Correlation between copy number variation genes (focal events) and molecular subtypes
Brain Lower Grade Glioma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C1R210M1
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1R210M1
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 52 focal events and 12 molecular subtypes across 513 patients, 357 significant findings detected with P value < 0.05 and Q value < 0.25.

  • amp_1q22 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • amp_1q32.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_2p24.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

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

  • amp_4q12 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • amp_7q32.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_8q24.13 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • amp_10p15.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_11q24.1 cnv correlated to 'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_12p13.32 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • amp_12q14.1 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_13q34 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • amp_15q26.3 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • amp_17q25.1 cnv correlated to 'RPPA_CHIERARCHICAL'.

  • amp_19p13.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_19p13.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_xp11.22 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • amp_xp11.22 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_1p36.32 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_1p32.3 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • del_2q37.3 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

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

  • del_3q13.31 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

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

  • del_4q34.3 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_5p15.33 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • del_5q34 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • del_6p25.3 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • del_6q22.31 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_6q24.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_7p22.3 cnv correlated to 'CN_CNMF'.

  • del_8q24.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_9p23 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

  • del_11p15.1 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

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

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

  • del_14q24.3 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_18q23 cnv correlated to 'METHLYATION_CNMF'.

  • del_19q13.41 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_19q13.42 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_22q13.31 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_xq21.1 cnv correlated to 'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 52 focal events and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 357 significant findings detected.

