Correlation between copy number variation genes (focal events) and molecular subtypes
Stomach Adenocarcinoma (Primary solid tumor)
15 July 2014  |  analyses__2014_07_15
Maintainer Information
Citation Information
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C12Z14BV
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 81 focal events and 10 molecular subtypes across 369 patients, 333 significant findings detected with P value < 0.05 and Q value < 0.25.

  • amp_1p36.22 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

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

  • amp_1q42.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_3q26.2 cnv correlated to 'CN_CNMF'.

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

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

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

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

  • amp_6q21 cnv correlated to 'CN_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_7p22.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_7p11.2 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • amp_7q21.2 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • amp_8p23.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

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

  • amp_9p24.1 cnv correlated to 'CN_CNMF'.

  • amp_9q34.3 cnv correlated to 'CN_CNMF'.

  • amp_10p11.22 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_10q22.2 cnv correlated to 'CN_CNMF'.

  • amp_10q26.13 cnv correlated to 'CN_CNMF'.

  • amp_11p13 cnv correlated to 'MIRSEQ_CHIERARCHICAL'.

  • amp_11q13.3 cnv correlated to 'CN_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • amp_12p12.1 cnv correlated to 'CN_CNMF'.

  • amp_12q15 cnv correlated to 'CN_CNMF'.

  • amp_13q12.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • amp_15q26.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

  • amp_18q11.2 cnv correlated to 'CN_CNMF'.

  • amp_19p13.2 cnv correlated to 'CN_CNMF'.

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

  • amp_20q13.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_xq27.3 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

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

  • del_1p13.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • del_2q37.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_3p26.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • del_3q26.31 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

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

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

  • del_5q11.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_5q23.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_6p25.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_6q14.1 cnv correlated to 'CN_CNMF'.

  • del_6q26 cnv correlated to 'CN_CNMF'.

  • del_7q31.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • del_7q36.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_8p23.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • del_9p21.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • del_10p15.3 cnv correlated to 'CN_CNMF'.

  • del_10q22.3 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • del_11p15.4 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

  • del_12p13.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_13q12.11 cnv correlated to 'CN_CNMF'.

  • del_14q23.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_14q32.33 cnv correlated to 'CN_CNMF'.

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

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

  • del_16p13.3 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_16q23.1 cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.

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

  • del_17q24.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

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

  • del_19q13.11 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_21q11.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_21q22.13 cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • del_22q13.31 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • del_xp21.1 cnv correlated to 'CN_CNMF'.

  • del_xq21.33 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 81 focal events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 333 significant findings detected.

Clinical
Features
CN
CNMF
METHLYATION
CNMF
RPPA
CNMF
RPPA
CHIERARCHICAL
MRNASEQ
CNMF
MRNASEQ
CHIERARCHICAL
MIRSEQ
CNMF
MIRSEQ
CHIERARCHICAL
MIRSEQ
MATURE
CNMF
MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
amp 1q21 3 135 (37%) 234 1e-05
(0.0081)
1e-05
(0.0081)
0.033
(1.00)
0.027
(1.00)
1e-05
(0.0081)
1e-05
(0.0081)
1e-05
(0.0081)
1e-05
(0.0081)
1e-05
(0.0081)
1e-05
(0.0081)
amp 5p15 33 104 (28%) 265 1e-05
(0.0081)
1e-05
(0.0081)
0.126
(1.00)
0.985
(1.00)
1e-05
(0.0081)
5e-05
(0.0288)
1e-05
(0.0081)
2e-05
(0.0124)
0.0001
(0.055)
1e-05
(0.0081)
amp 13q22 1 149 (40%) 220 1e-05
(0.0081)
1e-05
(0.0081)
0.2
(1.00)
0.679
(1.00)
2e-05
(0.0124)
1e-05
(0.0081)
0.00044
(0.215)
2e-05
(0.0124)
1e-05
(0.0081)
1e-05
(0.0081)
del 3p14 2 131 (36%) 238 1e-05
(0.0081)
1e-05
(0.0081)
0.409
(1.00)
0.371
(1.00)
8e-05
(0.0446)
0.00019
(0.101)
1e-05
(0.0081)
1e-05
(0.0081)
0.00042
(0.207)
1e-05
(0.0081)
del 4p16 3 142 (38%) 227 1e-05
(0.0081)
0.00052
(0.249)
0.46
(1.00)
0.201
(1.00)
3e-05
(0.0179)
5e-05
(0.0288)
0.00046
(0.224)
1e-05
(0.0081)
0.00015
(0.0811)
1e-05
(0.0081)
del 4q34 3 163 (44%) 206 1e-05
(0.0081)
1e-05
(0.0081)
0.0519
(1.00)
0.00887
(1.00)
1e-05
(0.0081)
2e-05
(0.0124)
4e-05
(0.0234)
1e-05
(0.0081)
2e-05
(0.0124)
2e-05
(0.0124)
del 5q11 2 134 (36%) 235 1e-05
(0.0081)
1e-05
(0.0081)
0.24
(1.00)
0.224
(1.00)
1e-05
(0.0081)
1e-05
(0.0081)
1e-05
(0.0081)
1e-05
(0.0081)
1e-05
(0.0081)
1e-05
(0.0081)
del 5q23 2 122 (33%) 247 1e-05
(0.0081)
1e-05
(0.0081)
0.123
(1.00)
0.109
(1.00)
1e-05
(0.0081)
1e-05
(0.0081)
1e-05
(0.0081)
1e-05
(0.0081)
1e-05
(0.0081)
1e-05
(0.0081)
del 10q23 31 90 (24%) 279 1e-05
(0.0081)
0.00015
(0.0811)
0.0634
(1.00)
0.00019
(0.101)
1e-05
(0.0081)
1e-05
(0.0081)
0.00013
(0.0706)
6e-05
(0.0341)
0.00115
(0.509)
1e-05
(0.0081)
del 15q11 2 101 (27%) 268 1e-05
(0.0081)
3e-05
(0.0179)
0.00177
(0.74)
0.267
(1.00)
1e-05
(0.0081)
2e-05
(0.0124)
0.00024
(0.125)
2e-05
(0.0124)
1e-05
(0.0081)
1e-05
(0.0081)
del 17p12 141 (38%) 228 1e-05
(0.0081)
1e-05
(0.0081)
0.401
(1.00)
0.00824
(1.00)
1e-05
(0.0081)
1e-05
(0.0081)
4e-05
(0.0234)
1e-05
(0.0081)
1e-05
(0.0081)
1e-05
(0.0081)
del 19p13 3 127 (34%) 242 1e-05
(0.0081)
1e-05
(0.0081)
0.00364
(1.00)
0.00495
(1.00)
1e-05
(0.0081)
1e-05
(0.0081)
1e-05
(0.0081)
1e-05
(0.0081)
1e-05
(0.0081)
1e-05
(0.0081)
amp 1q42 3 122 (33%) 247 1e-05
(0.0081)
1e-05
(0.0081)
0.402
(1.00)
0.0965
(1.00)
1e-05
(0.0081)
9e-05
(0.0498)
1e-05
(0.0081)
1e-05
(0.0081)
0.00446
(1.00)
1e-05
(0.0081)
amp 5p13 1 103 (28%) 266 1e-05
(0.0081)
1e-05
(0.0081)
0.74
(1.00)
0.86
(1.00)
1e-05
(0.0081)
0.0005
(0.241)
0.00018
(0.0965)
0.00011
(0.0604)
0.00117
(0.516)
1e-05
(0.0081)
amp 19q12 111 (30%) 258 1e-05
(0.0081)
1e-05
(0.0081)
0.00618
(1.00)
0.115
(1.00)
1e-05
(0.0081)
1e-05
(0.0081)
2e-05
(0.0124)
1e-05
(0.0081)
0.00374
(1.00)
1e-05
(0.0081)
amp 20q13 2 243 (66%) 126 1e-05
(0.0081)
1e-05
(0.0081)
0.00637
(1.00)
0.0119
(1.00)
1e-05
(0.0081)
1e-05
(0.0081)
2e-05
(0.0124)
1e-05
(0.0081)
0.00378
(1.00)
1e-05
(0.0081)
del 3p26 1 115 (31%) 254 1e-05
(0.0081)
2e-05
(0.0124)
0.343
(1.00)
0.194
(1.00)
0.00663
(1.00)
5e-05
(0.0288)
9e-05
(0.0498)
4e-05
(0.0234)
0.00043
(0.212)
1e-05
(0.0081)
del 7q36 3 78 (21%) 291 1e-05
(0.0081)
2e-05
(0.0124)
0.38
(1.00)
0.0792
(1.00)
2e-05
(0.0124)
0.00034
(0.17)
0.00021
(0.111)
1e-05
(0.0081)
0.00198
(0.816)
2e-05
(0.0124)
del 8p23 3 102 (28%) 267 1e-05
(0.0081)
1e-05
(0.0081)
0.0756
(1.00)
0.594
(1.00)
1e-05
(0.0081)
1e-05
(0.0081)
0.00111
(0.497)
1e-05
(0.0081)
6e-05
(0.0341)
1e-05
(0.0081)
del 9p21 3 153 (41%) 216 1e-05
(0.0081)
1e-05
(0.0081)
7e-05
(0.0393)
1e-05
(0.0081)
1e-05
(0.0081)
1e-05
(0.0081)
0.00498
(1.00)
0.00075
(0.347)
0.00676
(1.00)
4e-05
(0.0234)
del 15q15 1 103 (28%) 266 1e-05
(0.0081)
1e-05
(0.0081)
0.00356
(1.00)
0.294
(1.00)
1e-05
(0.0081)
2e-05
(0.0124)
0.00117
(0.516)
1e-05
(0.0081)
1e-05
(0.0081)
1e-05
(0.0081)
del 16p13 3 75 (20%) 294 1e-05
(0.0081)
0.00057
(0.27)
0.7
(1.00)
0.817
(1.00)
1e-05
(0.0081)
1e-05
(0.0081)
1e-05
(0.0081)
5e-05
(0.0288)
1e-05
(0.0081)
1e-05
(0.0081)
del 19q13 11 57 (15%) 312 1e-05
(0.0081)
1e-05
(0.0081)
0.0634
(1.00)
0.711
(1.00)
2e-05
(0.0124)
0.00055
(0.262)
0.00024
(0.125)
1e-05
(0.0081)
0.00027
(0.139)
6e-05
(0.0341)
amp 6p21 1 99 (27%) 270 1e-05
(0.0081)
1e-05
(0.0081)
0.348
(1.00)
0.165
(1.00)
0.00065
(0.304)
0.00077
(0.356)
0.00033
(0.167)
0.00029
(0.148)
0.00034
(0.17)
2e-05
(0.0124)
amp 6q12 73 (20%) 296 1e-05
(0.0081)
1e-05
(0.0081)
0.0669
(1.00)
0.883
(1.00)
7e-05
(0.0393)
0.00037
(0.184)
0.00104
(0.468)
0.00032
(0.163)
0.00062
(0.291)
3e-05
(0.0179)
amp 7p22 1 189 (51%) 180 1e-05
(0.0081)
5e-05
(0.0288)
0.636
(1.00)
0.864
(1.00)
0.00021
(0.111)
3e-05
(0.0179)
0.00213
(0.861)
0.00051
(0.245)
0.00172
(0.724)
1e-05
(0.0081)
amp 8q24 21 256 (69%) 113 1e-05
(0.0081)
0.00033
(0.167)
0.385
(1.00)
0.382
(1.00)
0.0058
(1.00)
0.0108
(1.00)
8e-05
(0.0446)
0.00029
(0.148)
1e-05
(0.0081)
1e-05
(0.0081)
amp 13q12 3 144 (39%) 225 1e-05
(0.0081)
1e-05
(0.0081)
0.33
(1.00)
0.153
(1.00)
0.0165
(1.00)
3e-05
(0.0179)
0.00033
(0.167)
0.00461
(1.00)
0.0004
(0.198)
0.00027
(0.139)
amp 17q12 116 (31%) 253 1e-05
(0.0081)
1e-05
(0.0081)
0.795
(1.00)
0.0398
(1.00)
0.00021
(0.111)
0.00019
(0.101)
4e-05
(0.0234)
0.00021
(0.111)
0.0018
(0.747)
0.00092
(0.42)
del 1p36 11 104 (28%) 265 1e-05
(0.0081)
1e-05
(0.0081)
0.156
(1.00)
0.00095
(0.43)
0.00033
(0.167)
1e-05
(0.0081)
0.00962
(1.00)
0.00011
(0.0604)
0.00218
(0.876)
1e-05
(0.0081)
del 6p25 3 93 (25%) 276 1e-05
(0.0081)
0.0002
(0.106)
0.138
(1.00)
0.821
(1.00)
0.00011
(0.0604)
6e-05
(0.0341)
0.00069
(0.322)
2e-05
(0.0124)
0.00729
(1.00)
0.00043
(0.212)
del 14q23 3 108 (29%) 261 1e-05
(0.0081)
1e-05
(0.0081)
0.752
(1.00)
0.43
(1.00)
4e-05
(0.0234)
0.00043
(0.212)
0.00129
(0.557)
3e-05
(0.0179)
0.00074
(0.344)
0.00012
(0.0654)
del 12p13 1 57 (15%) 312 1e-05
(0.0081)
1e-05
(0.0081)
0.541
(1.00)
0.419
(1.00)
3e-05
(0.0179)
3e-05
(0.0179)
0.0187
(1.00)
0.012
(1.00)
0.0114
(1.00)
5e-05
(0.0288)
del 21q11 2 140 (38%) 229 1e-05
(0.0081)
0.00027
(0.139)
0.342
(1.00)
0.202
(1.00)
0.0024
(0.953)
0.00445
(1.00)
6e-05
(0.0341)
0.0113
(1.00)
4e-05
(0.0234)
0.00032
(0.163)
del 22q13 31 129 (35%) 240 1e-05
(0.0081)
1e-05
(0.0081)
0.0486
(1.00)
0.00646
(1.00)
0.0013
(0.56)
0.00435
(1.00)
3e-05
(0.0179)
1e-05
(0.0081)
0.00086
(0.395)
1e-05
(0.0081)
del xp22 2 67 (18%) 302 1e-05
(0.0081)
2e-05
(0.0124)
0.367
(1.00)
0.059
(1.00)
0.00019
(0.101)
0.00024
(0.125)
0.091
(1.00)
0.00298
(1.00)
0.215
(1.00)
0.00016
(0.0862)
amp 10p11 22 98 (27%) 271 1e-05
(0.0081)
1e-05
(0.0081)
0.147
(1.00)
0.523
(1.00)
0.00112
(0.5)
0.00927
(1.00)
0.00343
(1.00)
0.00013
(0.0706)
0.00184
(0.762)
9e-05
(0.0498)
amp 15q26 1 88 (24%) 281 1e-05
(0.0081)
0.00024
(0.125)
0.464
(1.00)
0.288
(1.00)
1e-05
(0.0081)
2e-05
(0.0124)
0.00797
(1.00)
0.00953
(1.00)
0.00577
(1.00)
0.00305
(1.00)
del 3q26 31 46 (12%) 323 1e-05
(0.0081)
1e-05
(0.0081)
0.134
(1.00)
0.373
(1.00)
0.00043
(0.212)
0.00046
(0.224)
0.00123
(0.536)
0.00056
(0.265)
0.00178
(0.742)
0.00282
(1.00)
del 4q22 1 160 (43%) 209 1e-05
(0.0081)
6e-05
(0.0341)
0.108
(1.00)
0.268
(1.00)
0.00253
(0.999)
3e-05
(0.0179)
0.0291
(1.00)
0.00203
(0.832)
0.0304
(1.00)
0.00047
(0.227)
del 10q22 3 61 (17%) 308 1e-05
(0.0081)
0.0136
(1.00)
0.749
(1.00)
0.0577
(1.00)
0.00018
(0.0965)
0.00035
(0.174)
0.00584
(1.00)
0.00532
(1.00)
0.00332
(1.00)
0.00022
(0.115)
del 11p15 4 79 (21%) 290 1e-05
(0.0081)
1e-05
(0.0081)
2e-05
(0.0124)
0.0008
(0.368)
0.00145
(0.621)
0.0127
(1.00)
0.00108
(0.485)
8e-05
(0.0446)
0.038
(1.00)
0.00118
(0.517)
del 18q21 2 169 (46%) 200 1e-05
(0.0081)
0.00046
(0.224)
0.667
(1.00)
0.452
(1.00)
0.00031
(0.158)
0.0041
(1.00)
0.00115
(0.509)
0.00278
(1.00)
0.0002
(0.106)
0.00374
(1.00)
del 21q22 13 152 (41%) 217 1e-05
(0.0081)
0.0224
(1.00)
0.102
(1.00)
0.24
(1.00)
0.00203
(0.832)
0.00037
(0.184)
0.00023
(0.12)
0.00088
(0.403)
4e-05
(0.0234)
0.00074
(0.344)
amp 6q21 68 (18%) 301 1e-05
(0.0081)
0.00055
(0.262)
0.383
(1.00)
0.406
(1.00)
0.00143
(0.613)
0.00151
(0.645)
0.00125
(0.542)
0.00051
(0.245)
0.00225
(0.9)
1e-05
(0.0081)
amp 11q13 3 90 (24%) 279 1e-05
(0.0081)
0.0181
(1.00)
0.19
(1.00)
0.639
(1.00)
0.127
(1.00)
0.037
(1.00)
0.00032
(0.163)
0.00619
(1.00)
0.00017
(0.0915)
0.00172
(0.724)
del 2q37 2 54 (15%) 315 1e-05
(0.0081)
5e-05
(0.0288)
0.273
(1.00)
0.345
(1.00)
0.00333
(1.00)
0.214
(1.00)
0.0225
(1.00)
1e-05
(0.0081)
0.08
(1.00)
0.00167
(0.706)
del 9p23 156 (42%) 213 1e-05
(0.0081)
2e-05
(0.0124)
0.0291
(1.00)
0.00113
(0.502)
1e-05
(0.0081)
0.00176
(0.737)
0.00159
(0.676)
0.00356
(1.00)
0.0354
(1.00)
0.00092
(0.42)
del 9q21 11 93 (25%) 276 1e-05
(0.0081)
0.00346
(1.00)
0.139
(1.00)
0.0565
(1.00)
0.00155
(0.66)
0.0354
(1.00)
0.00478
(1.00)
0.00049
(0.237)
0.00171
(0.722)
0.00024
(0.125)
del 17q24 3 68 (18%) 301 1e-05
(0.0081)
0.00011
(0.0604)
0.19
(1.00)
0.22
(1.00)
0.00161
(0.683)
0.00235
(0.935)
0.0697
(1.00)
0.00041
(0.203)
0.00363
(1.00)
0.00135
(0.58)
amp 1p36 22 52 (14%) 317 1e-05
(0.0081)
0.0229
(1.00)
0.518
(1.00)
0.242
(1.00)
0.00021
(0.111)
0.119
(1.00)
0.11
(1.00)
0.0425
(1.00)
0.119
(1.00)
0.0301
(1.00)
amp 7p11 2 172 (47%) 197 1e-05
(0.0081)
0.00117
(0.516)
0.906
(1.00)
0.851
(1.00)
0.0437
(1.00)
0.00051
(0.245)
0.00949
(1.00)
0.0408
(1.00)
0.00199
(0.818)
0.00123
(0.536)
amp 7q21 2 168 (46%) 201 1e-05
(0.0081)
0.00063
(0.295)
0.199
(1.00)
0.671
(1.00)
0.516
(1.00)
7e-05
(0.0393)
0.0219
(1.00)
0.0581
(1.00)
0.0493
(1.00)
0.00255
(1.00)
amp 8p23 1 146 (40%) 223 6e-05
(0.0341)
8e-05
(0.0446)
0.591
(1.00)
0.602
(1.00)
0.0548
(1.00)
0.0178
(1.00)
0.364
(1.00)
0.344
(1.00)
0.0371
(1.00)
0.055
(1.00)
amp xq27 3 67 (18%) 302 7e-05
(0.0393)
0.00324
(1.00)
0.598
(1.00)
0.963
(1.00)
0.187
(1.00)
1e-05
(0.0081)
0.0297
(1.00)
0.969
(1.00)
0.0544
(1.00)
0.0723
(1.00)
del 1p13 2 75 (20%) 294 1e-05
(0.0081)
1e-05
(0.0081)
0.0806
(1.00)
0.0636
(1.00)
0.00122
(0.533)
0.00091
(0.416)
0.182
(1.00)
0.017
(1.00)
0.0194
(1.00)
0.00317
(1.00)
del 7q31 1 54 (15%) 315 1e-05
(0.0081)
4e-05
(0.0234)
0.715
(1.00)
0.498
(1.00)
0.00852
(1.00)
0.277
(1.00)
0.0196
(1.00)
0.00707
(1.00)
0.00376
(1.00)
0.00427
(1.00)
del 11q23 2 82 (22%) 287 1e-05
(0.0081)
0.00818
(1.00)
0.701
(1.00)
0.153
(1.00)
0.00112
(0.5)
0.00012
(0.0654)
0.0914
(1.00)
0.204
(1.00)
0.0279
(1.00)
0.0426
(1.00)
del 16q23 1 146 (40%) 223 1e-05
(0.0081)
0.00272
(1.00)
0.47
(1.00)
0.17
(1.00)
0.00187
(0.772)
0.0091
(1.00)
0.00442
(1.00)
0.0185
(1.00)
5e-05
(0.0288)
0.00097
(0.438)
del xq21 33 46 (12%) 323 3e-05
(0.0179)
0.00021
(0.111)
0.815
(1.00)
0.0353
(1.00)
0.00817
(1.00)
0.0521
(1.00)
0.174
(1.00)
0.204
(1.00)
0.523
(1.00)
0.0924
(1.00)
amp 3q26 2 125 (34%) 244 1e-05
(0.0081)
0.00256
(1.00)
0.821
(1.00)
0.0112
(1.00)
0.448
(1.00)
0.0287
(1.00)
0.0141
(1.00)
0.0177
(1.00)
0.0195
(1.00)
0.00437
(1.00)
amp 9p24 1 57 (15%) 312 2e-05
(0.0124)
0.449
(1.00)
0.617
(1.00)
0.219
(1.00)
0.109
(1.00)
0.00557
(1.00)
0.0311
(1.00)
0.308
(1.00)
0.038
(1.00)
0.129
(1.00)
amp 9q34 3 98 (27%) 271 0.00025
(0.129)
0.179
(1.00)
0.712
(1.00)
0.56
(1.00)
0.0286
(1.00)
0.297
(1.00)
0.0287
(1.00)
0.429
(1.00)
0.167
(1.00)
0.094
(1.00)
amp 10q22 2 68 (18%) 301 1e-05
(0.0081)
0.0201
(1.00)
0.0269
(1.00)
0.252
(1.00)
0.0182
(1.00)
0.023
(1.00)
0.202
(1.00)
0.184
(1.00)
0.0976
(1.00)
0.0236
(1.00)
amp 10q26 13 72 (20%) 297 1e-05
(0.0081)
0.0022
(0.882)
0.0363
(1.00)
0.33
(1.00)
0.00556
(1.00)
0.0318
(1.00)
0.633
(1.00)
0.11
(1.00)
0.899
(1.00)
0.0827
(1.00)
amp 11p13 70 (19%) 299 0.00053
(0.253)
0.041
(1.00)
0.643
(1.00)
0.116
(1.00)
0.00057
(0.27)
0.0059
(1.00)
0.0596
(1.00)
0.00017
(0.0915)
0.0642
(1.00)
0.00456
(1.00)
amp 12p12 1 109 (30%) 260 1e-05
(0.0081)
0.0377
(1.00)
0.428
(1.00)
0.348
(1.00)
0.209
(1.00)
0.367
(1.00)
0.00308
(1.00)
0.23
(1.00)
0.00437
(1.00)
0.0511
(1.00)
amp 12q15 92 (25%) 277 1e-05
(0.0081)
0.361
(1.00)
0.22
(1.00)
0.329
(1.00)
0.276
(1.00)
0.0752
(1.00)
0.0895
(1.00)
0.389
(1.00)
0.254
(1.00)
0.716
(1.00)
amp 18q11 2 117 (32%) 252 1e-05
(0.0081)
0.00216
(0.87)
0.294
(1.00)
0.286
(1.00)
0.0152
(1.00)
0.00386
(1.00)
0.00126
(0.546)
0.00208
(0.847)
0.00093
(0.422)
0.0049
(1.00)
amp 19p13 2 41 (11%) 328 0.00033
(0.167)
0.119
(1.00)
0.905
(1.00)
0.757
(1.00)
0.733
(1.00)
0.16
(1.00)
0.977
(1.00)
0.976
(1.00)
0.875
(1.00)
0.744
(1.00)
del 6q14 1 72 (20%) 297 1e-05
(0.0081)
0.00111
(0.497)
0.214
(1.00)
0.844
(1.00)
0.00061
(0.287)
0.00505
(1.00)
0.123
(1.00)
0.0164
(1.00)
0.0722
(1.00)
0.0481
(1.00)
del 6q26 82 (22%) 287 1e-05
(0.0081)
0.00824
(1.00)
0.792
(1.00)
0.702
(1.00)
0.00078
(0.36)
0.00247
(0.978)
0.159
(1.00)
0.0116
(1.00)
0.0775
(1.00)
0.0064
(1.00)
del 10p15 3 62 (17%) 307 3e-05
(0.0179)
0.0188
(1.00)
0.304
(1.00)
0.417
(1.00)
0.06
(1.00)
0.102
(1.00)
0.0603
(1.00)
0.0376
(1.00)
0.00865
(1.00)
0.00664
(1.00)
del 13q12 11 52 (14%) 317 1e-05
(0.0081)
0.109
(1.00)
0.426
(1.00)
0.366
(1.00)
0.0658
(1.00)
0.0222
(1.00)
0.39
(1.00)
0.423
(1.00)
0.179
(1.00)
0.219
(1.00)
del 14q32 33 106 (29%) 263 1e-05
(0.0081)
0.0007
(0.326)
0.928
(1.00)
0.222
(1.00)
0.00209
(0.847)
0.00524
(1.00)
0.0216
(1.00)
0.0319
(1.00)
0.0292
(1.00)
0.0683
(1.00)
del xp21 1 64 (17%) 305 1e-05
(0.0081)
0.00338
(1.00)
0.0929
(1.00)
0.0225
(1.00)
0.0141
(1.00)
0.0254
(1.00)
0.197
(1.00)
0.336
(1.00)
0.217
(1.00)
0.0415
(1.00)
amp 9p13 3 71 (19%) 298 0.00274
(1.00)
0.483
(1.00)
0.267
(1.00)
0.316
(1.00)
0.00983
(1.00)
0.232
(1.00)
0.00732
(1.00)
0.434
(1.00)
0.00179
(0.745)
0.171
(1.00)
del 1q25 1 13 (4%) 356 0.0373
(1.00)
0.0944
(1.00)
0.168
(1.00)
0.895
(1.00)
0.444
(1.00)
0.415
(1.00)
0.207
(1.00)
0.71
(1.00)
0.188
(1.00)
0.0718
(1.00)
del 1q44 23 (6%) 346 0.00313
(1.00)
0.00103
(0.465)
0.309
(1.00)
0.373
(1.00)
0.739
(1.00)
0.337
(1.00)
0.0145
(1.00)
0.443
(1.00)
0.0106
(1.00)
0.155
(1.00)
del 2q32 1 53 (14%) 316 0.0089
(1.00)
0.0988
(1.00)
0.49
(1.00)
0.0826
(1.00)
0.0904
(1.00)
0.24
(1.00)
0.377
(1.00)
0.00206
(0.84)
0.153
(1.00)
0.147
(1.00)
del 20p12 1 31 (8%) 338 0.00208
(0.847)
0.00233
(0.93)
0.658
(1.00)
0.192
(1.00)
0.0154
(1.00)
0.0855
(1.00)
0.0292
(1.00)
0.112
(1.00)
0.0262
(1.00)
0.0663
(1.00)
'amp_1p36.22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S1.  Gene #1: 'amp_1p36.22' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
AMP PEAK 1(1P36.22) MUTATED 5 3 16 1 27
AMP PEAK 1(1P36.22) WILD-TYPE 164 30 50 9 64

