Correlation between copy number variation genes (focal events) and molecular subtypes
Head and Neck Squamous Cell Carcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
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 (2016): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1SB455G
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 76 focal events and 10 molecular subtypes across 522 patients, 397 significant findings detected with P value < 0.05 and Q value < 0.25.

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

  • amp_2q31.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

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

  • amp_5p12 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

  • amp_18p11.31 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

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

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

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

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

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

  • del_2q21.2 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

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

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

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

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

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

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

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

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

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

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

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

  • del_5q12.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

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

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

  • del_7q31.1 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.

  • del_7q36.1 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.

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

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

  • del_9p21.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

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

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

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

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

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

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

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

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

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

  • del_15q15.1 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

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

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

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

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

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

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

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

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

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

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

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

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 76 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, 397 significant findings detected.

Clinical
Features
CN
CNMF
METHLYATION
CNMF
RPPA
CNMF
RPPA
CHIERARCHICAL
MRNASEQ
CNMF
MRNASEQ
CHIERARCHICAL
MIRSEQ
CNMF
MIRSEQ
CHIERARCHICAL
MIRSEQ
MATURE
CNMF
MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
del 1p36 21 95 (18%) 427 1e-05
(4.94e-05)
1e-05
(4.94e-05)
0.021
(0.0463)
0.00578
(0.015)
7e-05
(0.000277)
1e-05
(4.94e-05)
0.00709
(0.0176)
0.0405
(0.0807)
0.00355
(0.00992)
0.00681
(0.017)
amp 8q24 21 386 (74%) 136 1e-05
(4.94e-05)
1e-05
(4.94e-05)
0.00599
(0.0153)
0.447
(0.555)
1e-05
(4.94e-05)
1e-05
(4.94e-05)
1e-05
(4.94e-05)
0.00109
(0.00345)
0.00268
(0.00766)
0.0009
(0.00286)
del 4p15 2 208 (40%) 314 1e-05
(4.94e-05)
1e-05
(4.94e-05)
0.0248
(0.053)
0.336
(0.446)
0.00569
(0.0148)
1e-05
(4.94e-05)
0.00646
(0.0163)
0.0302
(0.0626)
0.00111
(0.00349)
0.00296
(0.00839)
amp 8q11 21 310 (59%) 212 1e-05
(4.94e-05)
1e-05
(4.94e-05)
0.0224
(0.0489)
0.635
(0.724)
1e-05
(4.94e-05)
1e-05
(4.94e-05)
0.00222
(0.00656)
0.00522
(0.0136)
0.0934
(0.161)
0.00434
(0.0117)
del 8p23 2 305 (58%) 217 1e-05
(4.94e-05)
1e-05
(4.94e-05)
0.122
(0.203)
0.322
(0.434)
1e-05
(4.94e-05)
1e-05
(4.94e-05)
1e-05
(4.94e-05)
0.00316
(0.00889)
0.0265
(0.0562)
5e-05
(0.000203)
del 1p13 2 133 (25%) 389 1e-05
(4.94e-05)
1e-05
(4.94e-05)
0.0108
(0.0256)
0.00712
(0.0176)
0.156
(0.251)
2e-05
(8.94e-05)
0.00081
(0.0026)
0.0001
(0.000382)
0.0769
(0.14)
0.628
(0.72)
del 3p26 2 348 (67%) 174 1e-05
(4.94e-05)
1e-05
(4.94e-05)
0.178
(0.276)
0.211
(0.316)
5e-05
(0.000203)
1e-05
(4.94e-05)
1e-05
(4.94e-05)
1e-05
(4.94e-05)
0.0534
(0.101)
0.0198
(0.0442)
del 3p24 1 368 (70%) 154 1e-05
(4.94e-05)
1e-05
(4.94e-05)
0.224
(0.329)
0.113
(0.19)
0.00126
(0.00394)
1e-05
(4.94e-05)
6e-05
(0.000241)
5e-05
(0.000203)
0.0142
(0.0326)
0.111
(0.188)
del 3p14 2 372 (71%) 150 1e-05
(4.94e-05)
1e-05
(4.94e-05)
0.359
(0.471)
0.175
(0.272)
0.00579
(0.015)
1e-05
(4.94e-05)
0.00144
(0.0044)
0.00041
(0.00141)
0.0319
(0.0655)
0.214
(0.318)
del 9p21 3 302 (58%) 220 1e-05
(4.94e-05)
1e-05
(4.94e-05)
0.152
(0.244)
0.361
(0.471)
4e-05
(0.000168)
1e-05
(4.94e-05)
1e-05
(4.94e-05)
1e-05
(4.94e-05)
0.277
(0.382)
0.0364
(0.0742)
del 10p11 21 163 (31%) 359 1e-05
(4.94e-05)
1e-05
(4.94e-05)
0.549
(0.645)
0.22
(0.324)
6e-05
(0.000241)
0.0221
(0.0485)
2e-05
(8.94e-05)
0.0111
(0.0261)
0.0386
(0.0774)
0.86
(0.89)
del 11p15 5 163 (31%) 359 1e-05
(4.94e-05)
1e-05
(4.94e-05)
0.769
(0.821)
0.282
(0.388)
0.00084
(0.00268)
0.0137
(0.0317)
2e-05
(8.94e-05)
0.0038
(0.0104)
0.336
(0.446)
0.0142
(0.0325)
del 11q23 1 246 (47%) 276 2e-05
(8.94e-05)
1e-05
(4.94e-05)
0.343
(0.452)
0.166
(0.261)
2e-05
(8.94e-05)
1e-05
(4.94e-05)
1e-05
(4.94e-05)
0.0132
(0.0304)
0.0446
(0.0871)
0.16
(0.255)
del 16q23 1 98 (19%) 424 0.00037
(0.00128)
1e-05
(4.94e-05)
0.789
(0.834)
0.455
(0.561)
1e-05
(4.94e-05)
1e-05
(4.94e-05)
1e-05
(4.94e-05)
0.0408
(0.0812)
0.273
(0.378)
0.00065
(0.00215)
del 17q25 3 71 (14%) 451 0.0144
(0.0328)
2e-05
(8.94e-05)
0.1
(0.172)
0.691
(0.766)
0.00266
(0.00763)
0.0831
(0.147)
0.00357
(0.00994)
0.0496
(0.0949)
0.028
(0.0592)
0.00597
(0.0153)
del 18q23 288 (55%) 234 1e-05
(4.94e-05)
1e-05
(4.94e-05)
0.181
(0.279)
0.246
(0.347)
1e-05
(4.94e-05)
1e-05
(4.94e-05)
2e-05
(8.94e-05)
1e-05
(4.94e-05)
0.0824
(0.146)
0.0169
(0.0382)
amp 2q11 2 107 (20%) 415 1e-05
(4.94e-05)
1e-05
(4.94e-05)
0.0416
(0.0821)
0.543
(0.642)
0.085
(0.149)
1e-05
(4.94e-05)
0.00065
(0.00215)
0.00068
(0.00223)
0.701
(0.771)
0.736
(0.792)
amp 2q31 2 112 (21%) 410 1e-05
(4.94e-05)
1e-05
(4.94e-05)
0.163
(0.259)
0.312
(0.423)
0.0412
(0.0816)
1e-05
(4.94e-05)
0.00442
(0.0118)
0.00667
(0.0168)
0.257
(0.358)
0.557
(0.654)
amp 7p11 2 222 (43%) 300 1e-05
(4.94e-05)
1e-05
(4.94e-05)
0.854
(0.887)
0.671
(0.754)
0.0238
(0.0513)
1e-05
(4.94e-05)
0.00022
(0.000789)
1e-05
(4.94e-05)
0.226
(0.329)
0.219
(0.323)
amp 9p24 1 126 (24%) 396 1e-05
(4.94e-05)
2e-05
(8.94e-05)
0.134
(0.22)
0.251
(0.352)
0.00075
(0.00243)
0.0143
(0.0326)
0.00385
(0.0105)
0.00129
(0.004)
0.263
(0.364)
0.326
(0.438)
amp 9p23 124 (24%) 398 1e-05
(4.94e-05)
0.00014
(0.000527)
0.387
(0.496)
0.425
(0.536)
0.00136
(0.0042)
0.0195
(0.0435)
0.00163
(0.00492)
0.00218
(0.00647)
0.331
(0.442)
0.534
(0.634)
amp 11q13 3 229 (44%) 293 1e-05
(4.94e-05)
1e-05
(4.94e-05)
0.797
(0.841)
0.733
(0.79)
1e-05
(4.94e-05)
0.0318
(0.0655)
0.0301
(0.0626)
0.0046
(0.0121)
0.381
(0.492)
0.201
(0.303)
amp 17q12 91 (17%) 431 1e-05
(4.94e-05)
1e-05
(4.94e-05)
0.698
(0.77)
0.722
(0.787)
0.00255
(0.00737)
3e-05
(0.000129)
0.0207
(0.0458)
4e-05
(0.000168)
0.705
(0.773)
0.224
(0.329)
amp 18p11 31 156 (30%) 366 1e-05
(4.94e-05)
1e-05
(4.94e-05)
0.211
(0.316)
0.516
(0.617)
0.00946
(0.0228)
1e-05
(4.94e-05)
0.0106
(0.0253)
0.0002
(0.000724)
0.95
(0.957)
0.222
(0.327)
amp 20q11 22 227 (43%) 295 1e-05
(4.94e-05)
3e-05
(0.000129)
0.0487
(0.0938)
0.832
(0.87)
0.0587
(0.11)
0.0287
(0.0603)
0.91
(0.924)
0.0236
(0.0511)
0.579
(0.672)
0.0173
(0.039)
del 1q44 48 (9%) 474 9e-05
(0.000349)
0.012
(0.0281)
0.8
(0.842)
0.91
(0.924)
0.00853
(0.0207)
0.0102
(0.0244)
0.00037
(0.00128)
0.0459
(0.0891)
0.242
(0.343)
0.486
(0.587)
del 3p12 1 343 (66%) 179 1e-05
(4.94e-05)
1e-05
(4.94e-05)
0.669
(0.753)
0.902
(0.92)
0.00161
(0.00487)
1e-05
(4.94e-05)
0.00014
(0.000527)
0.00047
(0.00159)
0.0808
(0.144)
0.482
(0.585)
del 4p16 3 205 (39%) 317 1e-05
(4.94e-05)
1e-05
(4.94e-05)
0.196
(0.297)
0.408
(0.518)
0.00246
(0.00716)
1e-05
(4.94e-05)
0.0641
(0.119)
0.0695
(0.128)
0.00814
(0.0199)
0.0412
(0.0816)
del 4q21 3 156 (30%) 366 1e-05
(4.94e-05)
1e-05
(4.94e-05)
0.732
(0.79)
0.0465
(0.0899)
0.146
(0.238)
2e-05
(8.94e-05)
0.259
(0.36)
0.0315
(0.065)
0.443
(0.552)
0.0296
(0.0619)
del 5q12 1 215 (41%) 307 1e-05
(4.94e-05)
1e-05
(4.94e-05)
0.00419
(0.0113)
0.361
(0.471)
0.0735
(0.135)
1e-05
(4.94e-05)
0.00264
(0.0076)
3e-05
(0.000129)
0.351
(0.461)
0.523
(0.623)
del 5q15 226 (43%) 296 1e-05
(4.94e-05)
1e-05
(4.94e-05)
0.0188
(0.0422)
0.431
(0.544)
0.311
(0.423)
1e-05
(4.94e-05)
0.0121
(0.0283)
2e-05
(8.94e-05)
0.651
(0.738)
0.78
(0.828)
del 5q35 3 199 (38%) 323 1e-05
(4.94e-05)
1e-05
(4.94e-05)
0.121
(0.202)
0.723
(0.787)
0.00702
(0.0174)
1e-05
(4.94e-05)
0.0377
(0.0763)
4e-05
(0.000168)
0.361
(0.471)
0.229
(0.332)
del 9p23 239 (46%) 283 1e-05
(4.94e-05)
1e-05
(4.94e-05)
0.124
(0.205)
0.113
(0.191)
0.00052
(0.00175)
1e-05
(4.94e-05)
1e-05
(4.94e-05)
9e-05
(0.000349)
0.485
(0.587)
0.979
(0.98)
del 10p15 3 170 (33%) 352 1e-05
(4.94e-05)
1e-05
(4.94e-05)
0.757
(0.812)
0.709
(0.776)
0.0008
(0.00258)
0.003
(0.00848)
0.00021
(0.000756)
0.0803
(0.144)
0.0276
(0.0585)
0.686
(0.764)
del 13q14 2 217 (42%) 305 1e-05
(4.94e-05)
1e-05
(4.94e-05)
0.214
(0.318)
0.566
(0.661)
3e-05
(0.000129)
7e-05
(0.000277)
0.0011
(0.00347)
0.216
(0.32)
0.91
(0.924)
0.0214
(0.0472)
del 14q32 32 75 (14%) 447 0.00129
(0.004)
1e-05
(4.94e-05)
0.0535
(0.101)
0.466
(0.568)
2e-05
(8.94e-05)
1e-05
(4.94e-05)
1e-05
(4.94e-05)
0.0289
(0.0605)
0.382
(0.492)
0.112
(0.189)
del 16q23 3 105 (20%) 417 0.00066
(0.00217)
1e-05
(4.94e-05)
0.42
(0.532)
0.233
(0.337)
1e-05
(4.94e-05)
1e-05
(4.94e-05)
5e-05
(0.000203)
0.165
(0.261)
0.379
(0.492)
0.0218
(0.0479)
del 19p13 3 175 (34%) 347 1e-05
(4.94e-05)
3e-05
(0.000129)
0.542
(0.642)
0.366
(0.476)
0.00073
(0.00237)
0.00069
(0.00225)
0.0466
(0.09)
0.0002
(0.000724)
0.536
(0.635)
0.252
(0.353)
del 21q22 3 208 (40%) 314 1e-05
(4.94e-05)
1e-05
(4.94e-05)
0.656
(0.739)
0.727
(0.789)
0.0459
(0.0891)
1e-05
(4.94e-05)
0.00028
(0.000985)
5e-05
(0.000203)
0.0842
(0.148)
0.19
(0.289)
del xq21 33 80 (15%) 442 3e-05
(0.000129)
1e-05
(4.94e-05)
0.585
(0.677)
0.128
(0.21)
0.00345
(0.00968)
0.00383
(0.0105)
0.00683
(0.017)
0.0123
(0.0288)
0.236
(0.339)
0.0778
(0.141)
amp 3q26 33 380 (73%) 142 1e-05
(4.94e-05)
1e-05
(4.94e-05)
0.0809
(0.144)
0.309
(0.422)
1e-05
(4.94e-05)
0.00023
(0.000821)
0.00057
(0.00191)
0.594
(0.685)
0.2
(0.302)
0.227
(0.33)
amp 7q21 3 169 (32%) 353 1e-05
(4.94e-05)
1e-05
(4.94e-05)
0.765
(0.818)
0.442
(0.552)
0.0128
(0.0297)
1e-05
(4.94e-05)
0.0827
(0.147)
0.00015
(0.000562)
0.242
(0.343)
0.935
(0.945)
amp 12p13 33 167 (32%) 355 1e-05
(4.94e-05)
1e-05
(4.94e-05)
0.251
(0.352)
0.524
(0.624)
0.00177
(0.0053)
9e-05
(0.000349)
0.0259
(0.0552)
0.0875
(0.152)
0.672
(0.754)
0.771
(0.822)
amp 18q11 2 106 (20%) 416 2e-05
(8.94e-05)
0.00033
(0.00116)
0.773
(0.823)
0.207
(0.311)
0.107
(0.182)
0.0126
(0.0293)
0.00799
(0.0196)
0.0287
(0.0603)
0.798
(0.841)
0.681
(0.76)
del 6p25 3 96 (18%) 426 0.00582
(0.015)
1e-05
(4.94e-05)
0.298
(0.409)
0.0107
(0.0254)
0.0036
(0.00999)
0.172
(0.269)
0.0373
(0.0756)
0.726
(0.789)
0.681
(0.76)
0.672
(0.754)
del 9q21 11 108 (21%) 414 1e-05
(4.94e-05)
1e-05
(4.94e-05)
0.703
(0.772)
0.237
(0.339)
0.0745
(0.136)
0.0228
(0.0497)
0.00234
(0.00684)
0.00061
(0.00203)
0.444
(0.553)
0.122
(0.203)
del 10q23 31 138 (26%) 384 1e-05
(4.94e-05)
1e-05
(4.94e-05)
0.237
(0.339)
0.98
(0.98)
0.00047
(0.00159)
0.00281
(0.008)
0.00035
(0.00122)
0.462
(0.565)
0.33
(0.441)
0.456
(0.561)
del 13q12 11 233 (45%) 289 1e-05
(4.94e-05)
1e-05
(4.94e-05)
0.162
(0.258)
0.24
(0.342)
0.0787
(0.142)
2e-05
(8.94e-05)
0.0199
(0.0443)
0.0308
(0.0638)
0.63
(0.721)
0.837
(0.873)
del xp22 2 157 (30%) 365 1e-05
(4.94e-05)
1e-05
(4.94e-05)
0.622
(0.714)
0.00247
(0.00716)
0.484
(0.586)
0.0173
(0.039)
0.00852
(0.0207)
0.158
(0.253)
0.867
(0.894)
0.891
(0.913)
amp 5p15 33 240 (46%) 282 1e-05
(4.94e-05)
1e-05
(4.94e-05)
0.517
(0.617)
0.83
(0.868)
0.00506
(0.0133)
0.687
(0.764)
0.695
(0.769)
0.0337
(0.0689)
0.573
(0.665)
0.636
(0.725)
amp 6p12 1 110 (21%) 412 1e-05
(4.94e-05)
2e-05
(8.94e-05)
0.499
(0.6)
0.951
(0.957)
0.112
(0.189)
0.0372
(0.0756)
0.562
(0.658)
0.0023
(0.00675)
0.402
(0.512)
0.237
(0.339)
amp 8p11 23 161 (31%) 361 1e-05
(4.94e-05)
0.0385
(0.0774)
0.949
(0.957)
0.874
(0.899)
0.241
(0.343)
0.17
(0.266)
0.0664
(0.123)
0.0109
(0.0258)
0.404
(0.514)
0.0453
(0.0883)
amp 9p13 3 139 (27%) 383 1e-05
(4.94e-05)
0.00389
(0.0106)
0.247
(0.348)
0.122
(0.203)
0.00027
(0.000954)
0.00144
(0.0044)
0.226
(0.329)
0.0595
(0.111)
0.758
(0.812)
0.454
(0.561)
amp 9q34 3 177 (34%) 345 1e-05
(4.94e-05)
0.00012
(0.000456)
0.652
(0.738)
0.0237
(0.0511)
0.38
(0.492)
0.00446
(0.0118)
0.225
(0.329)
0.0862
(0.151)
0.96
(0.965)
0.968
(0.972)
del 2q21 2 78 (15%) 444 0.0495
(0.0949)
0.0551
(0.104)
0.504
(0.605)
0.212
(0.317)
0.0063
(0.016)
0.0002
(0.000724)
0.0386
(0.0774)
0.259
(0.36)
0.311
(0.423)
0.171
(0.267)
del 2q22 1 121 (23%) 401 0.00468
(0.0123)
0.0001
(0.000382)
0.387
(0.496)
0.837
(0.873)
0.123
(0.204)
0.00972
(0.0233)
0.0811
(0.144)
0.00139
(0.00428)
0.89
(0.912)
0.572
(0.665)
del 2q36 2 157 (30%) 365 1e-05
(4.94e-05)
1e-05
(4.94e-05)
0.186
(0.285)
0.859
(0.89)
0.0088
(0.0213)
0.0659
(0.122)
0.0696
(0.128)
0.0248
(0.053)
0.103
(0.176)
0.0901
(0.156)
del 4q22 1 169 (32%) 353 1e-05
(4.94e-05)
1e-05
(4.94e-05)
0.477
(0.581)
0.0745
(0.136)
0.12
(0.201)
0.00024
(0.000852)
0.443
(0.552)
0.04
(0.08)
0.446
(0.554)
0.0871
(0.152)
del 4q35 2 213 (41%) 309 1e-05
(4.94e-05)
1e-05
(4.94e-05)
0.871
(0.897)
0.186
(0.285)
0.0807
(0.144)
0.00017
(0.000633)
0.235
(0.339)
0.00601
(0.0153)
0.147
(0.238)
0.164
(0.26)
del 14q11 2 75 (14%) 447 0.00365
(0.0101)
0.00672
(0.0169)
0.171
(0.267)
0.898
(0.919)
0.241
(0.342)
0.149
(0.242)
0.00447
(0.0118)
0.0326
(0.0668)
0.387
(0.496)
0.654
(0.738)
del 19q13 43 97 (19%) 425 1e-05
(4.94e-05)
1e-05
(4.94e-05)
0.214
(0.318)
0.587
(0.678)
0.338
(0.448)
5e-05
(0.000203)
0.0427
(0.0839)
0.0658
(0.122)
0.165
(0.261)
0.58
(0.672)
amp 5p12 205 (39%) 317 1e-05
(4.94e-05)
1e-05
(4.94e-05)
0.179
(0.276)
0.146
(0.238)
0.0502
(0.0959)
0.234
(0.338)
0.436
(0.548)
0.0162
(0.0367)
0.698
(0.77)
0.713
(0.778)
amp 6q12 96 (18%) 426 1e-05
(4.94e-05)
8e-05
(0.000315)
0.689
(0.766)
0.9
(0.919)
0.089
(0.155)
0.00612
(0.0156)
0.183
(0.281)
0.234
(0.338)
0.842
(0.876)
0.547
(0.645)
amp 11p13 102 (20%) 420 0.00223
(0.00657)
0.00049
(0.00166)
0.173
(0.269)
0.177
(0.274)
0.0839
(0.148)
0.565
(0.661)
0.632
(0.722)
0.492
(0.593)
0.905
(0.922)
0.0422
(0.083)
amp 12q15 103 (20%) 419 2e-05
(8.94e-05)
7e-05
(0.000277)
0.303
(0.415)
0.205
(0.309)
0.102
(0.175)
0.00167
(0.00502)
0.88
(0.904)
0.322
(0.434)
0.396
(0.506)
0.737
(0.792)
amp 13q34 106 (20%) 416 1e-05
(4.94e-05)
0.00047
(0.00159)
0.779
(0.828)
0.492
(0.593)
0.244
(0.344)
0.00402
(0.0109)
0.124
(0.205)
0.133
(0.217)
0.466
(0.568)
0.31
(0.423)
del 7q31 1 77 (15%) 445 0.00018
(0.000667)
0.342
(0.452)
0.73
(0.79)
0.381
(0.492)
0.00364
(0.0101)
0.548
(0.645)
0.00217
(0.00647)
0.176
(0.272)
0.187
(0.285)
0.398
(0.507)
del 7q36 1 132 (25%) 390 2e-05
(8.94e-05)
0.327
(0.439)
0.314
(0.426)
0.674
(0.754)
0.0429
(0.084)
0.805
(0.846)
0.00718
(0.0177)
0.331
(0.442)
0.517
(0.617)
0.29
(0.399)
del 9q34 3 79 (15%) 443 1e-05
(4.94e-05)
0.0002
(0.000724)
0.828
(0.868)
0.369
(0.48)
0.434
(0.546)
0.442
(0.552)
0.788
(0.834)
0.00958
(0.023)
0.452
(0.56)
0.26
(0.36)
del xp21 3 159 (30%) 363 1e-05
(4.94e-05)
4e-05
(0.000168)
0.787
(0.834)
0.0552
(0.104)
0.81
(0.85)
0.0233
(0.0505)
0.152
(0.245)
0.0848
(0.149)
0.712
(0.778)
0.457
(0.561)
amp 13q22 1 105 (20%) 417 1e-05
(4.94e-05)
1e-05
(4.94e-05)
0.384
(0.494)
0.157
(0.251)
0.65
(0.737)
0.0764
(0.139)
0.332
(0.442)
0.162
(0.258)
0.461
(0.565)
0.619
(0.712)
amp 15q26 3 105 (20%) 417 3e-05
(0.000129)
0.00443
(0.0118)
0.699
(0.77)
0.327
(0.439)
0.224
(0.329)
0.0757
(0.138)
0.549
(0.645)
0.051
(0.0969)
0.529
(0.629)
0.0794
(0.143)
amp xq28 150 (29%) 372 1e-05
(4.94e-05)
0.0001
(0.000382)
0.745
(0.8)
0.196
(0.297)
0.257
(0.358)
0.315
(0.427)
0.568
(0.662)
0.0946
(0.163)
0.694
(0.769)
0.605
(0.697)
del 12q24 33 63 (12%) 459 1e-05
(4.94e-05)
0.0002
(0.000724)
0.843
(0.877)
0.456
(0.561)
0.35
(0.461)
0.104
(0.178)
0.351
(0.461)
0.121
(0.202)
0.438
(0.55)
0.732
(0.79)
del 15q15 1 124 (24%) 398 1e-05
(4.94e-05)
0.0504
(0.096)
0.65
(0.737)
0.414
(0.525)
0.0248
(0.053)
0.0635
(0.119)
0.73
(0.79)
0.64
(0.728)
0.482
(0.585)
0.933
(0.944)
del 17p11 2 99 (19%) 423 1e-05
(4.94e-05)
0.00147
(0.00447)
0.858
(0.89)
0.973
(0.976)
0.193
(0.294)
0.1
(0.172)
0.14
(0.229)
0.126
(0.207)
0.867
(0.894)
0.933
(0.944)
'amp_2q11.2' versus 'CN_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
AMP PEAK 1(2Q11.2) MUTATED 55 42 4 6
AMP PEAK 1(2Q11.2) WILD-TYPE 148 86 141 40

