 33 13 15
AMP PEAK 21(20P12.1) WILD-TYPE 23 28 16 6

Figure S109.  Get High-res Image Gene #21: 'amp_20p12.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20p12.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00087 (Fisher's exact test), Q value = 0.0033

Table S110.  Gene #21: 'amp_20p12.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
AMP PEAK 21(20P12.1) MUTATED 11 44 18
AMP PEAK 21(20P12.1) WILD-TYPE 31 28 14

Figure S110.  Get High-res Image Gene #21: 'amp_20p12.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20p12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S111.  Gene #21: 'amp_20p12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
AMP PEAK 21(20P12.1) MUTATED 65 104 39
AMP PEAK 21(20P12.1) WILD-TYPE 137 66 39

Figure S111.  Get High-res Image Gene #21: 'amp_20p12.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20p12.1' versus 'RPPA_CNMF'

P value = 0.0379 (Fisher's exact test), Q value = 0.089

Table S112.  Gene #21: 'amp_20p12.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 144 125
AMP PEAK 21(20P12.1) MUTATED 45 63 44
AMP PEAK 21(20P12.1) WILD-TYPE 40 81 81

Figure S112.  Get High-res Image Gene #21: 'amp_20p12.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_20p12.1' versus 'MRNASEQ_CNMF'

P value = 0.0221 (Fisher's exact test), Q value = 0.056

Table S113.  Gene #21: 'amp_20p12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
AMP PEAK 21(20P12.1) MUTATED 62 38 37 69
AMP PEAK 21(20P12.1) WILD-TYPE 59 69 53 61

Figure S113.  Get High-res Image Gene #21: 'amp_20p12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20p12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S114.  Gene #21: 'amp_20p12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
AMP PEAK 21(20P12.1) MUTATED 39 55 29 77 6
AMP PEAK 21(20P12.1) WILD-TYPE 40 53 67 52 30

Figure S114.  Get High-res Image Gene #21: 'amp_20p12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20p11.21' versus 'MRNA_CNMF'

P value = 0.00211 (Fisher's exact test), Q value = 0.0074

Table S115.  Gene #22: 'amp_20p11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
AMP PEAK 22(20P11.21) MUTATED 12 41 13 16
AMP PEAK 22(20P11.21) WILD-TYPE 23 20 16 5

Figure S115.  Get High-res Image Gene #22: 'amp_20p11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20p11.21' versus 'MRNA_CHIERARCHICAL'

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

Table S116.  Gene #22: 'amp_20p11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
AMP PEAK 22(20P11.21) MUTATED 11 48 23
AMP PEAK 22(20P11.21) WILD-TYPE 31 24 9

Figure S116.  Get High-res Image Gene #22: '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 = 6.1e-05

Table S117.  Gene #22: 'amp_20p11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
AMP PEAK 22(20P11.21) MUTATED 69 138 45
AMP PEAK 22(20P11.21) WILD-TYPE 133 32 33

Figure S117.  Get High-res Image Gene #22: '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 = 6.1e-05

Table S118.  Gene #22: 'amp_20p11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
AMP PEAK 22(20P11.21) MUTATED 89 44 33
AMP PEAK 22(20P11.21) WILD-TYPE 31 53 43

Figure S118.  Get High-res Image Gene #22: 'amp_20p11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20p11.21' versus 'RPPA_CNMF'

P value = 0.00639 (Fisher's exact test), Q value = 0.02

Table S119.  Gene #22: 'amp_20p11.21' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 144 125
AMP PEAK 22(20P11.21) MUTATED 56 81 55
AMP PEAK 22(20P11.21) WILD-TYPE 29 63 70

Figure S119.  Get High-res Image Gene #22: 'amp_20p11.21' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_20p11.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S120.  Gene #22: 'amp_20p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
AMP PEAK 22(20P11.21) MUTATED 91 38 47 74
AMP PEAK 22(20P11.21) WILD-TYPE 30 69 43 56

Figure S120.  Get High-res Image Gene #22: '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 = 6.1e-05

Table S121.  Gene #22: 'amp_20p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
AMP PEAK 22(20P11.21) MUTATED 51 75 31 87 6
AMP PEAK 22(20P11.21) WILD-TYPE 28 33 65 42 30

Figure S121.  Get High-res Image Gene #22: 'amp_20p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20p11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0375 (Fisher's exact test), Q value = 0.089

Table S122.  Gene #22: 'amp_20p11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 50 77 135
AMP PEAK 22(20P11.21) MUTATED 74 25 54 69
AMP PEAK 22(20P11.21) WILD-TYPE 61 25 23 66

Figure S122.  Get High-res Image Gene #22: '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 = 6.1e-05

Table S123.  Gene #23: 'amp_20q11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
AMP PEAK 23(20Q11.21) MUTATED 13 58 16 18
AMP PEAK 23(20Q11.21) WILD-TYPE 22 3 13 3

Figure S123.  Get High-res Image Gene #23: '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 = 6.1e-05

Table S124.  Gene #23: 'amp_20q11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
AMP PEAK 23(20Q11.21) MUTATED 12 62 31
AMP PEAK 23(20Q11.21) WILD-TYPE 30 10 1

Figure S124.  Get High-res Image Gene #23: '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 = 6.1e-05

Table S125.  Gene #23: 'amp_20q11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
AMP PEAK 23(20Q11.21) MUTATED 89 170 64
AMP PEAK 23(20Q11.21) WILD-TYPE 113 0 14

Figure S125.  Get High-res Image Gene #23: '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 = 6.1e-05

Table S126.  Gene #23: 'amp_20q11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
AMP PEAK 23(20Q11.21) MUTATED 117 50 45
AMP PEAK 23(20Q11.21) WILD-TYPE 3 47 31

Figure S126.  Get High-res Image Gene #23: 'amp_20q11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20q11.21' versus 'RPPA_CNMF'

P value = 0.00948 (Fisher's exact test), Q value = 0.028

Table S127.  Gene #23: 'amp_20q11.21' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 144 125
AMP PEAK 23(20Q11.21) MUTATED 67 107 76
AMP PEAK 23(20Q11.21) WILD-TYPE 18 37 49

Figure S127.  Get High-res Image Gene #23: 'amp_20q11.21' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_20q11.21' versus 'RPPA_CHIERARCHICAL'

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

Table S128.  Gene #23: 'amp_20q11.21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 51 33 35 39 42 86 22 20 26
AMP PEAK 23(20Q11.21) MUTATED 46 20 29 25 31 49 11 16 23
AMP PEAK 23(20Q11.21) WILD-TYPE 5 13 6 14 11 37 11 4 3

Figure S128.  Get High-res Image Gene #23: 'amp_20q11.21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_20q11.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S129.  Gene #23: 'amp_20q11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
AMP PEAK 23(20Q11.21) MUTATED 117 46 64 94
AMP PEAK 23(20Q11.21) WILD-TYPE 4 61 26 36

Figure S129.  Get High-res Image Gene #23: '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 = 6.1e-05

Table S130.  Gene #23: 'amp_20q11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
AMP PEAK 23(20Q11.21) MUTATED 73 96 34 111 7
AMP PEAK 23(20Q11.21) WILD-TYPE 6 12 62 18 29

Figure S130.  Get High-res Image Gene #23: 'amp_20q11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20q11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00166 (Fisher's exact test), Q value = 0.0059

Table S131.  Gene #23: 'amp_20q11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 50 77 135
AMP PEAK 23(20Q11.21) MUTATED 92 36 68 88
AMP PEAK 23(20Q11.21) WILD-TYPE 43 14 9 47

Figure S131.  Get High-res Image Gene #23: 'amp_20q11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20q11.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00405 (Fisher's exact test), Q value = 0.013

Table S132.  Gene #23: 'amp_20q11.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 22 17 24 10
AMP PEAK 23(20Q11.21) MUTATED 12 19 14 12 9
AMP PEAK 23(20Q11.21) WILD-TYPE 0 3 3 12 1

Figure S132.  Get High-res Image Gene #23: '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 = 6.1e-05

Table S133.  Gene #24: 'amp_20q12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
AMP PEAK 24(20Q12) MUTATED 12 58 15 18
AMP PEAK 24(20Q12) WILD-TYPE 23 3 14 3

Figure S133.  Get High-res Image Gene #24: 'amp_20q12' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20q12' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S134.  Gene #24: 'amp_20q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
AMP PEAK 24(20Q12) MUTATED 11 61 31
AMP PEAK 24(20Q12) WILD-TYPE 31 11 1

Figure S134.  Get High-res Image Gene #24: 'amp_20q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S135.  Gene #24: 'amp_20q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
AMP PEAK 24(20Q12) MUTATED 88 170 66
AMP PEAK 24(20Q12) WILD-TYPE 114 0 12

Figure S135.  Get High-res Image Gene #24: 'amp_20q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S136.  Gene #24: 'amp_20q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
AMP PEAK 24(20Q12) MUTATED 117 52 46
AMP PEAK 24(20Q12) WILD-TYPE 3 45 30

Figure S136.  Get High-res Image Gene #24: 'amp_20q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20q12' versus 'RPPA_CNMF'

P value = 0.0187 (Fisher's exact test), Q value = 0.049

Table S137.  Gene #24: 'amp_20q12' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 144 125
AMP PEAK 24(20Q12) MUTATED 66 108 77
AMP PEAK 24(20Q12) WILD-TYPE 19 36 48

Figure S137.  Get High-res Image Gene #24: 'amp_20q12' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_20q12' versus 'RPPA_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00042

Table S138.  Gene #24: 'amp_20q12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 51 33 35 39 42 86 22 20 26
AMP PEAK 24(20Q12) MUTATED 46 19 29 27 31 49 11 16 23
AMP PEAK 24(20Q12) WILD-TYPE 5 14 6 12 11 37 11 4 3

Figure S138.  Get High-res Image Gene #24: 'amp_20q12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_20q12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S139.  Gene #24: 'amp_20q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
AMP PEAK 24(20Q12) MUTATED 117 47 66 92
AMP PEAK 24(20Q12) WILD-TYPE 4 60 24 38

Figure S139.  Get High-res Image Gene #24: 'amp_20q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S140.  Gene #24: 'amp_20q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
AMP PEAK 24(20Q12) MUTATED 74 96 36 110 6
AMP PEAK 24(20Q12) WILD-TYPE 5 12 60 19 30

Figure S140.  Get High-res Image Gene #24: 'amp_20q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00129 (Fisher's exact test), Q value = 0.0047

Table S141.  Gene #24: 'amp_20q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 50 77 135
AMP PEAK 24(20Q12) MUTATED 92 37 68 88
AMP PEAK 24(20Q12) WILD-TYPE 43 13 9 47

Figure S141.  Get High-res Image Gene #24: 'amp_20q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00559 (Fisher's exact test), Q value = 0.018