Figure S1.  Get High-res Image Gene #1: 'amp_1p36.22' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1p36.22' versus 'MRNASEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.11

Table S2.  Gene #1: 'amp_1p36.22' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
AMP PEAK 1(1P36.22) MUTATED 2 2 6 6 16
AMP PEAK 1(1P36.22) WILD-TYPE 63 60 40 31 46

Figure S2.  Get High-res Image Gene #1: 'amp_1p36.22' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_1q21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S3.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
AMP PEAK 2(1Q21.3) MUTATED 15 13 31 8 68
AMP PEAK 2(1Q21.3) WILD-TYPE 154 20 35 2 23

Figure S3.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q21.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S4.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
AMP PEAK 2(1Q21.3) MUTATED 35 61 22
AMP PEAK 2(1Q21.3) WILD-TYPE 85 31 87

Figure S4.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_1q21.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S5.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
AMP PEAK 2(1Q21.3) MUTATED 12 10 16 13 47
AMP PEAK 2(1Q21.3) WILD-TYPE 53 52 30 24 15

Figure S5.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_1q21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S6.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 38 21 49 62 41 40 21
AMP PEAK 2(1Q21.3) MUTATED 12 3 7 26 22 27 1
AMP PEAK 2(1Q21.3) WILD-TYPE 26 18 42 36 19 13 20

Figure S6.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_1q21.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S7.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 108 141
AMP PEAK 2(1Q21.3) MUTATED 34 22 78
AMP PEAK 2(1Q21.3) WILD-TYPE 85 86 63

Figure S7.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_1q21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S8.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 83 106
AMP PEAK 2(1Q21.3) MUTATED 52 21 61
AMP PEAK 2(1Q21.3) WILD-TYPE 127 62 45

Figure S8.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_1q21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S9.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 144 100
AMP PEAK 2(1Q21.3) MUTATED 17 78 22
AMP PEAK 2(1Q21.3) WILD-TYPE 60 66 78

Figure S9.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_1q21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S10.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 62 82
AMP PEAK 2(1Q21.3) MUTATED 58 9 50
AMP PEAK 2(1Q21.3) WILD-TYPE 119 53 32

Figure S10.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_1q42.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S11.  Gene #3: 'amp_1q42.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
AMP PEAK 3(1Q42.3) MUTATED 18 12 23 7 62
AMP PEAK 3(1Q42.3) WILD-TYPE 151 21 43 3 29

Figure S11.  Get High-res Image Gene #3: 'amp_1q42.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q42.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S12.  Gene #3: 'amp_1q42.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
AMP PEAK 3(1Q42.3) MUTATED 31 50 25
AMP PEAK 3(1Q42.3) WILD-TYPE 89 42 84

Figure S12.  Get High-res Image Gene #3: 'amp_1q42.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_1q42.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S13.  Gene #3: 'amp_1q42.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
AMP PEAK 3(1Q42.3) MUTATED 13 13 12 12 41
AMP PEAK 3(1Q42.3) WILD-TYPE 52 49 34 25 21

Figure S13.  Get High-res Image Gene #3: 'amp_1q42.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_1q42.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.05

Table S14.  Gene #3: 'amp_1q42.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 38 21 49 62 41 40 21
AMP PEAK 3(1Q42.3) MUTATED 12 3 10 20 20 24 2
AMP PEAK 3(1Q42.3) WILD-TYPE 26 18 39 42 21 16 19

Figure S14.  Get High-res Image Gene #3: 'amp_1q42.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_1q42.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S15.  Gene #3: 'amp_1q42.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 108 141
AMP PEAK 3(1Q42.3) MUTATED 28 25 69
AMP PEAK 3(1Q42.3) WILD-TYPE 91 83 72

Figure S15.  Get High-res Image Gene #3: 'amp_1q42.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_1q42.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S16.  Gene #3: 'amp_1q42.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 83 106
AMP PEAK 3(1Q42.3) MUTATED 41 22 59
AMP PEAK 3(1Q42.3) WILD-TYPE 138 61 47