Clinical
Features 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
del 1p36 32 206 (40%) 307 0.00057
(0.00182) 		0.00013
(0.000469) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		0.00061
(0.0019) 		0.0003
(0.00102) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05)
del 1p32 3 196 (38%) 317 0.0293
(0.0563) 		0.00016
(0.000564) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		0.00166
(0.00441) 		0.00061
(0.0019) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05)
del 19q13 41 267 (52%) 246 0.0347
(0.0652) 		0.0102
(0.0223) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		0.00494
(0.0117) 		0.0138
(0.0291) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05)
del 19q13 42 278 (54%) 235 0.035
(0.0655) 		0.0213
(0.043) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		0.00663
(0.0153) 		0.0224
(0.0444) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05)
del 22q13 31 77 (15%) 436 0.251
(0.336) 		0.0421
(0.0765) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		0.00079
(0.00237) 		0.0415
(0.0759) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		0.0352
(0.0656) 		2e-05
(8.49e-05) 		0.00144
(0.00389) 		8e-05
(0.000301)
amp 7p11 2 128 (25%) 385 0.763
(0.842) 		0.402
(0.495) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		0.00065
(0.00201) 		0.00228
(0.0059) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		0.00037
(0.00123) 		1e-05
(4.49e-05) 		8e-05
(0.000301) 		1e-05
(4.49e-05)
del 10q26 3 151 (29%) 362 0.0841
(0.136) 		0.707
(0.788) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		0.00131
(0.00357) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05)
del 14q24 3 121 (24%) 392 0.303
(0.393) 		0.098
(0.154) 		0.0043
(0.0104) 		0.0116
(0.0249) 		0.00058
(0.00185) 		0.0222
(0.0441) 		0.00093
(0.00274) 		0.00065
(0.00201) 		0.00033
(0.00112) 		0.00468
(0.0112) 		0.00166
(0.00441) 		0.00114
(0.00322)
amp 4q12 30 (6%) 483 1
(1.00) 		0.0427
(0.0766) 		0.00017
(0.000596) 		0.00037
(0.00123) 		0.0002
(0.000697) 		0.332
(0.422) 		0.00014
(0.000499) 		2e-05
(8.49e-05) 		0.00304
(0.00768) 		7e-05
(0.000268) 		0.944
(1.00) 		0.00374
(0.00919)
amp 12q14 1 37 (7%) 476 1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		0.0138
(0.029) 		0.347
(0.438) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		0.00277
(0.00705) 		1e-05
(4.49e-05) 		0.0425
(0.0766) 		2e-05
(8.49e-05)
del 3p21 31 49 (10%) 464 1
(1.00) 		0.00731
(0.0165) 		0.0001
(0.000367) 		0.00229
(0.0059) 		6e-05
(0.000233) 		0.0433
(0.0775) 		0.0426
(0.0766) 		0.00106
(0.00303) 		0.00059
(0.00187) 		0.00218
(0.00567) 		0.726
(0.806) 		0.0517
(0.0898)
del 4q34 3 138 (27%) 375 1
(1.00) 		0.354
(0.443) 		0.0132
(0.028) 		1e-05
(4.49e-05) 		0.0448
(0.0795) 		0.36
(0.446) 		0.0238
(0.047) 		9e-05
(0.000334) 		0.0307
(0.0586) 		0.0386
(0.0714) 		0.00123
(0.00343) 		0.00618
(0.0144)
del 9p21 3 176 (34%) 337 0.332
(0.422) 		0.0629
(0.105) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		6e-05
(0.000233) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		0.251
(0.336) 		1e-05
(4.49e-05) 		0.00078
(0.00236) 		1e-05
(4.49e-05)
del 11p15 1 72 (14%) 441 1
(1.00) 		0.0314
(0.0598) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		0.00149
(0.00401) 		0.615
(0.704) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		7e-05
(0.000268) 		0.873
(0.948) 		0.0332
(0.0628)
amp 3q26 33 21 (4%) 492 1
(1.00) 		0.579
(0.674) 		1e-05
(4.49e-05) 		0.00095
(0.00277) 		0.0241
(0.0475) 		0.286
(0.375) 		0.00049
(0.00161) 		0.00129
(0.00353) 		0.00118
(0.0033) 		0.0183
(0.0375) 		0.0547
(0.094) 		0.00363
(0.00895)
amp 7q31 2 174 (34%) 339 1
(1.00) 		0.815
(0.89) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		0.0718
(0.119) 		0.128
(0.193) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		0.0105
(0.0227) 		1e-05
(4.49e-05) 		0.00858
(0.0191) 		1e-05
(4.49e-05)
amp 10p15 3 71 (14%) 442 0.525
(0.62) 		0.0862
(0.139) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		0.00816
(0.0183) 		0.00152
(0.00407) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		0.00105
(0.00303) 		0.0745
(0.122) 		0.336
(0.426) 		0.00012
(0.000435)
amp 12p13 32 72 (14%) 441 0.864
(0.94) 		0.0984
(0.155) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		0.00561
(0.0132) 		0.145
(0.215) 		0.00125
(0.00347) 		1e-05
(4.49e-05) 		0.0101
(0.0221) 		0.00667
(0.0153) 		0.0246
(0.0482) 		0.0865
(0.139)
amp 19p13 3 129 (25%) 384 0.0766
(0.125) 		0.149
(0.219) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		0.248
(0.334) 		0.00481
(0.0114) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		0.00012
(0.000435) 		0.155
(0.224) 		0.0459
(0.0812) 		0.0008
(0.00239)
amp 19p13 2 122 (24%) 391 0.0761
(0.125) 		0.149
(0.219) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		0.0557
(0.0945) 		0.00075
(0.00228) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		0.00016
(0.000564) 		0.141
(0.21) 		0.0415
(0.0759) 		0.00053
(0.00171)
del 2q37 3 77 (15%) 436 0.37
(0.457) 		0.0126
(0.0268) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		0.0011
(0.00313) 		0.0146
(0.0306) 		0.00094
(0.00275) 		1e-05
(4.49e-05) 		0.0149
(0.0309) 		0.138
(0.207) 		0.102
(0.16) 		0.0806
(0.131)
del 6q22 31 78 (15%) 435 0.614
(0.704) 		0.579
(0.674) 		4e-05
(0.00016) 		2e-05
(8.49e-05) 		0.0624
(0.104) 		0.0154
(0.032) 		0.00461
(0.0111) 		0.00128
(0.00352) 		0.00079
(0.00237) 		0.12
(0.183) 		0.00661
(0.0153) 		1e-05
(4.49e-05)
del 6q24 3 82 (16%) 431 0.168
(0.238) 		0.279
(0.369) 		0.00028
(0.00096) 		1e-05
(4.49e-05) 		0.0526
(0.091) 		0.00965
(0.0214) 		0.00139
(0.00377) 		0.00039
(0.00129) 		0.0001
(0.000367) 		0.162
(0.231) 		0.021
(0.0425) 		2e-05
(8.49e-05)
del 13q14 2 142 (28%) 371 0.18
(0.251) 		8e-05
(0.000301) 		1e-05
(4.49e-05) 		4e-05
(0.00016) 		0.0335
(0.0632) 		0.656
(0.741) 		0.00708
(0.0161) 		1e-05
(4.49e-05) 		0.018
(0.0369) 		0.00612
(0.0143) 		0.474
(0.566) 		0.414
(0.507)
del 13q14 2 144 (28%) 369 0.182
(0.254) 		5e-05
(0.000197) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		0.0286
(0.0552) 		0.787
(0.863) 		0.00363
(0.00895) 		2e-05
(8.49e-05) 		0.0161
(0.0331) 		0.00381
(0.00932) 		0.434
(0.528) 		0.358
(0.446)
amp 1q32 1 43 (8%) 470 1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		0.291
(0.379) 		0.445
(0.536) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		0.252
(0.336) 		1e-05
(4.49e-05) 		0.00115
(0.00323) 		1e-05
(4.49e-05)
amp 7q32 3 182 (35%) 331 0.694
(0.777) 		1
(1.00) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		0.107
(0.167) 		0.111
(0.171) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		0.0553
(0.0945) 		1e-05
(4.49e-05) 		0.0218
(0.0439) 		1e-05
(4.49e-05)
amp 8q24 13 100 (19%) 413 0.368
(0.456) 		0.238
(0.322) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		0.197
(0.27) 		0.422
(0.515) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		0.0289
(0.0557) 		0.00106
(0.00303) 		0.11
(0.171) 		2e-05
(8.49e-05)
del 5q34 64 (12%) 449 0.445
(0.536) 		0.238
(0.322) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		0.0365
(0.0677) 		0.0469
(0.0824) 		3e-05
(0.000125) 		1e-05
(4.49e-05) 		4e-05
(0.00016) 		0.147
(0.216) 		0.618
(0.705) 		0.666
(0.75)
del 8q24 3 29 (6%) 484 1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		0.338
(0.427) 		0.12
(0.183) 		0.00333
(0.00828) 		0.00674
(0.0154) 		0.00476
(0.0113) 		0.00317
(0.00794) 		0.167
(0.237) 		0.0297
(0.0569)
del 9p23 150 (29%) 363 0.446
(0.536) 		0.656
(0.741) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		0.00626
(0.0145) 		4e-05
(0.00016) 		0.022
(0.0441) 		0.00027
(0.000931) 		0.916
(0.981) 		0.113
(0.174) 		0.409
(0.502) 		0.00309
(0.00777)
del 11p15 5 104 (20%) 409 0.643
(0.732) 		0.00061
(0.0019) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		0.0551
(0.0944) 		0.899
(0.966) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		3e-05
(0.000125) 		0.00447
(0.0108) 		0.99
(1.00) 		0.888
(0.957)
del 13q34 110 (21%) 403 0.507
(0.6) 		0.15
(0.22) 		9e-05
(0.000334) 		0.0112
(0.0241) 		0.0219
(0.0439) 		0.384
(0.473) 		0.0427
(0.0766) 		0.00085
(0.00253) 		0.0259
(0.0502) 		0.00262
(0.0067) 		0.311
(0.402) 		0.175
(0.246)
amp xp11 22 63 (12%) 450 0.65
(0.738) 		1
(1.00) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		0.144
(0.215) 		0.104
(0.162) 		2e-05
(8.49e-05) 		1e-05
(4.49e-05) 		0.00037
(0.00123) 		0.35
(0.44) 		0.0769
(0.125) 		0.0093
(0.0207)
del 3q13 31 39 (8%) 474 0.175
(0.246) 		0.883
(0.953) 		4e-05
(0.00016) 		0.00401
(0.00977) 		0.0097
(0.0214) 		0.0194
(0.0395) 		0.15
(0.22) 		0.0125
(0.0266) 		0.156
(0.225) 		0.0005
(0.00163) 		0.573
(0.669) 		0.117
(0.178)
del 3q29 47 (9%) 466 0.175
(0.246) 		0.883
(0.953) 		1e-05
(4.49e-05) 		0.00051
(0.00166) 		0.436
(0.529) 		0.606
(0.699) 		0.016
(0.0331) 		4e-05
(0.00016) 		0.13
(0.195) 		0.00462
(0.0111) 		0.691
(0.777) 		0.17
(0.241)
del 5p15 33 50 (10%) 463 1
(1.00) 		0.0682
(0.113) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		0.777
(0.854) 		0.652
(0.739) 		0.00057
(0.00182) 		6e-05
(0.000233) 		0.00212
(0.00554) 		0.205
(0.28) 		0.947
(1.00) 		0.44
(0.532)
del 12p13 1 38 (7%) 475 0.00068
(0.00209) 		0.00197
(0.00516) 		0.23
(0.312) 		0.581
(0.675) 		0.0101
(0.0221) 		0.00685
(0.0156) 		0.057
(0.0964) 		0.0445
(0.0791) 		0.956
(1.00) 		0.252
(0.336)
del 12q12 72 (14%) 441 1
(1.00) 		0.151
(0.22) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		0.426
(0.519) 		0.983
(1.00) 		0.00188
(0.00495) 		1e-05
(4.49e-05) 		0.013
(0.0276) 		0.498
(0.593) 		0.911
(0.976) 		0.963
(1.00)
del xq21 1 78 (15%) 435 0.839
(0.915) 		0.267
(0.354) 		0.194
(0.267) 		0.0526
(0.091) 		0.00087
(0.00257) 		0.0144
(0.0302) 		0.00837
(0.0187) 		5e-05
(0.000197) 		0.00101
(0.00293) 		0.36
(0.446) 		0.121
(0.184) 		0.158
(0.227)
amp 2p24 3 24 (5%) 489 0.614
(0.704) 		0.582
(0.675) 		0.00256
(0.00657) 		0.0323
(0.0613) 		0.0905
(0.144) 		0.0874
(0.14) 		0.177
(0.247) 		0.0028
(0.0071) 		0.722
(0.803) 		0.035
(0.0655) 		0.438
(0.531) 		0.116
(0.178)
amp 13q34 22 (4%) 491 0.00186
(0.00492) 		0.00126
(0.00348) 		0.136
(0.204) 		0.768
(0.845) 		0.0387
(0.0714) 		0.0222
(0.0441) 		0.296
(0.385) 		0.692
(0.777) 		0.962
(1.00) 		0.0505
(0.0881)
amp 15q26 3 19 (4%) 494 1
(1.00) 		0.0425
(0.0766) 		1e-05
(4.49e-05) 		0.00071
(0.00217) 		0.162
(0.231) 		0.194
(0.267) 		0.0256
(0.0498) 		0.0621
(0.104) 		0.497
(0.593) 		0.284
(0.374) 		0.592
(0.686) 		0.193
(0.267)
amp xp11 22 48 (9%) 465 0.649
(0.738) 		1
(1.00) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		0.449
(0.538) 		0.166
(0.237) 		0.00112
(0.00318) 		3e-05
(0.000125) 		0.0557
(0.0945) 		0.597
(0.69) 		0.332
(0.422) 		0.109
(0.169)
amp 1q22 42 (8%) 471 0.00038
(0.00126) 		0.00755
(0.017) 		0.085
(0.137) 		0.707
(0.788) 		0.00549
(0.0129) 		0.0575
(0.097) 		0.568
(0.664) 		0.0904
(0.144) 		0.154
(0.223) 		0.313
(0.404)
amp 9q34 3 46 (9%) 467 0.506
(0.6) 		0.883
(0.953) 		0.0948
(0.15) 		0.0491
(0.0858) 		0.0185
(0.0377) 		1
(1.00) 		0.0694
(0.115) 		0.00022
(0.000763) 		0.201
(0.275) 		0.0848
(0.137) 		0.281
(0.37) 		0.287
(0.375)
amp 11q24 1 87 (17%) 426 0.0715
(0.118) 		0.12
(0.183) 		0.614
(0.704) 		0.0113
(0.0243) 		0.24
(0.325) 		0.0467
(0.0823) 		0.1
(0.157) 		0.159
(0.228) 		0.764
(0.842) 		0.113
(0.174) 		0.852
(0.927) 		0.0435
(0.0775)
del 1q43 31 (6%) 482 0.318
(0.409) 		0.00975
(0.0214) 		0.176
(0.246) 		0.351
(0.44) 		0.0259
(0.0502) 		0.0388
(0.0715) 		0.229
(0.312) 		0.755
(0.835) 		0.794
(0.87) 		0.303
(0.393)
del 6p25 3 50 (10%) 463 0.00014
(0.000499) 		0.0416
(0.0759) 		0.265
(0.352) 		0.328
(0.42) 		0.181
(0.253) 		0.0727
(0.12) 		0.412
(0.505) 		0.252
(0.336) 		0.145
(0.215) 		0.0883
(0.141)
amp 17q25 1 44 (9%) 469 0.0555
(0.0945) 		0.358
(0.446) 		0.0624
(0.104) 		0.0484
(0.0848) 		0.141
(0.211) 		0.053
(0.0913) 		0.151
(0.22) 		0.566
(0.664) 		0.188
(0.261) 		0.562
(0.66)
del 7p22 3 23 (4%) 490 0.0255
(0.0498) 		0.124
(0.187) 		0.314
(0.405) 		0.157
(0.226) 		0.558
(0.657) 		0.706
(0.788) 		0.506
(0.6) 		0.0974
(0.154) 		0.735
(0.814) 		0.351
(0.44)
del 18q23 78 (15%) 435 0.321
(0.412) 		0.33
(0.422) 		0.455
(0.544) 		0.00327
(0.00816) 		0.983
(1.00) 		0.262
(0.349) 		0.281
(0.37) 		0.225
(0.307) 		0.347
(0.438) 		0.616
(0.704) 		0.531
(0.627) 		0.9
(0.966)
'amp_1q22' versus 'CN_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.0013

Table S1.  Gene #1: 'amp_1q22' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
AMP PEAK 1(1Q22) MUTATED 15 19 8
AMP PEAK 1(1Q22) WILD-TYPE 157 101 213

Figure S1.  Get High-res Image Gene #1: 'amp_1q22' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1q22' versus 'METHLYATION_CNMF'

P value = 0.00755 (Fisher's exact test), Q value = 0.017

Table S2.  Gene #1: 'amp_1q22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
AMP PEAK 1(1Q22) MUTATED 19 14 8 1
AMP PEAK 1(1Q22) WILD-TYPE 206 67 159 39