Table S142.  Gene #24: 'amp_20q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 22 17 24 10
AMP PEAK 24(20Q12) MUTATED 12 20 14 13 9
AMP PEAK 24(20Q12) WILD-TYPE 0 2 3 11 1

Figure S142.  Get High-res Image Gene #24: 'amp_20q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20q13.12' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S143.  Gene #25: 'amp_20q13.12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
AMP PEAK 25(20Q13.12) MUTATED 13 58 16 18
AMP PEAK 25(20Q13.12) WILD-TYPE 22 3 13 3

Figure S143.  Get High-res Image Gene #25: 'amp_20q13.12' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20q13.12' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S144.  Gene #25: 'amp_20q13.12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
AMP PEAK 25(20Q13.12) MUTATED 12 62 31
AMP PEAK 25(20Q13.12) WILD-TYPE 30 10 1

Figure S144.  Get High-res Image Gene #25: 'amp_20q13.12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20q13.12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S145.  Gene #25: 'amp_20q13.12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
AMP PEAK 25(20Q13.12) MUTATED 88 170 68
AMP PEAK 25(20Q13.12) WILD-TYPE 114 0 10

Figure S145.  Get High-res Image Gene #25: 'amp_20q13.12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20q13.12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S146.  Gene #25: 'amp_20q13.12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
AMP PEAK 25(20Q13.12) MUTATED 117 52 46
AMP PEAK 25(20Q13.12) WILD-TYPE 3 45 30

Figure S146.  Get High-res Image Gene #25: 'amp_20q13.12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20q13.12' versus 'RPPA_CNMF'

P value = 0.0112 (Fisher's exact test), Q value = 0.032

Table S147.  Gene #25: 'amp_20q13.12' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 144 125
AMP PEAK 25(20Q13.12) MUTATED 66 110 77
AMP PEAK 25(20Q13.12) WILD-TYPE 19 34 48

Figure S147.  Get High-res Image Gene #25: 'amp_20q13.12' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_20q13.12' versus 'RPPA_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 3e-04

Table S148.  Gene #25: 'amp_20q13.12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 51 33 35 39 42 86 22 20 26
AMP PEAK 25(20Q13.12) MUTATED 46 19 29 28 32 49 11 16 23
AMP PEAK 25(20Q13.12) WILD-TYPE 5 14 6 11 10 37 11 4 3

Figure S148.  Get High-res Image Gene #25: 'amp_20q13.12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_20q13.12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S149.  Gene #25: 'amp_20q13.12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
AMP PEAK 25(20Q13.12) MUTATED 117 48 66 93
AMP PEAK 25(20Q13.12) WILD-TYPE 4 59 24 37

Figure S149.  Get High-res Image Gene #25: 'amp_20q13.12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20q13.12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S150.  Gene #25: 'amp_20q13.12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
AMP PEAK 25(20Q13.12) MUTATED 74 96 36 111 7
AMP PEAK 25(20Q13.12) WILD-TYPE 5 12 60 18 29

Figure S150.  Get High-res Image Gene #25: 'amp_20q13.12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20q13.12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00268 (Fisher's exact test), Q value = 0.0092

Table S151.  Gene #25: 'amp_20q13.12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 50 77 135
AMP PEAK 25(20Q13.12) MUTATED 93 37 68 90
AMP PEAK 25(20Q13.12) WILD-TYPE 42 13 9 45

Figure S151.  Get High-res Image Gene #25: 'amp_20q13.12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20q13.12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00589 (Fisher's exact test), Q value = 0.018

Table S152.  Gene #25: 'amp_20q13.12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 22 17 24 10
AMP PEAK 25(20Q13.12) MUTATED 12 20 14 13 9
AMP PEAK 25(20Q13.12) WILD-TYPE 0 2 3 11 1

Figure S152.  Get High-res Image Gene #25: 'amp_20q13.12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p36.11' versus 'MRNA_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00034

Table S153.  Gene #26: 'del_1p36.11' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
DEL PEAK 1(1P36.11) MUTATED 9 36 4 10
DEL PEAK 1(1P36.11) WILD-TYPE 26 25 25 11

Figure S153.  Get High-res Image Gene #26: 'del_1p36.11' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_1p36.11' versus 'MRNA_CHIERARCHICAL'

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

Table S154.  Gene #26: 'del_1p36.11' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
DEL PEAK 1(1P36.11) MUTATED 9 33 17
DEL PEAK 1(1P36.11) WILD-TYPE 33 39 15

Figure S154.  Get High-res Image Gene #26: '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 = 6.1e-05

Table S155.  Gene #26: 'del_1p36.11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
DEL PEAK 1(1P36.11) MUTATED 43 101 24
DEL PEAK 1(1P36.11) WILD-TYPE 159 69 54

Figure S155.  Get High-res Image Gene #26: '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 = 6.1e-05

Table S156.  Gene #26: 'del_1p36.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
DEL PEAK 1(1P36.11) MUTATED 64 21 22
DEL PEAK 1(1P36.11) WILD-TYPE 56 76 54

Figure S156.  Get High-res Image Gene #26: 'del_1p36.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p36.11' versus 'RPPA_CHIERARCHICAL'

P value = 0.028 (Fisher's exact test), Q value = 0.069

Table S157.  Gene #26: 'del_1p36.11' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 51 33 35 39 42 86 22 20 26
DEL PEAK 1(1P36.11) MUTATED 22 12 15 15 19 17 8 10 12
DEL PEAK 1(1P36.11) WILD-TYPE 29 21 20 24 23 69 14 10 14

Figure S157.  Get High-res Image Gene #26: 'del_1p36.11' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_1p36.11' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S158.  Gene #26: 'del_1p36.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
DEL PEAK 1(1P36.11) MUTATED 64 17 34 52
DEL PEAK 1(1P36.11) WILD-TYPE 57 90 56 78

Figure S158.  Get High-res Image Gene #26: '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 = 6.1e-05

Table S159.  Gene #26: 'del_1p36.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
DEL PEAK 1(1P36.11) MUTATED 42 48 12 61 4
DEL PEAK 1(1P36.11) WILD-TYPE 37 60 84 68 32

Figure S159.  Get High-res Image Gene #26: 'del_1p36.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0203 (Fisher's exact test), Q value = 0.052

Table S160.  Gene #26: 'del_1p36.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 50 77 135
DEL PEAK 1(1P36.11) MUTATED 45 17 41 46
DEL PEAK 1(1P36.11) WILD-TYPE 90 33 36 89

Figure S160.  Get High-res Image Gene #26: 'del_1p36.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_1p33' versus 'MRNA_CNMF'

P value = 0.0159 (Fisher's exact test), Q value = 0.043

Table S161.  Gene #27: 'del_1p33' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
DEL PEAK 2(1P33) MUTATED 10 23 2 5
DEL PEAK 2(1P33) WILD-TYPE 25 38 27 16

Figure S161.  Get High-res Image Gene #27: 'del_1p33' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_1p33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S162.  Gene #27: 'del_1p33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
DEL PEAK 2(1P33) MUTATED 33 80 10
DEL PEAK 2(1P33) WILD-TYPE 169 90 68

Figure S162.  Get High-res Image Gene #27: 'del_1p33' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p33' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 3e-04

Table S163.  Gene #27: 'del_1p33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
DEL PEAK 2(1P33) MUTATED 49 15 17
DEL PEAK 2(1P33) WILD-TYPE 71 82 59

Figure S163.  Get High-res Image Gene #27: 'del_1p33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p33' versus 'MRNASEQ_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.0011

Table S164.  Gene #27: 'del_1p33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
DEL PEAK 2(1P33) MUTATED 46 14 24 38
DEL PEAK 2(1P33) WILD-TYPE 75 93 66 92

Figure S164.  Get High-res Image Gene #27: 'del_1p33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

Table S165.  Gene #27: 'del_1p33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
DEL PEAK 2(1P33) MUTATED 34 33 10 39 6
DEL PEAK 2(1P33) WILD-TYPE 45 75 86 90 30

Figure S165.  Get High-res Image Gene #27: 'del_1p33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S166.  Gene #28: 'del_1p13.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
DEL PEAK 3(1P13.1) MUTATED 36 76 7
DEL PEAK 3(1P13.1) WILD-TYPE 166 94 71

Figure S166.  Get High-res Image Gene #28: 'del_1p13.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p13.1' versus 'METHLYATION_CNMF'

P value = 0.00131 (Fisher's exact test), Q value = 0.0047

Table S167.  Gene #28: 'del_1p13.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
DEL PEAK 3(1P13.1) MUTATED 46 17 16
DEL PEAK 3(1P13.1) WILD-TYPE 74 80 60

Figure S167.  Get High-res Image Gene #28: 'del_1p13.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p13.1' versus 'MRNASEQ_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.00095

Table S168.  Gene #28: 'del_1p13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
DEL PEAK 3(1P13.1) MUTATED 43 12 24 39
DEL PEAK 3(1P13.1) WILD-TYPE 78 95 66 91

Figure S168.  Get High-res Image Gene #28: 'del_1p13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00042

Table S169.  Gene #28: 'del_1p13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
DEL PEAK 3(1P13.1) MUTATED 31 31 12 40 4
DEL PEAK 3(1P13.1) WILD-TYPE 48 77 84 89 32

Figure S169.  Get High-res Image Gene #28: 'del_1p13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1q43' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

Table S170.  Gene #29: 'del_1q43' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
DEL PEAK 4(1Q43) MUTATED 9 35 10
DEL PEAK 4(1Q43) WILD-TYPE 193 135 68

Figure S170.  Get High-res Image Gene #29: 'del_1q43' versus Molecular Subtype #3: 'CN_CNMF'

'del_1q43' versus 'METHLYATION_CNMF'

P value = 0.00254 (Fisher's exact test), Q value = 0.0088

Table S171.  Gene #29: 'del_1q43' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
DEL PEAK 4(1Q43) MUTATED 25 5 9
DEL PEAK 4(1Q43) WILD-TYPE 95 92 67

Figure S171.  Get High-res Image Gene #29: 'del_1q43' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1q43' versus 'MRNASEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00042

Table S172.  Gene #29: 'del_1q43' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
DEL PEAK 4(1Q43) MUTATED 23 2 15 13
DEL PEAK 4(1Q43) WILD-TYPE 98 105 75 117

Figure S172.  Get High-res Image Gene #29: 'del_1q43' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1q43' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S173.  Gene #29: 'del_1q43' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
DEL PEAK 4(1Q43) MUTATED 18 17 3 14 1
DEL PEAK 4(1Q43) WILD-TYPE 61 91 93 115 35

Figure S173.  Get High-res Image Gene #29: 'del_1q43' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1q43' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00062 (Fisher's exact test), Q value = 0.0024

Table S174.  Gene #29: 'del_1q43' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 50 77 135
DEL PEAK 4(1Q43) MUTATED 16 9 17 6
DEL PEAK 4(1Q43) WILD-TYPE 119 41 60 129