Figure S16.  Get High-res Image Gene #3: 'amp_1q42.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_1q42.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S17.  Gene #3: 'amp_1q42.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 62 82
AMP PEAK 3(1Q42.3) MUTATED 49 13 45
AMP PEAK 3(1Q42.3) WILD-TYPE 128 49 37

Figure S17.  Get High-res Image Gene #3: 'amp_1q42.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_3q26.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S18.  Gene #4: 'amp_3q26.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
AMP PEAK 4(3Q26.2) MUTATED 31 8 36 5 45
AMP PEAK 4(3Q26.2) WILD-TYPE 138 25 30 5 46

Figure S18.  Get High-res Image Gene #4: 'amp_3q26.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5p15.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S19.  Gene #5: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
AMP PEAK 5(5P15.33) MUTATED 15 7 18 2 62
AMP PEAK 5(5P15.33) WILD-TYPE 154 26 48 8 29

Figure S19.  Get High-res Image Gene #5: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5p15.33' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S20.  Gene #5: 'amp_5p15.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
AMP PEAK 5(5P15.33) MUTATED 19 50 22
AMP PEAK 5(5P15.33) WILD-TYPE 101 42 87

Figure S20.  Get High-res Image Gene #5: 'amp_5p15.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_5p15.33' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
AMP PEAK 5(5P15.33) MUTATED 11 6 10 10 38
AMP PEAK 5(5P15.33) WILD-TYPE 54 56 36 27 24

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

'amp_5p15.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.029

Table S22.  Gene #5: 'amp_5p15.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 38 21 49 62 41 40 21
AMP PEAK 5(5P15.33) MUTATED 7 5 6 16 16 23 2
AMP PEAK 5(5P15.33) WILD-TYPE 31 16 43 46 25 17 19

Figure S22.  Get High-res Image Gene #5: 'amp_5p15.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S23.  Gene #5: 'amp_5p15.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 108 141
AMP PEAK 5(5P15.33) MUTATED 29 16 58
AMP PEAK 5(5P15.33) WILD-TYPE 90 92 83

Figure S23.  Get High-res Image Gene #5: 'amp_5p15.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_5p15.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S24.  Gene #5: 'amp_5p15.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 83 106
AMP PEAK 5(5P15.33) MUTATED 39 15 49
AMP PEAK 5(5P15.33) WILD-TYPE 140 68 57

Figure S24.  Get High-res Image Gene #5: 'amp_5p15.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.055

Table S25.  Gene #5: 'amp_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 144 100
AMP PEAK 5(5P15.33) MUTATED 19 56 15
AMP PEAK 5(5P15.33) WILD-TYPE 58 88 85

Figure S25.  Get High-res Image Gene #5: 'amp_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_5p15.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S26.  Gene #5: 'amp_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 62 82
AMP PEAK 5(5P15.33) MUTATED 42 5 43
AMP PEAK 5(5P15.33) WILD-TYPE 135 57 39

Figure S26.  Get High-res Image Gene #5: 'amp_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_5p13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S27.  Gene #6: 'amp_5p13.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
AMP PEAK 6(5P13.1) MUTATED 15 7 17 2 62
AMP PEAK 6(5P13.1) WILD-TYPE 154 26 49 8 29

Figure S27.  Get High-res Image Gene #6: 'amp_5p13.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5p13.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S28.  Gene #6: 'amp_5p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
AMP PEAK 6(5P13.1) MUTATED 22 45 21
AMP PEAK 6(5P13.1) WILD-TYPE 98 47 88

Figure S28.  Get High-res Image Gene #6: 'amp_5p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_5p13.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S29.  Gene #6: 'amp_5p13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
AMP PEAK 6(5P13.1) MUTATED 11 8 10 9 37
AMP PEAK 6(5P13.1) WILD-TYPE 54 54 36 28 25

Figure S29.  Get High-res Image Gene #6: 'amp_5p13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_5p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-04 (Fisher's exact test), Q value = 0.24

Table S30.  Gene #6: 'amp_5p13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 38 21 49 62 41 40 21
AMP PEAK 6(5P13.1) MUTATED 9 4 7 17 14 22 2
AMP PEAK 6(5P13.1) WILD-TYPE 29 17 42 45 27 18 19

Figure S30.  Get High-res Image Gene #6: 'amp_5p13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_5p13.1' versus 'MIRSEQ_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.096

Table S31.  Gene #6: 'amp_5p13.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 108 141
AMP PEAK 6(5P13.1) MUTATED 27 19 57
AMP PEAK 6(5P13.1) WILD-TYPE 92 89 84

Figure S31.  Get High-res Image Gene #6: 'amp_5p13.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_5p13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.06

Table S32.  Gene #6: 'amp_5p13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 83 106
AMP PEAK 6(5P13.1) MUTATED 39 17 47
AMP PEAK 6(5P13.1) WILD-TYPE 140 66 59

Figure S32.  Get High-res Image Gene #6: 'amp_5p13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_5p13.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S33.  Gene #6: 'amp_5p13.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 62 82
AMP PEAK 6(5P13.1) MUTATED 40 7 41
AMP PEAK 6(5P13.1) WILD-TYPE 137 55 41

Figure S33.  Get High-res Image Gene #6: 'amp_5p13.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_6p21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S34.  Gene #7: 'amp_6p21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
AMP PEAK 7(6P21.1) MUTATED 8 10 23 4 54
AMP PEAK 7(6P21.1) WILD-TYPE 161 23 43 6 37

Figure S34.  Get High-res Image Gene #7: 'amp_6p21.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6p21.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S35.  Gene #7: 'amp_6p21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
AMP PEAK 7(6P21.1) MUTATED 23 48 12
AMP PEAK 7(6P21.1) WILD-TYPE 97 44 97

Figure S35.  Get High-res Image Gene #7: 'amp_6p21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6p21.1' versus 'MIRSEQ_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.17

Table S36.  Gene #7: 'amp_6p21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 108 141
AMP PEAK 7(6P21.1) MUTATED 26 18 54
AMP PEAK 7(6P21.1) WILD-TYPE 93 90 87

Figure S36.  Get High-res Image Gene #7: 'amp_6p21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_6p21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.15

Table S37.  Gene #7: 'amp_6p21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 83 106
AMP PEAK 7(6P21.1) MUTATED 39 15 44
AMP PEAK 7(6P21.1) WILD-TYPE 140 68 62

Figure S37.  Get High-res Image Gene #7: 'amp_6p21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_6p21.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.17

Table S38.  Gene #7: 'amp_6p21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 144 100
AMP PEAK 7(6P21.1) MUTATED 13 53 17
AMP PEAK 7(6P21.1) WILD-TYPE 64 91 83

Figure S38.  Get High-res Image Gene #7: 'amp_6p21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_6p21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S39.  Gene #7: 'amp_6p21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 62 82
AMP PEAK 7(6P21.1) MUTATED 40 7 36
AMP PEAK 7(6P21.1) WILD-TYPE 137 55 46

Figure S39.  Get High-res Image Gene #7: 'amp_6p21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_6q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S40.  Gene #8: 'amp_6q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
AMP PEAK 8(6Q12) MUTATED 8 7 14 3 41
AMP PEAK 8(6Q12) WILD-TYPE 161 26 52 7 50

Figure S40.  Get High-res Image Gene #8: 'amp_6q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S41.  Gene #8: 'amp_6q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
AMP PEAK 8(6Q12) MUTATED 15 34 10
AMP PEAK 8(6Q12) WILD-TYPE 105 58 99

Figure S41.  Get High-res Image Gene #8: 'amp_6q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6q12' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.039

Table S42.  Gene #8: 'amp_6q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
AMP PEAK 8(6Q12) MUTATED 6 7 9 6 26
AMP PEAK 8(6Q12) WILD-TYPE 59 55 37 31 36

Figure S42.  Get High-res Image Gene #8: 'amp_6q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_6q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00037 (Fisher's exact test), Q value = 0.18

Table S43.  Gene #8: 'amp_6q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 38 21 49 62 41 40 21
AMP PEAK 8(6Q12) MUTATED 7 1 3 12 12 17 2
AMP PEAK 8(6Q12) WILD-TYPE 31 20 46 50 29 23 19

Figure S43.  Get High-res Image Gene #8: 'amp_6q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_6q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00032 (Fisher's exact test), Q value = 0.16

Table S44.  Gene #8: 'amp_6q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 83 106
AMP PEAK 8(6Q12) MUTATED 26 11 35
AMP PEAK 8(6Q12) WILD-TYPE 153 72 71

Figure S44.  Get High-res Image Gene #8: 'amp_6q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_6q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.018

Table S45.  Gene #8: 'amp_6q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 62 82
AMP PEAK 8(6Q12) MUTATED 25 4 29
AMP PEAK 8(6Q12) WILD-TYPE 152 58 53

Figure S45.  Get High-res Image Gene #8: 'amp_6q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_6q21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S46.  Gene #9: 'amp_6q21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
AMP PEAK 9(6Q21) MUTATED 8 6 17 2 35
AMP PEAK 9(6Q21) WILD-TYPE 161 27 49 8 56

Figure S46.  Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6q21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00051 (Fisher's exact test), Q value = 0.25

Table S47.  Gene #9: 'amp_6q21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 83 106
AMP PEAK 9(6Q21) MUTATED 27 8 32
AMP PEAK 9(6Q21) WILD-TYPE 152 75 74

Figure S47.  Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_6q21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S48.  Gene #9: 'amp_6q21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 62 82
AMP PEAK 9(6Q21) MUTATED 23 3 28
AMP PEAK 9(6Q21) WILD-TYPE 154 59 54

Figure S48.  Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7p22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S49.  Gene #10: 'amp_7p22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
AMP PEAK 10(7P22.1) MUTATED 47 32 39 5 66
AMP PEAK 10(7P22.1) WILD-TYPE 122 1 27 5 25

Figure S49.  Get High-res Image Gene #10: 'amp_7p22.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7p22.1' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.029

Table S50.  Gene #10: 'amp_7p22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
AMP PEAK 10(7P22.1) MUTATED 60 64 41
AMP PEAK 10(7P22.1) WILD-TYPE 60 28 68

Figure S50.  Get High-res Image Gene #10: 'amp_7p22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7p22.1' versus 'MRNASEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.11

Table S51.  Gene #10: 'amp_7p22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
AMP PEAK 10(7P22.1) MUTATED 29 25 16 20 46
AMP PEAK 10(7P22.1) WILD-TYPE 36 37 30 17 16

Figure S51.  Get High-res Image Gene #10: 'amp_7p22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_7p22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.018

Table S52.  Gene #10: 'amp_7p22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 38 21 49 62 41 40 21
AMP PEAK 10(7P22.1) MUTATED 17 11 15 31 30 28 4
AMP PEAK 10(7P22.1) WILD-TYPE 21 10 34 31 11 12 17

Figure S52.  Get High-res Image Gene #10: 'amp_7p22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_7p22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00051 (Fisher's exact test), Q value = 0.25

Table S53.  Gene #10: 'amp_7p22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 83 106
AMP PEAK 10(7P22.1) MUTATED 82 35 71
AMP PEAK 10(7P22.1) WILD-TYPE 97 48 35

Figure S53.  Get High-res Image Gene #10: 'amp_7p22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_7p22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S54.  Gene #10: 'amp_7p22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 62 82
AMP PEAK 10(7P22.1) MUTATED 87 18 59
AMP PEAK 10(7P22.1) WILD-TYPE 90 44 23

Figure S54.  Get High-res Image Gene #10: 'amp_7p22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S55.  Gene #11: 'amp_7p11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
AMP PEAK 11(7P11.2) MUTATED 46 31 38 6 51
AMP PEAK 11(7P11.2) WILD-TYPE 123 2 28 4 40

Figure S55.  Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00051 (Fisher's exact test), Q value = 0.25

Table S56.  Gene #11: 'amp_7p11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 38 21 49 62 41 40 21
AMP PEAK 11(7P11.2) MUTATED 15 11 15 29 28 22 3
AMP PEAK 11(7P11.2) WILD-TYPE 23 10 34 33 13 18 18

Figure S56.  Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_7q21.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S57.  Gene #12: 'amp_7q21.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
AMP PEAK 12(7Q21.2) MUTATED 47 30 41 7 43
AMP PEAK 12(7Q21.2) WILD-TYPE 122 3 25 3 48

Figure S57.  Get High-res Image Gene #12: 'amp_7q21.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7q21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.039

Table S58.  Gene #12: 'amp_7q21.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 38 21 49 62 41 40 21
AMP PEAK 12(7Q21.2) MUTATED 15 13 14 26 30 19 3
AMP PEAK 12(7Q21.2) WILD-TYPE 23 8 35 36 11 21 18

Figure S58.  Get High-res Image Gene #12: 'amp_7q21.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_8p23.1' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.034

Table S59.  Gene #13: 'amp_8p23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
AMP PEAK 13(8P23.1) MUTATED 75 13 22 10 26
AMP PEAK 13(8P23.1) WILD-TYPE 94 20 44 0 65

Figure S59.  Get High-res Image Gene #13: 'amp_8p23.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8p23.1' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.045

Table S60.  Gene #13: 'amp_8p23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
AMP PEAK 13(8P23.1) MUTATED 64 27 32
AMP PEAK 13(8P23.1) WILD-TYPE 56 65 77

Figure S60.  Get High-res Image Gene #13: 'amp_8p23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S61.  Gene #14: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
AMP PEAK 14(8Q24.21) MUTATED 96 28 41 10 81
AMP PEAK 14(8Q24.21) WILD-TYPE 73 5 25 0 10

Figure S61.  Get High-res Image Gene #14: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.17

Table S62.  Gene #14: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
AMP PEAK 14(8Q24.21) MUTATED 87 73 59
AMP PEAK 14(8Q24.21) WILD-TYPE 33 19 50

Figure S62.  Get High-res Image Gene #14: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'MIRSEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.045

Table S63.  Gene #14: 'amp_8q24.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 108 141
AMP PEAK 14(8Q24.21) MUTATED 80 60 115
AMP PEAK 14(8Q24.21) WILD-TYPE 39 48 26

Figure S63.  Get High-res Image Gene #14: 'amp_8q24.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_8q24.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.15

Table S64.  Gene #14: 'amp_8q24.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 83 106
AMP PEAK 14(8Q24.21) MUTATED 117 49 89
AMP PEAK 14(8Q24.21) WILD-TYPE 62 34 17

Figure S64.  Get High-res Image Gene #14: 'amp_8q24.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S65.  Gene #14: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 144 100
AMP PEAK 14(8Q24.21) MUTATED 46 121 52
AMP PEAK 14(8Q24.21) WILD-TYPE 31 23 48

Figure S65.  Get High-res Image Gene #14: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S66.  Gene #14: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 62 82
AMP PEAK 14(8Q24.21) MUTATED 122 28 69
AMP PEAK 14(8Q24.21) WILD-TYPE 55 34 13

Figure S66.  Get High-res Image Gene #14: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_9p24.1' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S67.  Gene #15: 'amp_9p24.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
AMP PEAK 15(9P24.1) MUTATED 26 1 1 2 27
AMP PEAK 15(9P24.1) WILD-TYPE 143 32 65 8 64

Figure S67.  Get High-res Image Gene #15: 'amp_9p24.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_9q34.3' versus 'CN_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.13

Table S68.  Gene #17: 'amp_9q34.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
AMP PEAK 17(9Q34.3) MUTATED 28 11 19 2 38
AMP PEAK 17(9Q34.3) WILD-TYPE 141 22 47 8 53

Figure S68.  Get High-res Image Gene #17: 'amp_9q34.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_10p11.22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S69.  Gene #18: 'amp_10p11.22' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
AMP PEAK 18(10P11.22) MUTATED 13 8 34 1 42
AMP PEAK 18(10P11.22) WILD-TYPE 156 25 32 9 49

Figure S69.  Get High-res Image Gene #18: 'amp_10p11.22' versus Molecular Subtype #1: 'CN_CNMF'

'amp_10p11.22' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S70.  Gene #18: 'amp_10p11.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
AMP PEAK 18(10P11.22) MUTATED 24 43 19
AMP PEAK 18(10P11.22) WILD-TYPE 96 49 90