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

'amp_2q11.2' versus 'METHLYATION_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
AMP PEAK 1(2Q11.2) MUTATED 7 34 7 38 2 17 2
AMP PEAK 1(2Q11.2) WILD-TYPE 77 53 96 51 76 58 4

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

'amp_2q11.2' versus 'RPPA_CNMF'

P value = 0.0416 (Fisher's exact test), Q value = 0.082

Table S3.  Gene #1: 'amp_2q11.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 50 29 31 29 67
AMP PEAK 1(2Q11.2) MUTATED 13 3 14 7 15
AMP PEAK 1(2Q11.2) WILD-TYPE 37 26 17 22 52

Figure S3.  Get High-res Image Gene #1: 'amp_2q11.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_2q11.2' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S4.  Gene #1: 'amp_2q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

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

Figure S4.  Get High-res Image Gene #1: 'amp_2q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_2q11.2' versus 'MIRSEQ_CNMF'

P value = 0.00065 (Fisher's exact test), Q value = 0.0021

Table S5.  Gene #1: 'amp_2q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 139 131 91 76
AMP PEAK 1(2Q11.2) MUTATED 32 22 21 17 13
AMP PEAK 1(2Q11.2) WILD-TYPE 49 117 110 74 63

Figure S5.  Get High-res Image Gene #1: 'amp_2q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_2q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00068 (Fisher's exact test), Q value = 0.0022

Table S6.  Gene #1: 'amp_2q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

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

Figure S6.  Get High-res Image Gene #1: 'amp_2q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_2q31.2' versus 'CN_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
AMP PEAK 2(2Q31.2) MUTATED 56 46 6 4
AMP PEAK 2(2Q31.2) WILD-TYPE 147 82 139 42

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

'amp_2q31.2' versus 'METHLYATION_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
AMP PEAK 2(2Q31.2) MUTATED 8 27 8 47 5 15 2
AMP PEAK 2(2Q31.2) WILD-TYPE 76 60 95 42 73 60 4

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

'amp_2q31.2' versus 'MRNASEQ_CNMF'

P value = 0.0412 (Fisher's exact test), Q value = 0.082

Table S9.  Gene #2: 'amp_2q31.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 171 95
AMP PEAK 2(2Q31.2) MUTATED 33 14 43 22
AMP PEAK 2(2Q31.2) WILD-TYPE 102 99 128 73

Figure S9.  Get High-res Image Gene #2: 'amp_2q31.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_2q31.2' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S10.  Gene #2: 'amp_2q31.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

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

Figure S10.  Get High-res Image Gene #2: 'amp_2q31.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_2q31.2' versus 'MIRSEQ_CNMF'

P value = 0.00442 (Fisher's exact test), Q value = 0.012

Table S11.  Gene #2: 'amp_2q31.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 139 131 91 76
AMP PEAK 2(2Q31.2) MUTATED 30 21 23 19 17
AMP PEAK 2(2Q31.2) WILD-TYPE 51 118 108 72 59

Figure S11.  Get High-res Image Gene #2: 'amp_2q31.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_2q31.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00667 (Fisher's exact test), Q value = 0.017

Table S12.  Gene #2: 'amp_2q31.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

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

Figure S12.  Get High-res Image Gene #2: 'amp_2q31.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_3q26.33' versus 'CN_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
AMP PEAK 3(3Q26.33) MUTATED 171 118 56 35
AMP PEAK 3(3Q26.33) WILD-TYPE 32 10 89 11

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

'amp_3q26.33' versus 'METHLYATION_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
AMP PEAK 3(3Q26.33) MUTATED 48 74 45 82 62 63 6
AMP PEAK 3(3Q26.33) WILD-TYPE 36 13 58 7 16 12 0

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

'amp_3q26.33' versus 'MRNASEQ_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 171 95
AMP PEAK 3(3Q26.33) MUTATED 99 58 148 71
AMP PEAK 3(3Q26.33) WILD-TYPE 36 55 23 24

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

'amp_3q26.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.00082

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

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

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

'amp_3q26.33' versus 'MIRSEQ_CNMF'

P value = 0.00057 (Fisher's exact test), Q value = 0.0019

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 139 131 91 76
AMP PEAK 3(3Q26.33) MUTATED 66 87 109 62 52
AMP PEAK 3(3Q26.33) WILD-TYPE 15 52 22 29 24

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

'amp_5p15.33' versus 'CN_CNMF'

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

Table S18.  Gene #4: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
AMP PEAK 4(5P15.33) MUTATED 116 82 24 18
AMP PEAK 4(5P15.33) WILD-TYPE 87 46 121 28

Figure S18.  Get High-res Image Gene #4: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5p15.33' versus 'METHLYATION_CNMF'

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

Table S19.  Gene #4: 'amp_5p15.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
AMP PEAK 4(5P15.33) MUTATED 27 52 27 50 35 46 3
AMP PEAK 4(5P15.33) WILD-TYPE 57 35 76 39 43 29 3

Figure S19.  Get High-res Image Gene #4: 'amp_5p15.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_5p15.33' versus 'MRNASEQ_CNMF'

P value = 0.00506 (Fisher's exact test), Q value = 0.013

Table S20.  Gene #4: 'amp_5p15.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 171 95
AMP PEAK 4(5P15.33) MUTATED 74 37 82 46
AMP PEAK 4(5P15.33) WILD-TYPE 61 76 89 49

Figure S20.  Get High-res Image Gene #4: 'amp_5p15.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_5p15.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0337 (Fisher's exact test), Q value = 0.069

Table S21.  Gene #4: 'amp_5p15.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

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

Figure S21.  Get High-res Image Gene #4: 'amp_5p15.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_5p12' versus 'CN_CNMF'

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

Table S22.  Gene #5: 'amp_5p12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
AMP PEAK 5(5P12) MUTATED 98 72 17 18
AMP PEAK 5(5P12) WILD-TYPE 105 56 128 28

Figure S22.  Get High-res Image Gene #5: 'amp_5p12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5p12' versus 'METHLYATION_CNMF'

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

Table S23.  Gene #5: 'amp_5p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
AMP PEAK 5(5P12) MUTATED 21 47 25 40 28 41 3
AMP PEAK 5(5P12) WILD-TYPE 63 40 78 49 50 34 3

Figure S23.  Get High-res Image Gene #5: 'amp_5p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_5p12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0162 (Fisher's exact test), Q value = 0.037

Table S24.  Gene #5: 'amp_5p12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
AMP PEAK 5(5P12) MUTATED 74 68 60
AMP PEAK 5(5P12) WILD-TYPE 116 74 126

Figure S24.  Get High-res Image Gene #5: 'amp_5p12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_6p12.1' versus 'CN_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
AMP PEAK 6(6P12.1) MUTATED 59 30 9 12
AMP PEAK 6(6P12.1) WILD-TYPE 144 98 136 34

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

'amp_6p12.1' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 8.9e-05

Table S26.  Gene #6: 'amp_6p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
AMP PEAK 6(6P12.1) MUTATED 9 27 15 24 7 26 2
AMP PEAK 6(6P12.1) WILD-TYPE 75 60 88 65 71 49 4

Figure S26.  Get High-res Image Gene #6: 'amp_6p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6p12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0372 (Fisher's exact test), Q value = 0.076

Table S27.  Gene #6: 'amp_6p12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

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

Figure S27.  Get High-res Image Gene #6: 'amp_6p12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_6p12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0023 (Fisher's exact test), Q value = 0.0067

Table S28.  Gene #6: 'amp_6p12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

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

Figure S28.  Get High-res Image Gene #6: 'amp_6p12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_6q12' versus 'CN_CNMF'

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

Table S29.  Gene #7: 'amp_6q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
AMP PEAK 7(6Q12) MUTATED 54 25 7 10
AMP PEAK 7(6Q12) WILD-TYPE 149 103 138 36

Figure S29.  Get High-res Image Gene #7: 'amp_6q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6q12' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00032

Table S30.  Gene #7: 'amp_6q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
AMP PEAK 7(6Q12) MUTATED 9 20 14 24 4 23 2
AMP PEAK 7(6Q12) WILD-TYPE 75 67 89 65 74 52 4

Figure S30.  Get High-res Image Gene #7: 'amp_6q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00612 (Fisher's exact test), Q value = 0.016

Table S31.  Gene #7: 'amp_6q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
AMP PEAK 7(6Q12) MUTATED 31 24 35 3
AMP PEAK 7(6Q12) WILD-TYPE 145 79 135 62

Figure S31.  Get High-res Image Gene #7: 'amp_6q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_7p11.2' versus 'CN_CNMF'

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

Table S32.  Gene #8: 'amp_7p11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
AMP PEAK 8(7P11.2) MUTATED 111 68 26 17
AMP PEAK 8(7P11.2) WILD-TYPE 92 60 119 29

Figure S32.  Get High-res Image Gene #8: 'amp_7p11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7p11.2' versus 'METHLYATION_CNMF'

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

Table S33.  Gene #8: 'amp_7p11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
AMP PEAK 8(7P11.2) MUTATED 30 48 41 54 6 40 3
AMP PEAK 8(7P11.2) WILD-TYPE 54 39 62 35 72 35 3

Figure S33.  Get High-res Image Gene #8: 'amp_7p11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7p11.2' versus 'MRNASEQ_CNMF'

P value = 0.0238 (Fisher's exact test), Q value = 0.051

Table S34.  Gene #8: 'amp_7p11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 171 95
AMP PEAK 8(7P11.2) MUTATED 71 47 60 41
AMP PEAK 8(7P11.2) WILD-TYPE 64 66 111 54

Figure S34.  Get High-res Image Gene #8: 'amp_7p11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_7p11.2' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S35.  Gene #8: 'amp_7p11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
AMP PEAK 8(7P11.2) MUTATED 76 57 81 5
AMP PEAK 8(7P11.2) WILD-TYPE 100 46 89 60

Figure S35.  Get High-res Image Gene #8: 'amp_7p11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_7p11.2' versus 'MIRSEQ_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.00079

Table S36.  Gene #8: 'amp_7p11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 139 131 91 76
AMP PEAK 8(7P11.2) MUTATED 48 60 36 42 33
AMP PEAK 8(7P11.2) WILD-TYPE 33 79 95 49 43

Figure S36.  Get High-res Image Gene #8: 'amp_7p11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_7p11.2' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S37.  Gene #8: 'amp_7p11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
AMP PEAK 8(7P11.2) MUTATED 84 83 52
AMP PEAK 8(7P11.2) WILD-TYPE 106 59 134

Figure S37.  Get High-res Image Gene #8: 'amp_7p11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_7q21.3' versus 'CN_CNMF'

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

Table S38.  Gene #9: 'amp_7q21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
AMP PEAK 9(7Q21.3) MUTATED 88 55 17 9
AMP PEAK 9(7Q21.3) WILD-TYPE 115 73 128 37

Figure S38.  Get High-res Image Gene #9: 'amp_7q21.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7q21.3' versus 'METHLYATION_CNMF'

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

Table S39.  Gene #9: 'amp_7q21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
AMP PEAK 9(7Q21.3) MUTATED 14 39 24 60 9 22 1
AMP PEAK 9(7Q21.3) WILD-TYPE 70 48 79 29 69 53 5

Figure S39.  Get High-res Image Gene #9: 'amp_7q21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7q21.3' versus 'MRNASEQ_CNMF'

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

Table S40.  Gene #9: 'amp_7q21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 171 95
AMP PEAK 9(7Q21.3) MUTATED 56 25 57 29
AMP PEAK 9(7Q21.3) WILD-TYPE 79 88 114 66

Figure S40.  Get High-res Image Gene #9: 'amp_7q21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_7q21.3' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S41.  Gene #9: 'amp_7q21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
AMP PEAK 9(7Q21.3) MUTATED 47 52 60 8
AMP PEAK 9(7Q21.3) WILD-TYPE 129 51 110 57

Figure S41.  Get High-res Image Gene #9: 'amp_7q21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_7q21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.00056

Table S42.  Gene #9: 'amp_7q21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
AMP PEAK 9(7Q21.3) MUTATED 56 65 45
AMP PEAK 9(7Q21.3) WILD-TYPE 134 77 141

Figure S42.  Get High-res Image Gene #9: 'amp_7q21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_8p11.23' versus 'CN_CNMF'

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

Table S43.  Gene #10: 'amp_8p11.23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
AMP PEAK 10(8P11.23) MUTATED 53 64 31 13
AMP PEAK 10(8P11.23) WILD-TYPE 150 64 114 33

Figure S43.  Get High-res Image Gene #10: 'amp_8p11.23' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8p11.23' versus 'METHLYATION_CNMF'

P value = 0.0385 (Fisher's exact test), Q value = 0.077

Table S44.  Gene #10: 'amp_8p11.23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
AMP PEAK 10(8P11.23) MUTATED 20 34 24 35 26 22 0
AMP PEAK 10(8P11.23) WILD-TYPE 64 53 79 54 52 53 6

Figure S44.  Get High-res Image Gene #10: 'amp_8p11.23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8p11.23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0109 (Fisher's exact test), Q value = 0.026

Table S45.  Gene #10: 'amp_8p11.23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
AMP PEAK 10(8P11.23) MUTATED 47 57 55
AMP PEAK 10(8P11.23) WILD-TYPE 143 85 131

Figure S45.  Get High-res Image Gene #10: 'amp_8p11.23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_8p11.23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0453 (Fisher's exact test), Q value = 0.088

Table S46.  Gene #10: 'amp_8p11.23' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 104 198
AMP PEAK 10(8P11.23) MUTATED 40 34 69
AMP PEAK 10(8P11.23) WILD-TYPE 131 70 129

Figure S46.  Get High-res Image Gene #10: 'amp_8p11.23' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8q11.21' versus 'CN_CNMF'

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

Table S47.  Gene #11: 'amp_8q11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
AMP PEAK 11(8Q11.21) MUTATED 154 66 57 33
AMP PEAK 11(8Q11.21) WILD-TYPE 49 62 88 13

Figure S47.  Get High-res Image Gene #11: 'amp_8q11.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q11.21' versus 'METHLYATION_CNMF'

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

Table S48.  Gene #11: 'amp_8q11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
AMP PEAK 11(8Q11.21) MUTATED 53 48 63 51 29 62 4
AMP PEAK 11(8Q11.21) WILD-TYPE 31 39 40 38 49 13 2

Figure S48.  Get High-res Image Gene #11: 'amp_8q11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8q11.21' versus 'RPPA_CNMF'