Figure S174.  Get High-res Image Gene #29: 'del_1q43' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_1q43' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0275 (Fisher's exact test), Q value = 0.068

Table S175.  Gene #29: 'del_1q43' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 32 24
DEL PEAK 4(1Q43) MUTATED 9 2 6
DEL PEAK 4(1Q43) WILD-TYPE 20 30 18

Figure S175.  Get High-res Image Gene #29: 'del_1q43' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_3p26.2' versus 'CN_CNMF'

P value = 0.0012 (Fisher's exact test), Q value = 0.0044

Table S176.  Gene #32: 'del_3p26.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
DEL PEAK 7(3P26.2) MUTATED 21 41 10
DEL PEAK 7(3P26.2) WILD-TYPE 181 129 68

Figure S176.  Get High-res Image Gene #32: 'del_3p26.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p26.2' versus 'MRNASEQ_CNMF'

P value = 0.00718 (Fisher's exact test), Q value = 0.022

Table S177.  Gene #32: 'del_3p26.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
DEL PEAK 7(3P26.2) MUTATED 23 7 14 28
DEL PEAK 7(3P26.2) WILD-TYPE 98 100 76 102

Figure S177.  Get High-res Image Gene #32: 'del_3p26.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3p26.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00327 (Fisher's exact test), Q value = 0.011

Table S178.  Gene #32: 'del_3p26.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
DEL PEAK 7(3P26.2) MUTATED 18 16 7 29 2
DEL PEAK 7(3P26.2) WILD-TYPE 61 92 89 100 34

Figure S178.  Get High-res Image Gene #32: 'del_3p26.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0411 (Fisher's exact test), Q value = 0.096

Table S179.  Gene #33: 'del_3p14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
DEL PEAK 8(3P14.2) MUTATED 19 25 9 29 6
DEL PEAK 8(3P14.2) WILD-TYPE 60 83 87 100 30

Figure S179.  Get High-res Image Gene #33: 'del_3p14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4p16.2' versus 'MRNA_CNMF'

P value = 0.00073 (Fisher's exact test), Q value = 0.0029

Table S180.  Gene #35: 'del_4p16.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
DEL PEAK 10(4P16.2) MUTATED 7 29 3 9
DEL PEAK 10(4P16.2) WILD-TYPE 28 32 26 12

Figure S180.  Get High-res Image Gene #35: 'del_4p16.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_4p16.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00159 (Fisher's exact test), Q value = 0.0057

Table S181.  Gene #35: 'del_4p16.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
DEL PEAK 10(4P16.2) MUTATED 7 23 18
DEL PEAK 10(4P16.2) WILD-TYPE 35 49 14

Figure S181.  Get High-res Image Gene #35: '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 = 6.1e-05

Table S182.  Gene #35: 'del_4p16.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
DEL PEAK 10(4P16.2) MUTATED 33 87 19
DEL PEAK 10(4P16.2) WILD-TYPE 169 83 59

Figure S182.  Get High-res Image Gene #35: 'del_4p16.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_4p16.2' versus 'METHLYATION_CNMF'

P value = 0.00413 (Fisher's exact test), Q value = 0.014

Table S183.  Gene #35: 'del_4p16.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
DEL PEAK 10(4P16.2) MUTATED 48 19 21
DEL PEAK 10(4P16.2) WILD-TYPE 72 78 55

Figure S183.  Get High-res Image Gene #35: 'del_4p16.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4p16.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00437 (Fisher's exact test), Q value = 0.014

Table S184.  Gene #35: 'del_4p16.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 51 33 35 39 42 86 22 20 26
DEL PEAK 10(4P16.2) MUTATED 18 7 12 12 19 14 7 1 9
DEL PEAK 10(4P16.2) WILD-TYPE 33 26 23 27 23 72 15 19 17

Figure S184.  Get High-res Image Gene #35: 'del_4p16.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_4p16.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S185.  Gene #35: 'del_4p16.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
DEL PEAK 10(4P16.2) MUTATED 52 13 30 43
DEL PEAK 10(4P16.2) WILD-TYPE 69 94 60 87

Figure S185.  Get High-res Image Gene #35: 'del_4p16.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4p16.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S186.  Gene #35: 'del_4p16.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
DEL PEAK 10(4P16.2) MUTATED 36 38 8 52 4
DEL PEAK 10(4P16.2) WILD-TYPE 43 70 88 77 32

Figure S186.  Get High-res Image Gene #35: 'del_4p16.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4q22.1' versus 'MRNA_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.0015

Table S187.  Gene #36: 'del_4q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
DEL PEAK 11(4Q22.1) MUTATED 9 27 2 11
DEL PEAK 11(4Q22.1) WILD-TYPE 26 34 27 10

Figure S187.  Get High-res Image Gene #36: 'del_4q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_4q22.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.004 (Fisher's exact test), Q value = 0.013

Table S188.  Gene #36: 'del_4q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
DEL PEAK 11(4Q22.1) MUTATED 7 25 17
DEL PEAK 11(4Q22.1) WILD-TYPE 35 47 15

Figure S188.  Get High-res Image Gene #36: '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 = 6.1e-05

Table S189.  Gene #36: 'del_4q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
DEL PEAK 11(4Q22.1) MUTATED 35 96 20
DEL PEAK 11(4Q22.1) WILD-TYPE 167 74 58

Figure S189.  Get High-res Image Gene #36: 'del_4q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q22.1' versus 'METHLYATION_CNMF'

P value = 0.00079 (Fisher's exact test), Q value = 0.003

Table S190.  Gene #36: 'del_4q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
DEL PEAK 11(4Q22.1) MUTATED 55 21 25
DEL PEAK 11(4Q22.1) WILD-TYPE 65 76 51

Figure S190.  Get High-res Image Gene #36: 'del_4q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q22.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S191.  Gene #36: 'del_4q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
DEL PEAK 11(4Q22.1) MUTATED 57 16 28 49
DEL PEAK 11(4Q22.1) WILD-TYPE 64 91 62 81

Figure S191.  Get High-res Image Gene #36: '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 = 6.1e-05

Table S192.  Gene #36: 'del_4q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
DEL PEAK 11(4Q22.1) MUTATED 40 44 9 53 4
DEL PEAK 11(4Q22.1) WILD-TYPE 39 64 87 76 32

Figure S192.  Get High-res Image Gene #36: 'del_4q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4q35.1' versus 'MRNA_CNMF'

P value = 0.00093 (Fisher's exact test), Q value = 0.0035

Table S193.  Gene #37: 'del_4q35.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
DEL PEAK 12(4Q35.1) MUTATED 8 30 4 11
DEL PEAK 12(4Q35.1) WILD-TYPE 27 31 25 10

Figure S193.  Get High-res Image Gene #37: 'del_4q35.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_4q35.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00767 (Fisher's exact test), Q value = 0.023

Table S194.  Gene #37: 'del_4q35.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
DEL PEAK 12(4Q35.1) MUTATED 8 28 17
DEL PEAK 12(4Q35.1) WILD-TYPE 34 44 15

Figure S194.  Get High-res Image Gene #37: 'del_4q35.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_4q35.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S195.  Gene #37: 'del_4q35.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
DEL PEAK 12(4Q35.1) MUTATED 36 101 22
DEL PEAK 12(4Q35.1) WILD-TYPE 166 69 56

Figure S195.  Get High-res Image Gene #37: 'del_4q35.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q35.1' versus 'METHLYATION_CNMF'

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

Table S196.  Gene #37: 'del_4q35.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
DEL PEAK 12(4Q35.1) MUTATED 59 17 26
DEL PEAK 12(4Q35.1) WILD-TYPE 61 80 50

Figure S196.  Get High-res Image Gene #37: 'del_4q35.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q35.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S197.  Gene #37: 'del_4q35.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
DEL PEAK 12(4Q35.1) MUTATED 61 19 29 49
DEL PEAK 12(4Q35.1) WILD-TYPE 60 88 61 81

Figure S197.  Get High-res Image Gene #37: 'del_4q35.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4q35.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S198.  Gene #37: 'del_4q35.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
DEL PEAK 12(4Q35.1) MUTATED 40 44 12 56 6
DEL PEAK 12(4Q35.1) WILD-TYPE 39 64 84 73 30

Figure S198.  Get High-res Image Gene #37: 'del_4q35.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5q12.1' versus 'MRNA_CNMF'

P value = 0.0012 (Fisher's exact test), Q value = 0.0044

Table S199.  Gene #38: 'del_5q12.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
DEL PEAK 13(5Q12.1) MUTATED 8 20 0 6
DEL PEAK 13(5Q12.1) WILD-TYPE 27 41 29 15

Figure S199.  Get High-res Image Gene #38: 'del_5q12.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_5q12.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.0031 (Fisher's exact test), Q value = 0.011

Table S200.  Gene #38: 'del_5q12.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
DEL PEAK 13(5Q12.1) MUTATED 7 12 15
DEL PEAK 13(5Q12.1) WILD-TYPE 35 60 17

Figure S200.  Get High-res Image Gene #38: '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 = 6.1e-05

Table S201.  Gene #38: 'del_5q12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
DEL PEAK 13(5Q12.1) MUTATED 19 63 24
DEL PEAK 13(5Q12.1) WILD-TYPE 183 107 54

Figure S201.  Get High-res Image Gene #38: 'del_5q12.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q12.1' versus 'METHLYATION_CNMF'

P value = 0.0138 (Fisher's exact test), Q value = 0.038

Table S202.  Gene #38: 'del_5q12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
DEL PEAK 13(5Q12.1) MUTATED 39 15 18
DEL PEAK 13(5Q12.1) WILD-TYPE 81 82 58

Figure S202.  Get High-res Image Gene #38: 'del_5q12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5q12.1' versus 'RPPA_CNMF'

P value = 0.0254 (Fisher's exact test), Q value = 0.063

Table S203.  Gene #38: 'del_5q12.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 144 125
DEL PEAK 13(5Q12.1) MUTATED 28 27 23
DEL PEAK 13(5Q12.1) WILD-TYPE 57 117 102

Figure S203.  Get High-res Image Gene #38: 'del_5q12.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_5q12.1' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00025

Table S204.  Gene #38: 'del_5q12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
DEL PEAK 13(5Q12.1) MUTATED 41 9 23 33
DEL PEAK 13(5Q12.1) WILD-TYPE 80 98 67 97

Figure S204.  Get High-res Image Gene #38: 'del_5q12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_5q12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00034

Table S205.  Gene #38: 'del_5q12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
DEL PEAK 13(5Q12.1) MUTATED 29 29 9 35 4
DEL PEAK 13(5Q12.1) WILD-TYPE 50 79 87 94 32

Figure S205.  Get High-res Image Gene #38: 'del_5q12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5q21.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.0439 (Fisher's exact test), Q value = 0.1

Table S206.  Gene #39: 'del_5q21.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
DEL PEAK 14(5Q21.1) MUTATED 9 18 15
DEL PEAK 14(5Q21.1) WILD-TYPE 33 54 17