Figure S70.  Get High-res Image Gene #18: 'amp_10p11.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_10p11.22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.071

Table S71.  Gene #18: 'amp_10p11.22' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 83 106
AMP PEAK 18(10P11.22) MUTATED 34 19 44
AMP PEAK 18(10P11.22) WILD-TYPE 145 64 62

Figure S71.  Get High-res Image Gene #18: 'amp_10p11.22' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_10p11.22' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.05

Table S72.  Gene #18: 'amp_10p11.22' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 62 82
AMP PEAK 18(10P11.22) MUTATED 41 8 36
AMP PEAK 18(10P11.22) WILD-TYPE 136 54 46

Figure S72.  Get High-res Image Gene #18: 'amp_10p11.22' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_10q22.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S73.  Gene #19: 'amp_10q22.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
AMP PEAK 19(10Q22.2) MUTATED 11 3 31 2 21
AMP PEAK 19(10Q22.2) WILD-TYPE 158 30 35 8 70

Figure S73.  Get High-res Image Gene #19: 'amp_10q22.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_10q26.13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S74.  Gene #20: 'amp_10q26.13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
AMP PEAK 20(10Q26.13) MUTATED 15 7 24 0 26
AMP PEAK 20(10Q26.13) WILD-TYPE 154 26 42 10 65

Figure S74.  Get High-res Image Gene #20: 'amp_10q26.13' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11p13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.091

Table S75.  Gene #21: 'amp_11p13' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 83 106
AMP PEAK 21(11P13) MUTATED 21 14 34
AMP PEAK 21(11P13) WILD-TYPE 158 69 72

Figure S75.  Get High-res Image Gene #21: 'amp_11p13' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_11q13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S76.  Gene #22: 'amp_11q13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
AMP PEAK 22(11Q13.3) MUTATED 16 5 34 4 31
AMP PEAK 22(11Q13.3) WILD-TYPE 153 28 32 6 60

Figure S76.  Get High-res Image Gene #22: 'amp_11q13.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11q13.3' versus 'MIRSEQ_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.16

Table S77.  Gene #22: 'amp_11q13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 108 141
AMP PEAK 22(11Q13.3) MUTATED 23 16 50
AMP PEAK 22(11Q13.3) WILD-TYPE 96 92 91

Figure S77.  Get High-res Image Gene #22: 'amp_11q13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_11q13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.091

Table S78.  Gene #22: 'amp_11q13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 144 100
AMP PEAK 22(11Q13.3) MUTATED 10 51 16
AMP PEAK 22(11Q13.3) WILD-TYPE 67 93 84

Figure S78.  Get High-res Image Gene #22: 'amp_11q13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_12p12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S79.  Gene #23: 'amp_12p12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
AMP PEAK 23(12P12.1) MUTATED 26 12 35 5 31
AMP PEAK 23(12P12.1) WILD-TYPE 143 21 31 5 60

Figure S79.  Get High-res Image Gene #23: 'amp_12p12.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12q15' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S80.  Gene #24: 'amp_12q15' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
AMP PEAK 24(12Q15) MUTATED 26 6 32 2 26
AMP PEAK 24(12Q15) WILD-TYPE 143 27 34 8 65

Figure S80.  Get High-res Image Gene #24: 'amp_12q15' versus Molecular Subtype #1: 'CN_CNMF'

'amp_13q12.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S81.  Gene #25: 'amp_13q12.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
AMP PEAK 25(13Q12.3) MUTATED 35 29 20 5 55
AMP PEAK 25(13Q12.3) WILD-TYPE 134 4 46 5 36

Figure S81.  Get High-res Image Gene #25: 'amp_13q12.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_13q12.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S82.  Gene #25: 'amp_13q12.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
AMP PEAK 25(13Q12.3) MUTATED 38 56 31
AMP PEAK 25(13Q12.3) WILD-TYPE 82 36 78

Figure S82.  Get High-res Image Gene #25: 'amp_13q12.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_13q12.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.018

Table S83.  Gene #25: 'amp_13q12.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 38 21 49 62 41 40 21
AMP PEAK 25(13Q12.3) MUTATED 4 5 17 23 25 22 5
AMP PEAK 25(13Q12.3) WILD-TYPE 34 16 32 39 16 18 16

Figure S83.  Get High-res Image Gene #25: 'amp_13q12.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_13q12.3' versus 'MIRSEQ_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.17

Table S84.  Gene #25: 'amp_13q12.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 108 141
AMP PEAK 25(13Q12.3) MUTATED 42 29 72
AMP PEAK 25(13Q12.3) WILD-TYPE 77 79 69

Figure S84.  Get High-res Image Gene #25: 'amp_13q12.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_13q12.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.2

Table S85.  Gene #25: 'amp_13q12.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 144 100
AMP PEAK 25(13Q12.3) MUTATED 23 73 28
AMP PEAK 25(13Q12.3) WILD-TYPE 54 71 72

Figure S85.  Get High-res Image Gene #25: 'amp_13q12.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_13q12.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 0.14

Table S86.  Gene #25: 'amp_13q12.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 62 82
AMP PEAK 25(13Q12.3) MUTATED 63 15 46
AMP PEAK 25(13Q12.3) WILD-TYPE 114 47 36

Figure S86.  Get High-res Image Gene #25: 'amp_13q12.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_13q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S87.  Gene #26: 'amp_13q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
AMP PEAK 26(13Q22.1) MUTATED 39 28 18 4 60
AMP PEAK 26(13Q22.1) WILD-TYPE 130 5 48 6 31

Figure S87.  Get High-res Image Gene #26: 'amp_13q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_13q22.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S88.  Gene #26: 'amp_13q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
AMP PEAK 26(13Q22.1) MUTATED 37 57 33
AMP PEAK 26(13Q22.1) WILD-TYPE 83 35 76

Figure S88.  Get High-res Image Gene #26: 'amp_13q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_13q22.1' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S89.  Gene #26: 'amp_13q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
AMP PEAK 26(13Q22.1) MUTATED 23 16 9 17 39
AMP PEAK 26(13Q22.1) WILD-TYPE 42 46 37 20 23

Figure S89.  Get High-res Image Gene #26: 'amp_13q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_13q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S90.  Gene #26: 'amp_13q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 38 21 49 62 41 40 21
AMP PEAK 26(13Q22.1) MUTATED 7 7 15 18 24 28 5
AMP PEAK 26(13Q22.1) WILD-TYPE 31 14 34 44 17 12 16

Figure S90.  Get High-res Image Gene #26: 'amp_13q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_13q22.1' versus 'MIRSEQ_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.21

Table S91.  Gene #26: 'amp_13q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 108 141
AMP PEAK 26(13Q22.1) MUTATED 44 30 74
AMP PEAK 26(13Q22.1) WILD-TYPE 75 78 67

Figure S91.  Get High-res Image Gene #26: 'amp_13q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_13q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S92.  Gene #26: 'amp_13q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 83 106
AMP PEAK 26(13Q22.1) MUTATED 58 26 64
AMP PEAK 26(13Q22.1) WILD-TYPE 121 57 42

Figure S92.  Get High-res Image Gene #26: 'amp_13q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_13q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S93.  Gene #26: 'amp_13q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 144 100
AMP PEAK 26(13Q22.1) MUTATED 23 77 27
AMP PEAK 26(13Q22.1) WILD-TYPE 54 67 73

Figure S93.  Get High-res Image Gene #26: 'amp_13q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_13q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S94.  Gene #26: 'amp_13q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 62 82
AMP PEAK 26(13Q22.1) MUTATED 59 15 53
AMP PEAK 26(13Q22.1) WILD-TYPE 118 47 29

Figure S94.  Get High-res Image Gene #26: 'amp_13q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_15q26.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S95.  Gene #27: 'amp_15q26.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
AMP PEAK 27(15Q26.1) MUTATED 11 5 26 0 46
AMP PEAK 27(15Q26.1) WILD-TYPE 158 28 40 10 45

Figure S95.  Get High-res Image Gene #27: 'amp_15q26.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_15q26.1' versus 'METHLYATION_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.12

Table S96.  Gene #27: 'amp_15q26.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
AMP PEAK 27(15Q26.1) MUTATED 21 37 19
AMP PEAK 27(15Q26.1) WILD-TYPE 99 55 90

Figure S96.  Get High-res Image Gene #27: 'amp_15q26.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_15q26.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S97.  Gene #27: 'amp_15q26.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
AMP PEAK 27(15Q26.1) MUTATED 12 4 11 9 28
AMP PEAK 27(15Q26.1) WILD-TYPE 53 58 35 28 34

Figure S97.  Get High-res Image Gene #27: 'amp_15q26.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_15q26.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S98.  Gene #27: 'amp_15q26.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 38 21 49 62 41 40 21
AMP PEAK 27(15Q26.1) MUTATED 13 1 4 14 11 20 1
AMP PEAK 27(15Q26.1) WILD-TYPE 25 20 45 48 30 20 20

Figure S98.  Get High-res Image Gene #27: 'amp_15q26.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_17q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S99.  Gene #28: 'amp_17q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
AMP PEAK 28(17Q12) MUTATED 17 15 21 2 61
AMP PEAK 28(17Q12) WILD-TYPE 152 18 45 8 30

Figure S99.  Get High-res Image Gene #28: 'amp_17q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S100.  Gene #28: 'amp_17q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
AMP PEAK 28(17Q12) MUTATED 31 52 19
AMP PEAK 28(17Q12) WILD-TYPE 89 40 90

Figure S100.  Get High-res Image Gene #28: 'amp_17q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_17q12' versus 'MRNASEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.11

Table S101.  Gene #28: 'amp_17q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
AMP PEAK 28(17Q12) MUTATED 14 10 15 8 32
AMP PEAK 28(17Q12) WILD-TYPE 51 52 31 29 30

Figure S101.  Get High-res Image Gene #28: 'amp_17q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_17q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.1

Table S102.  Gene #28: 'amp_17q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 38 21 49 62 41 40 21
AMP PEAK 28(17Q12) MUTATED 13 7 5 20 13 20 1
AMP PEAK 28(17Q12) WILD-TYPE 25 14 44 42 28 20 20

Figure S102.  Get High-res Image Gene #28: 'amp_17q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.023

Table S103.  Gene #28: 'amp_17q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 108 141
AMP PEAK 28(17Q12) MUTATED 31 21 63
AMP PEAK 28(17Q12) WILD-TYPE 88 87 78

Figure S103.  Get High-res Image Gene #28: 'amp_17q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_17q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.11

Table S104.  Gene #28: 'amp_17q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 83 106
AMP PEAK 28(17Q12) MUTATED 47 18 50
AMP PEAK 28(17Q12) WILD-TYPE 132 65 56

Figure S104.  Get High-res Image Gene #28: 'amp_17q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_18q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S105.  Gene #29: 'amp_18q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
AMP PEAK 29(18Q11.2) MUTATED 24 11 34 4 44
AMP PEAK 29(18Q11.2) WILD-TYPE 145 22 32 6 47

Figure S105.  Get High-res Image Gene #29: 'amp_18q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19p13.2' versus 'CN_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.17

Table S106.  Gene #30: 'amp_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
AMP PEAK 30(19P13.2) MUTATED 8 9 12 0 12
AMP PEAK 30(19P13.2) WILD-TYPE 161 24 54 10 79

Figure S106.  Get High-res Image Gene #30: 'amp_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S107.  Gene #31: 'amp_19q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
AMP PEAK 31(19Q12) MUTATED 18 9 17 1 66
AMP PEAK 31(19Q12) WILD-TYPE 151 24 49 9 25

Figure S107.  Get High-res Image Gene #31: 'amp_19q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S108.  Gene #31: 'amp_19q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
AMP PEAK 31(19Q12) MUTATED 21 50 28
AMP PEAK 31(19Q12) WILD-TYPE 99 42 81

Figure S108.  Get High-res Image Gene #31: 'amp_19q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_19q12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S109.  Gene #31: 'amp_19q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
AMP PEAK 31(19Q12) MUTATED 10 9 10 6 44
AMP PEAK 31(19Q12) WILD-TYPE 55 53 36 31 18

Figure S109.  Get High-res Image Gene #31: 'amp_19q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_19q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S110.  Gene #31: 'amp_19q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 38 21 49 62 41 40 21
AMP PEAK 31(19Q12) MUTATED 10 5 6 15 11 29 3
AMP PEAK 31(19Q12) WILD-TYPE 28 16 43 47 30 11 18

Figure S110.  Get High-res Image Gene #31: 'amp_19q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S111.  Gene #31: 'amp_19q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 108 141
AMP PEAK 31(19Q12) MUTATED 25 22 63
AMP PEAK 31(19Q12) WILD-TYPE 94 86 78

Figure S111.  Get High-res Image Gene #31: 'amp_19q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_19q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S112.  Gene #31: 'amp_19q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 83 106
AMP PEAK 31(19Q12) MUTATED 29 18 63
AMP PEAK 31(19Q12) WILD-TYPE 150 65 43

Figure S112.  Get High-res Image Gene #31: 'amp_19q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S113.  Gene #31: 'amp_19q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 62 82
AMP PEAK 31(19Q12) MUTATED 33 11 55
AMP PEAK 31(19Q12) WILD-TYPE 144 51 27

Figure S113.  Get High-res Image Gene #31: 'amp_19q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20q13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S114.  Gene #32: 'amp_20q13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
AMP PEAK 32(20Q13.2) MUTATED 65 31 55 9 83
AMP PEAK 32(20Q13.2) WILD-TYPE 104 2 11 1 8

Figure S114.  Get High-res Image Gene #32: 'amp_20q13.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20q13.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S115.  Gene #32: 'amp_20q13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
AMP PEAK 32(20Q13.2) MUTATED 64 84 63
AMP PEAK 32(20Q13.2) WILD-TYPE 56 8 46

Figure S115.  Get High-res Image Gene #32: 'amp_20q13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_20q13.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S116.  Gene #32: 'amp_20q13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
AMP PEAK 32(20Q13.2) MUTATED 31 31 31 24 59
AMP PEAK 32(20Q13.2) WILD-TYPE 34 31 15 13 3

Figure S116.  Get High-res Image Gene #32: 'amp_20q13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_20q13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S117.  Gene #32: 'amp_20q13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 38 21 49 62 41 40 21
AMP PEAK 32(20Q13.2) MUTATED 23 19 19 43 31 38 3
AMP PEAK 32(20Q13.2) WILD-TYPE 15 2 30 19 10 2 18

Figure S117.  Get High-res Image Gene #32: 'amp_20q13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_20q13.2' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S118.  Gene #32: 'amp_20q13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 108 141
AMP PEAK 32(20Q13.2) MUTATED 71 56 115
AMP PEAK 32(20Q13.2) WILD-TYPE 48 52 26

Figure S118.  Get High-res Image Gene #32: 'amp_20q13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_20q13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S119.  Gene #32: 'amp_20q13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 83 106
AMP PEAK 32(20Q13.2) MUTATED 103 44 95
AMP PEAK 32(20Q13.2) WILD-TYPE 76 39 11

Figure S119.  Get High-res Image Gene #32: 'amp_20q13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_20q13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S120.  Gene #32: 'amp_20q13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 62 82
AMP PEAK 32(20Q13.2) MUTATED 106 29 76
AMP PEAK 32(20Q13.2) WILD-TYPE 71 33 6

Figure S120.  Get High-res Image Gene #32: 'amp_20q13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_xq27.3' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.039

Table S121.  Gene #33: 'amp_xq27.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
AMP PEAK 33(XQ27.3) MUTATED 15 13 14 3 22
AMP PEAK 33(XQ27.3) WILD-TYPE 154 20 52 7 69

Figure S121.  Get High-res Image Gene #33: 'amp_xq27.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xq27.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S122.  Gene #33: 'amp_xq27.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 38 21 49 62 41 40 21
AMP PEAK 33(XQ27.3) MUTATED 8 4 2 9 20 3 2
AMP PEAK 33(XQ27.3) WILD-TYPE 30 17 47 53 21 37 19