P value = 0.0224 (Fisher's exact test), Q value = 0.049

Table S49.  Gene #11: 'amp_8q11.21' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 50 29 31 29 67
AMP PEAK 11(8Q11.21) MUTATED 26 11 15 19 47
AMP PEAK 11(8Q11.21) WILD-TYPE 24 18 16 10 20

Figure S49.  Get High-res Image Gene #11: 'amp_8q11.21' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_8q11.21' versus 'MRNASEQ_CNMF'

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

Table S50.  Gene #11: 'amp_8q11.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 171 95
AMP PEAK 11(8Q11.21) MUTATED 89 70 75 71
AMP PEAK 11(8Q11.21) WILD-TYPE 46 43 96 24

Figure S50.  Get High-res Image Gene #11: 'amp_8q11.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_8q11.21' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S51.  Gene #11: 'amp_8q11.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
AMP PEAK 11(8Q11.21) MUTATED 123 51 109 22
AMP PEAK 11(8Q11.21) WILD-TYPE 53 52 61 43

Figure S51.  Get High-res Image Gene #11: 'amp_8q11.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_8q11.21' versus 'MIRSEQ_CNMF'

P value = 0.00222 (Fisher's exact test), Q value = 0.0066

Table S52.  Gene #11: 'amp_8q11.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 139 131 91 76
AMP PEAK 11(8Q11.21) MUTATED 54 89 58 58 49
AMP PEAK 11(8Q11.21) WILD-TYPE 27 50 73 33 27

Figure S52.  Get High-res Image Gene #11: 'amp_8q11.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_8q11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00522 (Fisher's exact test), Q value = 0.014

Table S53.  Gene #11: 'amp_8q11.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
AMP PEAK 11(8Q11.21) MUTATED 129 83 96
AMP PEAK 11(8Q11.21) WILD-TYPE 61 59 90

Figure S53.  Get High-res Image Gene #11: 'amp_8q11.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_8q11.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00434 (Fisher's exact test), Q value = 0.012

Table S54.  Gene #11: 'amp_8q11.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 104 198
AMP PEAK 11(8Q11.21) MUTATED 116 63 101
AMP PEAK 11(8Q11.21) WILD-TYPE 55 41 97

Figure S54.  Get High-res Image Gene #11: 'amp_8q11.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8q24.21' versus 'CN_CNMF'

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

Table S55.  Gene #12: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
AMP PEAK 12(8Q24.21) MUTATED 185 89 74 38
AMP PEAK 12(8Q24.21) WILD-TYPE 18 39 71 8

Figure S55.  Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

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

Table S56.  Gene #12: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
AMP PEAK 12(8Q24.21) MUTATED 64 64 77 71 35 69 6
AMP PEAK 12(8Q24.21) WILD-TYPE 20 23 26 18 43 6 0

Figure S56.  Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'RPPA_CNMF'

P value = 0.00599 (Fisher's exact test), Q value = 0.015

Table S57.  Gene #12: 'amp_8q24.21' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 50 29 31 29 67
AMP PEAK 12(8Q24.21) MUTATED 32 15 25 22 57
AMP PEAK 12(8Q24.21) WILD-TYPE 18 14 6 7 10

Figure S57.  Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CNMF'

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

Table S58.  Gene #12: 'amp_8q24.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 171 95
AMP PEAK 12(8Q24.21) MUTATED 114 85 100 81
AMP PEAK 12(8Q24.21) WILD-TYPE 21 28 71 14

Figure S58.  Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S59.  Gene #12: 'amp_8q24.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
AMP PEAK 12(8Q24.21) MUTATED 142 75 136 27
AMP PEAK 12(8Q24.21) WILD-TYPE 34 28 34 38

Figure S59.  Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_CNMF'

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

Table S60.  Gene #12: 'amp_8q24.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 139 131 91 76
AMP PEAK 12(8Q24.21) MUTATED 67 110 74 77 55
AMP PEAK 12(8Q24.21) WILD-TYPE 14 29 57 14 21

Figure S60.  Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_8q24.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00109 (Fisher's exact test), Q value = 0.0035

Table S61.  Gene #12: 'amp_8q24.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
AMP PEAK 12(8Q24.21) MUTATED 154 109 120
AMP PEAK 12(8Q24.21) WILD-TYPE 36 33 66

Figure S61.  Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00268 (Fisher's exact test), Q value = 0.0077

Table S62.  Gene #12: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 189 143
AMP PEAK 12(8Q24.21) MUTATED 110 149 90
AMP PEAK 12(8Q24.21) WILD-TYPE 31 40 53

Figure S62.  Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9e-04 (Fisher's exact test), Q value = 0.0029

Table S63.  Gene #12: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 104 198
AMP PEAK 12(8Q24.21) MUTATED 138 83 128
AMP PEAK 12(8Q24.21) WILD-TYPE 33 21 70

Figure S63.  Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_9p24.1' versus 'CN_CNMF'

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

Table S64.  Gene #13: 'amp_9p24.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
AMP PEAK 13(9P24.1) MUTATED 40 19 29 38
AMP PEAK 13(9P24.1) WILD-TYPE 163 109 116 8

Figure S64.  Get High-res Image Gene #13: 'amp_9p24.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_9p24.1' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 8.9e-05

Table S65.  Gene #13: 'amp_9p24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
AMP PEAK 13(9P24.1) MUTATED 15 9 45 19 20 17 1
AMP PEAK 13(9P24.1) WILD-TYPE 69 78 58 70 58 58 5

Figure S65.  Get High-res Image Gene #13: 'amp_9p24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_9p24.1' versus 'MRNASEQ_CNMF'

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

Table S66.  Gene #13: 'amp_9p24.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 171 95
AMP PEAK 13(9P24.1) MUTATED 31 42 27 22
AMP PEAK 13(9P24.1) WILD-TYPE 104 71 144 73

Figure S66.  Get High-res Image Gene #13: 'amp_9p24.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_9p24.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0143 (Fisher's exact test), Q value = 0.033

Table S67.  Gene #13: 'amp_9p24.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
AMP PEAK 13(9P24.1) MUTATED 40 17 54 11
AMP PEAK 13(9P24.1) WILD-TYPE 136 86 116 54

Figure S67.  Get High-res Image Gene #13: 'amp_9p24.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_9p24.1' versus 'MIRSEQ_CNMF'

P value = 0.00385 (Fisher's exact test), Q value = 0.01

Table S68.  Gene #13: 'amp_9p24.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 139 131 91 76
AMP PEAK 13(9P24.1) MUTATED 9 44 32 27 14
AMP PEAK 13(9P24.1) WILD-TYPE 72 95 99 64 62

Figure S68.  Get High-res Image Gene #13: 'amp_9p24.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_9p24.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00129 (Fisher's exact test), Q value = 0.004

Table S69.  Gene #13: 'amp_9p24.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
AMP PEAK 13(9P24.1) MUTATED 43 22 61
AMP PEAK 13(9P24.1) WILD-TYPE 147 120 125

Figure S69.  Get High-res Image Gene #13: 'amp_9p24.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_9p23' versus 'CN_CNMF'

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

Table S70.  Gene #14: 'amp_9p23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
AMP PEAK 14(9P23) MUTATED 37 21 29 37
AMP PEAK 14(9P23) WILD-TYPE 166 107 116 9

Figure S70.  Get High-res Image Gene #14: 'amp_9p23' versus Molecular Subtype #1: 'CN_CNMF'

'amp_9p23' versus 'METHLYATION_CNMF'

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

Table S71.  Gene #14: 'amp_9p23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
AMP PEAK 14(9P23) MUTATED 16 9 43 19 19 17 1
AMP PEAK 14(9P23) WILD-TYPE 68 78 60 70 59 58 5

Figure S71.  Get High-res Image Gene #14: 'amp_9p23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_9p23' versus 'MRNASEQ_CNMF'

P value = 0.00136 (Fisher's exact test), Q value = 0.0042

Table S72.  Gene #14: 'amp_9p23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 171 95
AMP PEAK 14(9P23) MUTATED 32 40 26 23
AMP PEAK 14(9P23) WILD-TYPE 103 73 145 72

Figure S72.  Get High-res Image Gene #14: 'amp_9p23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_9p23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0195 (Fisher's exact test), Q value = 0.043

Table S73.  Gene #14: 'amp_9p23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
AMP PEAK 14(9P23) MUTATED 42 16 52 11
AMP PEAK 14(9P23) WILD-TYPE 134 87 118 54

Figure S73.  Get High-res Image Gene #14: 'amp_9p23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_9p23' versus 'MIRSEQ_CNMF'

P value = 0.00163 (Fisher's exact test), Q value = 0.0049

Table S74.  Gene #14: 'amp_9p23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 139 131 91 76
AMP PEAK 14(9P23) MUTATED 8 43 31 28 14
AMP PEAK 14(9P23) WILD-TYPE 73 96 100 63 62

Figure S74.  Get High-res Image Gene #14: 'amp_9p23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_9p23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00218 (Fisher's exact test), Q value = 0.0065

Table S75.  Gene #14: 'amp_9p23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
AMP PEAK 14(9P23) MUTATED 45 21 58
AMP PEAK 14(9P23) WILD-TYPE 145 121 128

Figure S75.  Get High-res Image Gene #14: 'amp_9p23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_9p13.3' versus 'CN_CNMF'

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

Table S76.  Gene #15: 'amp_9p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
AMP PEAK 15(9P13.3) MUTATED 48 29 29 33
AMP PEAK 15(9P13.3) WILD-TYPE 155 99 116 13

Figure S76.  Get High-res Image Gene #15: 'amp_9p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_9p13.3' versus 'METHLYATION_CNMF'

P value = 0.00389 (Fisher's exact test), Q value = 0.011

Table S77.  Gene #15: 'amp_9p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
AMP PEAK 15(9P13.3) MUTATED 19 17 44 24 14 19 2
AMP PEAK 15(9P13.3) WILD-TYPE 65 70 59 65 64 56 4

Figure S77.  Get High-res Image Gene #15: 'amp_9p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_9p13.3' versus 'MRNASEQ_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.00095

Table S78.  Gene #15: 'amp_9p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 171 95
AMP PEAK 15(9P13.3) MUTATED 30 43 30 33
AMP PEAK 15(9P13.3) WILD-TYPE 105 70 141 62

Figure S78.  Get High-res Image Gene #15: 'amp_9p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_9p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00144 (Fisher's exact test), Q value = 0.0044

Table S79.  Gene #15: 'amp_9p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
AMP PEAK 15(9P13.3) MUTATED 51 24 55 6
AMP PEAK 15(9P13.3) WILD-TYPE 125 79 115 59

Figure S79.  Get High-res Image Gene #15: 'amp_9p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_9q34.3' versus 'CN_CNMF'

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

Table S80.  Gene #16: 'amp_9q34.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
AMP PEAK 16(9Q34.3) MUTATED 59 55 30 33
AMP PEAK 16(9Q34.3) WILD-TYPE 144 73 115 13

Figure S80.  Get High-res Image Gene #16: 'amp_9q34.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_9q34.3' versus 'METHLYATION_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00046

Table S81.  Gene #16: 'amp_9q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
AMP PEAK 16(9Q34.3) MUTATED 20 23 51 37 22 19 5
AMP PEAK 16(9Q34.3) WILD-TYPE 64 64 52 52 56 56 1

Figure S81.  Get High-res Image Gene #16: 'amp_9q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_9q34.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0237 (Fisher's exact test), Q value = 0.051

Table S82.  Gene #16: 'amp_9q34.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 82 48
AMP PEAK 16(9Q34.3) MUTATED 36 32 11
AMP PEAK 16(9Q34.3) WILD-TYPE 40 50 37

Figure S82.  Get High-res Image Gene #16: 'amp_9q34.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_9q34.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00446 (Fisher's exact test), Q value = 0.012

Table S83.  Gene #16: 'amp_9q34.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
AMP PEAK 16(9Q34.3) MUTATED 60 33 70 11
AMP PEAK 16(9Q34.3) WILD-TYPE 116 70 100 54

Figure S83.  Get High-res Image Gene #16: 'amp_9q34.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_11p13' versus 'CN_CNMF'

P value = 0.00223 (Fisher's exact test), Q value = 0.0066

Table S84.  Gene #17: 'amp_11p13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
AMP PEAK 17(11P13) MUTATED 54 17 19 12
AMP PEAK 17(11P13) WILD-TYPE 149 111 126 34

Figure S84.  Get High-res Image Gene #17: 'amp_11p13' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11p13' versus 'METHLYATION_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.0017

Table S85.  Gene #17: 'amp_11p13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
AMP PEAK 17(11P13) MUTATED 8 12 22 24 9 26 1
AMP PEAK 17(11P13) WILD-TYPE 76 75 81 65 69 49 5

Figure S85.  Get High-res Image Gene #17: 'amp_11p13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_11p13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0422 (Fisher's exact test), Q value = 0.083

Table S86.  Gene #17: 'amp_11p13' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 104 198
AMP PEAK 17(11P13) MUTATED 32 29 31
AMP PEAK 17(11P13) WILD-TYPE 139 75 167

Figure S86.  Get High-res Image Gene #17: 'amp_11p13' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_11q13.3' versus 'CN_CNMF'

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

Table S87.  Gene #18: 'amp_11q13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
AMP PEAK 18(11Q13.3) MUTATED 135 59 22 13
AMP PEAK 18(11Q13.3) WILD-TYPE 68 69 123 33

Figure S87.  Get High-res Image Gene #18: 'amp_11q13.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11q13.3' versus 'METHLYATION_CNMF'

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

Table S88.  Gene #18: 'amp_11q13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
AMP PEAK 18(11Q13.3) MUTATED 30 38 37 53 15 51 5
AMP PEAK 18(11Q13.3) WILD-TYPE 54 49 66 36 63 24 1

Figure S88.  Get High-res Image Gene #18: 'amp_11q13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_11q13.3' versus 'MRNASEQ_CNMF'

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

Table S89.  Gene #18: 'amp_11q13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 171 95
AMP PEAK 18(11Q13.3) MUTATED 84 45 54 44
AMP PEAK 18(11Q13.3) WILD-TYPE 51 68 117 51

Figure S89.  Get High-res Image Gene #18: 'amp_11q13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_11q13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0318 (Fisher's exact test), Q value = 0.065

Table S90.  Gene #18: 'amp_11q13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
AMP PEAK 18(11Q13.3) MUTATED 82 42 84 19
AMP PEAK 18(11Q13.3) WILD-TYPE 94 61 86 46

Figure S90.  Get High-res Image Gene #18: 'amp_11q13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_11q13.3' versus 'MIRSEQ_CNMF'

P value = 0.0301 (Fisher's exact test), Q value = 0.063

Table S91.  Gene #18: 'amp_11q13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 139 131 91 76
AMP PEAK 18(11Q13.3) MUTATED 42 67 45 45 28
AMP PEAK 18(11Q13.3) WILD-TYPE 39 72 86 46 48

Figure S91.  Get High-res Image Gene #18: 'amp_11q13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_11q13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0046 (Fisher's exact test), Q value = 0.012

Table S92.  Gene #18: 'amp_11q13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
AMP PEAK 18(11Q13.3) MUTATED 91 72 64
AMP PEAK 18(11Q13.3) WILD-TYPE 99 70 122

Figure S92.  Get High-res Image Gene #18: 'amp_11q13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_12p13.33' versus 'CN_CNMF'

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

Table S93.  Gene #19: 'amp_12p13.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
AMP PEAK 19(12P13.33) MUTATED 77 62 12 16
AMP PEAK 19(12P13.33) WILD-TYPE 126 66 133 30

Figure S93.  Get High-res Image Gene #19: 'amp_12p13.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12p13.33' versus 'METHLYATION_CNMF'

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

Table S94.  Gene #19: 'amp_12p13.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
AMP PEAK 19(12P13.33) MUTATED 14 40 15 44 23 30 1
AMP PEAK 19(12P13.33) WILD-TYPE 70 47 88 45 55 45 5

Figure S94.  Get High-res Image Gene #19: 'amp_12p13.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_12p13.33' versus 'MRNASEQ_CNMF'

P value = 0.00177 (Fisher's exact test), Q value = 0.0053

Table S95.  Gene #19: 'amp_12p13.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 171 95
AMP PEAK 19(12P13.33) MUTATED 44 21 67 34
AMP PEAK 19(12P13.33) WILD-TYPE 91 92 104 61

Figure S95.  Get High-res Image Gene #19: 'amp_12p13.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_12p13.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00035

Table S96.  Gene #19: 'amp_12p13.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
AMP PEAK 19(12P13.33) MUTATED 61 50 39 16
AMP PEAK 19(12P13.33) WILD-TYPE 115 53 131 49

Figure S96.  Get High-res Image Gene #19: 'amp_12p13.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_12p13.33' versus 'MIRSEQ_CNMF'

P value = 0.0259 (Fisher's exact test), Q value = 0.055

Table S97.  Gene #19: 'amp_12p13.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 139 131 91 76
AMP PEAK 19(12P13.33) MUTATED 32 34 52 29 19
AMP PEAK 19(12P13.33) WILD-TYPE 49 105 79 62 57

Figure S97.  Get High-res Image Gene #19: 'amp_12p13.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_12q15' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 8.9e-05

Table S98.  Gene #20: 'amp_12q15' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
AMP PEAK 20(12Q15) MUTATED 46 37 10 10
AMP PEAK 20(12Q15) WILD-TYPE 157 91 135 36

Figure S98.  Get High-res Image Gene #20: 'amp_12q15' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12q15' versus 'METHLYATION_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00028

Table S99.  Gene #20: 'amp_12q15' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
AMP PEAK 20(12Q15) MUTATED 8 22 9 29 13 21 1
AMP PEAK 20(12Q15) WILD-TYPE 76 65 94 60 65 54 5

Figure S99.  Get High-res Image Gene #20: 'amp_12q15' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_12q15' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00167 (Fisher's exact test), Q value = 0.005

Table S100.  Gene #20: 'amp_12q15' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
AMP PEAK 20(12Q15) MUTATED 35 34 25 8
AMP PEAK 20(12Q15) WILD-TYPE 141 69 145 57

Figure S100.  Get High-res Image Gene #20: 'amp_12q15' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_13q22.1' versus 'CN_CNMF'

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

Table S101.  Gene #21: 'amp_13q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
AMP PEAK 21(13Q22.1) MUTATED 74 16 11 4
AMP PEAK 21(13Q22.1) WILD-TYPE 129 112 134 42

Figure S101.  Get High-res Image Gene #21: 'amp_13q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_13q22.1' versus 'METHLYATION_CNMF'

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

Table S102.  Gene #21: 'amp_13q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
AMP PEAK 21(13Q22.1) MUTATED 9 23 12 17 12 30 2
AMP PEAK 21(13Q22.1) WILD-TYPE 75 64 91 72 66 45 4

Figure S102.  Get High-res Image Gene #21: 'amp_13q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_13q34' versus 'CN_CNMF'

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

Table S103.  Gene #22: 'amp_13q34' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
AMP PEAK 22(13Q34) MUTATED 71 14 13 8
AMP PEAK 22(13Q34) WILD-TYPE 132 114 132 38

Figure S103.  Get High-res Image Gene #22: 'amp_13q34' versus Molecular Subtype #1: 'CN_CNMF'

'amp_13q34' versus 'METHLYATION_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.0016

Table S104.  Gene #22: 'amp_13q34' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
AMP PEAK 22(13Q34) MUTATED 12 20 14 19 10 30 1
AMP PEAK 22(13Q34) WILD-TYPE 72 67 89 70 68 45 5

Figure S104.  Get High-res Image Gene #22: 'amp_13q34' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_13q34' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00402 (Fisher's exact test), Q value = 0.011

Table S105.  Gene #22: 'amp_13q34' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

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

Figure S105.  Get High-res Image Gene #22: 'amp_13q34' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_15q26.3' versus 'CN_CNMF'

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

Table S106.  Gene #23: 'amp_15q26.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
AMP PEAK 23(15Q26.3) MUTATED 54 33 13 5
AMP PEAK 23(15Q26.3) WILD-TYPE 149 95 132 41

Figure S106.  Get High-res Image Gene #23: 'amp_15q26.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_15q26.3' versus 'METHLYATION_CNMF'