Figure S206.  Get High-res Image Gene #39: 'del_5q21.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_5q21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S207.  Gene #39: 'del_5q21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
DEL PEAK 14(5Q21.1) MUTATED 30 71 26
DEL PEAK 14(5Q21.1) WILD-TYPE 172 99 52

Figure S207.  Get High-res Image Gene #39: 'del_5q21.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q21.1' versus 'METHLYATION_CNMF'

P value = 0.00443 (Fisher's exact test), Q value = 0.014

Table S208.  Gene #39: 'del_5q21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
DEL PEAK 14(5Q21.1) MUTATED 45 17 23
DEL PEAK 14(5Q21.1) WILD-TYPE 75 80 53

Figure S208.  Get High-res Image Gene #39: 'del_5q21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5q21.1' versus 'RPPA_CNMF'

P value = 0.0475 (Fisher's exact test), Q value = 0.11

Table S209.  Gene #39: 'del_5q21.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 144 125
DEL PEAK 14(5Q21.1) MUTATED 31 33 28
DEL PEAK 14(5Q21.1) WILD-TYPE 54 111 97

Figure S209.  Get High-res Image Gene #39: 'del_5q21.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_5q21.1' versus 'MRNASEQ_CNMF'

P value = 0.00703 (Fisher's exact test), Q value = 0.022

Table S210.  Gene #39: 'del_5q21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
DEL PEAK 14(5Q21.1) MUTATED 47 20 22 38
DEL PEAK 14(5Q21.1) WILD-TYPE 74 87 68 92

Figure S210.  Get High-res Image Gene #39: 'del_5q21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_5q21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.0012

Table S211.  Gene #39: 'del_5q21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
DEL PEAK 14(5Q21.1) MUTATED 29 36 12 44 6
DEL PEAK 14(5Q21.1) WILD-TYPE 50 72 84 85 30

Figure S211.  Get High-res Image Gene #39: 'del_5q21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5q22.2' versus 'MRNA_CNMF'

P value = 0.0136 (Fisher's exact test), Q value = 0.038

Table S212.  Gene #40: 'del_5q22.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
DEL PEAK 15(5Q22.2) MUTATED 8 23 2 6
DEL PEAK 15(5Q22.2) WILD-TYPE 27 38 27 15

Figure S212.  Get High-res Image Gene #40: 'del_5q22.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_5q22.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00916 (Fisher's exact test), Q value = 0.027

Table S213.  Gene #40: 'del_5q22.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
DEL PEAK 15(5Q22.2) MUTATED 6 18 15
DEL PEAK 15(5Q22.2) WILD-TYPE 36 54 17

Figure S213.  Get High-res Image Gene #40: '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 = 6.1e-05

Table S214.  Gene #40: 'del_5q22.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
DEL PEAK 15(5Q22.2) MUTATED 30 72 28
DEL PEAK 15(5Q22.2) WILD-TYPE 172 98 50

Figure S214.  Get High-res Image Gene #40: 'del_5q22.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q22.2' versus 'METHLYATION_CNMF'

P value = 0.0289 (Fisher's exact test), Q value = 0.07

Table S215.  Gene #40: 'del_5q22.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
DEL PEAK 15(5Q22.2) MUTATED 46 21 23
DEL PEAK 15(5Q22.2) WILD-TYPE 74 76 53

Figure S215.  Get High-res Image Gene #40: 'del_5q22.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5q22.2' versus 'MRNASEQ_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.0011

Table S216.  Gene #40: 'del_5q22.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
DEL PEAK 15(5Q22.2) MUTATED 51 17 24 37
DEL PEAK 15(5Q22.2) WILD-TYPE 70 90 66 93

Figure S216.  Get High-res Image Gene #40: 'del_5q22.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_5q22.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 3e-04

Table S217.  Gene #40: 'del_5q22.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
DEL PEAK 15(5Q22.2) MUTATED 29 38 15 44 3
DEL PEAK 15(5Q22.2) WILD-TYPE 50 70 81 85 33

Figure S217.  Get High-res Image Gene #40: 'del_5q22.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_6p25.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0435 (Fisher's exact test), Q value = 0.1

Table S218.  Gene #41: 'del_6p25.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 22 17 24 10
DEL PEAK 16(6P25.3) MUTATED 1 0 1 5 3
DEL PEAK 16(6P25.3) WILD-TYPE 11 22 16 19 7

Figure S218.  Get High-res Image Gene #41: 'del_6p25.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q26' versus 'RPPA_CNMF'

P value = 0.0286 (Fisher's exact test), Q value = 0.07

Table S219.  Gene #42: 'del_6q26' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 144 125
DEL PEAK 17(6Q26) MUTATED 16 22 9
DEL PEAK 17(6Q26) WILD-TYPE 69 122 116

Figure S219.  Get High-res Image Gene #42: 'del_6q26' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_8p23.3' versus 'MRNA_CNMF'

P value = 0.0122 (Fisher's exact test), Q value = 0.035

Table S220.  Gene #44: 'del_8p23.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
DEL PEAK 19(8P23.3) MUTATED 12 33 6 11
DEL PEAK 19(8P23.3) WILD-TYPE 23 28 23 10

Figure S220.  Get High-res Image Gene #44: 'del_8p23.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_8p23.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.00072

Table S221.  Gene #44: 'del_8p23.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
DEL PEAK 19(8P23.3) MUTATED 10 29 23
DEL PEAK 19(8P23.3) WILD-TYPE 32 43 9

Figure S221.  Get High-res Image Gene #44: 'del_8p23.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_8p23.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S222.  Gene #44: 'del_8p23.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
DEL PEAK 19(8P23.3) MUTATED 35 99 55
DEL PEAK 19(8P23.3) WILD-TYPE 167 71 23

Figure S222.  Get High-res Image Gene #44: 'del_8p23.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_8p23.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S223.  Gene #44: 'del_8p23.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
DEL PEAK 19(8P23.3) MUTATED 70 28 27
DEL PEAK 19(8P23.3) WILD-TYPE 50 69 49

Figure S223.  Get High-res Image Gene #44: 'del_8p23.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_8p23.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S224.  Gene #44: 'del_8p23.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
DEL PEAK 19(8P23.3) MUTATED 65 22 43 59
DEL PEAK 19(8P23.3) WILD-TYPE 56 85 47 71

Figure S224.  Get High-res Image Gene #44: 'del_8p23.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_8p23.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S225.  Gene #44: 'del_8p23.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
DEL PEAK 19(8P23.3) MUTATED 47 50 19 67 6
DEL PEAK 19(8P23.3) WILD-TYPE 32 58 77 62 30

Figure S225.  Get High-res Image Gene #44: 'del_8p23.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0436 (Fisher's exact test), Q value = 0.1

Table S226.  Gene #44: 'del_8p23.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 22 17 24 10
DEL PEAK 19(8P23.3) MUTATED 9 12 10 6 5
DEL PEAK 19(8P23.3) WILD-TYPE 3 10 7 18 5

Figure S226.  Get High-res Image Gene #44: 'del_8p23.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p22' versus 'MRNA_CNMF'

P value = 0.00436 (Fisher's exact test), Q value = 0.014

Table S227.  Gene #45: 'del_8p22' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
DEL PEAK 20(8P22) MUTATED 9 35 8 11
DEL PEAK 20(8P22) WILD-TYPE 26 26 21 10

Figure S227.  Get High-res Image Gene #45: 'del_8p22' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_8p22' versus 'MRNA_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.00075

Table S228.  Gene #45: 'del_8p22' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
DEL PEAK 20(8P22) MUTATED 8 34 21
DEL PEAK 20(8P22) WILD-TYPE 34 38 11

Figure S228.  Get High-res Image Gene #45: 'del_8p22' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_8p22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S229.  Gene #45: 'del_8p22' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
DEL PEAK 20(8P22) MUTATED 36 108 59
DEL PEAK 20(8P22) WILD-TYPE 166 62 19

Figure S229.  Get High-res Image Gene #45: 'del_8p22' versus Molecular Subtype #3: 'CN_CNMF'

'del_8p22' versus 'METHLYATION_CNMF'

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

Table S230.  Gene #45: 'del_8p22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
DEL PEAK 20(8P22) MUTATED 77 32 29
DEL PEAK 20(8P22) WILD-TYPE 43 65 47

Figure S230.  Get High-res Image Gene #45: 'del_8p22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_8p22' versus 'RPPA_CHIERARCHICAL'

P value = 0.0174 (Fisher's exact test), Q value = 0.046

Table S231.  Gene #45: 'del_8p22' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 51 33 35 39 42 86 22 20 26
DEL PEAK 20(8P22) MUTATED 33 12 16 15 17 31 5 9 15
DEL PEAK 20(8P22) WILD-TYPE 18 21 19 24 25 55 17 11 11

Figure S231.  Get High-res Image Gene #45: 'del_8p22' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_8p22' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S232.  Gene #45: 'del_8p22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
DEL PEAK 20(8P22) MUTATED 73 27 46 57
DEL PEAK 20(8P22) WILD-TYPE 48 80 44 73

Figure S232.  Get High-res Image Gene #45: 'del_8p22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_8p22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S233.  Gene #45: 'del_8p22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
DEL PEAK 20(8P22) MUTATED 52 54 23 69 5
DEL PEAK 20(8P22) WILD-TYPE 27 54 73 60 31

Figure S233.  Get High-res Image Gene #45: 'del_8p22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_8p22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0145 (Fisher's exact test), Q value = 0.04

Table S234.  Gene #45: 'del_8p22' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 50 77 135
DEL PEAK 20(8P22) MUTATED 55 26 46 53
DEL PEAK 20(8P22) WILD-TYPE 80 24 31 82

Figure S234.  Get High-res Image Gene #45: 'del_8p22' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_8p22' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0477 (Fisher's exact test), Q value = 0.11

Table S235.  Gene #45: 'del_8p22' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 22 17 24 10
DEL PEAK 20(8P22) MUTATED 8 14 10 6 5
DEL PEAK 20(8P22) WILD-TYPE 4 8 7 18 5

Figure S235.  Get High-res Image Gene #45: 'del_8p22' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8q11.1' versus 'CN_CNMF'

P value = 0.0164 (Fisher's exact test), Q value = 0.044

Table S236.  Gene #46: 'del_8q11.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
DEL PEAK 21(8Q11.1) MUTATED 11 18 1
DEL PEAK 21(8Q11.1) WILD-TYPE 191 152 77

Figure S236.  Get High-res Image Gene #46: 'del_8q11.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p21.3' versus 'CN_CNMF'

P value = 0.00399 (Fisher's exact test), Q value = 0.013

Table S237.  Gene #47: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
DEL PEAK 22(9P21.3) MUTATED 16 32 14
DEL PEAK 22(9P21.3) WILD-TYPE 186 138 64