Figure S2.  Get High-res Image Gene #1: 'amp_1q22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_1q22' versus 'MRNASEQ_CNMF'

P value = 0.00549 (Fisher's exact test), Q value = 0.013

Table S3.  Gene #1: 'amp_1q22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 134 109 108 132 30
AMP PEAK 1(1Q22) MUTATED 8 19 4 9 2
AMP PEAK 1(1Q22) WILD-TYPE 126 90 104 123 28

Figure S3.  Get High-res Image Gene #1: 'amp_1q22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_1q32.1' versus 'CN_CNMF'

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

Table S4.  Gene #2: 'amp_1q32.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
AMP PEAK 2(1Q32.1) MUTATED 10 28 5
AMP PEAK 2(1Q32.1) WILD-TYPE 162 92 216

Figure S4.  Get High-res Image Gene #2: 'amp_1q32.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1q32.1' versus 'METHLYATION_CNMF'

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

Table S5.  Gene #2: 'amp_1q32.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
AMP PEAK 2(1Q32.1) MUTATED 12 24 6 1
AMP PEAK 2(1Q32.1) WILD-TYPE 213 57 161 39

Figure S5.  Get High-res Image Gene #2: 'amp_1q32.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_1q32.1' versus 'MRNASEQ_CNMF'

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

Table S6.  Gene #2: 'amp_1q32.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 134 109 108 132 30
AMP PEAK 2(1Q32.1) MUTATED 2 25 2 12 2
AMP PEAK 2(1Q32.1) WILD-TYPE 132 84 106 120 28

Figure S6.  Get High-res Image Gene #2: 'amp_1q32.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_1q32.1' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S7.  Gene #2: 'amp_1q32.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
AMP PEAK 2(1Q32.1) MUTATED 3 20 3 6 2 4 5
AMP PEAK 2(1Q32.1) WILD-TYPE 132 51 33 62 88 37 67

Figure S7.  Get High-res Image Gene #2: 'amp_1q32.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_1q32.1' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S8.  Gene #2: 'amp_1q32.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
AMP PEAK 2(1Q32.1) MUTATED 8 13 22
AMP PEAK 2(1Q32.1) WILD-TYPE 214 171 81

Figure S8.  Get High-res Image Gene #2: 'amp_1q32.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_1q32.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00115 (Fisher's exact test), Q value = 0.0032

Table S9.  Gene #2: 'amp_1q32.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 185 161 159
AMP PEAK 2(1Q32.1) MUTATED 23 4 16
AMP PEAK 2(1Q32.1) WILD-TYPE 162 157 143

Figure S9.  Get High-res Image Gene #2: 'amp_1q32.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_1q32.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S10.  Gene #2: 'amp_1q32.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 137 188 89
AMP PEAK 2(1Q32.1) MUTATED 5 3 14 21
AMP PEAK 2(1Q32.1) WILD-TYPE 86 134 174 68

Figure S10.  Get High-res Image Gene #2: 'amp_1q32.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_2p24.3' versus 'CN_CNMF'

P value = 0.00256 (Fisher's exact test), Q value = 0.0066

Table S11.  Gene #3: 'amp_2p24.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
AMP PEAK 3(2P24.3) MUTATED 6 13 5
AMP PEAK 3(2P24.3) WILD-TYPE 166 107 216

Figure S11.  Get High-res Image Gene #3: 'amp_2p24.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_2p24.3' versus 'METHLYATION_CNMF'

P value = 0.0323 (Fisher's exact test), Q value = 0.061

Table S12.  Gene #3: 'amp_2p24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
AMP PEAK 3(2P24.3) MUTATED 10 9 4 1
AMP PEAK 3(2P24.3) WILD-TYPE 215 72 163 39

Figure S12.  Get High-res Image Gene #3: 'amp_2p24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_2p24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0028 (Fisher's exact test), Q value = 0.0071

Table S13.  Gene #3: 'amp_2p24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
AMP PEAK 3(2P24.3) MUTATED 3 7 1 6 2 5 0
AMP PEAK 3(2P24.3) WILD-TYPE 132 64 35 62 88 36 72

Figure S13.  Get High-res Image Gene #3: 'amp_2p24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_2p24.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.035 (Fisher's exact test), Q value = 0.065

Table S14.  Gene #3: 'amp_2p24.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
AMP PEAK 3(2P24.3) MUTATED 9 5 10
AMP PEAK 3(2P24.3) WILD-TYPE 213 179 93

Figure S14.  Get High-res Image Gene #3: 'amp_2p24.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_3q26.33' versus 'CN_CNMF'

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

Table S15.  Gene #4: 'amp_3q26.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
AMP PEAK 4(3Q26.33) MUTATED 1 17 3
AMP PEAK 4(3Q26.33) WILD-TYPE 171 103 218

Figure S15.  Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #3: 'CN_CNMF'

'amp_3q26.33' versus 'METHLYATION_CNMF'

P value = 0.00095 (Fisher's exact test), Q value = 0.0028

Table S16.  Gene #4: 'amp_3q26.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
AMP PEAK 4(3Q26.33) MUTATED 9 10 2 0
AMP PEAK 4(3Q26.33) WILD-TYPE 216 71 165 40

Figure S16.  Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_3q26.33' versus 'RPPA_CNMF'

P value = 0.0241 (Fisher's exact test), Q value = 0.048

Table S17.  Gene #4: 'amp_3q26.33' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 95 125 115
AMP PEAK 4(3Q26.33) MUTATED 2 8 3 1
AMP PEAK 4(3Q26.33) WILD-TYPE 89 87 122 114

Figure S17.  Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_3q26.33' versus 'MRNASEQ_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.0016

Table S18.  Gene #4: 'amp_3q26.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 134 109 108 132 30
AMP PEAK 4(3Q26.33) MUTATED 5 13 2 1 0
AMP PEAK 4(3Q26.33) WILD-TYPE 129 96 106 131 30

Figure S18.  Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_3q26.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00129 (Fisher's exact test), Q value = 0.0035

Table S19.  Gene #4: 'amp_3q26.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
AMP PEAK 4(3Q26.33) MUTATED 4 9 1 2 0 4 1
AMP PEAK 4(3Q26.33) WILD-TYPE 131 62 35 66 90 37 71

Figure S19.  Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_3q26.33' versus 'MIRSEQ_CNMF'

P value = 0.00118 (Fisher's exact test), Q value = 0.0033

Table S20.  Gene #4: 'amp_3q26.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 107 183 82
AMP PEAK 4(3Q26.33) MUTATED 11 7 1 2
AMP PEAK 4(3Q26.33) WILD-TYPE 126 100 182 80

Figure S20.  Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_3q26.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0183 (Fisher's exact test), Q value = 0.038

Table S21.  Gene #4: 'amp_3q26.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
AMP PEAK 4(3Q26.33) MUTATED 9 3 9
AMP PEAK 4(3Q26.33) WILD-TYPE 213 181 94

Figure S21.  Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_3q26.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00363 (Fisher's exact test), Q value = 0.009

Table S22.  Gene #4: 'amp_3q26.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 137 188 89
AMP PEAK 4(3Q26.33) MUTATED 6 2 4 9
AMP PEAK 4(3Q26.33) WILD-TYPE 85 135 184 80

Figure S22.  Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_4q12' versus 'MRNA_CHIERARCHICAL'

P value = 0.0427 (Fisher's exact test), Q value = 0.077

Table S23.  Gene #5: 'amp_4q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 7 7 6
AMP PEAK 5(4Q12) MUTATED 0 3 0 0
AMP PEAK 5(4Q12) WILD-TYPE 7 4 7 6

Figure S23.  Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_4q12' versus 'CN_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 6e-04

Table S24.  Gene #5: 'amp_4q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
AMP PEAK 5(4Q12) MUTATED 17 10 3
AMP PEAK 5(4Q12) WILD-TYPE 155 110 218

Figure S24.  Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_4q12' versus 'METHLYATION_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.0012

Table S25.  Gene #5: 'amp_4q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
AMP PEAK 5(4Q12) MUTATED 19 9 1 1
AMP PEAK 5(4Q12) WILD-TYPE 206 72 166 39

Figure S25.  Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_4q12' versus 'RPPA_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 7e-04

Table S26.  Gene #5: 'amp_4q12' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 95 125 115
AMP PEAK 5(4Q12) MUTATED 3 14 1 7
AMP PEAK 5(4Q12) WILD-TYPE 88 81 124 108

Figure S26.  Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_4q12' versus 'MRNASEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 5e-04

Table S27.  Gene #5: 'amp_4q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 134 109 108 132 30
AMP PEAK 5(4Q12) MUTATED 5 17 1 6 1
AMP PEAK 5(4Q12) WILD-TYPE 129 92 107 126 29

Figure S27.  Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_4q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 8.5e-05

Table S28.  Gene #5: 'amp_4q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
AMP PEAK 5(4Q12) MUTATED 5 8 0 2 0 11 4
AMP PEAK 5(4Q12) WILD-TYPE 130 63 36 66 90 30 68

Figure S28.  Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_4q12' versus 'MIRSEQ_CNMF'

P value = 0.00304 (Fisher's exact test), Q value = 0.0077

Table S29.  Gene #5: 'amp_4q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 107 183 82
AMP PEAK 5(4Q12) MUTATED 6 15 7 2
AMP PEAK 5(4Q12) WILD-TYPE 131 92 176 80