P value = 0.00443 (Fisher's exact test), Q value = 0.012

Table S107.  Gene #23: 'amp_15q26.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
AMP PEAK 23(15Q26.3) MUTATED 9 21 19 26 8 20 2
AMP PEAK 23(15Q26.3) WILD-TYPE 75 66 84 63 70 55 4

Figure S107.  Get High-res Image Gene #23: 'amp_15q26.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_17q12' versus 'CN_CNMF'

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

Table S108.  Gene #24: 'amp_17q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
AMP PEAK 24(17Q12) MUTATED 43 36 4 8
AMP PEAK 24(17Q12) WILD-TYPE 160 92 141 38

Figure S108.  Get High-res Image Gene #24: 'amp_17q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q12' versus 'METHLYATION_CNMF'

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

Table S109.  Gene #24: 'amp_17q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
AMP PEAK 24(17Q12) MUTATED 6 23 7 29 6 20 0
AMP PEAK 24(17Q12) WILD-TYPE 78 64 96 60 72 55 6

Figure S109.  Get High-res Image Gene #24: 'amp_17q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_17q12' versus 'MRNASEQ_CNMF'

P value = 0.00255 (Fisher's exact test), Q value = 0.0074

Table S110.  Gene #24: 'amp_17q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 171 95
AMP PEAK 24(17Q12) MUTATED 25 9 42 14
AMP PEAK 24(17Q12) WILD-TYPE 110 104 129 81

Figure S110.  Get High-res Image Gene #24: 'amp_17q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_17q12' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S111.  Gene #24: 'amp_17q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

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

Figure S111.  Get High-res Image Gene #24: 'amp_17q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_CNMF'

P value = 0.0207 (Fisher's exact test), Q value = 0.046

Table S112.  Gene #24: 'amp_17q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 139 131 91 76
AMP PEAK 24(17Q12) MUTATED 24 22 17 18 9
AMP PEAK 24(17Q12) WILD-TYPE 57 117 114 73 67

Figure S112.  Get High-res Image Gene #24: 'amp_17q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_17q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00017

Table S113.  Gene #24: 'amp_17q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
AMP PEAK 24(17Q12) MUTATED 31 41 18
AMP PEAK 24(17Q12) WILD-TYPE 159 101 168

Figure S113.  Get High-res Image Gene #24: 'amp_17q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_18p11.31' versus 'CN_CNMF'

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

Table S114.  Gene #25: 'amp_18p11.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
AMP PEAK 25(18P11.31) MUTATED 73 56 20 7
AMP PEAK 25(18P11.31) WILD-TYPE 130 72 125 39

Figure S114.  Get High-res Image Gene #25: 'amp_18p11.31' versus Molecular Subtype #1: 'CN_CNMF'

'amp_18p11.31' versus 'METHLYATION_CNMF'

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

Table S115.  Gene #25: 'amp_18p11.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
AMP PEAK 25(18P11.31) MUTATED 9 50 15 33 21 26 2
AMP PEAK 25(18P11.31) WILD-TYPE 75 37 88 56 57 49 4

Figure S115.  Get High-res Image Gene #25: 'amp_18p11.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_18p11.31' versus 'MRNASEQ_CNMF'

P value = 0.00946 (Fisher's exact test), Q value = 0.023

Table S116.  Gene #25: 'amp_18p11.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 171 95
AMP PEAK 25(18P11.31) MUTATED 42 23 65 24
AMP PEAK 25(18P11.31) WILD-TYPE 93 90 106 71

Figure S116.  Get High-res Image Gene #25: 'amp_18p11.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_18p11.31' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S117.  Gene #25: 'amp_18p11.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
AMP PEAK 25(18P11.31) MUTATED 46 52 39 17
AMP PEAK 25(18P11.31) WILD-TYPE 130 51 131 48

Figure S117.  Get High-res Image Gene #25: 'amp_18p11.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_18p11.31' versus 'MIRSEQ_CNMF'

P value = 0.0106 (Fisher's exact test), Q value = 0.025

Table S118.  Gene #25: 'amp_18p11.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 139 131 91 76
AMP PEAK 25(18P11.31) MUTATED 36 38 40 27 14
AMP PEAK 25(18P11.31) WILD-TYPE 45 101 91 64 62

Figure S118.  Get High-res Image Gene #25: 'amp_18p11.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_18p11.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.00072

Table S119.  Gene #25: 'amp_18p11.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
AMP PEAK 25(18P11.31) MUTATED 49 62 44
AMP PEAK 25(18P11.31) WILD-TYPE 141 80 142

Figure S119.  Get High-res Image Gene #25: 'amp_18p11.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_18q11.2' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 8.9e-05

Table S120.  Gene #26: 'amp_18q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
AMP PEAK 26(18Q11.2) MUTATED 44 42 15 5
AMP PEAK 26(18Q11.2) WILD-TYPE 159 86 130 41

Figure S120.  Get High-res Image Gene #26: 'amp_18q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_18q11.2' versus 'METHLYATION_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.0012

Table S121.  Gene #26: 'amp_18q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
AMP PEAK 26(18Q11.2) MUTATED 7 27 12 26 17 15 2
AMP PEAK 26(18Q11.2) WILD-TYPE 77 60 91 63 61 60 4

Figure S121.  Get High-res Image Gene #26: 'amp_18q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_18q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0126 (Fisher's exact test), Q value = 0.029

Table S122.  Gene #26: 'amp_18q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
AMP PEAK 26(18Q11.2) MUTATED 29 33 29 14
AMP PEAK 26(18Q11.2) WILD-TYPE 147 70 141 51

Figure S122.  Get High-res Image Gene #26: 'amp_18q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_18q11.2' versus 'MIRSEQ_CNMF'

P value = 0.00799 (Fisher's exact test), Q value = 0.02

Table S123.  Gene #26: 'amp_18q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 139 131 91 76
AMP PEAK 26(18Q11.2) MUTATED 26 19 30 20 10
AMP PEAK 26(18Q11.2) WILD-TYPE 55 120 101 71 66

Figure S123.  Get High-res Image Gene #26: 'amp_18q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_18q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0287 (Fisher's exact test), Q value = 0.06

Table S124.  Gene #26: 'amp_18q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
AMP PEAK 26(18Q11.2) MUTATED 33 40 32
AMP PEAK 26(18Q11.2) WILD-TYPE 157 102 154

Figure S124.  Get High-res Image Gene #26: 'amp_18q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_20q11.22' versus 'CN_CNMF'

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

Table S125.  Gene #27: 'amp_20q11.22' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
AMP PEAK 27(20Q11.22) MUTATED 115 55 35 22
AMP PEAK 27(20Q11.22) WILD-TYPE 88 73 110 24

Figure S125.  Get High-res Image Gene #27: 'amp_20q11.22' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20q11.22' versus 'METHLYATION_CNMF'

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

Table S126.  Gene #27: 'amp_20q11.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
AMP PEAK 27(20Q11.22) MUTATED 30 44 29 45 27 49 3
AMP PEAK 27(20Q11.22) WILD-TYPE 54 43 74 44 51 26 3

Figure S126.  Get High-res Image Gene #27: 'amp_20q11.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_20q11.22' versus 'RPPA_CNMF'

P value = 0.0487 (Fisher's exact test), Q value = 0.094

Table S127.  Gene #27: 'amp_20q11.22' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 50 29 31 29 67
AMP PEAK 27(20Q11.22) MUTATED 22 19 14 15 22
AMP PEAK 27(20Q11.22) WILD-TYPE 28 10 17 14 45

Figure S127.  Get High-res Image Gene #27: 'amp_20q11.22' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_20q11.22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0287 (Fisher's exact test), Q value = 0.06

Table S128.  Gene #27: 'amp_20q11.22' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
AMP PEAK 27(20Q11.22) MUTATED 90 44 69 20
AMP PEAK 27(20Q11.22) WILD-TYPE 86 59 101 45

Figure S128.  Get High-res Image Gene #27: 'amp_20q11.22' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_20q11.22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0236 (Fisher's exact test), Q value = 0.051

Table S129.  Gene #27: 'amp_20q11.22' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
AMP PEAK 27(20Q11.22) MUTATED 96 61 68
AMP PEAK 27(20Q11.22) WILD-TYPE 94 81 118

Figure S129.  Get High-res Image Gene #27: 'amp_20q11.22' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_20q11.22' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0173 (Fisher's exact test), Q value = 0.039

Table S130.  Gene #27: 'amp_20q11.22' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 104 198
AMP PEAK 27(20Q11.22) MUTATED 84 49 70
AMP PEAK 27(20Q11.22) WILD-TYPE 87 55 128

Figure S130.  Get High-res Image Gene #27: 'amp_20q11.22' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_xq28' versus 'CN_CNMF'

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

Table S131.  Gene #28: 'amp_xq28' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
AMP PEAK 28(XQ28) MUTATED 89 32 18 11
AMP PEAK 28(XQ28) WILD-TYPE 114 96 127 35

Figure S131.  Get High-res Image Gene #28: 'amp_xq28' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xq28' versus 'METHLYATION_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00038

Table S132.  Gene #28: 'amp_xq28' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
AMP PEAK 28(XQ28) MUTATED 10 25 25 36 20 32 2
AMP PEAK 28(XQ28) WILD-TYPE 74 62 78 53 58 43 4

Figure S132.  Get High-res Image Gene #28: 'amp_xq28' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p36.21' versus 'CN_CNMF'

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

Table S133.  Gene #29: 'del_1p36.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
DEL PEAK 1(1P36.21) MUTATED 36 43 9 7
DEL PEAK 1(1P36.21) WILD-TYPE 167 85 136 39

Figure S133.  Get High-res Image Gene #29: 'del_1p36.21' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.21' versus 'METHLYATION_CNMF'

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

Table S134.  Gene #29: 'del_1p36.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
DEL PEAK 1(1P36.21) MUTATED 5 17 11 48 8 6 0
DEL PEAK 1(1P36.21) WILD-TYPE 79 70 92 41 70 69 6

Figure S134.  Get High-res Image Gene #29: 'del_1p36.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p36.21' versus 'RPPA_CNMF'

P value = 0.021 (Fisher's exact test), Q value = 0.046

Table S135.  Gene #29: 'del_1p36.21' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 50 29 31 29 67
DEL PEAK 1(1P36.21) MUTATED 9 6 14 3 13
DEL PEAK 1(1P36.21) WILD-TYPE 41 23 17 26 54

Figure S135.  Get High-res Image Gene #29: 'del_1p36.21' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_1p36.21' versus 'RPPA_CHIERARCHICAL'

P value = 0.00578 (Fisher's exact test), Q value = 0.015

Table S136.  Gene #29: 'del_1p36.21' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

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

Figure S136.  Get High-res Image Gene #29: 'del_1p36.21' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_1p36.21' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00028

Table S137.  Gene #29: 'del_1p36.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 171 95
DEL PEAK 1(1P36.21) MUTATED 25 8 48 13
DEL PEAK 1(1P36.21) WILD-TYPE 110 105 123 82

Figure S137.  Get High-res Image Gene #29: 'del_1p36.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_1p36.21' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S138.  Gene #29: 'del_1p36.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

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

Figure S138.  Get High-res Image Gene #29: 'del_1p36.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.21' versus 'MIRSEQ_CNMF'

P value = 0.00709 (Fisher's exact test), Q value = 0.018

Table S139.  Gene #29: 'del_1p36.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 139 131 91 76
DEL PEAK 1(1P36.21) MUTATED 22 15 31 14 10
DEL PEAK 1(1P36.21) WILD-TYPE 59 124 100 77 66

Figure S139.  Get High-res Image Gene #29: 'del_1p36.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_1p36.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0405 (Fisher's exact test), Q value = 0.081

Table S140.  Gene #29: 'del_1p36.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

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

Figure S140.  Get High-res Image Gene #29: 'del_1p36.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00355 (Fisher's exact test), Q value = 0.0099

Table S141.  Gene #29: 'del_1p36.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 189 143
DEL PEAK 1(1P36.21) MUTATED 23 22 37
DEL PEAK 1(1P36.21) WILD-TYPE 118 167 106

Figure S141.  Get High-res Image Gene #29: 'del_1p36.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_1p36.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00681 (Fisher's exact test), Q value = 0.017

Table S142.  Gene #29: 'del_1p36.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 104 198
DEL PEAK 1(1P36.21) MUTATED 24 11 47
DEL PEAK 1(1P36.21) WILD-TYPE 147 93 151

Figure S142.  Get High-res Image Gene #29: 'del_1p36.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p13.2' versus 'CN_CNMF'

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

Table S143.  Gene #30: 'del_1p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
DEL PEAK 2(1P13.2) MUTATED 67 46 7 13
DEL PEAK 2(1P13.2) WILD-TYPE 136 82 138 33

Figure S143.  Get High-res Image Gene #30: 'del_1p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p13.2' versus 'METHLYATION_CNMF'

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

Table S144.  Gene #30: 'del_1p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
DEL PEAK 2(1P13.2) MUTATED 13 27 15 55 6 14 3
DEL PEAK 2(1P13.2) WILD-TYPE 71 60 88 34 72 61 3

Figure S144.  Get High-res Image Gene #30: 'del_1p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p13.2' versus 'RPPA_CNMF'

P value = 0.0108 (Fisher's exact test), Q value = 0.026

Table S145.  Gene #30: 'del_1p13.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 50 29 31 29 67
DEL PEAK 2(1P13.2) MUTATED 7 6 15 9 23
DEL PEAK 2(1P13.2) WILD-TYPE 43 23 16 20 44

Figure S145.  Get High-res Image Gene #30: 'del_1p13.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_1p13.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00712 (Fisher's exact test), Q value = 0.018

Table S146.  Gene #30: 'del_1p13.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

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

Figure S146.  Get High-res Image Gene #30: 'del_1p13.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_1p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 8.9e-05

Table S147.  Gene #30: 'del_1p13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

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

Figure S147.  Get High-res Image Gene #30: 'del_1p13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1p13.2' versus 'MIRSEQ_CNMF'

P value = 0.00081 (Fisher's exact test), Q value = 0.0026

Table S148.  Gene #30: 'del_1p13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 139 131 91 76
DEL PEAK 2(1P13.2) MUTATED 34 27 39 16 15
DEL PEAK 2(1P13.2) WILD-TYPE 47 112 92 75 61

Figure S148.  Get High-res Image Gene #30: 'del_1p13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_1p13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00038

Table S149.  Gene #30: 'del_1p13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

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

Figure S149.  Get High-res Image Gene #30: 'del_1p13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_1q44' versus 'CN_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00035

Table S150.  Gene #31: 'del_1q44' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
DEL PEAK 3(1Q44) MUTATED 28 7 4 9
DEL PEAK 3(1Q44) WILD-TYPE 175 121 141 37

Figure S150.  Get High-res Image Gene #31: 'del_1q44' versus Molecular Subtype #1: 'CN_CNMF'

'del_1q44' versus 'METHLYATION_CNMF'

P value = 0.012 (Fisher's exact test), Q value = 0.028

Table S151.  Gene #31: 'del_1q44' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
DEL PEAK 3(1Q44) MUTATED 8 6 12 7 1 14 0
DEL PEAK 3(1Q44) WILD-TYPE 76 81 91 82 77 61 6

Figure S151.  Get High-res Image Gene #31: 'del_1q44' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1q44' versus 'MRNASEQ_CNMF'

P value = 0.00853 (Fisher's exact test), Q value = 0.021

Table S152.  Gene #31: 'del_1q44' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 171 95
DEL PEAK 3(1Q44) MUTATED 14 16 6 10
DEL PEAK 3(1Q44) WILD-TYPE 121 97 165 85

Figure S152.  Get High-res Image Gene #31: 'del_1q44' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_1q44' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0102 (Fisher's exact test), Q value = 0.024

Table S153.  Gene #31: 'del_1q44' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

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

Figure S153.  Get High-res Image Gene #31: 'del_1q44' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1q44' versus 'MIRSEQ_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.0013

Table S154.  Gene #31: 'del_1q44' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 139 131 91 76
DEL PEAK 3(1Q44) MUTATED 4 23 3 7 10
DEL PEAK 3(1Q44) WILD-TYPE 77 116 128 84 66

Figure S154.  Get High-res Image Gene #31: 'del_1q44' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_1q44' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0459 (Fisher's exact test), Q value = 0.089

Table S155.  Gene #31: 'del_1q44' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

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

Figure S155.  Get High-res Image Gene #31: 'del_1q44' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_2q21.2' versus 'CN_CNMF'

P value = 0.0495 (Fisher's exact test), Q value = 0.095

Table S156.  Gene #32: 'del_2q21.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
DEL PEAK 4(2Q21.2) MUTATED 35 15 16 12
DEL PEAK 4(2Q21.2) WILD-TYPE 168 113 129 34

Figure S156.  Get High-res Image Gene #32: 'del_2q21.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q21.2' versus 'MRNASEQ_CNMF'

P value = 0.0063 (Fisher's exact test), Q value = 0.016

Table S157.  Gene #32: 'del_2q21.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 171 95
DEL PEAK 4(2Q21.2) MUTATED 29 21 17 8
DEL PEAK 4(2Q21.2) WILD-TYPE 106 92 154 87

Figure S157.  Get High-res Image Gene #32: 'del_2q21.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2q21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.00072

Table S158.  Gene #32: 'del_2q21.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

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

Figure S158.  Get High-res Image Gene #32: 'del_2q21.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_2q21.2' versus 'MIRSEQ_CNMF'

P value = 0.0386 (Fisher's exact test), Q value = 0.077

Table S159.  Gene #32: 'del_2q21.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 139 131 91 76
DEL PEAK 4(2Q21.2) MUTATED 17 28 16 10 6
DEL PEAK 4(2Q21.2) WILD-TYPE 64 111 115 81 70

Figure S159.  Get High-res Image Gene #32: 'del_2q21.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_2q22.1' versus 'CN_CNMF'

P value = 0.00468 (Fisher's exact test), Q value = 0.012

Table S160.  Gene #33: 'del_2q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
DEL PEAK 5(2Q22.1) MUTATED 55 33 19 14
DEL PEAK 5(2Q22.1) WILD-TYPE 148 95 126 32

Figure S160.  Get High-res Image Gene #33: 'del_2q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q22.1' versus 'METHLYATION_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00038

Table S161.  Gene #33: 'del_2q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
DEL PEAK 5(2Q22.1) MUTATED 10 18 24 39 11 18 1
DEL PEAK 5(2Q22.1) WILD-TYPE 74 69 79 50 67 57 5

Figure S161.  Get High-res Image Gene #33: 'del_2q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00972 (Fisher's exact test), Q value = 0.023

Table S162.  Gene #33: 'del_2q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 5(2Q22.1) MUTATED 34 30 47 7
DEL PEAK 5(2Q22.1) WILD-TYPE 142 73 123 58

Figure S162.  Get High-res Image Gene #33: 'del_2q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_2q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00139 (Fisher's exact test), Q value = 0.0043

Table S163.  Gene #33: 'del_2q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
DEL PEAK 5(2Q22.1) MUTATED 39 49 33
DEL PEAK 5(2Q22.1) WILD-TYPE 151 93 153

Figure S163.  Get High-res Image Gene #33: 'del_2q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_2q36.2' versus 'CN_CNMF'

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

Table S164.  Gene #34: 'del_2q36.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
DEL PEAK 6(2Q36.2) MUTATED 62 58 17 20
DEL PEAK 6(2Q36.2) WILD-TYPE 141 70 128 26

Figure S164.  Get High-res Image Gene #34: 'del_2q36.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q36.2' versus 'METHLYATION_CNMF'

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

Table S165.  Gene #34: 'del_2q36.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
DEL PEAK 6(2Q36.2) MUTATED 8 28 25 48 24 21 3
DEL PEAK 6(2Q36.2) WILD-TYPE 76 59 78 41 54 54 3

Figure S165.  Get High-res Image Gene #34: 'del_2q36.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q36.2' versus 'MRNASEQ_CNMF'

P value = 0.0088 (Fisher's exact test), Q value = 0.021

Table S166.  Gene #34: 'del_2q36.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 171 95
DEL PEAK 6(2Q36.2) MUTATED 49 25 60 20
DEL PEAK 6(2Q36.2) WILD-TYPE 86 88 111 75