Figure S237.  Get High-res Image Gene #47: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 0.0192 (Fisher's exact test), Q value = 0.049

Table S238.  Gene #47: 'del_9p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
DEL PEAK 22(9P21.3) MUTATED 26 8 13 15
DEL PEAK 22(9P21.3) WILD-TYPE 95 99 77 115

Figure S238.  Get High-res Image Gene #47: 'del_9p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00123 (Fisher's exact test), Q value = 0.0045

Table S239.  Gene #47: 'del_9p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
DEL PEAK 22(9P21.3) MUTATED 16 19 6 21 0
DEL PEAK 22(9P21.3) WILD-TYPE 63 89 90 108 36

Figure S239.  Get High-res Image Gene #47: 'del_9p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10p15.3' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

Table S240.  Gene #48: 'del_10p15.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
DEL PEAK 23(10P15.3) MUTATED 16 46 18
DEL PEAK 23(10P15.3) WILD-TYPE 186 124 60

Figure S240.  Get High-res Image Gene #48: 'del_10p15.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_10p15.3' versus 'METHLYATION_CNMF'

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

Table S241.  Gene #48: 'del_10p15.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
DEL PEAK 23(10P15.3) MUTATED 37 7 13
DEL PEAK 23(10P15.3) WILD-TYPE 83 90 63

Figure S241.  Get High-res Image Gene #48: 'del_10p15.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10p15.3' versus 'MRNASEQ_CNMF'

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

Table S242.  Gene #48: 'del_10p15.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
DEL PEAK 23(10P15.3) MUTATED 33 7 18 21
DEL PEAK 23(10P15.3) WILD-TYPE 88 100 72 109

Figure S242.  Get High-res Image Gene #48: 'del_10p15.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10p15.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.00063

Table S243.  Gene #48: 'del_10p15.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
DEL PEAK 23(10P15.3) MUTATED 27 19 7 23 3
DEL PEAK 23(10P15.3) WILD-TYPE 52 89 89 106 33

Figure S243.  Get High-res Image Gene #48: 'del_10p15.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10p15.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0218 (Fisher's exact test), Q value = 0.055

Table S244.  Gene #48: 'del_10p15.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 22 17 24 10
DEL PEAK 23(10P15.3) MUTATED 4 8 0 3 2
DEL PEAK 23(10P15.3) WILD-TYPE 8 14 17 21 8

Figure S244.  Get High-res Image Gene #48: 'del_10p15.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q21.1' versus 'MRNA_CNMF'

P value = 0.00312 (Fisher's exact test), Q value = 0.011

Table S245.  Gene #49: 'del_10q21.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
DEL PEAK 24(10Q21.1) MUTATED 3 19 1 4
DEL PEAK 24(10Q21.1) WILD-TYPE 32 42 28 17

Figure S245.  Get High-res Image Gene #49: 'del_10q21.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_10q21.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.0279 (Fisher's exact test), Q value = 0.069

Table S246.  Gene #49: 'del_10q21.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
DEL PEAK 24(10Q21.1) MUTATED 3 14 10
DEL PEAK 24(10Q21.1) WILD-TYPE 39 58 22

Figure S246.  Get High-res Image Gene #49: 'del_10q21.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_10q21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S247.  Gene #49: 'del_10q21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
DEL PEAK 24(10Q21.1) MUTATED 17 63 18
DEL PEAK 24(10Q21.1) WILD-TYPE 185 107 60

Figure S247.  Get High-res Image Gene #49: 'del_10q21.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q21.1' versus 'METHLYATION_CNMF'

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

Table S248.  Gene #49: 'del_10q21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
DEL PEAK 24(10Q21.1) MUTATED 44 12 14
DEL PEAK 24(10Q21.1) WILD-TYPE 76 85 62

Figure S248.  Get High-res Image Gene #49: 'del_10q21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10q21.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S249.  Gene #49: 'del_10q21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
DEL PEAK 24(10Q21.1) MUTATED 45 8 19 25
DEL PEAK 24(10Q21.1) WILD-TYPE 76 99 71 105

Figure S249.  Get High-res Image Gene #49: 'del_10q21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10q21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S250.  Gene #49: 'del_10q21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
DEL PEAK 24(10Q21.1) MUTATED 28 27 9 32 1
DEL PEAK 24(10Q21.1) WILD-TYPE 51 81 87 97 35

Figure S250.  Get High-res Image Gene #49: '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 = 6.1e-05

Table S251.  Gene #50: 'del_10q23.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
DEL PEAK 25(10Q23.31) MUTATED 25 63 21
DEL PEAK 25(10Q23.31) WILD-TYPE 177 107 57

Figure S251.  Get High-res Image Gene #50: 'del_10q23.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q23.31' versus 'METHLYATION_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.00083

Table S252.  Gene #50: 'del_10q23.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
DEL PEAK 25(10Q23.31) MUTATED 47 15 16
DEL PEAK 25(10Q23.31) WILD-TYPE 73 82 60

Figure S252.  Get High-res Image Gene #50: 'del_10q23.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10q23.31' versus 'MRNASEQ_CNMF'

P value = 0.00123 (Fisher's exact test), Q value = 0.0045

Table S253.  Gene #50: 'del_10q23.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
DEL PEAK 25(10Q23.31) MUTATED 45 18 20 25
DEL PEAK 25(10Q23.31) WILD-TYPE 76 89 70 105

Figure S253.  Get High-res Image Gene #50: 'del_10q23.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S254.  Gene #50: 'del_10q23.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
DEL PEAK 25(10Q23.31) MUTATED 29 32 12 33 2
DEL PEAK 25(10Q23.31) WILD-TYPE 50 76 84 96 34

Figure S254.  Get High-res Image Gene #50: 'del_10q23.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10q25.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.018 (Fisher's exact test), Q value = 0.047

Table S255.  Gene #51: 'del_10q25.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
DEL PEAK 26(10Q25.2) MUTATED 3 18 10
DEL PEAK 26(10Q25.2) WILD-TYPE 39 54 22

Figure S255.  Get High-res Image Gene #51: 'del_10q25.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_10q25.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S256.  Gene #51: 'del_10q25.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
DEL PEAK 26(10Q25.2) MUTATED 23 68 18
DEL PEAK 26(10Q25.2) WILD-TYPE 179 102 60

Figure S256.  Get High-res Image Gene #51: 'del_10q25.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q25.2' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

Table S257.  Gene #51: 'del_10q25.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
DEL PEAK 26(10Q25.2) MUTATED 49 13 13
DEL PEAK 26(10Q25.2) WILD-TYPE 71 84 63

Figure S257.  Get High-res Image Gene #51: 'del_10q25.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10q25.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S258.  Gene #51: 'del_10q25.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
DEL PEAK 26(10Q25.2) MUTATED 48 10 20 30
DEL PEAK 26(10Q25.2) WILD-TYPE 73 97 70 100

Figure S258.  Get High-res Image Gene #51: '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 = 6.1e-05

Table S259.  Gene #51: 'del_10q25.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
DEL PEAK 26(10Q25.2) MUTATED 32 29 7 39 1
DEL PEAK 26(10Q25.2) WILD-TYPE 47 79 89 90 35

Figure S259.  Get High-res Image Gene #51: 'del_10q25.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_12p13.2' versus 'MRNA_CNMF'

P value = 0.0104 (Fisher's exact test), Q value = 0.03

Table S260.  Gene #52: 'del_12p13.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
DEL PEAK 27(12P13.2) MUTATED 2 13 0 2
DEL PEAK 27(12P13.2) WILD-TYPE 33 48 29 19

Figure S260.  Get High-res Image Gene #52: 'del_12p13.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_12p13.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00321 (Fisher's exact test), Q value = 0.011

Table S261.  Gene #52: 'del_12p13.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
DEL PEAK 27(12P13.2) MUTATED 0 10 7
DEL PEAK 27(12P13.2) WILD-TYPE 42 62 25

Figure S261.  Get High-res Image Gene #52: 'del_12p13.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_12p13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S262.  Gene #52: 'del_12p13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
DEL PEAK 27(12P13.2) MUTATED 5 44 11
DEL PEAK 27(12P13.2) WILD-TYPE 197 126 67

Figure S262.  Get High-res Image Gene #52: 'del_12p13.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_12p13.2' versus 'METHLYATION_CNMF'

P value = 0.00444 (Fisher's exact test), Q value = 0.014

Table S263.  Gene #52: 'del_12p13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
DEL PEAK 27(12P13.2) MUTATED 28 10 6
DEL PEAK 27(12P13.2) WILD-TYPE 92 87 70

Figure S263.  Get High-res Image Gene #52: 'del_12p13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_12p13.2' versus 'MRNASEQ_CNMF'

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

Table S264.  Gene #52: 'del_12p13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
DEL PEAK 27(12P13.2) MUTATED 27 4 11 18
DEL PEAK 27(12P13.2) WILD-TYPE 94 103 79 112

Figure S264.  Get High-res Image Gene #52: 'del_12p13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_12p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S265.  Gene #52: 'del_12p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
DEL PEAK 27(12P13.2) MUTATED 16 21 2 21 0
DEL PEAK 27(12P13.2) WILD-TYPE 63 87 94 108 36

Figure S265.  Get High-res Image Gene #52: 'del_12p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_12p13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00195 (Fisher's exact test), Q value = 0.0069

Table S266.  Gene #52: 'del_12p13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 22 17 24 10
DEL PEAK 27(12P13.2) MUTATED 4 3 0 0 3
DEL PEAK 27(12P13.2) WILD-TYPE 8 19 17 24 7

Figure S266.  Get High-res Image Gene #52: 'del_12p13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_14q31.1' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S267.  Gene #54: 'del_14q31.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
DEL PEAK 29(14Q31.1) MUTATED 6 36 3 10
DEL PEAK 29(14Q31.1) WILD-TYPE 29 25 26 11

Figure S267.  Get High-res Image Gene #54: 'del_14q31.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_14q31.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.00055

Table S268.  Gene #54: 'del_14q31.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
DEL PEAK 29(14Q31.1) MUTATED 6 29 20
DEL PEAK 29(14Q31.1) WILD-TYPE 36 43 12

Figure S268.  Get High-res Image Gene #54: '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 = 6.1e-05

Table S269.  Gene #54: 'del_14q31.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
DEL PEAK 29(14Q31.1) MUTATED 28 107 15
DEL PEAK 29(14Q31.1) WILD-TYPE 174 63 63

Figure S269.  Get High-res Image Gene #54: 'del_14q31.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_14q31.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S270.  Gene #54: 'del_14q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
DEL PEAK 29(14Q31.1) MUTATED 57 18 18
DEL PEAK 29(14Q31.1) WILD-TYPE 63 79 58

Figure S270.  Get High-res Image Gene #54: 'del_14q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_14q31.1' versus 'RPPA_CNMF'