Figure S29.  Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_4q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00027

Table S30.  Gene #5: 'amp_4q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
AMP PEAK 5(4Q12) MUTATED 7 7 16
AMP PEAK 5(4Q12) WILD-TYPE 215 177 87

Figure S30.  Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_4q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00374 (Fisher's exact test), Q value = 0.0092

Table S31.  Gene #5: 'amp_4q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 137 188 89
AMP PEAK 5(4Q12) MUTATED 3 8 6 13
AMP PEAK 5(4Q12) WILD-TYPE 88 129 182 76

Figure S31.  Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7p11.2' versus 'CN_CNMF'

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

Table S32.  Gene #6: 'amp_7p11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
AMP PEAK 6(7P11.2) MUTATED 21 98 9
AMP PEAK 6(7P11.2) WILD-TYPE 151 22 212

Figure S32.  Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_7p11.2' versus 'METHLYATION_CNMF'

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

Table S33.  Gene #6: 'amp_7p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
AMP PEAK 6(7P11.2) MUTATED 40 64 15 9
AMP PEAK 6(7P11.2) WILD-TYPE 185 17 152 31

Figure S33.  Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_7p11.2' versus 'RPPA_CNMF'

P value = 0.00065 (Fisher's exact test), Q value = 0.002

Table S34.  Gene #6: 'amp_7p11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 95 125 115
AMP PEAK 6(7P11.2) MUTATED 23 37 20 22
AMP PEAK 6(7P11.2) WILD-TYPE 68 58 105 93

Figure S34.  Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_7p11.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00228 (Fisher's exact test), Q value = 0.0059

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 158 185
AMP PEAK 6(7P11.2) MUTATED 12 31 59
AMP PEAK 6(7P11.2) WILD-TYPE 71 127 126

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

'amp_7p11.2' versus 'MRNASEQ_CNMF'

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

Table S36.  Gene #6: 'amp_7p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 134 109 108 132 30
AMP PEAK 6(7P11.2) MUTATED 23 64 11 25 5
AMP PEAK 6(7P11.2) WILD-TYPE 111 45 97 107 25

Figure S36.  Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_7p11.2' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S37.  Gene #6: 'amp_7p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
AMP PEAK 6(7P11.2) MUTATED 19 57 3 27 7 9 6
AMP PEAK 6(7P11.2) WILD-TYPE 116 14 33 41 83 32 66

Figure S37.  Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_7p11.2' versus 'MIRSEQ_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.0012

Table S38.  Gene #6: 'amp_7p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 107 183 82
AMP PEAK 6(7P11.2) MUTATED 44 37 32 13
AMP PEAK 6(7P11.2) WILD-TYPE 93 70 151 69

Figure S38.  Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_7p11.2' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S39.  Gene #6: 'amp_7p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
AMP PEAK 6(7P11.2) MUTATED 37 28 61
AMP PEAK 6(7P11.2) WILD-TYPE 185 156 42

Figure S39.  Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_7p11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 3e-04

Table S40.  Gene #6: 'amp_7p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 185 161 159
AMP PEAK 6(7P11.2) MUTATED 66 26 33
AMP PEAK 6(7P11.2) WILD-TYPE 119 135 126

Figure S40.  Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_7p11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S41.  Gene #6: 'amp_7p11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 137 188 89
AMP PEAK 6(7P11.2) MUTATED 13 22 32 58
AMP PEAK 6(7P11.2) WILD-TYPE 78 115 156 31

Figure S41.  Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7q31.2' versus 'CN_CNMF'

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

Table S42.  Gene #7: 'amp_7q31.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
AMP PEAK 7(7Q31.2) MUTATED 46 105 23
AMP PEAK 7(7Q31.2) WILD-TYPE 126 15 198

Figure S42.  Get High-res Image Gene #7: 'amp_7q31.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_7q31.2' versus 'METHLYATION_CNMF'

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

Table S43.  Gene #7: 'amp_7q31.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
AMP PEAK 7(7Q31.2) MUTATED 77 59 29 9
AMP PEAK 7(7Q31.2) WILD-TYPE 148 22 138 31

Figure S43.  Get High-res Image Gene #7: 'amp_7q31.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_7q31.2' versus 'MRNASEQ_CNMF'

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

Table S44.  Gene #7: 'amp_7q31.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 134 109 108 132 30
AMP PEAK 7(7Q31.2) MUTATED 49 61 17 39 8
AMP PEAK 7(7Q31.2) WILD-TYPE 85 48 91 93 22

Figure S44.  Get High-res Image Gene #7: 'amp_7q31.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_7q31.2' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S45.  Gene #7: 'amp_7q31.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
AMP PEAK 7(7Q31.2) MUTATED 44 53 6 33 14 9 15
AMP PEAK 7(7Q31.2) WILD-TYPE 91 18 30 35 76 32 57

Figure S45.  Get High-res Image Gene #7: 'amp_7q31.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_7q31.2' versus 'MIRSEQ_CNMF'

P value = 0.0105 (Fisher's exact test), Q value = 0.023

Table S46.  Gene #7: 'amp_7q31.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 107 183 82
AMP PEAK 7(7Q31.2) MUTATED 56 44 52 20
AMP PEAK 7(7Q31.2) WILD-TYPE 81 63 131 62

Figure S46.  Get High-res Image Gene #7: 'amp_7q31.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_7q31.2' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S47.  Gene #7: 'amp_7q31.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
AMP PEAK 7(7Q31.2) MUTATED 65 48 59
AMP PEAK 7(7Q31.2) WILD-TYPE 157 136 44

Figure S47.  Get High-res Image Gene #7: 'amp_7q31.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_7q31.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00858 (Fisher's exact test), Q value = 0.019

Table S48.  Gene #7: 'amp_7q31.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 185 161 159
AMP PEAK 7(7Q31.2) MUTATED 76 41 54
AMP PEAK 7(7Q31.2) WILD-TYPE 109 120 105

Figure S48.  Get High-res Image Gene #7: 'amp_7q31.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_7q31.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S49.  Gene #7: 'amp_7q31.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 137 188 89
AMP PEAK 7(7Q31.2) MUTATED 24 35 57 55
AMP PEAK 7(7Q31.2) WILD-TYPE 67 102 131 34

Figure S49.  Get High-res Image Gene #7: 'amp_7q31.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7q32.3' versus 'CN_CNMF'

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

Table S50.  Gene #8: 'amp_7q32.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
AMP PEAK 8(7Q32.3) MUTATED 49 108 25
AMP PEAK 8(7Q32.3) WILD-TYPE 123 12 196

Figure S50.  Get High-res Image Gene #8: 'amp_7q32.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_7q32.3' versus 'METHLYATION_CNMF'

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

Table S51.  Gene #8: 'amp_7q32.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
AMP PEAK 8(7Q32.3) MUTATED 82 60 30 10
AMP PEAK 8(7Q32.3) WILD-TYPE 143 21 137 30

Figure S51.  Get High-res Image Gene #8: 'amp_7q32.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_7q32.3' versus 'MRNASEQ_CNMF'

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

Table S52.  Gene #8: 'amp_7q32.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 134 109 108 132 30
AMP PEAK 8(7Q32.3) MUTATED 53 61 18 42 8
AMP PEAK 8(7Q32.3) WILD-TYPE 81 48 90 90 22

Figure S52.  Get High-res Image Gene #8: 'amp_7q32.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_7q32.3' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S53.  Gene #8: 'amp_7q32.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
AMP PEAK 8(7Q32.3) MUTATED 47 53 6 37 15 9 15
AMP PEAK 8(7Q32.3) WILD-TYPE 88 18 30 31 75 32 57

Figure S53.  Get High-res Image Gene #8: 'amp_7q32.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_7q32.3' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S54.  Gene #8: 'amp_7q32.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
AMP PEAK 8(7Q32.3) MUTATED 68 52 60
AMP PEAK 8(7Q32.3) WILD-TYPE 154 132 43

Figure S54.  Get High-res Image Gene #8: 'amp_7q32.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_7q32.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0218 (Fisher's exact test), Q value = 0.044

Table S55.  Gene #8: 'amp_7q32.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 185 161 159
AMP PEAK 8(7Q32.3) MUTATED 78 45 56
AMP PEAK 8(7Q32.3) WILD-TYPE 107 116 103

Figure S55.  Get High-res Image Gene #8: 'amp_7q32.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_7q32.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S56.  Gene #8: 'amp_7q32.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 137 188 89
AMP PEAK 8(7Q32.3) MUTATED 28 37 59 55
AMP PEAK 8(7Q32.3) WILD-TYPE 63 100 129 34

Figure S56.  Get High-res Image Gene #8: 'amp_7q32.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8q24.13' versus 'CN_CNMF'

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

Table S57.  Gene #9: 'amp_8q24.13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
AMP PEAK 9(8Q24.13) MUTATED 66 19 15
AMP PEAK 9(8Q24.13) WILD-TYPE 106 101 206

Figure S57.  Get High-res Image Gene #9: 'amp_8q24.13' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8q24.13' versus 'METHLYATION_CNMF'

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

Table S58.  Gene #9: 'amp_8q24.13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
AMP PEAK 9(8Q24.13) MUTATED 82 4 10 4
AMP PEAK 9(8Q24.13) WILD-TYPE 143 77 157 36

Figure S58.  Get High-res Image Gene #9: 'amp_8q24.13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8q24.13' versus 'MRNASEQ_CNMF'