Figure S166.  Get High-res Image Gene #34: 'del_2q36.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2q36.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0248 (Fisher's exact test), Q value = 0.053

Table S167.  Gene #34: 'del_2q36.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
DEL PEAK 6(2Q36.2) MUTATED 49 55 50
DEL PEAK 6(2Q36.2) WILD-TYPE 141 87 136

Figure S167.  Get High-res Image Gene #34: 'del_2q36.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p26.2' versus 'CN_CNMF'

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

Table S168.  Gene #35: 'del_3p26.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
DEL PEAK 7(3P26.2) MUTATED 190 96 30 32
DEL PEAK 7(3P26.2) WILD-TYPE 13 32 115 14

Figure S168.  Get High-res Image Gene #35: 'del_3p26.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p26.2' versus 'METHLYATION_CNMF'

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

Table S169.  Gene #35: 'del_3p26.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
DEL PEAK 7(3P26.2) MUTATED 50 73 55 76 19 69 6
DEL PEAK 7(3P26.2) WILD-TYPE 34 14 48 13 59 6 0

Figure S169.  Get High-res Image Gene #35: 'del_3p26.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p26.2' versus 'MRNASEQ_CNMF'

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

Table S170.  Gene #35: 'del_3p26.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 171 95
DEL PEAK 7(3P26.2) MUTATED 103 64 100 76
DEL PEAK 7(3P26.2) WILD-TYPE 32 49 71 19

Figure S170.  Get High-res Image Gene #35: 'del_3p26.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p26.2' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S171.  Gene #35: 'del_3p26.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 7(3P26.2) MUTATED 134 83 107 19
DEL PEAK 7(3P26.2) WILD-TYPE 42 20 63 46

Figure S171.  Get High-res Image Gene #35: 'del_3p26.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p26.2' versus 'MIRSEQ_CNMF'

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

Table S172.  Gene #35: 'del_3p26.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 139 131 91 76
DEL PEAK 7(3P26.2) MUTATED 68 85 67 68 58
DEL PEAK 7(3P26.2) WILD-TYPE 13 54 64 23 18

Figure S172.  Get High-res Image Gene #35: 'del_3p26.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3p26.2' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S173.  Gene #35: 'del_3p26.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
DEL PEAK 7(3P26.2) MUTATED 144 106 96
DEL PEAK 7(3P26.2) WILD-TYPE 46 36 90

Figure S173.  Get High-res Image Gene #35: 'del_3p26.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p26.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0198 (Fisher's exact test), Q value = 0.044

Table S174.  Gene #35: 'del_3p26.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 104 198
DEL PEAK 7(3P26.2) MUTATED 127 68 120
DEL PEAK 7(3P26.2) WILD-TYPE 44 36 78

Figure S174.  Get High-res Image Gene #35: 'del_3p26.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p24.1' versus 'CN_CNMF'

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

Table S175.  Gene #36: 'del_3p24.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
DEL PEAK 8(3P24.1) MUTATED 191 107 36 34
DEL PEAK 8(3P24.1) WILD-TYPE 12 21 109 12

Figure S175.  Get High-res Image Gene #36: 'del_3p24.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p24.1' versus 'METHLYATION_CNMF'

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

Table S176.  Gene #36: 'del_3p24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
DEL PEAK 8(3P24.1) MUTATED 50 78 56 80 29 69 6
DEL PEAK 8(3P24.1) WILD-TYPE 34 9 47 9 49 6 0

Figure S176.  Get High-res Image Gene #36: 'del_3p24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p24.1' versus 'MRNASEQ_CNMF'

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

Table S177.  Gene #36: 'del_3p24.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 171 95
DEL PEAK 8(3P24.1) MUTATED 105 66 116 76
DEL PEAK 8(3P24.1) WILD-TYPE 30 47 55 19

Figure S177.  Get High-res Image Gene #36: 'del_3p24.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p24.1' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S178.  Gene #36: 'del_3p24.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 8(3P24.1) MUTATED 137 91 108 27
DEL PEAK 8(3P24.1) WILD-TYPE 39 12 62 38

Figure S178.  Get High-res Image Gene #36: 'del_3p24.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p24.1' versus 'MIRSEQ_CNMF'

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

Table S179.  Gene #36: 'del_3p24.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 139 131 91 76
DEL PEAK 8(3P24.1) MUTATED 70 87 78 70 60
DEL PEAK 8(3P24.1) WILD-TYPE 11 52 53 21 16

Figure S179.  Get High-res Image Gene #36: 'del_3p24.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3p24.1' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S180.  Gene #36: 'del_3p24.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
DEL PEAK 8(3P24.1) MUTATED 147 110 108
DEL PEAK 8(3P24.1) WILD-TYPE 43 32 78

Figure S180.  Get High-res Image Gene #36: 'del_3p24.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p24.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0142 (Fisher's exact test), Q value = 0.033

Table S181.  Gene #36: 'del_3p24.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 189 143
DEL PEAK 8(3P24.1) MUTATED 109 119 104
DEL PEAK 8(3P24.1) WILD-TYPE 32 70 39

Figure S181.  Get High-res Image Gene #36: 'del_3p24.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_3p14.2' versus 'CN_CNMF'

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

Table S182.  Gene #37: 'del_3p14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
DEL PEAK 9(3P14.2) MUTATED 190 110 36 36
DEL PEAK 9(3P14.2) WILD-TYPE 13 18 109 10

Figure S182.  Get High-res Image Gene #37: 'del_3p14.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p14.2' versus 'METHLYATION_CNMF'

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

Table S183.  Gene #37: 'del_3p14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
DEL PEAK 9(3P14.2) MUTATED 50 79 54 82 34 67 6
DEL PEAK 9(3P14.2) WILD-TYPE 34 8 49 7 44 8 0

Figure S183.  Get High-res Image Gene #37: 'del_3p14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p14.2' versus 'MRNASEQ_CNMF'

P value = 0.00579 (Fisher's exact test), Q value = 0.015

Table S184.  Gene #37: 'del_3p14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 171 95
DEL PEAK 9(3P14.2) MUTATED 105 67 121 74
DEL PEAK 9(3P14.2) WILD-TYPE 30 46 50 21

Figure S184.  Get High-res Image Gene #37: 'del_3p14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p14.2' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S185.  Gene #37: 'del_3p14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 9(3P14.2) MUTATED 135 93 108 31
DEL PEAK 9(3P14.2) WILD-TYPE 41 10 62 34

Figure S185.  Get High-res Image Gene #37: 'del_3p14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p14.2' versus 'MIRSEQ_CNMF'

P value = 0.00144 (Fisher's exact test), Q value = 0.0044

Table S186.  Gene #37: 'del_3p14.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 139 131 91 76
DEL PEAK 9(3P14.2) MUTATED 70 92 82 68 57
DEL PEAK 9(3P14.2) WILD-TYPE 11 47 49 23 19

Figure S186.  Get High-res Image Gene #37: 'del_3p14.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3p14.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00041 (Fisher's exact test), Q value = 0.0014

Table S187.  Gene #37: 'del_3p14.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
DEL PEAK 9(3P14.2) MUTATED 145 111 113
DEL PEAK 9(3P14.2) WILD-TYPE 45 31 73

Figure S187.  Get High-res Image Gene #37: 'del_3p14.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p14.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0319 (Fisher's exact test), Q value = 0.065

Table S188.  Gene #37: 'del_3p14.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 189 143
DEL PEAK 9(3P14.2) MUTATED 106 121 108
DEL PEAK 9(3P14.2) WILD-TYPE 35 68 35

Figure S188.  Get High-res Image Gene #37: 'del_3p14.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_3p12.1' versus 'CN_CNMF'

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

Table S189.  Gene #38: 'del_3p12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
DEL PEAK 10(3P12.1) MUTATED 180 104 28 31
DEL PEAK 10(3P12.1) WILD-TYPE 23 24 117 15

Figure S189.  Get High-res Image Gene #38: 'del_3p12.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p12.1' versus 'METHLYATION_CNMF'

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

Table S190.  Gene #38: 'del_3p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
DEL PEAK 10(3P12.1) MUTATED 46 75 51 82 24 60 5
DEL PEAK 10(3P12.1) WILD-TYPE 38 12 52 7 54 15 1

Figure S190.  Get High-res Image Gene #38: 'del_3p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p12.1' versus 'MRNASEQ_CNMF'

P value = 0.00161 (Fisher's exact test), Q value = 0.0049

Table S191.  Gene #38: 'del_3p12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 171 95
DEL PEAK 10(3P12.1) MUTATED 101 60 109 69
DEL PEAK 10(3P12.1) WILD-TYPE 34 53 62 26

Figure S191.  Get High-res Image Gene #38: 'del_3p12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p12.1' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S192.  Gene #38: 'del_3p12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 10(3P12.1) MUTATED 124 88 104 23
DEL PEAK 10(3P12.1) WILD-TYPE 52 15 66 42

Figure S192.  Get High-res Image Gene #38: 'del_3p12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p12.1' versus 'MIRSEQ_CNMF'

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

Table S193.  Gene #38: 'del_3p12.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 139 131 91 76
DEL PEAK 10(3P12.1) MUTATED 68 83 72 63 54
DEL PEAK 10(3P12.1) WILD-TYPE 13 56 59 28 22

Figure S193.  Get High-res Image Gene #38: 'del_3p12.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3p12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00047 (Fisher's exact test), Q value = 0.0016

Table S194.  Gene #38: 'del_3p12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
DEL PEAK 10(3P12.1) MUTATED 130 107 103
DEL PEAK 10(3P12.1) WILD-TYPE 60 35 83

Figure S194.  Get High-res Image Gene #38: 'del_3p12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_4p16.3' versus 'CN_CNMF'

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

Table S195.  Gene #39: 'del_4p16.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
DEL PEAK 11(4P16.3) MUTATED 95 84 10 16
DEL PEAK 11(4P16.3) WILD-TYPE 108 44 135 30

Figure S195.  Get High-res Image Gene #39: 'del_4p16.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_4p16.3' versus 'METHLYATION_CNMF'

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

Table S196.  Gene #39: 'del_4p16.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
DEL PEAK 11(4P16.3) MUTATED 20 47 26 61 20 26 5
DEL PEAK 11(4P16.3) WILD-TYPE 64 40 77 28 58 49 1

Figure S196.  Get High-res Image Gene #39: 'del_4p16.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4p16.3' versus 'MRNASEQ_CNMF'

P value = 0.00246 (Fisher's exact test), Q value = 0.0072

Table S197.  Gene #39: 'del_4p16.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 171 95
DEL PEAK 11(4P16.3) MUTATED 61 30 79 32
DEL PEAK 11(4P16.3) WILD-TYPE 74 83 92 63

Figure S197.  Get High-res Image Gene #39: 'del_4p16.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4p16.3' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S198.  Gene #39: 'del_4p16.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 11(4P16.3) MUTATED 72 63 51 16
DEL PEAK 11(4P16.3) WILD-TYPE 104 40 119 49

Figure S198.  Get High-res Image Gene #39: 'del_4p16.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4p16.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00814 (Fisher's exact test), Q value = 0.02

Table S199.  Gene #39: 'del_4p16.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 189 143
DEL PEAK 11(4P16.3) MUTATED 60 57 65
DEL PEAK 11(4P16.3) WILD-TYPE 81 132 78

Figure S199.  Get High-res Image Gene #39: 'del_4p16.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_4p16.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0412 (Fisher's exact test), Q value = 0.082

Table S200.  Gene #39: 'del_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 104 198
DEL PEAK 11(4P16.3) MUTATED 71 29 82
DEL PEAK 11(4P16.3) WILD-TYPE 100 75 116

Figure S200.  Get High-res Image Gene #39: 'del_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4p15.2' versus 'CN_CNMF'

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

Table S201.  Gene #40: 'del_4p15.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
DEL PEAK 12(4P15.2) MUTATED 95 86 10 17
DEL PEAK 12(4P15.2) WILD-TYPE 108 42 135 29

Figure S201.  Get High-res Image Gene #40: 'del_4p15.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_4p15.2' versus 'METHLYATION_CNMF'

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

Table S202.  Gene #40: 'del_4p15.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
DEL PEAK 12(4P15.2) MUTATED 22 47 25 65 21 23 5
DEL PEAK 12(4P15.2) WILD-TYPE 62 40 78 24 57 52 1

Figure S202.  Get High-res Image Gene #40: 'del_4p15.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4p15.2' versus 'RPPA_CNMF'

P value = 0.0248 (Fisher's exact test), Q value = 0.053

Table S203.  Gene #40: 'del_4p15.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 50 29 31 29 67
DEL PEAK 12(4P15.2) MUTATED 26 13 20 9 23
DEL PEAK 12(4P15.2) WILD-TYPE 24 16 11 20 44

Figure S203.  Get High-res Image Gene #40: 'del_4p15.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_4p15.2' versus 'MRNASEQ_CNMF'

P value = 0.00569 (Fisher's exact test), Q value = 0.015

Table S204.  Gene #40: 'del_4p15.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 171 95
DEL PEAK 12(4P15.2) MUTATED 58 30 80 37
DEL PEAK 12(4P15.2) WILD-TYPE 77 83 91 58

Figure S204.  Get High-res Image Gene #40: 'del_4p15.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4p15.2' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S205.  Gene #40: 'del_4p15.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 12(4P15.2) MUTATED 74 64 49 18
DEL PEAK 12(4P15.2) WILD-TYPE 102 39 121 47

Figure S205.  Get High-res Image Gene #40: 'del_4p15.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4p15.2' versus 'MIRSEQ_CNMF'

P value = 0.00646 (Fisher's exact test), Q value = 0.016

Table S206.  Gene #40: 'del_4p15.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 139 131 91 76
DEL PEAK 12(4P15.2) MUTATED 43 41 57 32 33
DEL PEAK 12(4P15.2) WILD-TYPE 38 98 74 59 43

Figure S206.  Get High-res Image Gene #40: 'del_4p15.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_4p15.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0302 (Fisher's exact test), Q value = 0.063

Table S207.  Gene #40: 'del_4p15.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
DEL PEAK 12(4P15.2) MUTATED 76 68 62
DEL PEAK 12(4P15.2) WILD-TYPE 114 74 124

Figure S207.  Get High-res Image Gene #40: 'del_4p15.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_4p15.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00111 (Fisher's exact test), Q value = 0.0035

Table S208.  Gene #40: 'del_4p15.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 189 143
DEL PEAK 12(4P15.2) MUTATED 64 55 66
DEL PEAK 12(4P15.2) WILD-TYPE 77 134 77

Figure S208.  Get High-res Image Gene #40: 'del_4p15.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_4p15.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00296 (Fisher's exact test), Q value = 0.0084

Table S209.  Gene #40: 'del_4p15.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 104 198
DEL PEAK 12(4P15.2) MUTATED 76 26 83
DEL PEAK 12(4P15.2) WILD-TYPE 95 78 115

Figure S209.  Get High-res Image Gene #40: 'del_4p15.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q21.3' versus 'CN_CNMF'

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

Table S210.  Gene #41: 'del_4q21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
DEL PEAK 13(4Q21.3) MUTATED 67 61 12 16
DEL PEAK 13(4Q21.3) WILD-TYPE 136 67 133 30

Figure S210.  Get High-res Image Gene #41: 'del_4q21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q21.3' versus 'METHLYATION_CNMF'

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

Table S211.  Gene #41: 'del_4q21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
DEL PEAK 13(4Q21.3) MUTATED 15 32 19 48 17 23 2
DEL PEAK 13(4Q21.3) WILD-TYPE 69 55 84 41 61 52 4

Figure S211.  Get High-res Image Gene #41: 'del_4q21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q21.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0465 (Fisher's exact test), Q value = 0.09

Table S212.  Gene #41: 'del_4q21.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 82 48
DEL PEAK 13(4Q21.3) MUTATED 21 32 9
DEL PEAK 13(4Q21.3) WILD-TYPE 55 50 39

Figure S212.  Get High-res Image Gene #41: 'del_4q21.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_4q21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 8.9e-05

Table S213.  Gene #41: 'del_4q21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 13(4Q21.3) MUTATED 63 44 30 15
DEL PEAK 13(4Q21.3) WILD-TYPE 113 59 140 50

Figure S213.  Get High-res Image Gene #41: 'del_4q21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0315 (Fisher's exact test), Q value = 0.065

Table S214.  Gene #41: 'del_4q21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
DEL PEAK 13(4Q21.3) MUTATED 63 48 42
DEL PEAK 13(4Q21.3) WILD-TYPE 127 94 144

Figure S214.  Get High-res Image Gene #41: 'del_4q21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_4q21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0296 (Fisher's exact test), Q value = 0.062

Table S215.  Gene #41: 'del_4q21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 104 198
DEL PEAK 13(4Q21.3) MUTATED 59 21 64
DEL PEAK 13(4Q21.3) WILD-TYPE 112 83 134

Figure S215.  Get High-res Image Gene #41: 'del_4q21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q22.1' versus 'CN_CNMF'

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

Table S216.  Gene #42: 'del_4q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
DEL PEAK 14(4Q22.1) MUTATED 75 66 11 17
DEL PEAK 14(4Q22.1) WILD-TYPE 128 62 134 29

Figure S216.  Get High-res Image Gene #42: 'del_4q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q22.1' versus 'METHLYATION_CNMF'

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

Table S217.  Gene #42: 'del_4q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
DEL PEAK 14(4Q22.1) MUTATED 12 34 22 58 18 23 2
DEL PEAK 14(4Q22.1) WILD-TYPE 72 53 81 31 60 52 4

Figure S217.  Get High-res Image Gene #42: 'del_4q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q22.1' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S218.  Gene #42: 'del_4q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 14(4Q22.1) MUTATED 63 48 40 15
DEL PEAK 14(4Q22.1) WILD-TYPE 113 55 130 50

Figure S218.  Get High-res Image Gene #42: 'del_4q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.04 (Fisher's exact test), Q value = 0.08

Table S219.  Gene #42: 'del_4q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
DEL PEAK 14(4Q22.1) MUTATED 66 53 47
DEL PEAK 14(4Q22.1) WILD-TYPE 124 89 139

Figure S219.  Get High-res Image Gene #42: 'del_4q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_4q35.2' versus 'CN_CNMF'

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

Table S220.  Gene #43: 'del_4q35.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
DEL PEAK 15(4Q35.2) MUTATED 102 70 16 25
DEL PEAK 15(4Q35.2) WILD-TYPE 101 58 129 21

Figure S220.  Get High-res Image Gene #43: 'del_4q35.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q35.2' versus 'METHLYATION_CNMF'

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

Table S221.  Gene #43: 'del_4q35.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
DEL PEAK 15(4Q35.2) MUTATED 24 43 34 55 20 35 2
DEL PEAK 15(4Q35.2) WILD-TYPE 60 44 69 34 58 40 4

Figure S221.  Get High-res Image Gene #43: 'del_4q35.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q35.2' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S222.  Gene #43: 'del_4q35.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 15(4Q35.2) MUTATED 79 55 59 15
DEL PEAK 15(4Q35.2) WILD-TYPE 97 48 111 50

Figure S222.  Get High-res Image Gene #43: 'del_4q35.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q35.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00601 (Fisher's exact test), Q value = 0.015

Table S223.  Gene #43: 'del_4q35.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
DEL PEAK 15(4Q35.2) MUTATED 84 68 59
DEL PEAK 15(4Q35.2) WILD-TYPE 106 74 127

Figure S223.  Get High-res Image Gene #43: 'del_4q35.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_5q12.1' versus 'CN_CNMF'

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

Table S224.  Gene #44: 'del_5q12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
DEL PEAK 16(5Q12.1) MUTATED 112 86 8 9
DEL PEAK 16(5Q12.1) WILD-TYPE 91 42 137 37

Figure S224.  Get High-res Image Gene #44: 'del_5q12.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q12.1' versus 'METHLYATION_CNMF'

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

Table S225.  Gene #44: 'del_5q12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
DEL PEAK 16(5Q12.1) MUTATED 16 56 22 62 10 46 3
DEL PEAK 16(5Q12.1) WILD-TYPE 68 31 81 27 68 29 3