P value = 0.019 (Fisher's exact test), Q value = 0.049

Table S271.  Gene #54: 'del_14q31.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 144 125
DEL PEAK 29(14Q31.1) MUTATED 31 57 30
DEL PEAK 29(14Q31.1) WILD-TYPE 54 87 95

Figure S271.  Get High-res Image Gene #54: 'del_14q31.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_14q31.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S272.  Gene #54: 'del_14q31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
DEL PEAK 29(14Q31.1) MUTATED 62 12 23 53
DEL PEAK 29(14Q31.1) WILD-TYPE 59 95 67 77

Figure S272.  Get High-res Image Gene #54: '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 = 6.1e-05

Table S273.  Gene #54: 'del_14q31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
DEL PEAK 29(14Q31.1) MUTATED 33 46 9 60 2
DEL PEAK 29(14Q31.1) WILD-TYPE 46 62 87 69 34

Figure S273.  Get High-res Image Gene #54: 'del_14q31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_14q31.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0219 (Fisher's exact test), Q value = 0.055

Table S274.  Gene #54: 'del_14q31.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 50 77 135
DEL PEAK 29(14Q31.1) MUTATED 42 9 34 45
DEL PEAK 29(14Q31.1) WILD-TYPE 93 41 43 90

Figure S274.  Get High-res Image Gene #54: 'del_14q31.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_14q31.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.014 (Fisher's exact test), Q value = 0.039

Table S275.  Gene #54: 'del_14q31.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 22 17 24 10
DEL PEAK 29(14Q31.1) MUTATED 5 8 7 4 8
DEL PEAK 29(14Q31.1) WILD-TYPE 7 14 10 20 2

Figure S275.  Get High-res Image Gene #54: 'del_14q31.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_15q11.2' versus 'MRNA_CNMF'

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

Table S276.  Gene #55: 'del_15q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
DEL PEAK 30(15Q11.2) MUTATED 8 35 6 11
DEL PEAK 30(15Q11.2) WILD-TYPE 27 26 23 10

Figure S276.  Get High-res Image Gene #55: 'del_15q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_15q11.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00078 (Fisher's exact test), Q value = 0.003

Table S277.  Gene #55: 'del_15q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
DEL PEAK 30(15Q11.2) MUTATED 8 33 19
DEL PEAK 30(15Q11.2) WILD-TYPE 34 39 13

Figure S277.  Get High-res Image Gene #55: '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 = 6.1e-05

Table S278.  Gene #55: 'del_15q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
DEL PEAK 30(15Q11.2) MUTATED 34 117 26
DEL PEAK 30(15Q11.2) WILD-TYPE 168 53 52

Figure S278.  Get High-res Image Gene #55: 'del_15q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q11.2' versus 'METHLYATION_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00055

Table S279.  Gene #55: 'del_15q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
DEL PEAK 30(15Q11.2) MUTATED 65 28 22
DEL PEAK 30(15Q11.2) WILD-TYPE 55 69 54

Figure S279.  Get High-res Image Gene #55: '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 = 6.1e-05

Table S280.  Gene #55: 'del_15q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
DEL PEAK 30(15Q11.2) MUTATED 64 18 36 58
DEL PEAK 30(15Q11.2) WILD-TYPE 57 89 54 72

Figure S280.  Get High-res Image Gene #55: '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 = 6.1e-05

Table S281.  Gene #55: 'del_15q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
DEL PEAK 30(15Q11.2) MUTATED 44 52 11 63 6
DEL PEAK 30(15Q11.2) WILD-TYPE 35 56 85 66 30

Figure S281.  Get High-res Image Gene #55: 'del_15q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_15q15.2' versus 'MRNA_CNMF'

P value = 0.00143 (Fisher's exact test), Q value = 0.0051

Table S282.  Gene #56: 'del_15q15.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
DEL PEAK 31(15Q15.2) MUTATED 8 33 6 11
DEL PEAK 31(15Q15.2) WILD-TYPE 27 28 23 10

Figure S282.  Get High-res Image Gene #56: 'del_15q15.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_15q15.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00062 (Fisher's exact test), Q value = 0.0024

Table S283.  Gene #56: 'del_15q15.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
DEL PEAK 31(15Q15.2) MUTATED 7 33 18
DEL PEAK 31(15Q15.2) WILD-TYPE 35 39 14

Figure S283.  Get High-res Image Gene #56: '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 = 6.1e-05

Table S284.  Gene #56: 'del_15q15.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
DEL PEAK 31(15Q15.2) MUTATED 35 112 25
DEL PEAK 31(15Q15.2) WILD-TYPE 167 58 53

Figure S284.  Get High-res Image Gene #56: 'del_15q15.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q15.2' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 3e-04

Table S285.  Gene #56: 'del_15q15.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
DEL PEAK 31(15Q15.2) MUTATED 64 26 22
DEL PEAK 31(15Q15.2) WILD-TYPE 56 71 54

Figure S285.  Get High-res Image Gene #56: 'del_15q15.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_15q15.2' versus 'RPPA_CNMF'

P value = 0.012 (Fisher's exact test), Q value = 0.034

Table S286.  Gene #56: 'del_15q15.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 144 125
DEL PEAK 31(15Q15.2) MUTATED 42 47 38
DEL PEAK 31(15Q15.2) WILD-TYPE 43 97 87

Figure S286.  Get High-res Image Gene #56: 'del_15q15.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_15q15.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S287.  Gene #56: 'del_15q15.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
DEL PEAK 31(15Q15.2) MUTATED 63 19 33 56
DEL PEAK 31(15Q15.2) WILD-TYPE 58 88 57 74

Figure S287.  Get High-res Image Gene #56: '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 = 6.1e-05

Table S288.  Gene #56: 'del_15q15.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
DEL PEAK 31(15Q15.2) MUTATED 41 50 12 63 5
DEL PEAK 31(15Q15.2) WILD-TYPE 38 58 84 66 31

Figure S288.  Get High-res Image Gene #56: 'del_15q15.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_15q21.1' versus 'MRNA_CNMF'

P value = 0.0192 (Fisher's exact test), Q value = 0.049

Table S289.  Gene #57: 'del_15q21.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
DEL PEAK 32(15Q21.1) MUTATED 11 31 6 11
DEL PEAK 32(15Q21.1) WILD-TYPE 24 30 23 10

Figure S289.  Get High-res Image Gene #57: 'del_15q21.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_15q21.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.0147 (Fisher's exact test), Q value = 0.04

Table S290.  Gene #57: 'del_15q21.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
DEL PEAK 32(15Q21.1) MUTATED 10 31 18
DEL PEAK 32(15Q21.1) WILD-TYPE 32 41 14

Figure S290.  Get High-res Image Gene #57: '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 = 6.1e-05

Table S291.  Gene #57: 'del_15q21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
DEL PEAK 32(15Q21.1) MUTATED 35 109 25
DEL PEAK 32(15Q21.1) WILD-TYPE 167 61 53

Figure S291.  Get High-res Image Gene #57: 'del_15q21.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q21.1' versus 'METHLYATION_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00063

Table S292.  Gene #57: 'del_15q21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
DEL PEAK 32(15Q21.1) MUTATED 61 25 22
DEL PEAK 32(15Q21.1) WILD-TYPE 59 72 54

Figure S292.  Get High-res Image Gene #57: 'del_15q21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_15q21.1' versus 'RPPA_CNMF'

P value = 0.0477 (Fisher's exact test), Q value = 0.11

Table S293.  Gene #57: 'del_15q21.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 144 125
DEL PEAK 32(15Q21.1) MUTATED 40 48 39
DEL PEAK 32(15Q21.1) WILD-TYPE 45 96 86

Figure S293.  Get High-res Image Gene #57: 'del_15q21.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_15q21.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S294.  Gene #57: 'del_15q21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
DEL PEAK 32(15Q21.1) MUTATED 61 18 32 57
DEL PEAK 32(15Q21.1) WILD-TYPE 60 89 58 73

Figure S294.  Get High-res Image Gene #57: '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 = 6.1e-05

Table S295.  Gene #57: 'del_15q21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
DEL PEAK 32(15Q21.1) MUTATED 39 49 11 61 8
DEL PEAK 32(15Q21.1) WILD-TYPE 40 59 85 68 28

Figure S295.  Get High-res Image Gene #57: 'del_15q21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_15q22.33' versus 'MRNA_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.0014

Table S296.  Gene #58: 'del_15q22.33' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
DEL PEAK 33(15Q22.33) MUTATED 8 31 3 10
DEL PEAK 33(15Q22.33) WILD-TYPE 27 30 26 11

Figure S296.  Get High-res Image Gene #58: 'del_15q22.33' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_15q22.33' versus 'MRNA_CHIERARCHICAL'

P value = 0.00042 (Fisher's exact test), Q value = 0.0017

Table S297.  Gene #58: 'del_15q22.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
DEL PEAK 33(15Q22.33) MUTATED 6 28 18
DEL PEAK 33(15Q22.33) WILD-TYPE 36 44 14

Figure S297.  Get High-res Image Gene #58: '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 = 6.1e-05

Table S298.  Gene #58: 'del_15q22.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
DEL PEAK 33(15Q22.33) MUTATED 29 109 23
DEL PEAK 33(15Q22.33) WILD-TYPE 173 61 55

Figure S298.  Get High-res Image Gene #58: 'del_15q22.33' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q22.33' versus 'METHLYATION_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00047

Table S299.  Gene #58: 'del_15q22.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
DEL PEAK 33(15Q22.33) MUTATED 62 23 23
DEL PEAK 33(15Q22.33) WILD-TYPE 58 74 53

Figure S299.  Get High-res Image Gene #58: 'del_15q22.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_15q22.33' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S300.  Gene #58: 'del_15q22.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
DEL PEAK 33(15Q22.33) MUTATED 61 15 32 52
DEL PEAK 33(15Q22.33) WILD-TYPE 60 92 58 78

Figure S300.  Get High-res Image Gene #58: '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 = 6.1e-05

Table S301.  Gene #58: 'del_15q22.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
DEL PEAK 33(15Q22.33) MUTATED 41 47 11 58 3
DEL PEAK 33(15Q22.33) WILD-TYPE 38 61 85 71 33

Figure S301.  Get High-res Image Gene #58: 'del_15q22.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00543 (Fisher's exact test), Q value = 0.017

Table S302.  Gene #60: 'del_16q23.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
DEL PEAK 35(16Q23.1) MUTATED 13 6 3
DEL PEAK 35(16Q23.1) WILD-TYPE 29 66 29

Figure S302.  Get High-res Image Gene #60: 'del_16q23.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_16q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0126 (Fisher's exact test), Q value = 0.035

Table S303.  Gene #60: 'del_16q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
DEL PEAK 35(16Q23.1) MUTATED 9 13 15 12 12
DEL PEAK 35(16Q23.1) WILD-TYPE 70 95 81 117 24