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

Table S59.  Gene #9: 'amp_8q24.13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 134 109 108 132 30
AMP PEAK 9(8Q24.13) MUTATED 50 11 6 26 7
AMP PEAK 9(8Q24.13) WILD-TYPE 84 98 102 106 23

Figure S59.  Get High-res Image Gene #9: 'amp_8q24.13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8q24.13' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S60.  Gene #9: 'amp_8q24.13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
AMP PEAK 9(8Q24.13) MUTATED 52 3 2 20 5 9 9
AMP PEAK 9(8Q24.13) WILD-TYPE 83 68 34 48 85 32 63

Figure S60.  Get High-res Image Gene #9: 'amp_8q24.13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.13' versus 'MIRSEQ_CNMF'

P value = 0.0289 (Fisher's exact test), Q value = 0.056

Table S61.  Gene #9: 'amp_8q24.13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 107 183 82
AMP PEAK 9(8Q24.13) MUTATED 33 22 36 7
AMP PEAK 9(8Q24.13) WILD-TYPE 104 85 147 75

Figure S61.  Get High-res Image Gene #9: 'amp_8q24.13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_8q24.13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00106 (Fisher's exact test), Q value = 0.003

Table S62.  Gene #9: 'amp_8q24.13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
AMP PEAK 9(8Q24.13) MUTATED 58 30 10
AMP PEAK 9(8Q24.13) WILD-TYPE 164 154 93

Figure S62.  Get High-res Image Gene #9: 'amp_8q24.13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_8q24.13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 8.5e-05

Table S63.  Gene #9: 'amp_8q24.13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 137 188 89
AMP PEAK 9(8Q24.13) MUTATED 34 21 35 8
AMP PEAK 9(8Q24.13) WILD-TYPE 57 116 153 81

Figure S63.  Get High-res Image Gene #9: 'amp_8q24.13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_9q34.3' versus 'METHLYATION_CNMF'

P value = 0.0491 (Fisher's exact test), Q value = 0.086

Table S64.  Gene #10: 'amp_9q34.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
AMP PEAK 10(9Q34.3) MUTATED 28 8 8 2
AMP PEAK 10(9Q34.3) WILD-TYPE 197 73 159 38

Figure S64.  Get High-res Image Gene #10: 'amp_9q34.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_9q34.3' versus 'RPPA_CNMF'

P value = 0.0185 (Fisher's exact test), Q value = 0.038

Table S65.  Gene #10: 'amp_9q34.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 95 125 115
AMP PEAK 10(9Q34.3) MUTATED 9 15 6 6
AMP PEAK 10(9Q34.3) WILD-TYPE 82 80 119 109

Figure S65.  Get High-res Image Gene #10: 'amp_9q34.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_9q34.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.00076

Table S66.  Gene #10: 'amp_9q34.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
AMP PEAK 10(9Q34.3) MUTATED 8 6 3 9 4 13 3
AMP PEAK 10(9Q34.3) WILD-TYPE 127 65 33 59 86 28 69

Figure S66.  Get High-res Image Gene #10: 'amp_9q34.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_10p15.3' versus 'CN_CNMF'

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

Table S67.  Gene #11: 'amp_10p15.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
AMP PEAK 11(10P15.3) MUTATED 58 9 4
AMP PEAK 11(10P15.3) WILD-TYPE 114 111 217

Figure S67.  Get High-res Image Gene #11: 'amp_10p15.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_10p15.3' versus 'METHLYATION_CNMF'

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

Table S68.  Gene #11: 'amp_10p15.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
AMP PEAK 11(10P15.3) MUTATED 65 3 0 3
AMP PEAK 11(10P15.3) WILD-TYPE 160 78 167 37

Figure S68.  Get High-res Image Gene #11: 'amp_10p15.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_10p15.3' versus 'RPPA_CNMF'

P value = 0.00816 (Fisher's exact test), Q value = 0.018

Table S69.  Gene #11: 'amp_10p15.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 95 125 115
AMP PEAK 11(10P15.3) MUTATED 18 15 19 6
AMP PEAK 11(10P15.3) WILD-TYPE 73 80 106 109

Figure S69.  Get High-res Image Gene #11: 'amp_10p15.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_10p15.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00152 (Fisher's exact test), Q value = 0.0041

Table S70.  Gene #11: 'amp_10p15.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 158 185
AMP PEAK 11(10P15.3) MUTATED 17 10 31
AMP PEAK 11(10P15.3) WILD-TYPE 66 148 154

Figure S70.  Get High-res Image Gene #11: 'amp_10p15.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_10p15.3' versus 'MRNASEQ_CNMF'

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

Table S71.  Gene #11: 'amp_10p15.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 134 109 108 132 30
AMP PEAK 11(10P15.3) MUTATED 41 11 1 16 2
AMP PEAK 11(10P15.3) WILD-TYPE 93 98 107 116 28

Figure S71.  Get High-res Image Gene #11: 'amp_10p15.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_10p15.3' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S72.  Gene #11: 'amp_10p15.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
AMP PEAK 11(10P15.3) MUTATED 40 1 0 14 0 12 4
AMP PEAK 11(10P15.3) WILD-TYPE 95 70 36 54 90 29 68

Figure S72.  Get High-res Image Gene #11: 'amp_10p15.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_10p15.3' versus 'MIRSEQ_CNMF'

P value = 0.00105 (Fisher's exact test), Q value = 0.003

Table S73.  Gene #11: 'amp_10p15.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 107 183 82
AMP PEAK 11(10P15.3) MUTATED 20 26 20 4
AMP PEAK 11(10P15.3) WILD-TYPE 117 81 163 78

Figure S73.  Get High-res Image Gene #11: 'amp_10p15.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_10p15.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.00044

Table S74.  Gene #11: 'amp_10p15.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 137 188 89
AMP PEAK 11(10P15.3) MUTATED 27 16 21 6
AMP PEAK 11(10P15.3) WILD-TYPE 64 121 167 83

Figure S74.  Get High-res Image Gene #11: 'amp_10p15.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_11q24.1' versus 'METHLYATION_CNMF'

P value = 0.0113 (Fisher's exact test), Q value = 0.024

Table S75.  Gene #12: 'amp_11q24.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
AMP PEAK 12(11Q24.1) MUTATED 50 7 27 3
AMP PEAK 12(11Q24.1) WILD-TYPE 175 74 140 37

Figure S75.  Get High-res Image Gene #12: 'amp_11q24.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_11q24.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0467 (Fisher's exact test), Q value = 0.082

Table S76.  Gene #12: 'amp_11q24.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 158 185
AMP PEAK 12(11Q24.1) MUTATED 14 19 41
AMP PEAK 12(11Q24.1) WILD-TYPE 69 139 144

Figure S76.  Get High-res Image Gene #12: 'amp_11q24.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_11q24.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0435 (Fisher's exact test), Q value = 0.078

Table S77.  Gene #12: 'amp_11q24.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 137 188 89
AMP PEAK 12(11Q24.1) MUTATED 20 24 36 7
AMP PEAK 12(11Q24.1) WILD-TYPE 71 113 152 82

Figure S77.  Get High-res Image Gene #12: 'amp_11q24.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12p13.32' versus 'CN_CNMF'

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

Table S78.  Gene #13: 'amp_12p13.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
AMP PEAK 13(12P13.32) MUTATED 46 17 9
AMP PEAK 13(12P13.32) WILD-TYPE 126 103 212

Figure S78.  Get High-res Image Gene #13: 'amp_12p13.32' versus Molecular Subtype #3: 'CN_CNMF'

'amp_12p13.32' versus 'METHLYATION_CNMF'

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

Table S79.  Gene #13: 'amp_12p13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
AMP PEAK 13(12P13.32) MUTATED 55 9 5 3
AMP PEAK 13(12P13.32) WILD-TYPE 170 72 162 37

Figure S79.  Get High-res Image Gene #13: 'amp_12p13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_12p13.32' versus 'RPPA_CNMF'

P value = 0.00561 (Fisher's exact test), Q value = 0.013

Table S80.  Gene #13: 'amp_12p13.32' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 95 125 115
AMP PEAK 13(12P13.32) MUTATED 13 24 12 11
AMP PEAK 13(12P13.32) WILD-TYPE 78 71 113 104

Figure S80.  Get High-res Image Gene #13: 'amp_12p13.32' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_12p13.32' versus 'MRNASEQ_CNMF'

P value = 0.00125 (Fisher's exact test), Q value = 0.0035

Table S81.  Gene #13: 'amp_12p13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 134 109 108 132 30
AMP PEAK 13(12P13.32) MUTATED 30 19 6 13 4
AMP PEAK 13(12P13.32) WILD-TYPE 104 90 102 119 26

Figure S81.  Get High-res Image Gene #13: 'amp_12p13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_12p13.32' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S82.  Gene #13: 'amp_12p13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
AMP PEAK 13(12P13.32) MUTATED 32 8 1 14 4 12 1
AMP PEAK 13(12P13.32) WILD-TYPE 103 63 35 54 86 29 71

Figure S82.  Get High-res Image Gene #13: 'amp_12p13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_12p13.32' versus 'MIRSEQ_CNMF'

P value = 0.0101 (Fisher's exact test), Q value = 0.022

Table S83.  Gene #13: 'amp_12p13.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 107 183 82
AMP PEAK 13(12P13.32) MUTATED 17 26 18 11
AMP PEAK 13(12P13.32) WILD-TYPE 120 81 165 71