Figure S225.  Get High-res Image Gene #44: 'del_5q12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q12.1' versus 'RPPA_CNMF'

P value = 0.00419 (Fisher's exact test), Q value = 0.011

Table S226.  Gene #44: 'del_5q12.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 50 29 31 29 67
DEL PEAK 16(5Q12.1) MUTATED 19 7 22 12 33
DEL PEAK 16(5Q12.1) WILD-TYPE 31 22 9 17 34

Figure S226.  Get High-res Image Gene #44: 'del_5q12.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_5q12.1' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S227.  Gene #44: 'del_5q12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 16(5Q12.1) MUTATED 81 70 48 14
DEL PEAK 16(5Q12.1) WILD-TYPE 95 33 122 51

Figure S227.  Get High-res Image Gene #44: 'del_5q12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_5q12.1' versus 'MIRSEQ_CNMF'

P value = 0.00264 (Fisher's exact test), Q value = 0.0076

Table S228.  Gene #44: 'del_5q12.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 139 131 91 76
DEL PEAK 16(5Q12.1) MUTATED 49 52 44 36 31
DEL PEAK 16(5Q12.1) WILD-TYPE 32 87 87 55 45

Figure S228.  Get High-res Image Gene #44: 'del_5q12.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_5q12.1' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S229.  Gene #44: 'del_5q12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
DEL PEAK 16(5Q12.1) MUTATED 84 75 53
DEL PEAK 16(5Q12.1) WILD-TYPE 106 67 133

Figure S229.  Get High-res Image Gene #44: 'del_5q12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_5q15' versus 'CN_CNMF'

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

Table S230.  Gene #45: 'del_5q15' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
DEL PEAK 17(5Q15) MUTATED 114 89 13 10
DEL PEAK 17(5Q15) WILD-TYPE 89 39 132 36

Figure S230.  Get High-res Image Gene #45: 'del_5q15' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q15' versus 'METHLYATION_CNMF'

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

Table S231.  Gene #45: 'del_5q15' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
DEL PEAK 17(5Q15) MUTATED 17 59 24 64 12 46 4
DEL PEAK 17(5Q15) WILD-TYPE 67 28 79 25 66 29 2

Figure S231.  Get High-res Image Gene #45: 'del_5q15' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q15' versus 'RPPA_CNMF'

P value = 0.0188 (Fisher's exact test), Q value = 0.042

Table S232.  Gene #45: 'del_5q15' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 50 29 31 29 67
DEL PEAK 17(5Q15) MUTATED 19 9 22 12 30
DEL PEAK 17(5Q15) WILD-TYPE 31 20 9 17 37

Figure S232.  Get High-res Image Gene #45: 'del_5q15' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_5q15' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S233.  Gene #45: 'del_5q15' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 17(5Q15) MUTATED 82 71 54 16
DEL PEAK 17(5Q15) WILD-TYPE 94 32 116 49

Figure S233.  Get High-res Image Gene #45: 'del_5q15' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_5q15' versus 'MIRSEQ_CNMF'

P value = 0.0121 (Fisher's exact test), Q value = 0.028

Table S234.  Gene #45: 'del_5q15' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 139 131 91 76
DEL PEAK 17(5Q15) MUTATED 49 56 49 40 29
DEL PEAK 17(5Q15) WILD-TYPE 32 83 82 51 47

Figure S234.  Get High-res Image Gene #45: 'del_5q15' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_5q15' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 8.9e-05

Table S235.  Gene #45: 'del_5q15' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
DEL PEAK 17(5Q15) MUTATED 86 80 57
DEL PEAK 17(5Q15) WILD-TYPE 104 62 129

Figure S235.  Get High-res Image Gene #45: 'del_5q15' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_5q35.3' versus 'CN_CNMF'

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

Table S236.  Gene #46: 'del_5q35.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
DEL PEAK 18(5Q35.3) MUTATED 94 87 7 11
DEL PEAK 18(5Q35.3) WILD-TYPE 109 41 138 35

Figure S236.  Get High-res Image Gene #46: 'del_5q35.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q35.3' versus 'METHLYATION_CNMF'

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

Table S237.  Gene #46: 'del_5q35.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
DEL PEAK 18(5Q35.3) MUTATED 17 63 15 49 11 39 5
DEL PEAK 18(5Q35.3) WILD-TYPE 67 24 88 40 67 36 1

Figure S237.  Get High-res Image Gene #46: 'del_5q35.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q35.3' versus 'MRNASEQ_CNMF'

P value = 0.00702 (Fisher's exact test), Q value = 0.017

Table S238.  Gene #46: 'del_5q35.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 171 95
DEL PEAK 18(5Q35.3) MUTATED 48 31 81 38
DEL PEAK 18(5Q35.3) WILD-TYPE 87 82 90 57

Figure S238.  Get High-res Image Gene #46: 'del_5q35.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_5q35.3' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S239.  Gene #46: 'del_5q35.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 18(5Q35.3) MUTATED 76 69 39 14
DEL PEAK 18(5Q35.3) WILD-TYPE 100 34 131 51

Figure S239.  Get High-res Image Gene #46: 'del_5q35.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_5q35.3' versus 'MIRSEQ_CNMF'

P value = 0.0377 (Fisher's exact test), Q value = 0.076

Table S240.  Gene #46: 'del_5q35.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 139 131 91 76
DEL PEAK 18(5Q35.3) MUTATED 43 51 42 31 29
DEL PEAK 18(5Q35.3) WILD-TYPE 38 88 89 60 47

Figure S240.  Get High-res Image Gene #46: 'del_5q35.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_5q35.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00017

Table S241.  Gene #46: 'del_5q35.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
DEL PEAK 18(5Q35.3) MUTATED 79 70 47
DEL PEAK 18(5Q35.3) WILD-TYPE 111 72 139

Figure S241.  Get High-res Image Gene #46: 'del_5q35.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_6p25.3' versus 'CN_CNMF'

P value = 0.00582 (Fisher's exact test), Q value = 0.015

Table S242.  Gene #47: 'del_6p25.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
DEL PEAK 19(6P25.3) MUTATED 41 32 14 9
DEL PEAK 19(6P25.3) WILD-TYPE 162 96 131 37

Figure S242.  Get High-res Image Gene #47: 'del_6p25.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_6p25.3' versus 'METHLYATION_CNMF'

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

Table S243.  Gene #47: 'del_6p25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
DEL PEAK 19(6P25.3) MUTATED 11 13 9 37 11 13 2
DEL PEAK 19(6P25.3) WILD-TYPE 73 74 94 52 67 62 4

Figure S243.  Get High-res Image Gene #47: 'del_6p25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6p25.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0107 (Fisher's exact test), Q value = 0.025

Table S244.  Gene #47: 'del_6p25.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 82 48
DEL PEAK 19(6P25.3) MUTATED 15 25 4
DEL PEAK 19(6P25.3) WILD-TYPE 61 57 44

Figure S244.  Get High-res Image Gene #47: 'del_6p25.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_6p25.3' versus 'MRNASEQ_CNMF'

P value = 0.0036 (Fisher's exact test), Q value = 0.01

Table S245.  Gene #47: 'del_6p25.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 171 95
DEL PEAK 19(6P25.3) MUTATED 29 9 32 24
DEL PEAK 19(6P25.3) WILD-TYPE 106 104 139 71

Figure S245.  Get High-res Image Gene #47: 'del_6p25.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6p25.3' versus 'MIRSEQ_CNMF'

P value = 0.0373 (Fisher's exact test), Q value = 0.076

Table S246.  Gene #47: 'del_6p25.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 139 131 91 76
DEL PEAK 19(6P25.3) MUTATED 13 18 32 13 20
DEL PEAK 19(6P25.3) WILD-TYPE 68 121 99 78 56

Figure S246.  Get High-res Image Gene #47: 'del_6p25.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_7q31.1' versus 'CN_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.00067

Table S247.  Gene #48: 'del_7q31.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
DEL PEAK 20(7Q31.1) MUTATED 42 17 8 10
DEL PEAK 20(7Q31.1) WILD-TYPE 161 111 137 36

Figure S247.  Get High-res Image Gene #48: 'del_7q31.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_7q31.1' versus 'MRNASEQ_CNMF'

P value = 0.00364 (Fisher's exact test), Q value = 0.01

Table S248.  Gene #48: 'del_7q31.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 171 95
DEL PEAK 20(7Q31.1) MUTATED 33 17 17 10
DEL PEAK 20(7Q31.1) WILD-TYPE 102 96 154 85

Figure S248.  Get High-res Image Gene #48: 'del_7q31.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_7q31.1' versus 'MIRSEQ_CNMF'

P value = 0.00217 (Fisher's exact test), Q value = 0.0065

Table S249.  Gene #48: 'del_7q31.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 139 131 91 76
DEL PEAK 20(7Q31.1) MUTATED 22 26 13 10 6
DEL PEAK 20(7Q31.1) WILD-TYPE 59 113 118 81 70

Figure S249.  Get High-res Image Gene #48: 'del_7q31.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_7q36.1' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 8.9e-05

Table S250.  Gene #49: 'del_7q36.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
DEL PEAK 21(7Q36.1) MUTATED 71 29 18 14
DEL PEAK 21(7Q36.1) WILD-TYPE 132 99 127 32

Figure S250.  Get High-res Image Gene #49: 'del_7q36.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_7q36.1' versus 'MRNASEQ_CNMF'

P value = 0.0429 (Fisher's exact test), Q value = 0.084

Table S251.  Gene #49: 'del_7q36.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 171 95
DEL PEAK 21(7Q36.1) MUTATED 46 21 41 23
DEL PEAK 21(7Q36.1) WILD-TYPE 89 92 130 72

Figure S251.  Get High-res Image Gene #49: 'del_7q36.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_7q36.1' versus 'MIRSEQ_CNMF'

P value = 0.00718 (Fisher's exact test), Q value = 0.018

Table S252.  Gene #49: 'del_7q36.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 139 131 91 76
DEL PEAK 21(7Q36.1) MUTATED 30 37 26 14 23
DEL PEAK 21(7Q36.1) WILD-TYPE 51 102 105 77 53

Figure S252.  Get High-res Image Gene #49: 'del_7q36.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_8p23.2' versus 'CN_CNMF'

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

Table S253.  Gene #50: 'del_8p23.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
DEL PEAK 22(8P23.2) MUTATED 169 59 49 28
DEL PEAK 22(8P23.2) WILD-TYPE 34 69 96 18

Figure S253.  Get High-res Image Gene #50: 'del_8p23.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p23.2' versus 'METHLYATION_CNMF'

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

Table S254.  Gene #50: 'del_8p23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
DEL PEAK 22(8P23.2) MUTATED 49 47 68 63 16 56 6
DEL PEAK 22(8P23.2) WILD-TYPE 35 40 35 26 62 19 0

Figure S254.  Get High-res Image Gene #50: 'del_8p23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_8p23.2' versus 'MRNASEQ_CNMF'

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

Table S255.  Gene #50: 'del_8p23.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 171 95
DEL PEAK 22(8P23.2) MUTATED 101 67 67 65
DEL PEAK 22(8P23.2) WILD-TYPE 34 46 104 30

Figure S255.  Get High-res Image Gene #50: 'del_8p23.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_8p23.2' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S256.  Gene #50: 'del_8p23.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 22(8P23.2) MUTATED 115 62 112 11
DEL PEAK 22(8P23.2) WILD-TYPE 61 41 58 54

Figure S256.  Get High-res Image Gene #50: 'del_8p23.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_CNMF'

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

Table S257.  Gene #50: 'del_8p23.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 139 131 91 76
DEL PEAK 22(8P23.2) MUTATED 53 93 46 64 47
DEL PEAK 22(8P23.2) WILD-TYPE 28 46 85 27 29

Figure S257.  Get High-res Image Gene #50: 'del_8p23.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_8p23.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00316 (Fisher's exact test), Q value = 0.0089

Table S258.  Gene #50: 'del_8p23.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
DEL PEAK 22(8P23.2) MUTATED 125 87 91
DEL PEAK 22(8P23.2) WILD-TYPE 65 55 95

Figure S258.  Get High-res Image Gene #50: 'del_8p23.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0265 (Fisher's exact test), Q value = 0.056

Table S259.  Gene #50: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 189 143
DEL PEAK 22(8P23.2) MUTATED 92 113 71
DEL PEAK 22(8P23.2) WILD-TYPE 49 76 72

Figure S259.  Get High-res Image Gene #50: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_8p23.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S260.  Gene #50: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 104 198
DEL PEAK 22(8P23.2) MUTATED 114 70 92
DEL PEAK 22(8P23.2) WILD-TYPE 57 34 106

Figure S260.  Get High-res Image Gene #50: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p23' versus 'CN_CNMF'

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

Table S261.  Gene #51: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
DEL PEAK 23(9P23) MUTATED 132 76 29 2
DEL PEAK 23(9P23) WILD-TYPE 71 52 116 44

Figure S261.  Get High-res Image Gene #51: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p23' versus 'METHLYATION_CNMF'

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

Table S262.  Gene #51: 'del_9p23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
DEL PEAK 23(9P23) MUTATED 28 64 35 63 9 37 3
DEL PEAK 23(9P23) WILD-TYPE 56 23 68 26 69 38 3

Figure S262.  Get High-res Image Gene #51: 'del_9p23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p23' versus 'MRNASEQ_CNMF'

P value = 0.00052 (Fisher's exact test), Q value = 0.0017

Table S263.  Gene #51: 'del_9p23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 171 95
DEL PEAK 23(9P23) MUTATED 82 40 75 40
DEL PEAK 23(9P23) WILD-TYPE 53 73 96 55

Figure S263.  Get High-res Image Gene #51: 'del_9p23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9p23' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S264.  Gene #51: 'del_9p23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 23(9P23) MUTATED 77 68 80 12
DEL PEAK 23(9P23) WILD-TYPE 99 35 90 53

Figure S264.  Get High-res Image Gene #51: 'del_9p23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_CNMF'

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

Table S265.  Gene #51: 'del_9p23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 139 131 91 76
DEL PEAK 23(9P23) MUTATED 57 64 42 38 35
DEL PEAK 23(9P23) WILD-TYPE 24 75 89 53 41

Figure S265.  Get High-res Image Gene #51: 'del_9p23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_9p23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00035

Table S266.  Gene #51: 'del_9p23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
DEL PEAK 23(9P23) MUTATED 85 85 66
DEL PEAK 23(9P23) WILD-TYPE 105 57 120

Figure S266.  Get High-res Image Gene #51: 'del_9p23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'CN_CNMF'

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

Table S267.  Gene #52: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
DEL PEAK 24(9P21.3) MUTATED 148 90 53 11
DEL PEAK 24(9P21.3) WILD-TYPE 55 38 92 35

Figure S267.  Get High-res Image Gene #52: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

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

Table S268.  Gene #52: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
DEL PEAK 24(9P21.3) MUTATED 43 73 54 67 11 49 5
DEL PEAK 24(9P21.3) WILD-TYPE 41 14 49 22 67 26 1

Figure S268.  Get High-res Image Gene #52: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00017

Table S269.  Gene #52: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 171 95
DEL PEAK 24(9P21.3) MUTATED 100 64 80 56
DEL PEAK 24(9P21.3) WILD-TYPE 35 49 91 39

Figure S269.  Get High-res Image Gene #52: '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 = 4.9e-05

Table S270.  Gene #52: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 24(9P21.3) MUTATED 103 75 107 15
DEL PEAK 24(9P21.3) WILD-TYPE 73 28 63 50

Figure S270.  Get High-res Image Gene #52: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_CNMF'

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

Table S271.  Gene #52: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 139 131 91 76
DEL PEAK 24(9P21.3) MUTATED 67 79 53 54 47
DEL PEAK 24(9P21.3) WILD-TYPE 14 60 78 37 29

Figure S271.  Get High-res Image Gene #52: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_9p21.3' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S272.  Gene #52: 'del_9p21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
DEL PEAK 24(9P21.3) MUTATED 113 108 79
DEL PEAK 24(9P21.3) WILD-TYPE 77 34 107

Figure S272.  Get High-res Image Gene #52: 'del_9p21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0364 (Fisher's exact test), Q value = 0.074

Table S273.  Gene #52: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 104 198
DEL PEAK 24(9P21.3) MUTATED 99 70 103
DEL PEAK 24(9P21.3) WILD-TYPE 72 34 95

Figure S273.  Get High-res Image Gene #52: '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 = 4.9e-05

Table S274.  Gene #53: 'del_9q21.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
DEL PEAK 25(9Q21.11) MUTATED 70 27 10 1
DEL PEAK 25(9Q21.11) WILD-TYPE 133 101 135 45

Figure S274.  Get High-res Image Gene #53: 'del_9q21.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_9q21.11' versus 'METHLYATION_CNMF'

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

Table S275.  Gene #53: 'del_9q21.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
DEL PEAK 25(9Q21.11) MUTATED 13 32 10 27 4 19 3
DEL PEAK 25(9Q21.11) WILD-TYPE 71 55 93 62 74 56 3

Figure S275.  Get High-res Image Gene #53: 'del_9q21.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9q21.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0228 (Fisher's exact test), Q value = 0.05

Table S276.  Gene #53: 'del_9q21.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 25(9Q21.11) MUTATED 33 28 40 6
DEL PEAK 25(9Q21.11) WILD-TYPE 143 75 130 59

Figure S276.  Get High-res Image Gene #53: 'del_9q21.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9q21.11' versus 'MIRSEQ_CNMF'

P value = 0.00234 (Fisher's exact test), Q value = 0.0068

Table S277.  Gene #53: 'del_9q21.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 139 131 91 76
DEL PEAK 25(9Q21.11) MUTATED 30 29 19 17 11
DEL PEAK 25(9Q21.11) WILD-TYPE 51 110 112 74 65

Figure S277.  Get High-res Image Gene #53: 'del_9q21.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_9q21.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00061 (Fisher's exact test), Q value = 0.002

Table S278.  Gene #53: 'del_9q21.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
DEL PEAK 25(9Q21.11) MUTATED 33 45 28
DEL PEAK 25(9Q21.11) WILD-TYPE 157 97 158

Figure S278.  Get High-res Image Gene #53: 'del_9q21.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_9q34.3' versus 'CN_CNMF'

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

Table S279.  Gene #54: 'del_9q34.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
DEL PEAK 26(9Q34.3) MUTATED 49 16 13 1
DEL PEAK 26(9Q34.3) WILD-TYPE 154 112 132 45

Figure S279.  Get High-res Image Gene #54: 'del_9q34.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9q34.3' versus 'METHLYATION_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.00072

Table S280.  Gene #54: 'del_9q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
DEL PEAK 26(9Q34.3) MUTATED 6 25 8 15 7 17 1
DEL PEAK 26(9Q34.3) WILD-TYPE 78 62 95 74 71 58 5

Figure S280.  Get High-res Image Gene #54: 'del_9q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9q34.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00958 (Fisher's exact test), Q value = 0.023

Table S281.  Gene #54: 'del_9q34.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
DEL PEAK 26(9Q34.3) MUTATED 28 32 19
DEL PEAK 26(9Q34.3) WILD-TYPE 162 110 167

Figure S281.  Get High-res Image Gene #54: 'del_9q34.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_10p15.3' versus 'CN_CNMF'

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

Table S282.  Gene #55: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
DEL PEAK 27(10P15.3) MUTATED 98 36 17 19
DEL PEAK 27(10P15.3) WILD-TYPE 105 92 128 27

Figure S282.  Get High-res Image Gene #55: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10p15.3' versus 'METHLYATION_CNMF'

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

Table S283.  Gene #55: 'del_10p15.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
DEL PEAK 27(10P15.3) MUTATED 18 27 35 43 10 34 3
DEL PEAK 27(10P15.3) WILD-TYPE 66 60 68 46 68 41 3

Figure S283.  Get High-res Image Gene #55: 'del_10p15.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10p15.3' versus 'MRNASEQ_CNMF'

P value = 8e-04 (Fisher's exact test), Q value = 0.0026

Table S284.  Gene #55: 'del_10p15.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 171 95
DEL PEAK 27(10P15.3) MUTATED 61 28 44 35
DEL PEAK 27(10P15.3) WILD-TYPE 74 85 127 60