Figure S303.  Get High-res Image Gene #60: 'del_16q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_17p12' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S304.  Gene #61: 'del_17p12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
DEL PEAK 36(17P12) MUTATED 10 49 8 15
DEL PEAK 36(17P12) WILD-TYPE 25 12 21 6

Figure S304.  Get High-res Image Gene #61: 'del_17p12' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_17p12' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S305.  Gene #61: 'del_17p12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
DEL PEAK 36(17P12) MUTATED 9 47 26
DEL PEAK 36(17P12) WILD-TYPE 33 25 6

Figure S305.  Get High-res Image Gene #61: 'del_17p12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_17p12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S306.  Gene #61: 'del_17p12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
DEL PEAK 36(17P12) MUTATED 53 147 54
DEL PEAK 36(17P12) WILD-TYPE 149 23 24

Figure S306.  Get High-res Image Gene #61: 'del_17p12' versus Molecular Subtype #3: 'CN_CNMF'

'del_17p12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S307.  Gene #61: 'del_17p12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
DEL PEAK 36(17P12) MUTATED 103 34 31
DEL PEAK 36(17P12) WILD-TYPE 17 63 45

Figure S307.  Get High-res Image Gene #61: 'del_17p12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_17p12' versus 'RPPA_CHIERARCHICAL'

P value = 0.00076 (Fisher's exact test), Q value = 0.0029

Table S308.  Gene #61: 'del_17p12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 51 33 35 39 42 86 22 20 26
DEL PEAK 36(17P12) MUTATED 35 14 26 22 23 37 8 10 21
DEL PEAK 36(17P12) WILD-TYPE 16 19 9 17 19 49 14 10 5

Figure S308.  Get High-res Image Gene #61: 'del_17p12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_17p12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S309.  Gene #61: 'del_17p12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
DEL PEAK 36(17P12) MUTATED 101 29 46 77
DEL PEAK 36(17P12) WILD-TYPE 20 78 44 53

Figure S309.  Get High-res Image Gene #61: 'del_17p12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_17p12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S310.  Gene #61: 'del_17p12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
DEL PEAK 36(17P12) MUTATED 55 83 20 91 4
DEL PEAK 36(17P12) WILD-TYPE 24 25 76 38 32

Figure S310.  Get High-res Image Gene #61: 'del_17p12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_17p12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0217 (Fisher's exact test), Q value = 0.055

Table S311.  Gene #61: 'del_17p12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 50 77 135
DEL PEAK 36(17P12) MUTATED 74 24 55 71
DEL PEAK 36(17P12) WILD-TYPE 61 26 22 64

Figure S311.  Get High-res Image Gene #61: 'del_17p12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_17p12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00131 (Fisher's exact test), Q value = 0.0047

Table S312.  Gene #61: 'del_17p12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 22 17 24 10
DEL PEAK 36(17P12) MUTATED 8 17 11 8 10
DEL PEAK 36(17P12) WILD-TYPE 4 5 6 16 0

Figure S312.  Get High-res Image Gene #61: 'del_17p12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17q24.3' versus 'CN_CNMF'

P value = 0.00407 (Fisher's exact test), Q value = 0.013

Table S313.  Gene #62: 'del_17q24.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
DEL PEAK 37(17Q24.3) MUTATED 20 38 11
DEL PEAK 37(17Q24.3) WILD-TYPE 182 132 67

Figure S313.  Get High-res Image Gene #62: 'del_17q24.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_17q24.3' versus 'MRNASEQ_CNMF'

P value = 0.044 (Fisher's exact test), Q value = 0.1

Table S314.  Gene #62: 'del_17q24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
DEL PEAK 37(17Q24.3) MUTATED 26 9 12 22
DEL PEAK 37(17Q24.3) WILD-TYPE 95 98 78 108

Figure S314.  Get High-res Image Gene #62: 'del_17q24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_18p11.31' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S315.  Gene #63: 'del_18p11.31' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
DEL PEAK 38(18P11.31) MUTATED 6 50 7 15
DEL PEAK 38(18P11.31) WILD-TYPE 29 11 22 6

Figure S315.  Get High-res Image Gene #63: '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 = 6.1e-05

Table S316.  Gene #63: 'del_18p11.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
DEL PEAK 38(18P11.31) MUTATED 5 47 26
DEL PEAK 38(18P11.31) WILD-TYPE 37 25 6

Figure S316.  Get High-res Image Gene #63: '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 = 6.1e-05

Table S317.  Gene #63: 'del_18p11.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
DEL PEAK 38(18P11.31) MUTATED 47 154 45
DEL PEAK 38(18P11.31) WILD-TYPE 155 16 33

Figure S317.  Get High-res Image Gene #63: '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 = 6.1e-05

Table S318.  Gene #63: 'del_18p11.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
DEL PEAK 38(18P11.31) MUTATED 105 27 33
DEL PEAK 38(18P11.31) WILD-TYPE 15 70 43

Figure S318.  Get High-res Image Gene #63: 'del_18p11.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_18p11.31' versus 'RPPA_CHIERARCHICAL'

P value = 0.0045 (Fisher's exact test), Q value = 0.014

Table S319.  Gene #63: 'del_18p11.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 51 33 35 39 42 86 22 20 26
DEL PEAK 38(18P11.31) MUTATED 29 19 23 19 23 35 8 11 22
DEL PEAK 38(18P11.31) WILD-TYPE 22 14 12 20 19 51 14 9 4

Figure S319.  Get High-res Image Gene #63: 'del_18p11.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_18p11.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S320.  Gene #63: 'del_18p11.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
DEL PEAK 38(18P11.31) MUTATED 106 21 46 72
DEL PEAK 38(18P11.31) WILD-TYPE 15 86 44 58

Figure S320.  Get High-res Image Gene #63: '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 = 6.1e-05

Table S321.  Gene #63: 'del_18p11.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
DEL PEAK 38(18P11.31) MUTATED 61 81 12 89 2
DEL PEAK 38(18P11.31) WILD-TYPE 18 27 84 40 34

Figure S321.  Get High-res Image Gene #63: 'del_18p11.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_18p11.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0111 (Fisher's exact test), Q value = 0.032

Table S322.  Gene #63: 'del_18p11.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 50 77 135
DEL PEAK 38(18P11.31) MUTATED 68 23 54 67
DEL PEAK 38(18P11.31) WILD-TYPE 67 27 23 68

Figure S322.  Get High-res Image Gene #63: 'del_18p11.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_18p11.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0036 (Fisher's exact test), Q value = 0.012

Table S323.  Gene #63: 'del_18p11.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 22 17 24 10
DEL PEAK 38(18P11.31) MUTATED 10 13 10 7 9
DEL PEAK 38(18P11.31) WILD-TYPE 2 9 7 17 1

Figure S323.  Get High-res Image Gene #63: '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 = 6.1e-05

Table S324.  Gene #64: 'del_18q12.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
DEL PEAK 39(18Q12.2) MUTATED 8 53 9 16
DEL PEAK 39(18Q12.2) WILD-TYPE 27 8 20 5

Figure S324.  Get High-res Image Gene #64: '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 = 6.1e-05

Table S325.  Gene #64: 'del_18q12.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
DEL PEAK 39(18Q12.2) MUTATED 7 51 28
DEL PEAK 39(18Q12.2) WILD-TYPE 35 21 4

Figure S325.  Get High-res Image Gene #64: '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 = 6.1e-05

Table S326.  Gene #64: 'del_18q12.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
DEL PEAK 39(18Q12.2) MUTATED 55 159 60
DEL PEAK 39(18Q12.2) WILD-TYPE 147 11 18

Figure S326.  Get High-res Image Gene #64: '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 = 6.1e-05

Table S327.  Gene #64: 'del_18q12.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
DEL PEAK 39(18Q12.2) MUTATED 112 35 36
DEL PEAK 39(18Q12.2) WILD-TYPE 8 62 40

Figure S327.  Get High-res Image Gene #64: 'del_18q12.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_18q12.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00444 (Fisher's exact test), Q value = 0.014

Table S328.  Gene #64: 'del_18q12.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 51 33 35 39 42 86 22 20 26
DEL PEAK 39(18Q12.2) MUTATED 36 17 25 23 26 38 9 13 21
DEL PEAK 39(18Q12.2) WILD-TYPE 15 16 10 16 16 48 13 7 5

Figure S328.  Get High-res Image Gene #64: 'del_18q12.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_18q12.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S329.  Gene #64: 'del_18q12.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
DEL PEAK 39(18Q12.2) MUTATED 108 28 55 82
DEL PEAK 39(18Q12.2) WILD-TYPE 13 79 35 48

Figure S329.  Get High-res Image Gene #64: '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 = 6.1e-05

Table S330.  Gene #64: 'del_18q12.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
DEL PEAK 39(18Q12.2) MUTATED 67 87 19 97 3
DEL PEAK 39(18Q12.2) WILD-TYPE 12 21 77 32 33

Figure S330.  Get High-res Image Gene #64: 'del_18q12.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_18q12.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.02 (Fisher's exact test), Q value = 0.051

Table S331.  Gene #64: 'del_18q12.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 50 77 135
DEL PEAK 39(18Q12.2) MUTATED 79 28 58 74
DEL PEAK 39(18Q12.2) WILD-TYPE 56 22 19 61

Figure S331.  Get High-res Image Gene #64: 'del_18q12.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_18q12.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00523 (Fisher's exact test), Q value = 0.017

Table S332.  Gene #64: 'del_18q12.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 22 17 24 10
DEL PEAK 39(18Q12.2) MUTATED 10 17 11 10 10
DEL PEAK 39(18Q12.2) WILD-TYPE 2 5 6 14 0

Figure S332.  Get High-res Image Gene #64: '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 = 6.1e-05

Table S333.  Gene #65: 'del_18q21.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
DEL PEAK 40(18Q21.2) MUTATED 8 53 10 16
DEL PEAK 40(18Q21.2) WILD-TYPE 27 8 19 5

Figure S333.  Get High-res Image Gene #65: '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 = 6.1e-05

Table S334.  Gene #65: 'del_18q21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
DEL PEAK 40(18Q21.2) MUTATED 7 52 28
DEL PEAK 40(18Q21.2) WILD-TYPE 35 20 4

Figure S334.  Get High-res Image Gene #65: '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 = 6.1e-05

Table S335.  Gene #65: 'del_18q21.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
DEL PEAK 40(18Q21.2) MUTATED 63 161 63
DEL PEAK 40(18Q21.2) WILD-TYPE 139 9 15

Figure S335.  Get High-res Image Gene #65: '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 = 6.1e-05

Table S336.  Gene #65: 'del_18q21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
DEL PEAK 40(18Q21.2) MUTATED 114 45 36
DEL PEAK 40(18Q21.2) WILD-TYPE 6 52 40

Figure S336.  Get High-res Image Gene #65: 'del_18q21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_18q21.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00707 (Fisher's exact test), Q value = 0.022