Figure S122.  Get High-res Image Gene #33: 'amp_xq27.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S123.  Gene #34: 'del_1p36.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
DEL PEAK 1(1P36.11) MUTATED 10 8 32 4 50
DEL PEAK 1(1P36.11) WILD-TYPE 159 25 34 6 41

Figure S123.  Get High-res Image Gene #34: 'del_1p36.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.11' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S124.  Gene #34: 'del_1p36.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
DEL PEAK 1(1P36.11) MUTATED 23 48 15
DEL PEAK 1(1P36.11) WILD-TYPE 97 44 94

Figure S124.  Get High-res Image Gene #34: 'del_1p36.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p36.11' versus 'MRNASEQ_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.17

Table S125.  Gene #34: 'del_1p36.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
DEL PEAK 1(1P36.11) MUTATED 12 8 17 11 28
DEL PEAK 1(1P36.11) WILD-TYPE 53 54 29 26 34

Figure S125.  Get High-res Image Gene #34: 'del_1p36.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_1p36.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S126.  Gene #34: 'del_1p36.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 38 21 49 62 41 40 21
DEL PEAK 1(1P36.11) MUTATED 10 2 4 21 15 22 2
DEL PEAK 1(1P36.11) WILD-TYPE 28 19 45 41 26 18 19

Figure S126.  Get High-res Image Gene #34: 'del_1p36.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.06

Table S127.  Gene #34: 'del_1p36.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 83 106
DEL PEAK 1(1P36.11) MUTATED 43 14 46
DEL PEAK 1(1P36.11) WILD-TYPE 136 69 60

Figure S127.  Get High-res Image Gene #34: 'del_1p36.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S128.  Gene #34: 'del_1p36.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 62 82
DEL PEAK 1(1P36.11) MUTATED 41 7 38
DEL PEAK 1(1P36.11) WILD-TYPE 136 55 44

Figure S128.  Get High-res Image Gene #34: 'del_1p36.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S129.  Gene #35: 'del_1p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
DEL PEAK 2(1P13.2) MUTATED 5 7 19 3 41
DEL PEAK 2(1P13.2) WILD-TYPE 164 26 47 7 50

Figure S129.  Get High-res Image Gene #35: 'del_1p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p13.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S130.  Gene #35: 'del_1p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
DEL PEAK 2(1P13.2) MUTATED 21 36 9
DEL PEAK 2(1P13.2) WILD-TYPE 99 56 100

Figure S130.  Get High-res Image Gene #35: 'del_1p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q37.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S131.  Gene #39: 'del_2q37.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
DEL PEAK 6(2Q37.2) MUTATED 9 4 14 3 24
DEL PEAK 6(2Q37.2) WILD-TYPE 160 29 52 7 67

Figure S131.  Get High-res Image Gene #39: 'del_2q37.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q37.2' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.029

Table S132.  Gene #39: 'del_2q37.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
DEL PEAK 6(2Q37.2) MUTATED 10 28 11
DEL PEAK 6(2Q37.2) WILD-TYPE 110 64 98

Figure S132.  Get High-res Image Gene #39: 'del_2q37.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q37.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S133.  Gene #39: 'del_2q37.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 83 106
DEL PEAK 6(2Q37.2) MUTATED 17 6 31
DEL PEAK 6(2Q37.2) WILD-TYPE 162 77 75

Figure S133.  Get High-res Image Gene #39: 'del_2q37.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p26.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S134.  Gene #40: 'del_3p26.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
DEL PEAK 7(3P26.1) MUTATED 19 18 29 4 45
DEL PEAK 7(3P26.1) WILD-TYPE 150 15 37 6 46

Figure S134.  Get High-res Image Gene #40: 'del_3p26.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p26.1' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S135.  Gene #40: 'del_3p26.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
DEL PEAK 7(3P26.1) MUTATED 29 47 25
DEL PEAK 7(3P26.1) WILD-TYPE 91 45 84

Figure S135.  Get High-res Image Gene #40: 'del_3p26.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p26.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.029

Table S136.  Gene #40: 'del_3p26.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 38 21 49 62 41 40 21
DEL PEAK 7(3P26.1) MUTATED 8 5 8 16 20 18 0
DEL PEAK 7(3P26.1) WILD-TYPE 30 16 41 46 21 22 21

Figure S136.  Get High-res Image Gene #40: 'del_3p26.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p26.1' versus 'MIRSEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.05

Table S137.  Gene #40: 'del_3p26.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 108 141
DEL PEAK 7(3P26.1) MUTATED 31 21 62
DEL PEAK 7(3P26.1) WILD-TYPE 88 87 79

Figure S137.  Get High-res Image Gene #40: 'del_3p26.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3p26.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.023

Table S138.  Gene #40: 'del_3p26.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 83 106
DEL PEAK 7(3P26.1) MUTATED 44 18 52
DEL PEAK 7(3P26.1) WILD-TYPE 135 65 54

Figure S138.  Get High-res Image Gene #40: 'del_3p26.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p26.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00043 (Fisher's exact test), Q value = 0.21

Table S139.  Gene #40: 'del_3p26.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 144 100
DEL PEAK 7(3P26.1) MUTATED 19 61 20
DEL PEAK 7(3P26.1) WILD-TYPE 58 83 80

Figure S139.  Get High-res Image Gene #40: 'del_3p26.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_3p26.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S140.  Gene #40: 'del_3p26.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 62 82
DEL PEAK 7(3P26.1) MUTATED 48 8 44
DEL PEAK 7(3P26.1) WILD-TYPE 129 54 38

Figure S140.  Get High-res Image Gene #40: 'del_3p26.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p14.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S141.  Gene #41: 'del_3p14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
DEL PEAK 8(3P14.2) MUTATED 27 15 36 5 48
DEL PEAK 8(3P14.2) WILD-TYPE 142 18 30 5 43

Figure S141.  Get High-res Image Gene #41: 'del_3p14.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p14.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S142.  Gene #41: 'del_3p14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
DEL PEAK 8(3P14.2) MUTATED 42 52 24
DEL PEAK 8(3P14.2) WILD-TYPE 78 40 85

Figure S142.  Get High-res Image Gene #41: 'del_3p14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p14.2' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.045

Table S143.  Gene #41: 'del_3p14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
DEL PEAK 8(3P14.2) MUTATED 16 10 15 13 34
DEL PEAK 8(3P14.2) WILD-TYPE 49 52 31 24 28

Figure S143.  Get High-res Image Gene #41: 'del_3p14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.1

Table S144.  Gene #41: 'del_3p14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 38 21 49 62 41 40 21
DEL PEAK 8(3P14.2) MUTATED 11 6 6 21 19 22 3
DEL PEAK 8(3P14.2) WILD-TYPE 27 15 43 41 22 18 18

Figure S144.  Get High-res Image Gene #41: 'del_3p14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p14.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S145.  Gene #41: 'del_3p14.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 108 141
DEL PEAK 8(3P14.2) MUTATED 36 25 70
DEL PEAK 8(3P14.2) WILD-TYPE 83 83 71

Figure S145.  Get High-res Image Gene #41: 'del_3p14.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3p14.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S146.  Gene #41: 'del_3p14.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 83 106
DEL PEAK 8(3P14.2) MUTATED 53 19 59
DEL PEAK 8(3P14.2) WILD-TYPE 126 64 47

Figure S146.  Get High-res Image Gene #41: 'del_3p14.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p14.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00042 (Fisher's exact test), Q value = 0.21

Table S147.  Gene #41: 'del_3p14.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 144 100
DEL PEAK 8(3P14.2) MUTATED 27 68 23
DEL PEAK 8(3P14.2) WILD-TYPE 50 76 77

Figure S147.  Get High-res Image Gene #41: 'del_3p14.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_3p14.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S148.  Gene #41: 'del_3p14.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 62 82
DEL PEAK 8(3P14.2) MUTATED 59 11 48
DEL PEAK 8(3P14.2) WILD-TYPE 118 51 34

Figure S148.  Get High-res Image Gene #41: 'del_3p14.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3q26.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S149.  Gene #42: 'del_3q26.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
DEL PEAK 9(3Q26.31) MUTATED 4 9 12 1 20
DEL PEAK 9(3Q26.31) WILD-TYPE 165 24 54 9 71

Figure S149.  Get High-res Image Gene #42: 'del_3q26.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_3q26.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S150.  Gene #42: 'del_3q26.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
DEL PEAK 9(3Q26.31) MUTATED 12 26 3
DEL PEAK 9(3Q26.31) WILD-TYPE 108 66 106

Figure S150.  Get High-res Image Gene #42: 'del_3q26.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3q26.31' versus 'MRNASEQ_CNMF'

P value = 0.00043 (Fisher's exact test), Q value = 0.21

Table S151.  Gene #42: 'del_3q26.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
DEL PEAK 9(3Q26.31) MUTATED 2 3 3 7 15
DEL PEAK 9(3Q26.31) WILD-TYPE 63 59 43 30 47

Figure S151.  Get High-res Image Gene #42: 'del_3q26.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3q26.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00046 (Fisher's exact test), Q value = 0.22

Table S152.  Gene #42: 'del_3q26.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 38 21 49 62 41 40 21
DEL PEAK 9(3Q26.31) MUTATED 4 1 1 4 11 9 0
DEL PEAK 9(3Q26.31) WILD-TYPE 34 20 48 58 30 31 21

Figure S152.  Get High-res Image Gene #42: 'del_3q26.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4p16.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S153.  Gene #43: 'del_4p16.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
DEL PEAK 10(4P16.3) MUTATED 29 13 40 3 57
DEL PEAK 10(4P16.3) WILD-TYPE 140 20 26 7 34

Figure S153.  Get High-res Image Gene #43: 'del_4p16.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_4p16.3' versus 'METHLYATION_CNMF'

P value = 0.00052 (Fisher's exact test), Q value = 0.25

Table S154.  Gene #43: 'del_4p16.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
DEL PEAK 10(4P16.3) MUTATED 34 50 39
DEL PEAK 10(4P16.3) WILD-TYPE 86 42 70

Figure S154.  Get High-res Image Gene #43: 'del_4p16.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4p16.3' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.018

Table S155.  Gene #43: 'del_4p16.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
DEL PEAK 10(4P16.3) MUTATED 11 23 15 11 38
DEL PEAK 10(4P16.3) WILD-TYPE 54 39 31 26 24

Figure S155.  Get High-res Image Gene #43: 'del_4p16.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4p16.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.029

Table S156.  Gene #43: 'del_4p16.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 38 21 49 62 41 40 21
DEL PEAK 10(4P16.3) MUTATED 10 4 18 18 17 28 3
DEL PEAK 10(4P16.3) WILD-TYPE 28 17 31 44 24 12 18

Figure S156.  Get High-res Image Gene #43: 'del_4p16.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4p16.3' versus 'MIRSEQ_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.22

Table S157.  Gene #43: 'del_4p16.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 108 141
DEL PEAK 10(4P16.3) MUTATED 30 43 69
DEL PEAK 10(4P16.3) WILD-TYPE 89 65 72

Figure S157.  Get High-res Image Gene #43: 'del_4p16.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_4p16.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S158.  Gene #43: 'del_4p16.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 83 106
DEL PEAK 10(4P16.3) MUTATED 49 29 64
DEL PEAK 10(4P16.3) WILD-TYPE 130 54 42

Figure S158.  Get High-res Image Gene #43: 'del_4p16.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_4p16.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.081

Table S159.  Gene #43: 'del_4p16.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 144 100
DEL PEAK 10(4P16.3) MUTATED 15 68 41
DEL PEAK 10(4P16.3) WILD-TYPE 62 76 59

Figure S159.  Get High-res Image Gene #43: 'del_4p16.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_4p16.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S160.  Gene #43: 'del_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 62 82
DEL PEAK 10(4P16.3) MUTATED 51 19 54
DEL PEAK 10(4P16.3) WILD-TYPE 126 43 28

Figure S160.  Get High-res Image Gene #43: 'del_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S161.  Gene #44: 'del_4q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
DEL PEAK 11(4Q22.1) MUTATED 25 17 50 4 64
DEL PEAK 11(4Q22.1) WILD-TYPE 144 16 16 6 27

Figure S161.  Get High-res Image Gene #44: 'del_4q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q22.1' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.034

Table S162.  Gene #44: 'del_4q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
DEL PEAK 11(4Q22.1) MUTATED 45 58 36
DEL PEAK 11(4Q22.1) WILD-TYPE 75 34 73

Figure S162.  Get High-res Image Gene #44: 'del_4q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.018

Table S163.  Gene #44: 'del_4q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 38 21 49 62 41 40 21
DEL PEAK 11(4Q22.1) MUTATED 16 4 16 23 25 27 3
DEL PEAK 11(4Q22.1) WILD-TYPE 22 17 33 39 16 13 18

Figure S163.  Get High-res Image Gene #44: 'del_4q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00047 (Fisher's exact test), Q value = 0.23

Table S164.  Gene #44: 'del_4q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 62 82
DEL PEAK 11(4Q22.1) MUTATED 70 19 50
DEL PEAK 11(4Q22.1) WILD-TYPE 107 43 32

Figure S164.  Get High-res Image Gene #44: 'del_4q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q34.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S165.  Gene #45: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
DEL PEAK 12(4Q34.3) MUTATED 27 15 50 4 67
DEL PEAK 12(4Q34.3) WILD-TYPE 142 18 16 6 24

Figure S165.  Get High-res Image Gene #45: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q34.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S166.  Gene #45: 'del_4q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
DEL PEAK 12(4Q34.3) MUTATED 40 63 41
DEL PEAK 12(4Q34.3) WILD-TYPE 80 29 68

Figure S166.  Get High-res Image Gene #45: 'del_4q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q34.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S167.  Gene #45: 'del_4q34.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
DEL PEAK 12(4Q34.3) MUTATED 14 21 21 16 41
DEL PEAK 12(4Q34.3) WILD-TYPE 51 41 25 21 21

Figure S167.  Get High-res Image Gene #45: 'del_4q34.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4q34.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S168.  Gene #45: 'del_4q34.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 38 21 49 62 41 40 21
DEL PEAK 12(4Q34.3) MUTATED 16 2 17 23 21 30 4
DEL PEAK 12(4Q34.3) WILD-TYPE 22 19 32 39 20 10 17

Figure S168.  Get High-res Image Gene #45: 'del_4q34.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.023

Table S169.  Gene #45: 'del_4q34.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 108 141
DEL PEAK 12(4Q34.3) MUTATED 40 39 84
DEL PEAK 12(4Q34.3) WILD-TYPE 79 69 57

Figure S169.  Get High-res Image Gene #45: 'del_4q34.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_4q34.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S170.  Gene #45: 'del_4q34.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 83 106
DEL PEAK 12(4Q34.3) MUTATED 65 29 69
DEL PEAK 12(4Q34.3) WILD-TYPE 114 54 37

Figure S170.  Get High-res Image Gene #45: 'del_4q34.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S171.  Gene #45: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 144 100
DEL PEAK 12(4Q34.3) MUTATED 23 85 37
DEL PEAK 12(4Q34.3) WILD-TYPE 54 59 63

Figure S171.  Get High-res Image Gene #45: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_4q34.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S172.  Gene #45: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 62 82
DEL PEAK 12(4Q34.3) MUTATED 69 20 56
DEL PEAK 12(4Q34.3) WILD-TYPE 108 42 26

Figure S172.  Get High-res Image Gene #45: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S173.  Gene #46: 'del_5q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
DEL PEAK 13(5Q11.2) MUTATED 13 13 34 5 69
DEL PEAK 13(5Q11.2) WILD-TYPE 156 20 32 5 22

Figure S173.  Get High-res Image Gene #46: 'del_5q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S174.  Gene #46: 'del_5q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
DEL PEAK 13(5Q11.2) MUTATED 32 67 21
DEL PEAK 13(5Q11.2) WILD-TYPE 88 25 88

Figure S174.  Get High-res Image Gene #46: 'del_5q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S175.  Gene #46: 'del_5q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
DEL PEAK 13(5Q11.2) MUTATED 17 4 11 14 44
DEL PEAK 13(5Q11.2) WILD-TYPE 48 58 35 23 18