Figure S284.  Get High-res Image Gene #55: 'del_10p15.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10p15.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.003 (Fisher's exact test), Q value = 0.0085

Table S285.  Gene #55: 'del_10p15.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 27(10P15.3) MUTATED 66 33 60 9
DEL PEAK 27(10P15.3) WILD-TYPE 110 70 110 56

Figure S285.  Get High-res Image Gene #55: 'del_10p15.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10p15.3' versus 'MIRSEQ_CNMF'

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

Table S286.  Gene #55: 'del_10p15.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 139 131 91 76
DEL PEAK 27(10P15.3) MUTATED 38 34 33 41 22
DEL PEAK 27(10P15.3) WILD-TYPE 43 105 98 50 54

Figure S286.  Get High-res Image Gene #55: 'del_10p15.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_10p15.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0276 (Fisher's exact test), Q value = 0.059

Table S287.  Gene #55: 'del_10p15.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 189 143
DEL PEAK 27(10P15.3) MUTATED 57 50 48
DEL PEAK 27(10P15.3) WILD-TYPE 84 139 95

Figure S287.  Get High-res Image Gene #55: 'del_10p15.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_10p11.21' versus 'CN_CNMF'

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

Table S288.  Gene #56: 'del_10p11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
DEL PEAK 28(10P11.21) MUTATED 98 38 12 15
DEL PEAK 28(10P11.21) WILD-TYPE 105 90 133 31

Figure S288.  Get High-res Image Gene #56: 'del_10p11.21' versus Molecular Subtype #1: 'CN_CNMF'

'del_10p11.21' versus 'METHLYATION_CNMF'

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

Table S289.  Gene #56: 'del_10p11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
DEL PEAK 28(10P11.21) MUTATED 14 28 29 42 12 35 3
DEL PEAK 28(10P11.21) WILD-TYPE 70 59 74 47 66 40 3

Figure S289.  Get High-res Image Gene #56: 'del_10p11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10p11.21' versus 'MRNASEQ_CNMF'

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

Table S290.  Gene #56: 'del_10p11.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 171 95
DEL PEAK 28(10P11.21) MUTATED 64 24 45 28
DEL PEAK 28(10P11.21) WILD-TYPE 71 89 126 67

Figure S290.  Get High-res Image Gene #56: 'del_10p11.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10p11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0221 (Fisher's exact test), Q value = 0.048

Table S291.  Gene #56: 'del_10p11.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 28(10P11.21) MUTATED 60 35 56 10
DEL PEAK 28(10P11.21) WILD-TYPE 116 68 114 55

Figure S291.  Get High-res Image Gene #56: 'del_10p11.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10p11.21' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 8.9e-05

Table S292.  Gene #56: 'del_10p11.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 139 131 91 76
DEL PEAK 28(10P11.21) MUTATED 41 33 32 38 17
DEL PEAK 28(10P11.21) WILD-TYPE 40 106 99 53 59

Figure S292.  Get High-res Image Gene #56: 'del_10p11.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_10p11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0111 (Fisher's exact test), Q value = 0.026

Table S293.  Gene #56: 'del_10p11.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
DEL PEAK 28(10P11.21) MUTATED 62 55 44
DEL PEAK 28(10P11.21) WILD-TYPE 128 87 142

Figure S293.  Get High-res Image Gene #56: 'del_10p11.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_10p11.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0386 (Fisher's exact test), Q value = 0.077

Table S294.  Gene #56: 'del_10p11.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 189 143
DEL PEAK 28(10P11.21) MUTATED 49 48 54
DEL PEAK 28(10P11.21) WILD-TYPE 92 141 89

Figure S294.  Get High-res Image Gene #56: 'del_10p11.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_10q23.31' versus 'CN_CNMF'

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

Table S295.  Gene #57: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
DEL PEAK 29(10Q23.31) MUTATED 60 50 18 10
DEL PEAK 29(10Q23.31) WILD-TYPE 143 78 127 36

Figure S295.  Get High-res Image Gene #57: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q23.31' versus 'METHLYATION_CNMF'

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

Table S296.  Gene #57: 'del_10q23.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
DEL PEAK 29(10Q23.31) MUTATED 8 29 12 38 24 24 3
DEL PEAK 29(10Q23.31) WILD-TYPE 76 58 91 51 54 51 3

Figure S296.  Get High-res Image Gene #57: 'del_10q23.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q23.31' versus 'MRNASEQ_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.0016

Table S297.  Gene #57: 'del_10q23.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 171 95
DEL PEAK 29(10Q23.31) MUTATED 35 17 63 21
DEL PEAK 29(10Q23.31) WILD-TYPE 100 96 108 74

Figure S297.  Get High-res Image Gene #57: 'del_10q23.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00281 (Fisher's exact test), Q value = 0.008

Table S298.  Gene #57: 'del_10q23.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 29(10Q23.31) MUTATED 45 39 31 21
DEL PEAK 29(10Q23.31) WILD-TYPE 131 64 139 44

Figure S298.  Get High-res Image Gene #57: 'del_10q23.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.0012

Table S299.  Gene #57: 'del_10q23.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 139 131 91 76
DEL PEAK 29(10Q23.31) MUTATED 29 25 47 23 11
DEL PEAK 29(10Q23.31) WILD-TYPE 52 114 84 68 65

Figure S299.  Get High-res Image Gene #57: 'del_10q23.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_11p15.5' versus 'CN_CNMF'

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

Table S300.  Gene #58: 'del_11p15.5' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
DEL PEAK 30(11P15.5) MUTATED 69 70 17 7
DEL PEAK 30(11P15.5) WILD-TYPE 134 58 128 39

Figure S300.  Get High-res Image Gene #58: 'del_11p15.5' versus Molecular Subtype #1: 'CN_CNMF'

'del_11p15.5' versus 'METHLYATION_CNMF'

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

Table S301.  Gene #58: 'del_11p15.5' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
DEL PEAK 30(11P15.5) MUTATED 19 31 14 53 26 19 1
DEL PEAK 30(11P15.5) WILD-TYPE 65 56 89 36 52 56 5

Figure S301.  Get High-res Image Gene #58: 'del_11p15.5' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11p15.5' versus 'MRNASEQ_CNMF'

P value = 0.00084 (Fisher's exact test), Q value = 0.0027

Table S302.  Gene #58: 'del_11p15.5' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 171 95
DEL PEAK 30(11P15.5) MUTATED 50 21 66 24
DEL PEAK 30(11P15.5) WILD-TYPE 85 92 105 71

Figure S302.  Get High-res Image Gene #58: 'del_11p15.5' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_11p15.5' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0137 (Fisher's exact test), Q value = 0.032

Table S303.  Gene #58: 'del_11p15.5' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 30(11P15.5) MUTATED 42 43 52 24
DEL PEAK 30(11P15.5) WILD-TYPE 134 60 118 41

Figure S303.  Get High-res Image Gene #58: 'del_11p15.5' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 8.9e-05

Table S304.  Gene #58: 'del_11p15.5' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 139 131 91 76
DEL PEAK 30(11P15.5) MUTATED 35 22 53 32 21
DEL PEAK 30(11P15.5) WILD-TYPE 46 117 78 59 55

Figure S304.  Get High-res Image Gene #58: 'del_11p15.5' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_11p15.5' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0038 (Fisher's exact test), Q value = 0.01

Table S305.  Gene #58: 'del_11p15.5' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
DEL PEAK 30(11P15.5) MUTATED 46 59 58
DEL PEAK 30(11P15.5) WILD-TYPE 144 83 128

Figure S305.  Get High-res Image Gene #58: 'del_11p15.5' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0142 (Fisher's exact test), Q value = 0.033

Table S306.  Gene #58: 'del_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 104 198
DEL PEAK 30(11P15.5) MUTATED 40 32 74
DEL PEAK 30(11P15.5) WILD-TYPE 131 72 124

Figure S306.  Get High-res Image Gene #58: 'del_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11q23.1' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 8.9e-05

Table S307.  Gene #59: 'del_11q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
DEL PEAK 31(11Q23.1) MUTATED 108 75 43 20
DEL PEAK 31(11Q23.1) WILD-TYPE 95 53 102 26

Figure S307.  Get High-res Image Gene #59: 'del_11q23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q23.1' versus 'METHLYATION_CNMF'

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

Table S308.  Gene #59: 'del_11q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
DEL PEAK 31(11Q23.1) MUTATED 27 35 27 48 65 41 3
DEL PEAK 31(11Q23.1) WILD-TYPE 57 52 76 41 13 34 3

Figure S308.  Get High-res Image Gene #59: 'del_11q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11q23.1' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 8.9e-05

Table S309.  Gene #59: 'del_11q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 171 95
DEL PEAK 31(11Q23.1) MUTATED 69 33 102 38
DEL PEAK 31(11Q23.1) WILD-TYPE 66 80 69 57

Figure S309.  Get High-res Image Gene #59: 'del_11q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_11q23.1' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S310.  Gene #59: 'del_11q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 31(11Q23.1) MUTATED 74 42 71 55
DEL PEAK 31(11Q23.1) WILD-TYPE 102 61 99 10

Figure S310.  Get High-res Image Gene #59: 'del_11q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11q23.1' versus 'MIRSEQ_CNMF'

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

Table S311.  Gene #59: 'del_11q23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 139 131 91 76
DEL PEAK 31(11Q23.1) MUTATED 36 49 88 38 34
DEL PEAK 31(11Q23.1) WILD-TYPE 45 90 43 53 42

Figure S311.  Get High-res Image Gene #59: 'del_11q23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_11q23.1' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S312.  Gene #59: 'del_11q23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
DEL PEAK 31(11Q23.1) MUTATED 80 61 104
DEL PEAK 31(11Q23.1) WILD-TYPE 110 81 82

Figure S312.  Get High-res Image Gene #59: 'del_11q23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_11q23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0446 (Fisher's exact test), Q value = 0.087

Table S313.  Gene #59: 'del_11q23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 189 143
DEL PEAK 31(11Q23.1) MUTATED 66 77 78
DEL PEAK 31(11Q23.1) WILD-TYPE 75 112 65

Figure S313.  Get High-res Image Gene #59: 'del_11q23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_12q24.33' versus 'CN_CNMF'

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

Table S314.  Gene #60: 'del_12q24.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
DEL PEAK 32(12Q24.33) MUTATED 41 18 1 3
DEL PEAK 32(12Q24.33) WILD-TYPE 162 110 144 43

Figure S314.  Get High-res Image Gene #60: 'del_12q24.33' versus Molecular Subtype #1: 'CN_CNMF'

'del_12q24.33' versus 'METHLYATION_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.00072

Table S315.  Gene #60: 'del_12q24.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
DEL PEAK 32(12Q24.33) MUTATED 5 14 6 23 4 10 1
DEL PEAK 32(12Q24.33) WILD-TYPE 79 73 97 66 74 65 5

Figure S315.  Get High-res Image Gene #60: 'del_12q24.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_13q12.11' versus 'CN_CNMF'

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

Table S316.  Gene #61: 'del_13q12.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
DEL PEAK 33(13Q12.11) MUTATED 100 94 19 20
DEL PEAK 33(13Q12.11) WILD-TYPE 103 34 126 26

Figure S316.  Get High-res Image Gene #61: 'del_13q12.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q12.11' versus 'METHLYATION_CNMF'

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

Table S317.  Gene #61: 'del_13q12.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
DEL PEAK 33(13Q12.11) MUTATED 21 58 28 58 25 41 2
DEL PEAK 33(13Q12.11) WILD-TYPE 63 29 75 31 53 34 4

Figure S317.  Get High-res Image Gene #61: 'del_13q12.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_13q12.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 8.9e-05

Table S318.  Gene #61: 'del_13q12.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 33(13Q12.11) MUTATED 83 66 62 19
DEL PEAK 33(13Q12.11) WILD-TYPE 93 37 108 46

Figure S318.  Get High-res Image Gene #61: 'del_13q12.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_13q12.11' versus 'MIRSEQ_CNMF'

P value = 0.0199 (Fisher's exact test), Q value = 0.044

Table S319.  Gene #61: 'del_13q12.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 139 131 91 76
DEL PEAK 33(13Q12.11) MUTATED 50 59 54 35 34
DEL PEAK 33(13Q12.11) WILD-TYPE 31 80 77 56 42

Figure S319.  Get High-res Image Gene #61: 'del_13q12.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_13q12.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0308 (Fisher's exact test), Q value = 0.064

Table S320.  Gene #61: 'del_13q12.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
DEL PEAK 33(13Q12.11) MUTATED 86 75 71
DEL PEAK 33(13Q12.11) WILD-TYPE 104 67 115

Figure S320.  Get High-res Image Gene #61: 'del_13q12.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_13q14.2' versus 'CN_CNMF'

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

Table S321.  Gene #62: 'del_13q14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
DEL PEAK 34(13Q14.2) MUTATED 71 95 32 19
DEL PEAK 34(13Q14.2) WILD-TYPE 132 33 113 27

Figure S321.  Get High-res Image Gene #62: 'del_13q14.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q14.2' versus 'METHLYATION_CNMF'

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

Table S322.  Gene #62: 'del_13q14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
DEL PEAK 34(13Q14.2) MUTATED 17 50 23 49 44 32 2
DEL PEAK 34(13Q14.2) WILD-TYPE 67 37 80 40 34 43 4

Figure S322.  Get High-res Image Gene #62: 'del_13q14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_13q14.2' versus 'MRNASEQ_CNMF'

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

Table S323.  Gene #62: 'del_13q14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 171 95
DEL PEAK 34(13Q14.2) MUTATED 58 31 94 32
DEL PEAK 34(13Q14.2) WILD-TYPE 77 82 77 63

Figure S323.  Get High-res Image Gene #62: 'del_13q14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_13q14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00028

Table S324.  Gene #62: 'del_13q14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 34(13Q14.2) MUTATED 70 55 52 38
DEL PEAK 34(13Q14.2) WILD-TYPE 106 48 118 27

Figure S324.  Get High-res Image Gene #62: 'del_13q14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_CNMF'

P value = 0.0011 (Fisher's exact test), Q value = 0.0035

Table S325.  Gene #62: 'del_13q14.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 139 131 91 76
DEL PEAK 34(13Q14.2) MUTATED 42 46 70 32 26
DEL PEAK 34(13Q14.2) WILD-TYPE 39 93 61 59 50

Figure S325.  Get High-res Image Gene #62: 'del_13q14.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_13q14.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0214 (Fisher's exact test), Q value = 0.047

Table S326.  Gene #62: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 104 198
DEL PEAK 34(13Q14.2) MUTATED 60 41 97
DEL PEAK 34(13Q14.2) WILD-TYPE 111 63 101

Figure S326.  Get High-res Image Gene #62: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_14q11.2' versus 'CN_CNMF'

P value = 0.00365 (Fisher's exact test), Q value = 0.01

Table S327.  Gene #63: 'del_14q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
DEL PEAK 35(14Q11.2) MUTATED 36 25 12 2
DEL PEAK 35(14Q11.2) WILD-TYPE 167 103 133 44

Figure S327.  Get High-res Image Gene #63: 'del_14q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q11.2' versus 'METHLYATION_CNMF'

P value = 0.00672 (Fisher's exact test), Q value = 0.017

Table S328.  Gene #63: 'del_14q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
DEL PEAK 35(14Q11.2) MUTATED 5 21 16 18 9 6 0
DEL PEAK 35(14Q11.2) WILD-TYPE 79 66 87 71 69 69 6

Figure S328.  Get High-res Image Gene #63: 'del_14q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_14q11.2' versus 'MIRSEQ_CNMF'

P value = 0.00447 (Fisher's exact test), Q value = 0.012

Table S329.  Gene #63: 'del_14q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 139 131 91 76
DEL PEAK 35(14Q11.2) MUTATED 21 17 20 10 4
DEL PEAK 35(14Q11.2) WILD-TYPE 60 122 111 81 72

Figure S329.  Get High-res Image Gene #63: 'del_14q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_14q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0326 (Fisher's exact test), Q value = 0.067

Table S330.  Gene #63: 'del_14q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
DEL PEAK 35(14Q11.2) MUTATED 20 29 23
DEL PEAK 35(14Q11.2) WILD-TYPE 170 113 163

Figure S330.  Get High-res Image Gene #63: 'del_14q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_14q32.32' versus 'CN_CNMF'

P value = 0.00129 (Fisher's exact test), Q value = 0.004

Table S331.  Gene #64: 'del_14q32.32' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
DEL PEAK 36(14Q32.32) MUTATED 15 28 25 7
DEL PEAK 36(14Q32.32) WILD-TYPE 188 100 120 39

Figure S331.  Get High-res Image Gene #64: 'del_14q32.32' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q32.32' versus 'METHLYATION_CNMF'

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

Table S332.  Gene #64: 'del_14q32.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
DEL PEAK 36(14Q32.32) MUTATED 3 14 5 17 32 4 0
DEL PEAK 36(14Q32.32) WILD-TYPE 81 73 98 72 46 71 6

Figure S332.  Get High-res Image Gene #64: 'del_14q32.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_14q32.32' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 8.9e-05

Table S333.  Gene #64: 'del_14q32.32' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 171 95
DEL PEAK 36(14Q32.32) MUTATED 12 7 43 11
DEL PEAK 36(14Q32.32) WILD-TYPE 123 106 128 84

Figure S333.  Get High-res Image Gene #64: 'del_14q32.32' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_14q32.32' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S334.  Gene #64: 'del_14q32.32' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 36(14Q32.32) MUTATED 21 15 9 28
DEL PEAK 36(14Q32.32) WILD-TYPE 155 88 161 37

Figure S334.  Get High-res Image Gene #64: 'del_14q32.32' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_14q32.32' versus 'MIRSEQ_CNMF'

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

Table S335.  Gene #64: 'del_14q32.32' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 139 131 91 76
DEL PEAK 36(14Q32.32) MUTATED 11 7 42 5 9
DEL PEAK 36(14Q32.32) WILD-TYPE 70 132 89 86 67

Figure S335.  Get High-res Image Gene #64: 'del_14q32.32' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_14q32.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0289 (Fisher's exact test), Q value = 0.061

Table S336.  Gene #64: 'del_14q32.32' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
DEL PEAK 36(14Q32.32) MUTATED 21 16 37
DEL PEAK 36(14Q32.32) WILD-TYPE 169 126 149

Figure S336.  Get High-res Image Gene #64: 'del_14q32.32' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_15q15.1' versus 'CN_CNMF'

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

Table S337.  Gene #65: 'del_15q15.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
DEL PEAK 37(15Q15.1) MUTATED 66 26 11 21
DEL PEAK 37(15Q15.1) WILD-TYPE 137 102 134 25

Figure S337.  Get High-res Image Gene #65: 'del_15q15.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_15q15.1' versus 'MRNASEQ_CNMF'

P value = 0.0248 (Fisher's exact test), Q value = 0.053

Table S338.  Gene #65: 'del_15q15.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 171 95
DEL PEAK 37(15Q15.1) MUTATED 39 16 42 27
DEL PEAK 37(15Q15.1) WILD-TYPE 96 97 129 68

Figure S338.  Get High-res Image Gene #65: 'del_15q15.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16q23.1' versus 'CN_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.0013

Table S339.  Gene #66: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
DEL PEAK 38(16Q23.1) MUTATED 27 36 20 15
DEL PEAK 38(16Q23.1) WILD-TYPE 176 92 125 31

Figure S339.  Get High-res Image Gene #66: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.1' versus 'METHLYATION_CNMF'

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

Table S340.  Gene #66: 'del_16q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
DEL PEAK 38(16Q23.1) MUTATED 5 17 10 30 27 8 1
DEL PEAK 38(16Q23.1) WILD-TYPE 79 70 93 59 51 67 5

Figure S340.  Get High-res Image Gene #66: 'del_16q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16q23.1' versus 'MRNASEQ_CNMF'

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

Table S341.  Gene #66: 'del_16q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 171 95
DEL PEAK 38(16Q23.1) MUTATED 17 8 60 13
DEL PEAK 38(16Q23.1) WILD-TYPE 118 105 111 82