Figure S83.  Get High-res Image Gene #13: 'amp_12p13.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_12p13.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00667 (Fisher's exact test), Q value = 0.015

Table S84.  Gene #13: 'amp_12p13.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
AMP PEAK 13(12P13.32) MUTATED 36 15 21
AMP PEAK 13(12P13.32) WILD-TYPE 186 169 82

Figure S84.  Get High-res Image Gene #13: 'amp_12p13.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_12p13.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0246 (Fisher's exact test), Q value = 0.048

Table S85.  Gene #13: 'amp_12p13.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 185 161 159
AMP PEAK 13(12P13.32) MUTATED 31 28 13
AMP PEAK 13(12P13.32) WILD-TYPE 154 133 146

Figure S85.  Get High-res Image Gene #13: 'amp_12p13.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_12q14.1' versus 'CN_CNMF'

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

Table S86.  Gene #14: 'amp_12q14.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
AMP PEAK 14(12Q14.1) MUTATED 10 22 5
AMP PEAK 14(12Q14.1) WILD-TYPE 162 98 216

Figure S86.  Get High-res Image Gene #14: 'amp_12q14.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_12q14.1' versus 'METHLYATION_CNMF'

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

Table S87.  Gene #14: 'amp_12q14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
AMP PEAK 14(12Q14.1) MUTATED 13 19 4 1
AMP PEAK 14(12Q14.1) WILD-TYPE 212 62 163 39

Figure S87.  Get High-res Image Gene #14: 'amp_12q14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_12q14.1' versus 'RPPA_CNMF'

P value = 0.0138 (Fisher's exact test), Q value = 0.029

Table S88.  Gene #14: 'amp_12q14.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 95 125 115
AMP PEAK 14(12Q14.1) MUTATED 3 13 6 4
AMP PEAK 14(12Q14.1) WILD-TYPE 88 82 119 111

Figure S88.  Get High-res Image Gene #14: 'amp_12q14.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_12q14.1' versus 'MRNASEQ_CNMF'

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

Table S89.  Gene #14: 'amp_12q14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 134 109 108 132 30
AMP PEAK 14(12Q14.1) MUTATED 4 25 4 3 1
AMP PEAK 14(12Q14.1) WILD-TYPE 130 84 104 129 29

Figure S89.  Get High-res Image Gene #14: 'amp_12q14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_12q14.1' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S90.  Gene #14: 'amp_12q14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
AMP PEAK 14(12Q14.1) MUTATED 3 18 1 4 3 8 0
AMP PEAK 14(12Q14.1) WILD-TYPE 132 53 35 64 87 33 72

Figure S90.  Get High-res Image Gene #14: 'amp_12q14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_12q14.1' versus 'MIRSEQ_CNMF'

P value = 0.00277 (Fisher's exact test), Q value = 0.0071

Table S91.  Gene #14: 'amp_12q14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 107 183 82
AMP PEAK 14(12Q14.1) MUTATED 13 15 6 3
AMP PEAK 14(12Q14.1) WILD-TYPE 124 92 177 79

Figure S91.  Get High-res Image Gene #14: 'amp_12q14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_12q14.1' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S92.  Gene #14: 'amp_12q14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
AMP PEAK 14(12Q14.1) MUTATED 10 5 22
AMP PEAK 14(12Q14.1) WILD-TYPE 212 179 81

Figure S92.  Get High-res Image Gene #14: 'amp_12q14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_12q14.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0425 (Fisher's exact test), Q value = 0.077

Table S93.  Gene #14: 'amp_12q14.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 185 161 159
AMP PEAK 14(12Q14.1) MUTATED 21 8 8
AMP PEAK 14(12Q14.1) WILD-TYPE 164 153 151

Figure S93.  Get High-res Image Gene #14: 'amp_12q14.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_12q14.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 8.5e-05

Table S94.  Gene #14: 'amp_12q14.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 137 188 89
AMP PEAK 14(12Q14.1) MUTATED 6 5 7 19
AMP PEAK 14(12Q14.1) WILD-TYPE 85 132 181 70

Figure S94.  Get High-res Image Gene #14: 'amp_12q14.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_13q34' versus 'CN_CNMF'

P value = 0.00186 (Fisher's exact test), Q value = 0.0049

Table S95.  Gene #15: 'amp_13q34' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
AMP PEAK 15(13Q34) MUTATED 12 8 2
AMP PEAK 15(13Q34) WILD-TYPE 160 112 219

Figure S95.  Get High-res Image Gene #15: 'amp_13q34' versus Molecular Subtype #3: 'CN_CNMF'

'amp_13q34' versus 'METHLYATION_CNMF'

P value = 0.00126 (Fisher's exact test), Q value = 0.0035

Table S96.  Gene #15: 'amp_13q34' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
AMP PEAK 15(13Q34) MUTATED 18 3 1 0
AMP PEAK 15(13Q34) WILD-TYPE 207 78 166 40

Figure S96.  Get High-res Image Gene #15: 'amp_13q34' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_13q34' versus 'MRNASEQ_CNMF'

P value = 0.0387 (Fisher's exact test), Q value = 0.071

Table S97.  Gene #15: 'amp_13q34' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 134 109 108 132 30
AMP PEAK 15(13Q34) MUTATED 7 8 0 6 1
AMP PEAK 15(13Q34) WILD-TYPE 127 101 108 126 29

Figure S97.  Get High-res Image Gene #15: 'amp_13q34' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_13q34' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0222 (Fisher's exact test), Q value = 0.044

Table S98.  Gene #15: 'amp_13q34' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
AMP PEAK 15(13Q34) MUTATED 8 3 0 4 0 5 2
AMP PEAK 15(13Q34) WILD-TYPE 127 68 36 64 90 36 70

Figure S98.  Get High-res Image Gene #15: 'amp_13q34' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_15q26.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.0425 (Fisher's exact test), Q value = 0.077

Table S99.  Gene #16: 'amp_15q26.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 7 7 6
AMP PEAK 16(15Q26.3) MUTATED 0 3 0 0
AMP PEAK 16(15Q26.3) WILD-TYPE 7 4 7 6

Figure S99.  Get High-res Image Gene #16: 'amp_15q26.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_15q26.3' versus 'CN_CNMF'

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

Table S100.  Gene #16: 'amp_15q26.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
AMP PEAK 16(15Q26.3) MUTATED 12 7 0
AMP PEAK 16(15Q26.3) WILD-TYPE 160 113 221

Figure S100.  Get High-res Image Gene #16: 'amp_15q26.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_15q26.3' versus 'METHLYATION_CNMF'

P value = 0.00071 (Fisher's exact test), Q value = 0.0022

Table S101.  Gene #16: 'amp_15q26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
AMP PEAK 16(15Q26.3) MUTATED 14 5 0 0
AMP PEAK 16(15Q26.3) WILD-TYPE 211 76 167 40

Figure S101.  Get High-res Image Gene #16: 'amp_15q26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_15q26.3' versus 'MRNASEQ_CNMF'

P value = 0.0256 (Fisher's exact test), Q value = 0.05

Table S102.  Gene #16: 'amp_15q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 134 109 108 132 30
AMP PEAK 16(15Q26.3) MUTATED 5 8 0 4 2
AMP PEAK 16(15Q26.3) WILD-TYPE 129 101 108 128 28

Figure S102.  Get High-res Image Gene #16: 'amp_15q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17q25.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0484 (Fisher's exact test), Q value = 0.085

Table S103.  Gene #17: 'amp_17q25.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 158 185
AMP PEAK 17(17Q25.1) MUTATED 11 7 12
AMP PEAK 17(17Q25.1) WILD-TYPE 72 151 173

Figure S103.  Get High-res Image Gene #17: 'amp_17q25.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_19p13.3' versus 'CN_CNMF'

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

Table S104.  Gene #18: 'amp_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
AMP PEAK 18(19P13.3) MUTATED 9 40 80
AMP PEAK 18(19P13.3) WILD-TYPE 163 80 141

Figure S104.  Get High-res Image Gene #18: 'amp_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19p13.3' versus 'METHLYATION_CNMF'

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

Table S105.  Gene #18: 'amp_19p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
AMP PEAK 18(19P13.3) MUTATED 19 27 80 3
AMP PEAK 18(19P13.3) WILD-TYPE 206 54 87 37

Figure S105.  Get High-res Image Gene #18: 'amp_19p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_19p13.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00481 (Fisher's exact test), Q value = 0.011

Table S106.  Gene #18: 'amp_19p13.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 158 185
AMP PEAK 18(19P13.3) MUTATED 12 34 59
AMP PEAK 18(19P13.3) WILD-TYPE 71 124 126

Figure S106.  Get High-res Image Gene #18: 'amp_19p13.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_19p13.3' versus 'MRNASEQ_CNMF'

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

Table S107.  Gene #18: 'amp_19p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 134 109 108 132 30
AMP PEAK 18(19P13.3) MUTATED 10 29 54 34 2
AMP PEAK 18(19P13.3) WILD-TYPE 124 80 54 98 28

Figure S107.  Get High-res Image Gene #18: 'amp_19p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_19p13.3' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S108.  Gene #18: 'amp_19p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
AMP PEAK 18(19P13.3) MUTATED 8 25 18 10 40 6 22
AMP PEAK 18(19P13.3) WILD-TYPE 127 46 18 58 50 35 50