Figure S175.  Get High-res Image Gene #46: 'del_5q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_5q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S176.  Gene #46: 'del_5q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 38 21 49 62 41 40 21
DEL PEAK 13(5Q11.2) MUTATED 12 4 3 23 18 28 2
DEL PEAK 13(5Q11.2) WILD-TYPE 26 17 46 39 23 12 19

Figure S176.  Get High-res Image Gene #46: 'del_5q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_5q11.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S177.  Gene #46: 'del_5q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 108 141
DEL PEAK 13(5Q11.2) MUTATED 38 18 78
DEL PEAK 13(5Q11.2) WILD-TYPE 81 90 63

Figure S177.  Get High-res Image Gene #46: 'del_5q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_5q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S178.  Gene #46: 'del_5q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 83 106
DEL PEAK 13(5Q11.2) MUTATED 53 14 67
DEL PEAK 13(5Q11.2) WILD-TYPE 126 69 39

Figure S178.  Get High-res Image Gene #46: 'del_5q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_5q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S179.  Gene #46: 'del_5q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 144 100
DEL PEAK 13(5Q11.2) MUTATED 22 82 17
DEL PEAK 13(5Q11.2) WILD-TYPE 55 62 83

Figure S179.  Get High-res Image Gene #46: 'del_5q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_5q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S180.  Gene #46: 'del_5q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 62 82
DEL PEAK 13(5Q11.2) MUTATED 55 6 60
DEL PEAK 13(5Q11.2) WILD-TYPE 122 56 22

Figure S180.  Get High-res Image Gene #46: 'del_5q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q23.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S181.  Gene #47: 'del_5q23.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
DEL PEAK 14(5Q23.2) MUTATED 10 13 26 5 68
DEL PEAK 14(5Q23.2) WILD-TYPE 159 20 40 5 23

Figure S181.  Get High-res Image Gene #47: 'del_5q23.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q23.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S182.  Gene #47: 'del_5q23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
DEL PEAK 14(5Q23.2) MUTATED 27 63 19
DEL PEAK 14(5Q23.2) WILD-TYPE 93 29 90

Figure S182.  Get High-res Image Gene #47: 'del_5q23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q23.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S183.  Gene #47: 'del_5q23.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
DEL PEAK 14(5Q23.2) MUTATED 15 3 10 11 42
DEL PEAK 14(5Q23.2) WILD-TYPE 50 59 36 26 20

Figure S183.  Get High-res Image Gene #47: 'del_5q23.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_5q23.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S184.  Gene #47: 'del_5q23.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 38 21 49 62 41 40 21
DEL PEAK 14(5Q23.2) MUTATED 7 5 2 21 17 27 2
DEL PEAK 14(5Q23.2) WILD-TYPE 31 16 47 41 24 13 19

Figure S184.  Get High-res Image Gene #47: 'del_5q23.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_5q23.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S185.  Gene #47: 'del_5q23.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 108 141
DEL PEAK 14(5Q23.2) MUTATED 30 15 76
DEL PEAK 14(5Q23.2) WILD-TYPE 89 93 65

Figure S185.  Get High-res Image Gene #47: 'del_5q23.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_5q23.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S186.  Gene #47: 'del_5q23.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 83 106
DEL PEAK 14(5Q23.2) MUTATED 49 10 62
DEL PEAK 14(5Q23.2) WILD-TYPE 130 73 44

Figure S186.  Get High-res Image Gene #47: 'del_5q23.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_5q23.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S187.  Gene #47: 'del_5q23.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 144 100
DEL PEAK 14(5Q23.2) MUTATED 16 77 16
DEL PEAK 14(5Q23.2) WILD-TYPE 61 67 84

Figure S187.  Get High-res Image Gene #47: 'del_5q23.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_5q23.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S188.  Gene #47: 'del_5q23.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 62 82
DEL PEAK 14(5Q23.2) MUTATED 50 4 55
DEL PEAK 14(5Q23.2) WILD-TYPE 127 58 27

Figure S188.  Get High-res Image Gene #47: 'del_5q23.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6p25.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S189.  Gene #48: 'del_6p25.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
DEL PEAK 15(6P25.3) MUTATED 17 8 29 1 38
DEL PEAK 15(6P25.3) WILD-TYPE 152 25 37 9 53

Figure S189.  Get High-res Image Gene #48: 'del_6p25.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_6p25.3' versus 'METHLYATION_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.11

Table S190.  Gene #48: 'del_6p25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
DEL PEAK 15(6P25.3) MUTATED 28 39 19
DEL PEAK 15(6P25.3) WILD-TYPE 92 53 90

Figure S190.  Get High-res Image Gene #48: 'del_6p25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6p25.3' versus 'MRNASEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.06

Table S191.  Gene #48: 'del_6p25.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
DEL PEAK 15(6P25.3) MUTATED 7 6 14 6 24
DEL PEAK 15(6P25.3) WILD-TYPE 58 56 32 31 38

Figure S191.  Get High-res Image Gene #48: 'del_6p25.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6p25.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.034

Table S192.  Gene #48: 'del_6p25.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 38 21 49 62 41 40 21
DEL PEAK 15(6P25.3) MUTATED 10 0 4 15 9 18 1
DEL PEAK 15(6P25.3) WILD-TYPE 28 21 45 47 32 22 20

Figure S192.  Get High-res Image Gene #48: 'del_6p25.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6p25.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S193.  Gene #48: 'del_6p25.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 83 106
DEL PEAK 15(6P25.3) MUTATED 38 11 44
DEL PEAK 15(6P25.3) WILD-TYPE 141 72 62

Figure S193.  Get High-res Image Gene #48: 'del_6p25.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_6p25.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00043 (Fisher's exact test), Q value = 0.21

Table S194.  Gene #48: 'del_6p25.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 62 82
DEL PEAK 15(6P25.3) MUTATED 49 6 31
DEL PEAK 15(6P25.3) WILD-TYPE 128 56 51

Figure S194.  Get High-res Image Gene #48: 'del_6p25.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q14.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S195.  Gene #49: 'del_6q14.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
DEL PEAK 16(6Q14.1) MUTATED 11 6 26 1 28
DEL PEAK 16(6Q14.1) WILD-TYPE 158 27 40 9 63

Figure S195.  Get High-res Image Gene #49: 'del_6q14.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q26' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S196.  Gene #50: 'del_6q26' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
DEL PEAK 17(6Q26) MUTATED 18 10 29 0 25
DEL PEAK 17(6Q26) WILD-TYPE 151 23 37 10 66

Figure S196.  Get High-res Image Gene #50: 'del_6q26' versus Molecular Subtype #1: 'CN_CNMF'

'del_7q31.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S197.  Gene #51: 'del_7q31.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
DEL PEAK 18(7Q31.1) MUTATED 8 2 19 1 24
DEL PEAK 18(7Q31.1) WILD-TYPE 161 31 47 9 67

Figure S197.  Get High-res Image Gene #51: 'del_7q31.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_7q31.1' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.023

Table S198.  Gene #51: 'del_7q31.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
DEL PEAK 18(7Q31.1) MUTATED 18 24 4
DEL PEAK 18(7Q31.1) WILD-TYPE 102 68 105

Figure S198.  Get High-res Image Gene #51: 'del_7q31.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_7q36.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S199.  Gene #52: 'del_7q36.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
DEL PEAK 19(7Q36.3) MUTATED 5 1 32 2 38
DEL PEAK 19(7Q36.3) WILD-TYPE 164 32 34 8 53

Figure S199.  Get High-res Image Gene #52: 'del_7q36.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_7q36.3' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S200.  Gene #52: 'del_7q36.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
DEL PEAK 19(7Q36.3) MUTATED 21 35 13
DEL PEAK 19(7Q36.3) WILD-TYPE 99 57 96

Figure S200.  Get High-res Image Gene #52: 'del_7q36.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_7q36.3' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S201.  Gene #52: 'del_7q36.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
DEL PEAK 19(7Q36.3) MUTATED 7 8 8 3 27
DEL PEAK 19(7Q36.3) WILD-TYPE 58 54 38 34 35

Figure S201.  Get High-res Image Gene #52: 'del_7q36.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_7q36.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00034 (Fisher's exact test), Q value = 0.17

Table S202.  Gene #52: 'del_7q36.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 38 21 49 62 41 40 21
DEL PEAK 19(7Q36.3) MUTATED 12 0 6 13 7 15 0
DEL PEAK 19(7Q36.3) WILD-TYPE 26 21 43 49 34 25 21

Figure S202.  Get High-res Image Gene #52: 'del_7q36.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_7q36.3' versus 'MIRSEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.11

Table S203.  Gene #52: 'del_7q36.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 108 141
DEL PEAK 19(7Q36.3) MUTATED 23 11 44
DEL PEAK 19(7Q36.3) WILD-TYPE 96 97 97

Figure S203.  Get High-res Image Gene #52: 'del_7q36.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_7q36.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S204.  Gene #52: 'del_7q36.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 83 106
DEL PEAK 19(7Q36.3) MUTATED 29 8 41
DEL PEAK 19(7Q36.3) WILD-TYPE 150 75 65

Figure S204.  Get High-res Image Gene #52: 'del_7q36.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_7q36.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S205.  Gene #52: 'del_7q36.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 62 82
DEL PEAK 19(7Q36.3) MUTATED 33 4 33
DEL PEAK 19(7Q36.3) WILD-TYPE 144 58 49

Figure S205.  Get High-res Image Gene #52: 'del_7q36.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p23.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S206.  Gene #53: 'del_8p23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
DEL PEAK 20(8P23.3) MUTATED 12 15 29 0 46
DEL PEAK 20(8P23.3) WILD-TYPE 157 18 37 10 45

Figure S206.  Get High-res Image Gene #53: 'del_8p23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p23.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S207.  Gene #53: 'del_8p23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
DEL PEAK 20(8P23.3) MUTATED 22 44 23
DEL PEAK 20(8P23.3) WILD-TYPE 98 48 86

Figure S207.  Get High-res Image Gene #53: 'del_8p23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_8p23.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S208.  Gene #53: 'del_8p23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
DEL PEAK 20(8P23.3) MUTATED 11 9 8 10 34
DEL PEAK 20(8P23.3) WILD-TYPE 54 53 38 27 28

Figure S208.  Get High-res Image Gene #53: 'del_8p23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_8p23.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S209.  Gene #53: 'del_8p23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 38 21 49 62 41 40 21
DEL PEAK 20(8P23.3) MUTATED 9 2 6 13 15 25 2
DEL PEAK 20(8P23.3) WILD-TYPE 29 19 43 49 26 15 19

Figure S209.  Get High-res Image Gene #53: 'del_8p23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S210.  Gene #53: 'del_8p23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 83 106
DEL PEAK 20(8P23.3) MUTATED 36 16 49
DEL PEAK 20(8P23.3) WILD-TYPE 143 67 57

Figure S210.  Get High-res Image Gene #53: 'del_8p23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_8p23.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.034

Table S211.  Gene #53: 'del_8p23.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 144 100
DEL PEAK 20(8P23.3) MUTATED 18 56 15
DEL PEAK 20(8P23.3) WILD-TYPE 59 88 85

Figure S211.  Get High-res Image Gene #53: 'del_8p23.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_8p23.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S212.  Gene #53: 'del_8p23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 62 82
DEL PEAK 20(8P23.3) MUTATED 40 8 41
DEL PEAK 20(8P23.3) WILD-TYPE 137 54 41

Figure S212.  Get High-res Image Gene #53: 'del_8p23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S213.  Gene #54: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
DEL PEAK 21(9P23) MUTATED 24 21 55 5 51
DEL PEAK 21(9P23) WILD-TYPE 145 12 11 5 40

Figure S213.  Get High-res Image Gene #54: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p23' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S214.  Gene #54: 'del_9p23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
DEL PEAK 21(9P23) MUTATED 40 58 39
DEL PEAK 21(9P23) WILD-TYPE 80 34 70

Figure S214.  Get High-res Image Gene #54: 'del_9p23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p23' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S215.  Gene #54: 'del_9p23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
DEL PEAK 21(9P23) MUTATED 14 18 23 13 40
DEL PEAK 21(9P23) WILD-TYPE 51 44 23 24 22

Figure S215.  Get High-res Image Gene #54: 'del_9p23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S216.  Gene #55: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
DEL PEAK 22(9P21.3) MUTATED 23 19 54 6 51
DEL PEAK 22(9P21.3) WILD-TYPE 146 14 12 4 40

Figure S216.  Get High-res Image Gene #55: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S217.  Gene #55: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
DEL PEAK 22(9P21.3) MUTATED 36 61 38
DEL PEAK 22(9P21.3) WILD-TYPE 84 31 71

Figure S217.  Get High-res Image Gene #55: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p21.3' versus 'RPPA_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.039

Table S218.  Gene #55: 'del_9p21.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 82 90 91
DEL PEAK 22(9P21.3) MUTATED 17 41 47
DEL PEAK 22(9P21.3) WILD-TYPE 65 49 44

Figure S218.  Get High-res Image Gene #55: 'del_9p21.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_9p21.3' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S219.  Gene #55: 'del_9p21.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 83 55 91
DEL PEAK 22(9P21.3) MUTATED 8 45 10 42
DEL PEAK 22(9P21.3) WILD-TYPE 26 38 45 49

Figure S219.  Get High-res Image Gene #55: 'del_9p21.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S220.  Gene #55: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
DEL PEAK 22(9P21.3) MUTATED 9 18 23 15 43
DEL PEAK 22(9P21.3) WILD-TYPE 56 44 23 22 19

Figure S220.  Get High-res Image Gene #55: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S221.  Gene #55: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 38 21 49 62 41 40 21
DEL PEAK 22(9P21.3) MUTATED 19 1 11 30 18 27 2
DEL PEAK 22(9P21.3) WILD-TYPE 19 20 38 32 23 13 19

Figure S221.  Get High-res Image Gene #55: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.023

Table S222.  Gene #55: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 62 82
DEL PEAK 22(9P21.3) MUTATED 63 20 52
DEL PEAK 22(9P21.3) WILD-TYPE 114 42 30

Figure S222.  Get High-res Image Gene #55: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9q21.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S223.  Gene #56: 'del_9q21.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
DEL PEAK 23(9Q21.11) MUTATED 11 11 34 2 35
DEL PEAK 23(9Q21.11) WILD-TYPE 158 22 32 8 56

Figure S223.  Get High-res Image Gene #56: 'del_9q21.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_9q21.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00049 (Fisher's exact test), Q value = 0.24

Table S224.  Gene #56: 'del_9q21.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 83 106
DEL PEAK 23(9Q21.11) MUTATED 34 17 42
DEL PEAK 23(9Q21.11) WILD-TYPE 145 66 64

Figure S224.  Get High-res Image Gene #56: 'del_9q21.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_9q21.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.12

Table S225.  Gene #56: 'del_9q21.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 62 82
DEL PEAK 23(9Q21.11) MUTATED 38 10 36
DEL PEAK 23(9Q21.11) WILD-TYPE 139 52 46

Figure S225.  Get High-res Image Gene #56: 'del_9q21.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10p15.3' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.018

Table S226.  Gene #57: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
DEL PEAK 24(10P15.3) MUTATED 11 8 17 2 24
DEL PEAK 24(10P15.3) WILD-TYPE 158 25 49 8 67

Figure S226.  Get High-res Image Gene #57: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S227.  Gene #58: 'del_10q22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
DEL PEAK 25(10Q22.3) MUTATED 6 14 7 3 31
DEL PEAK 25(10Q22.3) WILD-TYPE 163 19 59 7 60

Figure S227.  Get High-res Image Gene #58: 'del_10q22.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q22.3' versus 'MRNASEQ_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.096

Table S228.  Gene #58: 'del_10q22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
DEL PEAK 25(10Q22.3) MUTATED 7 2 4 8 19
DEL PEAK 25(10Q22.3) WILD-TYPE 58 60 42 29 43

Figure S228.  Get High-res Image Gene #58: 'del_10q22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10q22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00035 (Fisher's exact test), Q value = 0.17

Table S229.  Gene #58: 'del_10q22.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 38 21 49 62 41 40 21
DEL PEAK 25(10Q22.3) MUTATED 2 1 3 8 14 11 1
DEL PEAK 25(10Q22.3) WILD-TYPE 36 20 46 54 27 29 20