Table S337.  Gene #65: 'del_18q21.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 51 33 35 39 42 86 22 20 26
DEL PEAK 40(18Q21.2) MUTATED 38 18 25 26 27 41 10 15 21
DEL PEAK 40(18Q21.2) WILD-TYPE 13 15 10 13 15 45 12 5 5

Figure S337.  Get High-res Image Gene #65: 'del_18q21.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_18q21.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S338.  Gene #65: 'del_18q21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
DEL PEAK 40(18Q21.2) MUTATED 109 37 58 82
DEL PEAK 40(18Q21.2) WILD-TYPE 12 70 32 48

Figure S338.  Get High-res Image Gene #65: '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 = 6.1e-05

Table S339.  Gene #65: 'del_18q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
DEL PEAK 40(18Q21.2) MUTATED 69 89 27 97 4
DEL PEAK 40(18Q21.2) WILD-TYPE 10 19 69 32 32

Figure S339.  Get High-res Image Gene #65: 'del_18q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_18q21.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0345 (Fisher's exact test), Q value = 0.082

Table S340.  Gene #65: 'del_18q21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 50 77 135
DEL PEAK 40(18Q21.2) MUTATED 86 30 59 77
DEL PEAK 40(18Q21.2) WILD-TYPE 49 20 18 58

Figure S340.  Get High-res Image Gene #65: 'del_18q21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_18q21.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00818 (Fisher's exact test), Q value = 0.025

Table S341.  Gene #65: 'del_18q21.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 22 17 24 10
DEL PEAK 40(18Q21.2) MUTATED 10 17 14 11 10
DEL PEAK 40(18Q21.2) WILD-TYPE 2 5 3 13 0

Figure S341.  Get High-res Image Gene #65: 'del_18q21.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19p13.3' versus 'CN_CNMF'

P value = 0.00076 (Fisher's exact test), Q value = 0.0029

Table S342.  Gene #66: 'del_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
DEL PEAK 41(19P13.3) MUTATED 15 33 15
DEL PEAK 41(19P13.3) WILD-TYPE 187 137 63

Figure S342.  Get High-res Image Gene #66: 'del_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_19p13.3' versus 'MRNASEQ_CNMF'

P value = 0.004 (Fisher's exact test), Q value = 0.013

Table S343.  Gene #66: 'del_19p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
DEL PEAK 41(19P13.3) MUTATED 24 5 13 21
DEL PEAK 41(19P13.3) WILD-TYPE 97 102 77 109

Figure S343.  Get High-res Image Gene #66: 'del_19p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_19p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00102 (Fisher's exact test), Q value = 0.0038

Table S344.  Gene #66: 'del_19p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
DEL PEAK 41(19P13.3) MUTATED 10 20 5 27 1
DEL PEAK 41(19P13.3) WILD-TYPE 69 88 91 102 35

Figure S344.  Get High-res Image Gene #66: 'del_19p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0087 (Fisher's exact test), Q value = 0.026

Table S345.  Gene #66: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 50 77 135
DEL PEAK 41(19P13.3) MUTATED 18 1 17 20
DEL PEAK 41(19P13.3) WILD-TYPE 117 49 60 115

Figure S345.  Get High-res Image Gene #66: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_20p12.1' versus 'MRNA_CNMF'

P value = 0.048 (Fisher's exact test), Q value = 0.11

Table S346.  Gene #67: 'del_20p12.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
DEL PEAK 42(20P12.1) MUTATED 3 17 3 2
DEL PEAK 42(20P12.1) WILD-TYPE 32 44 26 19

Figure S346.  Get High-res Image Gene #67: 'del_20p12.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_20p12.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.0285 (Fisher's exact test), Q value = 0.07

Table S347.  Gene #67: 'del_20p12.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
DEL PEAK 42(20P12.1) MUTATED 3 12 10
DEL PEAK 42(20P12.1) WILD-TYPE 39 60 22

Figure S347.  Get High-res Image Gene #67: 'del_20p12.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_20p12.1' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

Table S348.  Gene #67: 'del_20p12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
DEL PEAK 42(20P12.1) MUTATED 19 47 20
DEL PEAK 42(20P12.1) WILD-TYPE 183 123 58

Figure S348.  Get High-res Image Gene #67: 'del_20p12.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_20p12.1' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00039

Table S349.  Gene #67: 'del_20p12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
DEL PEAK 42(20P12.1) MUTATED 39 9 12
DEL PEAK 42(20P12.1) WILD-TYPE 81 88 64

Figure S349.  Get High-res Image Gene #67: 'del_20p12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_20p12.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0166 (Fisher's exact test), Q value = 0.044

Table S350.  Gene #67: 'del_20p12.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 51 33 35 39 42 86 22 20 26
DEL PEAK 42(20P12.1) MUTATED 12 1 11 11 6 14 2 6 8
DEL PEAK 42(20P12.1) WILD-TYPE 39 32 24 28 36 72 20 14 18

Figure S350.  Get High-res Image Gene #67: 'del_20p12.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_20p12.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S351.  Gene #67: 'del_20p12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
DEL PEAK 42(20P12.1) MUTATED 44 7 15 20
DEL PEAK 42(20P12.1) WILD-TYPE 77 100 75 110

Figure S351.  Get High-res Image Gene #67: 'del_20p12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_20p12.1' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S352.  Gene #67: 'del_20p12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
DEL PEAK 42(20P12.1) MUTATED 24 30 5 23 4
DEL PEAK 42(20P12.1) WILD-TYPE 55 78 91 106 32

Figure S352.  Get High-res Image Gene #67: 'del_20p12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_20p12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0104 (Fisher's exact test), Q value = 0.03

Table S353.  Gene #67: 'del_20p12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 50 77 135
DEL PEAK 42(20P12.1) MUTATED 26 12 22 15
DEL PEAK 42(20P12.1) WILD-TYPE 109 38 55 120

Figure S353.  Get High-res Image Gene #67: 'del_20p12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_20p12.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0477 (Fisher's exact test), Q value = 0.11

Table S354.  Gene #67: 'del_20p12.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 22 17 24 10
DEL PEAK 42(20P12.1) MUTATED 2 5 6 1 4
DEL PEAK 42(20P12.1) WILD-TYPE 10 17 11 23 6

Figure S354.  Get High-res Image Gene #67: 'del_20p12.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_21q11.2' versus 'MRNA_CNMF'

P value = 0.0163 (Fisher's exact test), Q value = 0.044

Table S355.  Gene #68: 'del_21q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
DEL PEAK 43(21Q11.2) MUTATED 7 29 6 6
DEL PEAK 43(21Q11.2) WILD-TYPE 28 32 23 15

Figure S355.  Get High-res Image Gene #68: 'del_21q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_21q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S356.  Gene #68: 'del_21q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
DEL PEAK 43(21Q11.2) MUTATED 42 82 17
DEL PEAK 43(21Q11.2) WILD-TYPE 160 88 61

Figure S356.  Get High-res Image Gene #68: 'del_21q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_21q11.2' versus 'METHLYATION_CNMF'

P value = 0.00608 (Fisher's exact test), Q value = 0.019

Table S357.  Gene #68: 'del_21q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
DEL PEAK 43(21Q11.2) MUTATED 49 21 20
DEL PEAK 43(21Q11.2) WILD-TYPE 71 76 56

Figure S357.  Get High-res Image Gene #68: 'del_21q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_21q11.2' versus 'MRNASEQ_CNMF'

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

Table S358.  Gene #68: 'del_21q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
DEL PEAK 43(21Q11.2) MUTATED 57 17 26 40
DEL PEAK 43(21Q11.2) WILD-TYPE 64 90 64 90

Figure S358.  Get High-res Image Gene #68: 'del_21q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_21q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-04 (Fisher's exact test), Q value = 0.0016

Table S359.  Gene #68: 'del_21q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
DEL PEAK 43(21Q11.2) MUTATED 35 35 18 47 5
DEL PEAK 43(21Q11.2) WILD-TYPE 44 73 78 82 31

Figure S359.  Get High-res Image Gene #68: 'del_21q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.32' versus 'MRNA_CNMF'

P value = 0.00054 (Fisher's exact test), Q value = 0.0021

Table S360.  Gene #69: 'del_22q13.32' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
DEL PEAK 44(22Q13.32) MUTATED 8 34 5 10
DEL PEAK 44(22Q13.32) WILD-TYPE 27 27 24 11

Figure S360.  Get High-res Image Gene #69: 'del_22q13.32' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_22q13.32' versus 'MRNA_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.0011

Table S361.  Gene #69: 'del_22q13.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
DEL PEAK 44(22Q13.32) MUTATED 6 35 16
DEL PEAK 44(22Q13.32) WILD-TYPE 36 37 16

Figure S361.  Get High-res Image Gene #69: '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 = 6.1e-05

Table S362.  Gene #69: 'del_22q13.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
DEL PEAK 44(22Q13.32) MUTATED 40 98 22
DEL PEAK 44(22Q13.32) WILD-TYPE 162 72 56

Figure S362.  Get High-res Image Gene #69: 'del_22q13.32' versus Molecular Subtype #3: 'CN_CNMF'

'del_22q13.32' versus 'METHLYATION_CNMF'

P value = 0.00557 (Fisher's exact test), Q value = 0.018

Table S363.  Gene #69: 'del_22q13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
DEL PEAK 44(22Q13.32) MUTATED 50 21 28
DEL PEAK 44(22Q13.32) WILD-TYPE 70 76 48

Figure S363.  Get High-res Image Gene #69: 'del_22q13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_22q13.32' versus 'RPPA_CHIERARCHICAL'

P value = 0.0116 (Fisher's exact test), Q value = 0.033

Table S364.  Gene #69: 'del_22q13.32' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 51 33 35 39 42 86 22 20 26
DEL PEAK 44(22Q13.32) MUTATED 17 7 23 10 14 25 7 7 10
DEL PEAK 44(22Q13.32) WILD-TYPE 34 26 12 29 28 61 15 13 16

Figure S364.  Get High-res Image Gene #69: 'del_22q13.32' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_22q13.32' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S365.  Gene #69: 'del_22q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
DEL PEAK 44(22Q13.32) MUTATED 56 18 32 53
DEL PEAK 44(22Q13.32) WILD-TYPE 65 89 58 77

Figure S365.  Get High-res Image Gene #69: 'del_22q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_22q13.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S366.  Gene #69: 'del_22q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
DEL PEAK 44(22Q13.32) MUTATED 37 45 13 61 3
DEL PEAK 44(22Q13.32) WILD-TYPE 42 63 83 68 33

Figure S366.  Get High-res Image Gene #69: '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/COAD-TP/19780705/transformed.cor.cli.txt

  • Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/COAD-TP/20125559/COAD-TP.transferedmergedcluster.txt

  • Number of patients = 450

  • Number of significantly focal cnvs = 69

  • Number of molecular subtypes = 12

  • Exclude genes that fewer than K tumors have alterations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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