Figure S108.  Get High-res Image Gene #18: 'amp_19p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_19p13.3' versus 'MIRSEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00044

Table S109.  Gene #18: 'amp_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 107 183 82
AMP PEAK 18(19P13.3) MUTATED 24 23 45 37
AMP PEAK 18(19P13.3) WILD-TYPE 113 84 138 45

Figure S109.  Get High-res Image Gene #18: 'amp_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_19p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0459 (Fisher's exact test), Q value = 0.081

Table S110.  Gene #18: 'amp_19p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 185 161 159
AMP PEAK 18(19P13.3) MUTATED 37 51 41
AMP PEAK 18(19P13.3) WILD-TYPE 148 110 118

Figure S110.  Get High-res Image Gene #18: 'amp_19p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_19p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8e-04 (Fisher's exact test), Q value = 0.0024

Table S111.  Gene #18: 'amp_19p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 137 188 89
AMP PEAK 18(19P13.3) MUTATED 10 46 47 26
AMP PEAK 18(19P13.3) WILD-TYPE 81 91 141 63

Figure S111.  Get High-res Image Gene #18: 'amp_19p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19p13.2' versus 'CN_CNMF'

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

Table S112.  Gene #19: 'amp_19p13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
AMP PEAK 19(19P13.2) MUTATED 6 42 74
AMP PEAK 19(19P13.2) WILD-TYPE 166 78 147

Figure S112.  Get High-res Image Gene #19: 'amp_19p13.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19p13.2' versus 'METHLYATION_CNMF'

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

Table S113.  Gene #19: 'amp_19p13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
AMP PEAK 19(19P13.2) MUTATED 12 30 77 3
AMP PEAK 19(19P13.2) WILD-TYPE 213 51 90 37

Figure S113.  Get High-res Image Gene #19: 'amp_19p13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_19p13.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00075 (Fisher's exact test), Q value = 0.0023

Table S114.  Gene #19: 'amp_19p13.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 158 185
AMP PEAK 19(19P13.2) MUTATED 11 30 60
AMP PEAK 19(19P13.2) WILD-TYPE 72 128 125

Figure S114.  Get High-res Image Gene #19: 'amp_19p13.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_19p13.2' versus 'MRNASEQ_CNMF'

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

Table S115.  Gene #19: 'amp_19p13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 134 109 108 132 30
AMP PEAK 19(19P13.2) MUTATED 6 33 53 27 3
AMP PEAK 19(19P13.2) WILD-TYPE 128 76 55 105 27

Figure S115.  Get High-res Image Gene #19: 'amp_19p13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_19p13.2' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S116.  Gene #19: 'amp_19p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
AMP PEAK 19(19P13.2) MUTATED 6 28 18 7 39 5 19
AMP PEAK 19(19P13.2) WILD-TYPE 129 43 18 61 51 36 53

Figure S116.  Get High-res Image Gene #19: 'amp_19p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_19p13.2' versus 'MIRSEQ_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.00056

Table S117.  Gene #19: 'amp_19p13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 107 183 82
AMP PEAK 19(19P13.2) MUTATED 26 21 39 36
AMP PEAK 19(19P13.2) WILD-TYPE 111 86 144 46

Figure S117.  Get High-res Image Gene #19: 'amp_19p13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_19p13.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0415 (Fisher's exact test), Q value = 0.076

Table S118.  Gene #19: 'amp_19p13.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 185 161 159
AMP PEAK 19(19P13.2) MUTATED 36 50 36
AMP PEAK 19(19P13.2) WILD-TYPE 149 111 123

Figure S118.  Get High-res Image Gene #19: 'amp_19p13.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_19p13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00053 (Fisher's exact test), Q value = 0.0017

Table S119.  Gene #19: 'amp_19p13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 137 188 89
AMP PEAK 19(19P13.2) MUTATED 9 41 43 29
AMP PEAK 19(19P13.2) WILD-TYPE 82 96 145 60

Figure S119.  Get High-res Image Gene #19: 'amp_19p13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_xp11.22' versus 'CN_CNMF'

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

Table S120.  Gene #20: 'amp_xp11.22' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
AMP PEAK 20(XP11.22) MUTATED 33 8 7
AMP PEAK 20(XP11.22) WILD-TYPE 139 112 214

Figure S120.  Get High-res Image Gene #20: 'amp_xp11.22' versus Molecular Subtype #3: 'CN_CNMF'

'amp_xp11.22' versus 'METHLYATION_CNMF'

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

Table S121.  Gene #20: 'amp_xp11.22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
AMP PEAK 20(XP11.22) MUTATED 41 5 1 1
AMP PEAK 20(XP11.22) WILD-TYPE 184 76 166 39

Figure S121.  Get High-res Image Gene #20: 'amp_xp11.22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_xp11.22' versus 'MRNASEQ_CNMF'

P value = 0.00112 (Fisher's exact test), Q value = 0.0032

Table S122.  Gene #20: 'amp_xp11.22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 134 109 108 132 30
AMP PEAK 20(XP11.22) MUTATED 20 11 1 13 3
AMP PEAK 20(XP11.22) WILD-TYPE 114 98 107 119 27

Figure S122.  Get High-res Image Gene #20: 'amp_xp11.22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_xp11.22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00012

Table S123.  Gene #20: 'amp_xp11.22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
AMP PEAK 20(XP11.22) MUTATED 22 3 0 9 1 8 5
AMP PEAK 20(XP11.22) WILD-TYPE 113 68 36 59 89 33 67

Figure S123.  Get High-res Image Gene #20: 'amp_xp11.22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_xp11.22' versus 'CN_CNMF'

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

Table S124.  Gene #21: 'amp_xp11.22' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
AMP PEAK 21(XP11.22) MUTATED 47 7 9
AMP PEAK 21(XP11.22) WILD-TYPE 125 113 212

Figure S124.  Get High-res Image Gene #21: 'amp_xp11.22' versus Molecular Subtype #3: 'CN_CNMF'

'amp_xp11.22' versus 'METHLYATION_CNMF'

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

Table S125.  Gene #21: 'amp_xp11.22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
AMP PEAK 21(XP11.22) MUTATED 54 6 1 2
AMP PEAK 21(XP11.22) WILD-TYPE 171 75 166 38

Figure S125.  Get High-res Image Gene #21: 'amp_xp11.22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_xp11.22' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 8.5e-05

Table S126.  Gene #21: 'amp_xp11.22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 134 109 108 132 30
AMP PEAK 21(XP11.22) MUTATED 27 16 1 15 4
AMP PEAK 21(XP11.22) WILD-TYPE 107 93 107 117 26

Figure S126.  Get High-res Image Gene #21: 'amp_xp11.22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_xp11.22' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S127.  Gene #21: 'amp_xp11.22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
AMP PEAK 21(XP11.22) MUTATED 30 5 0 12 1 11 4
AMP PEAK 21(XP11.22) WILD-TYPE 105 66 36 56 89 30 68

Figure S127.  Get High-res Image Gene #21: 'amp_xp11.22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_xp11.22' versus 'MIRSEQ_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.0012

Table S128.  Gene #21: 'amp_xp11.22' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 107 183 82
AMP PEAK 21(XP11.22) MUTATED 22 19 20 1
AMP PEAK 21(XP11.22) WILD-TYPE 115 88 163 81

Figure S128.  Get High-res Image Gene #21: 'amp_xp11.22' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_xp11.22' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0093 (Fisher's exact test), Q value = 0.021

Table S129.  Gene #21: 'amp_xp11.22' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 137 188 89
AMP PEAK 21(XP11.22) MUTATED 21 11 21 9
AMP PEAK 21(XP11.22) WILD-TYPE 70 126 167 80

Figure S129.  Get High-res Image Gene #21: 'amp_xp11.22' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p36.32' versus 'MRNA_CNMF'

P value = 0.00057 (Fisher's exact test), Q value = 0.0018

Table S130.  Gene #22: 'del_1p36.32' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 9 10 8
DEL PEAK 1(1P36.32) MUTATED 0 8 2
DEL PEAK 1(1P36.32) WILD-TYPE 9 2 6

Figure S130.  Get High-res Image Gene #22: 'del_1p36.32' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_1p36.32' versus 'MRNA_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.00047

Table S131.  Gene #22: 'del_1p36.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 7 7 6
DEL PEAK 1(1P36.32) MUTATED 0 1 7 2
DEL PEAK 1(1P36.32) WILD-TYPE 7 6 0 4

Figure S131.  Get High-res Image Gene #22: 'del_1p36.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_1p36.32' versus 'CN_CNMF'

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

Table S132.  Gene #22: 'del_1p36.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
DEL PEAK 1(1P36.32) MUTATED 10 29 167
DEL PEAK 1(1P36.32) WILD-TYPE 162 91 54

Figure S132.  Get High-res Image Gene #22: 'del_1p36.32' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p36.32' versus 'METHLYATION_CNMF'

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

Table S133.  Gene #22: 'del_1p36.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
DEL PEAK 1(1P36.32) MUTATED 11 19 166 10
DEL PEAK 1(1P36.32) WILD-TYPE 214 62 1 30

Figure S133.  Get High-res Image Gene #22: 'del_1p36.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p36.32' versus 'RPPA_CNMF'