Figure S229.  Get High-res Image Gene #58: 'del_10q22.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10q22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.11

Table S230.  Gene #58: 'del_10q22.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 62 82
DEL PEAK 25(10Q22.3) MUTATED 27 2 23
DEL PEAK 25(10Q22.3) WILD-TYPE 150 60 59

Figure S230.  Get High-res Image Gene #58: 'del_10q22.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q23.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S231.  Gene #59: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
DEL PEAK 26(10Q23.31) MUTATED 11 13 15 4 47
DEL PEAK 26(10Q23.31) WILD-TYPE 158 20 51 6 44

Figure S231.  Get High-res Image Gene #59: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q23.31' versus 'METHLYATION_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.081

Table S232.  Gene #59: 'del_10q23.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
DEL PEAK 26(10Q23.31) MUTATED 22 37 17
DEL PEAK 26(10Q23.31) WILD-TYPE 98 55 92

Figure S232.  Get High-res Image Gene #59: 'del_10q23.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q23.31' versus 'RPPA_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.1

Table S233.  Gene #59: 'del_10q23.31' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 83 55 91
DEL PEAK 26(10Q23.31) MUTATED 7 34 8 13
DEL PEAK 26(10Q23.31) WILD-TYPE 27 49 47 78

Figure S233.  Get High-res Image Gene #59: 'del_10q23.31' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_10q23.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S234.  Gene #59: 'del_10q23.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
DEL PEAK 26(10Q23.31) MUTATED 8 4 9 12 28
DEL PEAK 26(10Q23.31) WILD-TYPE 57 58 37 25 34

Figure S234.  Get High-res Image Gene #59: 'del_10q23.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S235.  Gene #59: 'del_10q23.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 38 21 49 62 41 40 21
DEL PEAK 26(10Q23.31) MUTATED 2 3 4 16 18 17 1
DEL PEAK 26(10Q23.31) WILD-TYPE 36 18 45 46 23 23 20

Figure S235.  Get High-res Image Gene #59: 'del_10q23.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.071

Table S236.  Gene #59: 'del_10q23.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 108 141
DEL PEAK 26(10Q23.31) MUTATED 28 13 49
DEL PEAK 26(10Q23.31) WILD-TYPE 91 95 92

Figure S236.  Get High-res Image Gene #59: 'del_10q23.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_10q23.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.034

Table S237.  Gene #59: 'del_10q23.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 83 106
DEL PEAK 26(10Q23.31) MUTATED 43 8 39
DEL PEAK 26(10Q23.31) WILD-TYPE 136 75 67

Figure S237.  Get High-res Image Gene #59: 'del_10q23.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S238.  Gene #59: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 62 82
DEL PEAK 26(10Q23.31) MUTATED 40 3 33
DEL PEAK 26(10Q23.31) WILD-TYPE 137 59 49

Figure S238.  Get High-res Image Gene #59: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11p15.4' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S239.  Gene #60: 'del_11p15.4' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
DEL PEAK 27(11P15.4) MUTATED 10 6 21 2 40
DEL PEAK 27(11P15.4) WILD-TYPE 159 27 45 8 51

Figure S239.  Get High-res Image Gene #60: 'del_11p15.4' versus Molecular Subtype #1: 'CN_CNMF'

'del_11p15.4' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S240.  Gene #60: 'del_11p15.4' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
DEL PEAK 27(11P15.4) MUTATED 16 35 14
DEL PEAK 27(11P15.4) WILD-TYPE 104 57 95

Figure S240.  Get High-res Image Gene #60: 'del_11p15.4' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11p15.4' versus 'RPPA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S241.  Gene #60: 'del_11p15.4' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 82 90 91
DEL PEAK 27(11P15.4) MUTATED 6 15 35
DEL PEAK 27(11P15.4) WILD-TYPE 76 75 56

Figure S241.  Get High-res Image Gene #60: 'del_11p15.4' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_11p15.4' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.045

Table S242.  Gene #60: 'del_11p15.4' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 83 106
DEL PEAK 27(11P15.4) MUTATED 31 10 38
DEL PEAK 27(11P15.4) WILD-TYPE 148 73 68

Figure S242.  Get High-res Image Gene #60: 'del_11p15.4' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_11q23.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S243.  Gene #61: 'del_11q23.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
DEL PEAK 28(11Q23.2) MUTATED 17 8 24 2 31
DEL PEAK 28(11Q23.2) WILD-TYPE 152 25 42 8 60

Figure S243.  Get High-res Image Gene #61: 'del_11q23.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q23.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.065

Table S244.  Gene #61: 'del_11q23.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 38 21 49 62 41 40 21
DEL PEAK 28(11Q23.2) MUTATED 4 1 7 24 7 12 0
DEL PEAK 28(11Q23.2) WILD-TYPE 34 20 42 38 34 28 21

Figure S244.  Get High-res Image Gene #61: 'del_11q23.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_12p13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S245.  Gene #62: 'del_12p13.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
DEL PEAK 29(12P13.1) MUTATED 4 2 13 4 34
DEL PEAK 29(12P13.1) WILD-TYPE 165 31 53 6 57

Figure S245.  Get High-res Image Gene #62: 'del_12p13.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_12p13.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S246.  Gene #62: 'del_12p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
DEL PEAK 29(12P13.1) MUTATED 10 33 6
DEL PEAK 29(12P13.1) WILD-TYPE 110 59 103

Figure S246.  Get High-res Image Gene #62: 'del_12p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_12p13.1' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.018

Table S247.  Gene #62: 'del_12p13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
DEL PEAK 29(12P13.1) MUTATED 4 5 5 4 23
DEL PEAK 29(12P13.1) WILD-TYPE 61 57 41 33 39

Figure S247.  Get High-res Image Gene #62: 'del_12p13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_12p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.018

Table S248.  Gene #62: 'del_12p13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 38 21 49 62 41 40 21
DEL PEAK 29(12P13.1) MUTATED 7 0 3 8 6 17 0
DEL PEAK 29(12P13.1) WILD-TYPE 31 21 46 54 35 23 21

Figure S248.  Get High-res Image Gene #62: 'del_12p13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_12p13.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.029

Table S249.  Gene #62: 'del_12p13.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 62 82
DEL PEAK 29(12P13.1) MUTATED 21 3 25
DEL PEAK 29(12P13.1) WILD-TYPE 156 59 57

Figure S249.  Get High-res Image Gene #62: 'del_12p13.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_13q12.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S250.  Gene #63: 'del_13q12.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
DEL PEAK 30(13Q12.11) MUTATED 7 1 23 2 19
DEL PEAK 30(13Q12.11) WILD-TYPE 162 32 43 8 72

Figure S250.  Get High-res Image Gene #63: 'del_13q12.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q23.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S251.  Gene #64: 'del_14q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
DEL PEAK 31(14Q23.3) MUTATED 19 9 34 4 42
DEL PEAK 31(14Q23.3) WILD-TYPE 150 24 32 6 49

Figure S251.  Get High-res Image Gene #64: 'del_14q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q23.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S252.  Gene #64: 'del_14q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
DEL PEAK 31(14Q23.3) MUTATED 26 46 23
DEL PEAK 31(14Q23.3) WILD-TYPE 94 46 86

Figure S252.  Get High-res Image Gene #64: 'del_14q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_14q23.3' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.023

Table S253.  Gene #64: 'del_14q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
DEL PEAK 31(14Q23.3) MUTATED 11 14 13 6 33
DEL PEAK 31(14Q23.3) WILD-TYPE 54 48 33 31 29

Figure S253.  Get High-res Image Gene #64: 'del_14q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_14q23.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00043 (Fisher's exact test), Q value = 0.21

Table S254.  Gene #64: 'del_14q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 38 21 49 62 41 40 21
DEL PEAK 31(14Q23.3) MUTATED 9 5 10 15 10 25 3
DEL PEAK 31(14Q23.3) WILD-TYPE 29 16 39 47 31 15 18

Figure S254.  Get High-res Image Gene #64: 'del_14q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_14q23.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.018

Table S255.  Gene #64: 'del_14q23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 83 106
DEL PEAK 31(14Q23.3) MUTATED 40 18 50
DEL PEAK 31(14Q23.3) WILD-TYPE 139 65 56

Figure S255.  Get High-res Image Gene #64: 'del_14q23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_14q23.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.065

Table S256.  Gene #64: 'del_14q23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 62 82
DEL PEAK 31(14Q23.3) MUTATED 44 12 39
DEL PEAK 31(14Q23.3) WILD-TYPE 133 50 43

Figure S256.  Get High-res Image Gene #64: 'del_14q23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_14q32.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S257.  Gene #65: 'del_14q32.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
DEL PEAK 32(14Q32.33) MUTATED 21 9 36 2 38
DEL PEAK 32(14Q32.33) WILD-TYPE 148 24 30 8 53

Figure S257.  Get High-res Image Gene #65: 'del_14q32.33' versus Molecular Subtype #1: 'CN_CNMF'

'del_15q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S258.  Gene #66: 'del_15q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
DEL PEAK 33(15Q11.2) MUTATED 12 13 25 4 47
DEL PEAK 33(15Q11.2) WILD-TYPE 157 20 41 6 44

Figure S258.  Get High-res Image Gene #66: 'del_15q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_15q11.2' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.018

Table S259.  Gene #66: 'del_15q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
DEL PEAK 33(15Q11.2) MUTATED 25 44 22
DEL PEAK 33(15Q11.2) WILD-TYPE 95 48 87

Figure S259.  Get High-res Image Gene #66: 'del_15q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_15q11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S260.  Gene #66: 'del_15q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
DEL PEAK 33(15Q11.2) MUTATED 9 3 15 8 31
DEL PEAK 33(15Q11.2) WILD-TYPE 56 59 31 29 31

Figure S260.  Get High-res Image Gene #66: 'del_15q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_15q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S261.  Gene #66: 'del_15q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 38 21 49 62 41 40 21
DEL PEAK 33(15Q11.2) MUTATED 8 3 2 19 16 17 1
DEL PEAK 33(15Q11.2) WILD-TYPE 30 18 47 43 25 23 20

Figure S261.  Get High-res Image Gene #66: 'del_15q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_15q11.2' versus 'MIRSEQ_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.12

Table S262.  Gene #66: 'del_15q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 108 141
DEL PEAK 33(15Q11.2) MUTATED 28 18 55
DEL PEAK 33(15Q11.2) WILD-TYPE 91 90 86

Figure S262.  Get High-res Image Gene #66: 'del_15q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_15q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S263.  Gene #66: 'del_15q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 83 106
DEL PEAK 33(15Q11.2) MUTATED 44 10 47
DEL PEAK 33(15Q11.2) WILD-TYPE 135 73 59

Figure S263.  Get High-res Image Gene #66: 'del_15q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_15q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S264.  Gene #66: 'del_15q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 144 100
DEL PEAK 33(15Q11.2) MUTATED 16 61 14
DEL PEAK 33(15Q11.2) WILD-TYPE 61 83 86

Figure S264.  Get High-res Image Gene #66: 'del_15q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_15q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S265.  Gene #66: 'del_15q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 62 82
DEL PEAK 33(15Q11.2) MUTATED 49 4 38
DEL PEAK 33(15Q11.2) WILD-TYPE 128 58 44

Figure S265.  Get High-res Image Gene #66: 'del_15q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_15q15.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S266.  Gene #67: 'del_15q15.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
DEL PEAK 34(15Q15.1) MUTATED 13 12 27 4 47
DEL PEAK 34(15Q15.1) WILD-TYPE 156 21 39 6 44

Figure S266.  Get High-res Image Gene #67: 'del_15q15.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_15q15.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S267.  Gene #67: 'del_15q15.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
DEL PEAK 34(15Q15.1) MUTATED 24 46 20
DEL PEAK 34(15Q15.1) WILD-TYPE 96 46 89

Figure S267.  Get High-res Image Gene #67: 'del_15q15.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_15q15.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S268.  Gene #67: 'del_15q15.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
DEL PEAK 34(15Q15.1) MUTATED 11 3 16 7 31
DEL PEAK 34(15Q15.1) WILD-TYPE 54 59 30 30 31

Figure S268.  Get High-res Image Gene #67: 'del_15q15.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_15q15.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S269.  Gene #67: 'del_15q15.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 38 21 49 62 41 40 21
DEL PEAK 34(15Q15.1) MUTATED 10 4 1 19 14 19 1
DEL PEAK 34(15Q15.1) WILD-TYPE 28 17 48 43 27 21 20

Figure S269.  Get High-res Image Gene #67: 'del_15q15.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_15q15.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S270.  Gene #67: 'del_15q15.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 83 106
DEL PEAK 34(15Q15.1) MUTATED 46 9 48
DEL PEAK 34(15Q15.1) WILD-TYPE 133 74 58

Figure S270.  Get High-res Image Gene #67: 'del_15q15.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_15q15.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S271.  Gene #67: 'del_15q15.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 144 100
DEL PEAK 34(15Q15.1) MUTATED 18 59 13
DEL PEAK 34(15Q15.1) WILD-TYPE 59 85 87

Figure S271.  Get High-res Image Gene #67: 'del_15q15.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_15q15.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S272.  Gene #67: 'del_15q15.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 62 82
DEL PEAK 34(15Q15.1) MUTATED 49 4 37
DEL PEAK 34(15Q15.1) WILD-TYPE 128 58 45

Figure S272.  Get High-res Image Gene #67: 'del_15q15.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S273.  Gene #68: 'del_16p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
DEL PEAK 35(16P13.3) MUTATED 7 4 23 0 41
DEL PEAK 35(16P13.3) WILD-TYPE 162 29 43 10 50

Figure S273.  Get High-res Image Gene #68: 'del_16p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_16p13.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S274.  Gene #68: 'del_16p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
DEL PEAK 35(16P13.3) MUTATED 8 6 4 3 29
DEL PEAK 35(16P13.3) WILD-TYPE 57 56 42 34 33

Figure S274.  Get High-res Image Gene #68: 'del_16p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S275.  Gene #68: 'del_16p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 38 21 49 62 41 40 21
DEL PEAK 35(16P13.3) MUTATED 8 0 4 7 6 22 3
DEL PEAK 35(16P13.3) WILD-TYPE 30 21 45 55 35 18 18

Figure S275.  Get High-res Image Gene #68: 'del_16p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_16p13.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S276.  Gene #68: 'del_16p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 108 141
DEL PEAK 35(16P13.3) MUTATED 13 14 48
DEL PEAK 35(16P13.3) WILD-TYPE 106 94 93

Figure S276.  Get High-res Image Gene #68: 'del_16p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_16p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.029

Table S277.  Gene #68: 'del_16p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 83 106
DEL PEAK 35(16P13.3) MUTATED 27 10 38
DEL PEAK 35(16P13.3) WILD-TYPE 152 73 68

Figure S277.  Get High-res Image Gene #68: 'del_16p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_16p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S278.  Gene #68: 'del_16p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 144 100
DEL PEAK 35(16P13.3) MUTATED 5 47 15
DEL PEAK 35(16P13.3) WILD-TYPE 72 97 85

Figure S278.  Get High-res Image Gene #68: 'del_16p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_16p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S279.  Gene #68: 'del_16p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 62 82
DEL PEAK 35(16P13.3) MUTATED 28 5 34
DEL PEAK 35(16P13.3) WILD-TYPE 149 57 48

Figure S279.  Get High-res Image Gene #68: 'del_16p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q23.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S280.  Gene #69: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
DEL PEAK 36(16Q23.1) MUTATED 37 16 36 3 54
DEL PEAK 36(16Q23.1) WILD-TYPE 132 17 30 7 37

Figure S280.  Get High-res Image Gene #69: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.029

Table S281.  Gene #69: 'del_16q23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 144 100
DEL PEAK 36(16Q23.1) MUTATED 28 74 24
DEL PEAK 36(16Q23.1) WILD-TYPE 49 70 76

Figure S281.  Get High-res Image Gene #69: 'del_16q23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_17p12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S282.  Gene #70: 'del_17p12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
DEL PEAK 37(17P12) MUTATED 13 21 40 3 64
DEL PEAK 37(17P12) WILD-TYPE 156 12 26 7 27