Figure S341.  Get High-res Image Gene #66: 'del_16q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16q23.1' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S342.  Gene #66: 'del_16q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 38(16Q23.1) MUTATED 24 31 17 26
DEL PEAK 38(16Q23.1) WILD-TYPE 152 72 153 39

Figure S342.  Get High-res Image Gene #66: 'del_16q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_CNMF'

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

Table S343.  Gene #66: 'del_16q23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 139 131 91 76
DEL PEAK 38(16Q23.1) MUTATED 14 13 46 12 12
DEL PEAK 38(16Q23.1) WILD-TYPE 67 126 85 79 64

Figure S343.  Get High-res Image Gene #66: 'del_16q23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_16q23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0408 (Fisher's exact test), Q value = 0.081

Table S344.  Gene #66: 'del_16q23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
DEL PEAK 38(16Q23.1) MUTATED 25 30 42
DEL PEAK 38(16Q23.1) WILD-TYPE 165 112 144

Figure S344.  Get High-res Image Gene #66: 'del_16q23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00065 (Fisher's exact test), Q value = 0.0021

Table S345.  Gene #66: 'del_16q23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 104 198
DEL PEAK 38(16Q23.1) MUTATED 23 12 53
DEL PEAK 38(16Q23.1) WILD-TYPE 148 92 145

Figure S345.  Get High-res Image Gene #66: 'del_16q23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q23.3' versus 'CN_CNMF'

P value = 0.00066 (Fisher's exact test), Q value = 0.0022

Table S346.  Gene #67: 'del_16q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
DEL PEAK 39(16Q23.3) MUTATED 30 37 22 16
DEL PEAK 39(16Q23.3) WILD-TYPE 173 91 123 30

Figure S346.  Get High-res Image Gene #67: 'del_16q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.3' versus 'METHLYATION_CNMF'

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

Table S347.  Gene #67: 'del_16q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
DEL PEAK 39(16Q23.3) MUTATED 6 16 16 32 27 7 1
DEL PEAK 39(16Q23.3) WILD-TYPE 78 71 87 57 51 68 5

Figure S347.  Get High-res Image Gene #67: 'del_16q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16q23.3' versus 'MRNASEQ_CNMF'

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

Table S348.  Gene #67: 'del_16q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 171 95
DEL PEAK 39(16Q23.3) MUTATED 17 13 60 14
DEL PEAK 39(16Q23.3) WILD-TYPE 118 100 111 81

Figure S348.  Get High-res Image Gene #67: 'del_16q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16q23.3' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S349.  Gene #67: 'del_16q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 39(16Q23.3) MUTATED 27 31 19 27
DEL PEAK 39(16Q23.3) WILD-TYPE 149 72 151 38

Figure S349.  Get High-res Image Gene #67: 'del_16q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_16q23.3' versus 'MIRSEQ_CNMF'

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

Table S350.  Gene #67: 'del_16q23.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 139 131 91 76
DEL PEAK 39(16Q23.3) MUTATED 15 16 47 13 13
DEL PEAK 39(16Q23.3) WILD-TYPE 66 123 84 78 63

Figure S350.  Get High-res Image Gene #67: 'del_16q23.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_16q23.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0218 (Fisher's exact test), Q value = 0.048

Table S351.  Gene #67: 'del_16q23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 104 198
DEL PEAK 39(16Q23.3) MUTATED 29 14 51
DEL PEAK 39(16Q23.3) WILD-TYPE 142 90 147

Figure S351.  Get High-res Image Gene #67: 'del_16q23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17p11.2' versus 'CN_CNMF'

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

Table S352.  Gene #68: 'del_17p11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
DEL PEAK 40(17P11.2) MUTATED 49 36 5 9
DEL PEAK 40(17P11.2) WILD-TYPE 154 92 140 37

Figure S352.  Get High-res Image Gene #68: 'del_17p11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_17p11.2' versus 'METHLYATION_CNMF'

P value = 0.00147 (Fisher's exact test), Q value = 0.0045

Table S353.  Gene #68: 'del_17p11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
DEL PEAK 40(17P11.2) MUTATED 9 24 11 25 13 14 3
DEL PEAK 40(17P11.2) WILD-TYPE 75 63 92 64 65 61 3

Figure S353.  Get High-res Image Gene #68: 'del_17p11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17q25.3' versus 'CN_CNMF'

P value = 0.0144 (Fisher's exact test), Q value = 0.033

Table S354.  Gene #69: 'del_17q25.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
DEL PEAK 41(17Q25.3) MUTATED 31 25 10 5
DEL PEAK 41(17Q25.3) WILD-TYPE 172 103 135 41

Figure S354.  Get High-res Image Gene #69: 'del_17q25.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_17q25.3' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 8.9e-05

Table S355.  Gene #69: 'del_17q25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
DEL PEAK 41(17Q25.3) MUTATED 3 10 7 22 19 8 2
DEL PEAK 41(17Q25.3) WILD-TYPE 81 77 96 67 59 67 4

Figure S355.  Get High-res Image Gene #69: 'del_17q25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17q25.3' versus 'MRNASEQ_CNMF'

P value = 0.00266 (Fisher's exact test), Q value = 0.0076

Table S356.  Gene #69: 'del_17q25.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 171 95
DEL PEAK 41(17Q25.3) MUTATED 23 8 32 6
DEL PEAK 41(17Q25.3) WILD-TYPE 112 105 139 89

Figure S356.  Get High-res Image Gene #69: 'del_17q25.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_17q25.3' versus 'MIRSEQ_CNMF'

P value = 0.00357 (Fisher's exact test), Q value = 0.0099

Table S357.  Gene #69: 'del_17q25.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 139 131 91 76
DEL PEAK 41(17Q25.3) MUTATED 13 11 30 10 6
DEL PEAK 41(17Q25.3) WILD-TYPE 68 128 101 81 70

Figure S357.  Get High-res Image Gene #69: 'del_17q25.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_17q25.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0496 (Fisher's exact test), Q value = 0.095

Table S358.  Gene #69: 'del_17q25.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
DEL PEAK 41(17Q25.3) MUTATED 17 25 28
DEL PEAK 41(17Q25.3) WILD-TYPE 173 117 158

Figure S358.  Get High-res Image Gene #69: 'del_17q25.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_17q25.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.028 (Fisher's exact test), Q value = 0.059

Table S359.  Gene #69: 'del_17q25.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 189 143
DEL PEAK 41(17Q25.3) MUTATED 11 31 25
DEL PEAK 41(17Q25.3) WILD-TYPE 130 158 118

Figure S359.  Get High-res Image Gene #69: 'del_17q25.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_17q25.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00597 (Fisher's exact test), Q value = 0.015

Table S360.  Gene #69: 'del_17q25.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 104 198
DEL PEAK 41(17Q25.3) MUTATED 14 14 39
DEL PEAK 41(17Q25.3) WILD-TYPE 157 90 159

Figure S360.  Get High-res Image Gene #69: 'del_17q25.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18q23' versus 'CN_CNMF'

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

Table S361.  Gene #70: 'del_18q23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
DEL PEAK 42(18Q23) MUTATED 155 78 28 27
DEL PEAK 42(18Q23) WILD-TYPE 48 50 117 19

Figure S361.  Get High-res Image Gene #70: 'del_18q23' versus Molecular Subtype #1: 'CN_CNMF'

'del_18q23' versus 'METHLYATION_CNMF'

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

Table S362.  Gene #70: 'del_18q23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
DEL PEAK 42(18Q23) MUTATED 44 63 44 67 9 58 3
DEL PEAK 42(18Q23) WILD-TYPE 40 24 59 22 69 17 3

Figure S362.  Get High-res Image Gene #70: 'del_18q23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_18q23' versus 'MRNASEQ_CNMF'

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

Table S363.  Gene #70: 'del_18q23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 171 95
DEL PEAK 42(18Q23) MUTATED 94 56 73 61
DEL PEAK 42(18Q23) WILD-TYPE 41 57 98 34

Figure S363.  Get High-res Image Gene #70: 'del_18q23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_18q23' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S364.  Gene #70: 'del_18q23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 42(18Q23) MUTATED 110 70 95 9
DEL PEAK 42(18Q23) WILD-TYPE 66 33 75 56

Figure S364.  Get High-res Image Gene #70: 'del_18q23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_18q23' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 8.9e-05

Table S365.  Gene #70: 'del_18q23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 139 131 91 76
DEL PEAK 42(18Q23) MUTATED 58 79 48 54 47
DEL PEAK 42(18Q23) WILD-TYPE 23 60 83 37 29

Figure S365.  Get High-res Image Gene #70: 'del_18q23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_18q23' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S366.  Gene #70: 'del_18q23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
DEL PEAK 42(18Q23) MUTATED 119 92 75
DEL PEAK 42(18Q23) WILD-TYPE 71 50 111

Figure S366.  Get High-res Image Gene #70: 'del_18q23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_18q23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0169 (Fisher's exact test), Q value = 0.038

Table S367.  Gene #70: 'del_18q23' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 104 198
DEL PEAK 42(18Q23) MUTATED 106 62 95
DEL PEAK 42(18Q23) WILD-TYPE 65 42 103

Figure S367.  Get High-res Image Gene #70: 'del_18q23' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19p13.3' versus 'CN_CNMF'

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

Table S368.  Gene #71: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
DEL PEAK 43(19P13.3) MUTATED 96 43 18 18
DEL PEAK 43(19P13.3) WILD-TYPE 107 85 127 28

Figure S368.  Get High-res Image Gene #71: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_19p13.3' versus 'METHLYATION_CNMF'

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

Table S369.  Gene #71: 'del_19p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
DEL PEAK 43(19P13.3) MUTATED 18 31 34 40 14 38 0
DEL PEAK 43(19P13.3) WILD-TYPE 66 56 69 49 64 37 6

Figure S369.  Get High-res Image Gene #71: 'del_19p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19p13.3' versus 'MRNASEQ_CNMF'

P value = 0.00073 (Fisher's exact test), Q value = 0.0024

Table S370.  Gene #71: 'del_19p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 171 95
DEL PEAK 43(19P13.3) MUTATED 61 29 45 38
DEL PEAK 43(19P13.3) WILD-TYPE 74 84 126 57

Figure S370.  Get High-res Image Gene #71: 'del_19p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_19p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00069 (Fisher's exact test), Q value = 0.0023

Table S371.  Gene #71: 'del_19p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 43(19P13.3) MUTATED 71 39 54 9
DEL PEAK 43(19P13.3) WILD-TYPE 105 64 116 56

Figure S371.  Get High-res Image Gene #71: 'del_19p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_CNMF'

P value = 0.0466 (Fisher's exact test), Q value = 0.09

Table S372.  Gene #71: 'del_19p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 139 131 91 76
DEL PEAK 43(19P13.3) MUTATED 35 50 31 30 26
DEL PEAK 43(19P13.3) WILD-TYPE 46 89 100 61 50

Figure S372.  Get High-res Image Gene #71: 'del_19p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_19p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.00072

Table S373.  Gene #71: 'del_19p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
DEL PEAK 43(19P13.3) MUTATED 72 59 41
DEL PEAK 43(19P13.3) WILD-TYPE 118 83 145

Figure S373.  Get High-res Image Gene #71: 'del_19p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_19q13.43' versus 'CN_CNMF'

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

Table S374.  Gene #72: 'del_19q13.43' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
DEL PEAK 44(19Q13.43) MUTATED 54 33 2 8
DEL PEAK 44(19Q13.43) WILD-TYPE 149 95 143 38

Figure S374.  Get High-res Image Gene #72: 'del_19q13.43' versus Molecular Subtype #1: 'CN_CNMF'

'del_19q13.43' versus 'METHLYATION_CNMF'

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

Table S375.  Gene #72: 'del_19q13.43' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
DEL PEAK 44(19Q13.43) MUTATED 8 21 11 29 5 22 1
DEL PEAK 44(19Q13.43) WILD-TYPE 76 66 92 60 73 53 5

Figure S375.  Get High-res Image Gene #72: 'del_19q13.43' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19q13.43' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S376.  Gene #72: 'del_19q13.43' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 44(19Q13.43) MUTATED 34 34 23 4
DEL PEAK 44(19Q13.43) WILD-TYPE 142 69 147 61

Figure S376.  Get High-res Image Gene #72: 'del_19q13.43' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_19q13.43' versus 'MIRSEQ_CNMF'

P value = 0.0427 (Fisher's exact test), Q value = 0.084

Table S377.  Gene #72: 'del_19q13.43' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 139 131 91 76
DEL PEAK 44(19Q13.43) MUTATED 25 25 20 15 10
DEL PEAK 44(19Q13.43) WILD-TYPE 56 114 111 76 66

Figure S377.  Get High-res Image Gene #72: 'del_19q13.43' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_21q22.3' versus 'CN_CNMF'

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

Table S378.  Gene #73: 'del_21q22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
DEL PEAK 45(21Q22.3) MUTATED 113 59 11 25
DEL PEAK 45(21Q22.3) WILD-TYPE 90 69 134 21

Figure S378.  Get High-res Image Gene #73: 'del_21q22.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_21q22.3' versus 'METHLYATION_CNMF'

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

Table S379.  Gene #73: 'del_21q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
DEL PEAK 45(21Q22.3) MUTATED 24 39 34 50 12 47 2
DEL PEAK 45(21Q22.3) WILD-TYPE 60 48 69 39 66 28 4

Figure S379.  Get High-res Image Gene #73: 'del_21q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_21q22.3' versus 'MRNASEQ_CNMF'

P value = 0.0459 (Fisher's exact test), Q value = 0.089

Table S380.  Gene #73: 'del_21q22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 171 95
DEL PEAK 45(21Q22.3) MUTATED 65 39 59 42
DEL PEAK 45(21Q22.3) WILD-TYPE 70 74 112 53

Figure S380.  Get High-res Image Gene #73: 'del_21q22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_21q22.3' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S381.  Gene #73: 'del_21q22.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 45(21Q22.3) MUTATED 89 46 59 11
DEL PEAK 45(21Q22.3) WILD-TYPE 87 57 111 54

Figure S381.  Get High-res Image Gene #73: 'del_21q22.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_21q22.3' versus 'MIRSEQ_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.00099

Table S382.  Gene #73: 'del_21q22.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 139 131 91 76
DEL PEAK 45(21Q22.3) MUTATED 45 58 35 32 37
DEL PEAK 45(21Q22.3) WILD-TYPE 36 81 96 59 39

Figure S382.  Get High-res Image Gene #73: 'del_21q22.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_21q22.3' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S383.  Gene #73: 'del_21q22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
DEL PEAK 45(21Q22.3) MUTATED 88 68 51
DEL PEAK 45(21Q22.3) WILD-TYPE 102 74 135

Figure S383.  Get High-res Image Gene #73: 'del_21q22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_xp22.2' versus 'CN_CNMF'

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

Table S384.  Gene #74: 'del_xp22.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
DEL PEAK 46(XP22.2) MUTATED 85 46 16 10
DEL PEAK 46(XP22.2) WILD-TYPE 118 82 129 36

Figure S384.  Get High-res Image Gene #74: 'del_xp22.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_xp22.2' versus 'METHLYATION_CNMF'

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

Table S385.  Gene #74: 'del_xp22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
DEL PEAK 46(XP22.2) MUTATED 14 28 20 50 17 27 1
DEL PEAK 46(XP22.2) WILD-TYPE 70 59 83 39 61 48 5

Figure S385.  Get High-res Image Gene #74: 'del_xp22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xp22.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00247 (Fisher's exact test), Q value = 0.0072

Table S386.  Gene #74: 'del_xp22.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 82 48
DEL PEAK 46(XP22.2) MUTATED 19 39 11
DEL PEAK 46(XP22.2) WILD-TYPE 57 43 37

Figure S386.  Get High-res Image Gene #74: 'del_xp22.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_xp22.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0173 (Fisher's exact test), Q value = 0.039

Table S387.  Gene #74: 'del_xp22.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 46(XP22.2) MUTATED 60 40 38 18
DEL PEAK 46(XP22.2) WILD-TYPE 116 63 132 47

Figure S387.  Get High-res Image Gene #74: 'del_xp22.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_xp22.2' versus 'MIRSEQ_CNMF'

P value = 0.00852 (Fisher's exact test), Q value = 0.021

Table S388.  Gene #74: 'del_xp22.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 139 131 91 76
DEL PEAK 46(XP22.2) MUTATED 35 29 44 24 22
DEL PEAK 46(XP22.2) WILD-TYPE 46 110 87 67 54

Figure S388.  Get High-res Image Gene #74: 'del_xp22.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_xp21.3' versus 'CN_CNMF'

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

Table S389.  Gene #75: 'del_xp21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
DEL PEAK 47(XP21.3) MUTATED 90 43 17 9
DEL PEAK 47(XP21.3) WILD-TYPE 113 85 128 37

Figure S389.  Get High-res Image Gene #75: 'del_xp21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_xp21.3' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00017

Table S390.  Gene #75: 'del_xp21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
DEL PEAK 47(XP21.3) MUTATED 16 30 24 44 15 29 1
DEL PEAK 47(XP21.3) WILD-TYPE 68 57 79 45 63 46 5

Figure S390.  Get High-res Image Gene #75: 'del_xp21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xp21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0233 (Fisher's exact test), Q value = 0.051

Table S391.  Gene #75: 'del_xp21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 47(XP21.3) MUTATED 62 39 40 16
DEL PEAK 47(XP21.3) WILD-TYPE 114 64 130 49

Figure S391.  Get High-res Image Gene #75: 'del_xp21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_xq21.33' versus 'CN_CNMF'

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

Table S392.  Gene #76: 'del_xq21.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 203 128 145 46
DEL PEAK 48(XQ21.33) MUTATED 39 30 8 3
DEL PEAK 48(XQ21.33) WILD-TYPE 164 98 137 43

Figure S392.  Get High-res Image Gene #76: 'del_xq21.33' versus Molecular Subtype #1: 'CN_CNMF'

'del_xq21.33' versus 'METHLYATION_CNMF'

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

Table S393.  Gene #76: 'del_xq21.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 87 103 89 78 75 6
DEL PEAK 48(XQ21.33) MUTATED 4 16 5 30 11 13 1
DEL PEAK 48(XQ21.33) WILD-TYPE 80 71 98 59 67 62 5

Figure S393.  Get High-res Image Gene #76: 'del_xq21.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xq21.33' versus 'MRNASEQ_CNMF'

P value = 0.00345 (Fisher's exact test), Q value = 0.0097

Table S394.  Gene #76: 'del_xq21.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 113 171 95
DEL PEAK 48(XQ21.33) MUTATED 26 12 35 6
DEL PEAK 48(XQ21.33) WILD-TYPE 109 101 136 89

Figure S394.  Get High-res Image Gene #76: 'del_xq21.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_xq21.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00383 (Fisher's exact test), Q value = 0.01

Table S395.  Gene #76: 'del_xq21.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
DEL PEAK 48(XQ21.33) MUTATED 17 26 23 13
DEL PEAK 48(XQ21.33) WILD-TYPE 159 77 147 52

Figure S395.  Get High-res Image Gene #76: 'del_xq21.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_xq21.33' versus 'MIRSEQ_CNMF'

P value = 0.00683 (Fisher's exact test), Q value = 0.017

Table S396.  Gene #76: 'del_xq21.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 139 131 91 76
DEL PEAK 48(XQ21.33) MUTATED 21 16 26 9 7
DEL PEAK 48(XQ21.33) WILD-TYPE 60 123 105 82 69

Figure S396.  Get High-res Image Gene #76: 'del_xq21.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_xq21.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0123 (Fisher's exact test), Q value = 0.029

Table S397.  Gene #76: 'del_xq21.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
DEL PEAK 48(XQ21.33) MUTATED 18 29 32
DEL PEAK 48(XQ21.33) WILD-TYPE 172 113 154

Figure S397.  Get High-res Image Gene #76: 'del_xq21.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

Methods & Data
Input
  • Copy number data file = all_lesions.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/HNSC-TP/22508724/transformed.cor.cli.txt

  • Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/HNSC-TP/22541004/HNSC-TP.transferedmergedcluster.txt

  • Number of patients = 522

  • Number of significantly focal cnvs = 76

  • 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)