Figure S282.  Get High-res Image Gene #70: 'del_17p12' versus Molecular Subtype #1: 'CN_CNMF'

'del_17p12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S283.  Gene #70: 'del_17p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
DEL PEAK 37(17P12) MUTATED 36 66 23
DEL PEAK 37(17P12) WILD-TYPE 84 26 86

Figure S283.  Get High-res Image Gene #70: 'del_17p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17p12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S284.  Gene #70: 'del_17p12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
DEL PEAK 37(17P12) MUTATED 15 10 19 12 42
DEL PEAK 37(17P12) WILD-TYPE 50 52 27 25 20

Figure S284.  Get High-res Image Gene #70: 'del_17p12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_17p12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S285.  Gene #70: 'del_17p12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 38 21 49 62 41 40 21
DEL PEAK 37(17P12) MUTATED 14 2 7 25 17 30 3
DEL PEAK 37(17P12) WILD-TYPE 24 19 42 37 24 10 18

Figure S285.  Get High-res Image Gene #70: 'del_17p12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_17p12' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.023

Table S286.  Gene #70: 'del_17p12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 108 141
DEL PEAK 37(17P12) MUTATED 44 24 72
DEL PEAK 37(17P12) WILD-TYPE 75 84 69

Figure S286.  Get High-res Image Gene #70: 'del_17p12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_17p12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S287.  Gene #70: 'del_17p12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 83 106
DEL PEAK 37(17P12) MUTATED 60 18 62
DEL PEAK 37(17P12) WILD-TYPE 119 65 44

Figure S287.  Get High-res Image Gene #70: 'del_17p12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_17p12' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S288.  Gene #70: 'del_17p12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 144 100
DEL PEAK 37(17P12) MUTATED 26 77 22
DEL PEAK 37(17P12) WILD-TYPE 51 67 78

Figure S288.  Get High-res Image Gene #70: 'del_17p12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_17p12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S289.  Gene #70: 'del_17p12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 62 82
DEL PEAK 37(17P12) MUTATED 61 10 54
DEL PEAK 37(17P12) WILD-TYPE 116 52 28

Figure S289.  Get High-res Image Gene #70: 'del_17p12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17q24.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S290.  Gene #71: 'del_17q24.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
DEL PEAK 38(17Q24.3) MUTATED 7 9 16 3 33
DEL PEAK 38(17Q24.3) WILD-TYPE 162 24 50 7 58

Figure S290.  Get High-res Image Gene #71: 'del_17q24.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_17q24.3' versus 'METHLYATION_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.06

Table S291.  Gene #71: 'del_17q24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
DEL PEAK 38(17Q24.3) MUTATED 18 29 9
DEL PEAK 38(17Q24.3) WILD-TYPE 102 63 100

Figure S291.  Get High-res Image Gene #71: 'del_17q24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17q24.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00041 (Fisher's exact test), Q value = 0.2

Table S292.  Gene #71: 'del_17q24.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 83 106
DEL PEAK 38(17Q24.3) MUTATED 24 10 33
DEL PEAK 38(17Q24.3) WILD-TYPE 155 73 73

Figure S292.  Get High-res Image Gene #71: 'del_17q24.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_18q21.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S293.  Gene #72: 'del_18q21.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
DEL PEAK 39(18Q21.2) MUTATED 34 23 46 2 64
DEL PEAK 39(18Q21.2) WILD-TYPE 135 10 20 8 27

Figure S293.  Get High-res Image Gene #72: 'del_18q21.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_18q21.2' versus 'METHLYATION_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.22

Table S294.  Gene #72: 'del_18q21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
DEL PEAK 39(18Q21.2) MUTATED 48 58 41
DEL PEAK 39(18Q21.2) WILD-TYPE 72 34 68

Figure S294.  Get High-res Image Gene #72: 'del_18q21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_18q21.2' versus 'MRNASEQ_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.16

Table S295.  Gene #72: 'del_18q21.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
DEL PEAK 39(18Q21.2) MUTATED 26 19 23 11 41
DEL PEAK 39(18Q21.2) WILD-TYPE 39 43 23 26 21

Figure S295.  Get High-res Image Gene #72: 'del_18q21.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_18q21.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.11

Table S296.  Gene #72: 'del_18q21.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 144 100
DEL PEAK 39(18Q21.2) MUTATED 30 84 33
DEL PEAK 39(18Q21.2) WILD-TYPE 47 60 67

Figure S296.  Get High-res Image Gene #72: 'del_18q21.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_19p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S297.  Gene #73: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
DEL PEAK 40(19P13.3) MUTATED 7 13 35 4 68
DEL PEAK 40(19P13.3) WILD-TYPE 162 20 31 6 23

Figure S297.  Get High-res Image Gene #73: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_19p13.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S298.  Gene #73: 'del_19p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
DEL PEAK 40(19P13.3) MUTATED 26 63 22
DEL PEAK 40(19P13.3) WILD-TYPE 94 29 87

Figure S298.  Get High-res Image Gene #73: 'del_19p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19p13.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S299.  Gene #73: 'del_19p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
DEL PEAK 40(19P13.3) MUTATED 13 4 13 8 47
DEL PEAK 40(19P13.3) WILD-TYPE 52 58 33 29 15

Figure S299.  Get High-res Image Gene #73: 'del_19p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_19p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S300.  Gene #73: 'del_19p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 38 21 49 62 41 40 21
DEL PEAK 40(19P13.3) MUTATED 14 2 4 21 12 30 2
DEL PEAK 40(19P13.3) WILD-TYPE 24 19 45 41 29 10 19

Figure S300.  Get High-res Image Gene #73: 'del_19p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S301.  Gene #73: 'del_19p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 108 141
DEL PEAK 40(19P13.3) MUTATED 32 16 78
DEL PEAK 40(19P13.3) WILD-TYPE 87 92 63

Figure S301.  Get High-res Image Gene #73: 'del_19p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_19p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S302.  Gene #73: 'del_19p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 83 106
DEL PEAK 40(19P13.3) MUTATED 42 9 75
DEL PEAK 40(19P13.3) WILD-TYPE 137 74 31

Figure S302.  Get High-res Image Gene #73: 'del_19p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S303.  Gene #73: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 144 100
DEL PEAK 40(19P13.3) MUTATED 18 74 19
DEL PEAK 40(19P13.3) WILD-TYPE 59 70 81

Figure S303.  Get High-res Image Gene #73: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_19p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S304.  Gene #73: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 62 82
DEL PEAK 40(19P13.3) MUTATED 48 4 59
DEL PEAK 40(19P13.3) WILD-TYPE 129 58 23

Figure S304.  Get High-res Image Gene #73: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19q13.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S305.  Gene #74: 'del_19q13.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
DEL PEAK 41(19Q13.11) MUTATED 4 5 15 4 29
DEL PEAK 41(19Q13.11) WILD-TYPE 165 28 51 6 62

Figure S305.  Get High-res Image Gene #74: 'del_19q13.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_19q13.11' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S306.  Gene #74: 'del_19q13.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
DEL PEAK 41(19Q13.11) MUTATED 14 33 3
DEL PEAK 41(19Q13.11) WILD-TYPE 106 59 106

Figure S306.  Get High-res Image Gene #74: 'del_19q13.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19q13.11' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S307.  Gene #74: 'del_19q13.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
DEL PEAK 41(19Q13.11) MUTATED 6 2 6 3 21
DEL PEAK 41(19Q13.11) WILD-TYPE 59 60 40 34 41

Figure S307.  Get High-res Image Gene #74: 'del_19q13.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_19q13.11' versus 'MIRSEQ_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.12

Table S308.  Gene #74: 'del_19q13.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 108 141
DEL PEAK 41(19Q13.11) MUTATED 15 7 35
DEL PEAK 41(19Q13.11) WILD-TYPE 104 101 106

Figure S308.  Get High-res Image Gene #74: 'del_19q13.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_19q13.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S309.  Gene #74: 'del_19q13.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 83 106
DEL PEAK 41(19Q13.11) MUTATED 19 5 33
DEL PEAK 41(19Q13.11) WILD-TYPE 160 78 73

Figure S309.  Get High-res Image Gene #74: 'del_19q13.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_19q13.11' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.14

Table S310.  Gene #74: 'del_19q13.11' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 144 100
DEL PEAK 41(19Q13.11) MUTATED 9 35 6
DEL PEAK 41(19Q13.11) WILD-TYPE 68 109 94

Figure S310.  Get High-res Image Gene #74: 'del_19q13.11' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_19q13.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.034

Table S311.  Gene #74: 'del_19q13.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 62 82
DEL PEAK 41(19Q13.11) MUTATED 22 3 25
DEL PEAK 41(19Q13.11) WILD-TYPE 155 59 57

Figure S311.  Get High-res Image Gene #74: 'del_19q13.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_21q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S312.  Gene #76: 'del_21q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
DEL PEAK 43(21Q11.2) MUTATED 27 18 40 7 48
DEL PEAK 43(21Q11.2) WILD-TYPE 142 15 26 3 43

Figure S312.  Get High-res Image Gene #76: 'del_21q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_21q11.2' versus 'METHLYATION_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.14

Table S313.  Gene #76: 'del_21q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
DEL PEAK 43(21Q11.2) MUTATED 39 52 34
DEL PEAK 43(21Q11.2) WILD-TYPE 81 40 75

Figure S313.  Get High-res Image Gene #76: 'del_21q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_21q11.2' versus 'MIRSEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.034

Table S314.  Gene #76: 'del_21q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 108 141
DEL PEAK 43(21Q11.2) MUTATED 36 30 74
DEL PEAK 43(21Q11.2) WILD-TYPE 83 78 67

Figure S314.  Get High-res Image Gene #76: 'del_21q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_21q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.023

Table S315.  Gene #76: 'del_21q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 144 100
DEL PEAK 43(21Q11.2) MUTATED 20 75 30
DEL PEAK 43(21Q11.2) WILD-TYPE 57 69 70

Figure S315.  Get High-res Image Gene #76: 'del_21q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_21q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00032 (Fisher's exact test), Q value = 0.16

Table S316.  Gene #76: 'del_21q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 62 82
DEL PEAK 43(21Q11.2) MUTATED 61 17 47
DEL PEAK 43(21Q11.2) WILD-TYPE 116 45 35

Figure S316.  Get High-res Image Gene #76: 'del_21q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_21q22.13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S317.  Gene #77: 'del_21q22.13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
DEL PEAK 44(21Q22.13) MUTATED 30 17 46 7 52
DEL PEAK 44(21Q22.13) WILD-TYPE 139 16 20 3 39

Figure S317.  Get High-res Image Gene #77: 'del_21q22.13' versus Molecular Subtype #1: 'CN_CNMF'

'del_21q22.13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00037 (Fisher's exact test), Q value = 0.18

Table S318.  Gene #77: 'del_21q22.13' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 38 21 49 62 41 40 21
DEL PEAK 44(21Q22.13) MUTATED 19 2 16 20 17 24 3
DEL PEAK 44(21Q22.13) WILD-TYPE 19 19 33 42 24 16 18

Figure S318.  Get High-res Image Gene #77: 'del_21q22.13' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_21q22.13' versus 'MIRSEQ_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.12

Table S319.  Gene #77: 'del_21q22.13' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 108 141
DEL PEAK 44(21Q22.13) MUTATED 41 34 77
DEL PEAK 44(21Q22.13) WILD-TYPE 78 74 64

Figure S319.  Get High-res Image Gene #77: 'del_21q22.13' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_21q22.13' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.023

Table S320.  Gene #77: 'del_21q22.13' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 144 100
DEL PEAK 44(21Q22.13) MUTATED 24 79 31
DEL PEAK 44(21Q22.13) WILD-TYPE 53 65 69

Figure S320.  Get High-res Image Gene #77: 'del_21q22.13' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_22q13.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S321.  Gene #78: 'del_22q13.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
DEL PEAK 45(22Q13.31) MUTATED 17 10 42 6 54
DEL PEAK 45(22Q13.31) WILD-TYPE 152 23 24 4 37

Figure S321.  Get High-res Image Gene #78: 'del_22q13.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q13.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S322.  Gene #78: 'del_22q13.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
DEL PEAK 45(22Q13.31) MUTATED 35 55 22
DEL PEAK 45(22Q13.31) WILD-TYPE 85 37 87

Figure S322.  Get High-res Image Gene #78: 'del_22q13.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_22q13.31' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.018

Table S323.  Gene #78: 'del_22q13.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 108 141
DEL PEAK 45(22Q13.31) MUTATED 31 27 70
DEL PEAK 45(22Q13.31) WILD-TYPE 88 81 71

Figure S323.  Get High-res Image Gene #78: 'del_22q13.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_22q13.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S324.  Gene #78: 'del_22q13.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 83 106
DEL PEAK 45(22Q13.31) MUTATED 48 19 61
DEL PEAK 45(22Q13.31) WILD-TYPE 131 64 45

Figure S324.  Get High-res Image Gene #78: 'del_22q13.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_22q13.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S325.  Gene #78: 'del_22q13.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 62 82
DEL PEAK 45(22Q13.31) MUTATED 55 11 46
DEL PEAK 45(22Q13.31) WILD-TYPE 122 51 36

Figure S325.  Get High-res Image Gene #78: 'del_22q13.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xp22.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S326.  Gene #79: 'del_xp22.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
DEL PEAK 46(XP22.2) MUTATED 6 6 21 3 31
DEL PEAK 46(XP22.2) WILD-TYPE 163 27 45 7 60

Figure S326.  Get High-res Image Gene #79: 'del_xp22.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_xp22.2' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S327.  Gene #79: 'del_xp22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
DEL PEAK 46(XP22.2) MUTATED 17 34 10
DEL PEAK 46(XP22.2) WILD-TYPE 103 58 99

Figure S327.  Get High-res Image Gene #79: 'del_xp22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xp22.2' versus 'MRNASEQ_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.1

Table S328.  Gene #79: 'del_xp22.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
DEL PEAK 46(XP22.2) MUTATED 3 8 8 10 21
DEL PEAK 46(XP22.2) WILD-TYPE 62 54 38 27 41

Figure S328.  Get High-res Image Gene #79: 'del_xp22.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_xp22.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.12

Table S329.  Gene #79: 'del_xp22.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 38 21 49 62 41 40 21
DEL PEAK 46(XP22.2) MUTATED 11 0 5 10 15 9 0
DEL PEAK 46(XP22.2) WILD-TYPE 27 21 44 52 26 31 21

Figure S329.  Get High-res Image Gene #79: 'del_xp22.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_xp22.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.086

Table S330.  Gene #79: 'del_xp22.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 177 62 82
DEL PEAK 46(XP22.2) MUTATED 27 6 29
DEL PEAK 46(XP22.2) WILD-TYPE 150 56 53

Figure S330.  Get High-res Image Gene #79: 'del_xp22.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xp21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S331.  Gene #80: 'del_xp21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
DEL PEAK 47(XP21.1) MUTATED 6 8 21 2 27
DEL PEAK 47(XP21.1) WILD-TYPE 163 25 45 8 64

Figure S331.  Get High-res Image Gene #80: 'del_xp21.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_xq21.33' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.018

Table S332.  Gene #81: 'del_xq21.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 33 66 10 91
DEL PEAK 48(XQ21.33) MUTATED 6 6 14 0 20
DEL PEAK 48(XQ21.33) WILD-TYPE 163 27 52 10 71

Figure S332.  Get High-res Image Gene #81: 'del_xq21.33' versus Molecular Subtype #1: 'CN_CNMF'

'del_xq21.33' versus 'METHLYATION_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.11

Table S333.  Gene #81: 'del_xq21.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 92 109
DEL PEAK 48(XQ21.33) MUTATED 12 21 5
DEL PEAK 48(XQ21.33) WILD-TYPE 108 71 104

Figure S333.  Get High-res Image Gene #81: 'del_xq21.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

Methods & Data
Input
  • Copy number data file = transformed.cor.cli.txt

  • Molecular subtype file = STAD-TP.transferedmergedcluster.txt

  • Number of patients = 369

  • Number of significantly focal cnvs = 81

  • Number of molecular subtypes = 10

  • Exclude genes that fewer than K tumors have alterations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)