P value = 0.00061 (Fisher's exact test), Q value = 0.0019

Table S134.  Gene #22: 'del_1p36.32' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 95 125 115
DEL PEAK 1(1P36.32) MUTATED 25 37 52 64
DEL PEAK 1(1P36.32) WILD-TYPE 66 58 73 51

Figure S134.  Get High-res Image Gene #22: 'del_1p36.32' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_1p36.32' versus 'RPPA_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.001

Table S135.  Gene #22: 'del_1p36.32' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 158 185
DEL PEAK 1(1P36.32) MUTATED 26 85 67
DEL PEAK 1(1P36.32) WILD-TYPE 57 73 118

Figure S135.  Get High-res Image Gene #22: 'del_1p36.32' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_1p36.32' versus 'MRNASEQ_CNMF'

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

Table S136.  Gene #22: 'del_1p36.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 134 109 108 132 30
DEL PEAK 1(1P36.32) MUTATED 5 20 106 61 14
DEL PEAK 1(1P36.32) WILD-TYPE 129 89 2 71 16

Figure S136.  Get High-res Image Gene #22: 'del_1p36.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p36.32' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S137.  Gene #22: 'del_1p36.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
DEL PEAK 1(1P36.32) MUTATED 7 19 36 5 88 1 50
DEL PEAK 1(1P36.32) WILD-TYPE 128 52 0 63 2 40 22

Figure S137.  Get High-res Image Gene #22: 'del_1p36.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.32' versus 'MIRSEQ_CNMF'

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

Table S138.  Gene #22: 'del_1p36.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 107 183 82
DEL PEAK 1(1P36.32) MUTATED 33 13 92 68
DEL PEAK 1(1P36.32) WILD-TYPE 104 94 91 14

Figure S138.  Get High-res Image Gene #22: 'del_1p36.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_1p36.32' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S139.  Gene #22: 'del_1p36.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
DEL PEAK 1(1P36.32) MUTATED 84 101 21
DEL PEAK 1(1P36.32) WILD-TYPE 138 83 82

Figure S139.  Get High-res Image Gene #22: 'del_1p36.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.32' versus 'MIRSEQ_MATURE_CNMF'

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

Table S140.  Gene #22: 'del_1p36.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 185 161 159
DEL PEAK 1(1P36.32) MUTATED 44 83 79
DEL PEAK 1(1P36.32) WILD-TYPE 141 78 80

Figure S140.  Get High-res Image Gene #22: 'del_1p36.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_1p36.32' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S141.  Gene #22: 'del_1p36.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 137 188 89
DEL PEAK 1(1P36.32) MUTATED 7 83 95 21
DEL PEAK 1(1P36.32) WILD-TYPE 84 54 93 68

Figure S141.  Get High-res Image Gene #22: 'del_1p36.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p32.3' versus 'MRNA_CNMF'

P value = 0.0293 (Fisher's exact test), Q value = 0.056

Table S142.  Gene #23: 'del_1p32.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 9 10 8
DEL PEAK 2(1P32.3) MUTATED 1 7 2
DEL PEAK 2(1P32.3) WILD-TYPE 8 3 6

Figure S142.  Get High-res Image Gene #23: 'del_1p32.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_1p32.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.00056

Table S143.  Gene #23: 'del_1p32.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 7 7 6
DEL PEAK 2(1P32.3) MUTATED 0 1 7 2
DEL PEAK 2(1P32.3) WILD-TYPE 7 6 0 4

Figure S143.  Get High-res Image Gene #23: 'del_1p32.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_1p32.3' versus 'CN_CNMF'

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

Table S144.  Gene #23: 'del_1p32.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
DEL PEAK 2(1P32.3) MUTATED 6 24 166
DEL PEAK 2(1P32.3) WILD-TYPE 166 96 55

Figure S144.  Get High-res Image Gene #23: 'del_1p32.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p32.3' versus 'METHLYATION_CNMF'

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

Table S145.  Gene #23: 'del_1p32.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
DEL PEAK 2(1P32.3) MUTATED 5 15 166 10
DEL PEAK 2(1P32.3) WILD-TYPE 220 66 1 30

Figure S145.  Get High-res Image Gene #23: 'del_1p32.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p32.3' versus 'RPPA_CNMF'

P value = 0.00166 (Fisher's exact test), Q value = 0.0044

Table S146.  Gene #23: 'del_1p32.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 95 125 115
DEL PEAK 2(1P32.3) MUTATED 26 31 51 61
DEL PEAK 2(1P32.3) WILD-TYPE 65 64 74 54

Figure S146.  Get High-res Image Gene #23: 'del_1p32.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_1p32.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00061 (Fisher's exact test), Q value = 0.0019

Table S147.  Gene #23: 'del_1p32.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 158 185
DEL PEAK 2(1P32.3) MUTATED 24 81 64
DEL PEAK 2(1P32.3) WILD-TYPE 59 77 121

Figure S147.  Get High-res Image Gene #23: 'del_1p32.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_1p32.3' versus 'MRNASEQ_CNMF'

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

Table S148.  Gene #23: 'del_1p32.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 134 109 108 132 30
DEL PEAK 2(1P32.3) MUTATED 4 15 106 58 13
DEL PEAK 2(1P32.3) WILD-TYPE 130 94 2 74 17

Figure S148.  Get High-res Image Gene #23: 'del_1p32.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p32.3' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S149.  Gene #23: 'del_1p32.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
DEL PEAK 2(1P32.3) MUTATED 5 16 36 2 88 0 49
DEL PEAK 2(1P32.3) WILD-TYPE 130 55 0 66 2 41 23

Figure S149.  Get High-res Image Gene #23: 'del_1p32.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p32.3' versus 'MIRSEQ_CNMF'

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

Table S150.  Gene #23: 'del_1p32.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 107 183 82
DEL PEAK 2(1P32.3) MUTATED 33 10 86 67
DEL PEAK 2(1P32.3) WILD-TYPE 104 97 97 15

Figure S150.  Get High-res Image Gene #23: 'del_1p32.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_1p32.3' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S151.  Gene #23: 'del_1p32.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
DEL PEAK 2(1P32.3) MUTATED 82 96 18
DEL PEAK 2(1P32.3) WILD-TYPE 140 88 85

Figure S151.  Get High-res Image Gene #23: 'del_1p32.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_1p32.3' versus 'MIRSEQ_MATURE_CNMF'

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

Table S152.  Gene #23: 'del_1p32.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 185 161 159
DEL PEAK 2(1P32.3) MUTATED 39 82 75
DEL PEAK 2(1P32.3) WILD-TYPE 146 79 84

Figure S152.  Get High-res Image Gene #23: 'del_1p32.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_1p32.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S153.  Gene #23: 'del_1p32.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 137 188 89
DEL PEAK 2(1P32.3) MUTATED 7 82 90 17
DEL PEAK 2(1P32.3) WILD-TYPE 84 55 98 72

Figure S153.  Get High-res Image Gene #23: 'del_1p32.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1q43' versus 'METHLYATION_CNMF'

P value = 0.00975 (Fisher's exact test), Q value = 0.021

Table S154.  Gene #24: 'del_1q43' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
DEL PEAK 3(1Q43) MUTATED 20 4 3 4
DEL PEAK 3(1Q43) WILD-TYPE 205 77 164 36

Figure S154.  Get High-res Image Gene #24: 'del_1q43' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1q43' versus 'MRNASEQ_CNMF'

P value = 0.0259 (Fisher's exact test), Q value = 0.05

Table S155.  Gene #24: 'del_1q43' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 134 109 108 132 30
DEL PEAK 3(1Q43) MUTATED 14 7 1 8 1
DEL PEAK 3(1Q43) WILD-TYPE 120 102 107 124 29

Figure S155.  Get High-res Image Gene #24: 'del_1q43' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1q43' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0388 (Fisher's exact test), Q value = 0.071

Table S156.  Gene #24: 'del_1q43' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
DEL PEAK 3(1Q43) MUTATED 15 3 1 2 1 3 6
DEL PEAK 3(1Q43) WILD-TYPE 120 68 35 66 89 38 66

Figure S156.  Get High-res Image Gene #24: 'del_1q43' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_2q37.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.0126 (Fisher's exact test), Q value = 0.027

Table S157.  Gene #25: 'del_2q37.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 7 7 6
DEL PEAK 4(2Q37.3) MUTATED 0 4 0 2
DEL PEAK 4(2Q37.3) WILD-TYPE 7 3 7 4

Figure S157.  Get High-res Image Gene #25: 'del_2q37.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_2q37.3' versus 'CN_CNMF'

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

Table S158.  Gene #25: 'del_2q37.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
DEL PEAK 4(2Q37.3) MUTATED 44 22 11
DEL PEAK 4(2Q37.3) WILD-TYPE 128 98 210

Figure S158.  Get High-res Image Gene #25: 'del_2q37.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_2q37.3' versus 'METHLYATION_CNMF'

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

Table S159.  Gene #25: 'del_2q37.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
DEL PEAK 4(2Q37.3) MUTATED 64 4 6 3
DEL PEAK 4(2Q37.3) WILD-TYPE 161 77 161 37

Figure S159.  Get High-res Image Gene #25: 'del_2q37.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_2q37.3' versus 'RPPA_CNMF'

P value = 0.0011 (Fisher's exact test), Q value = 0.0031

Table S160.  Gene #25: 'del_2q37.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 95 125 115
DEL PEAK 4(2Q37.3) MUTATED 10 26 19 9
DEL PEAK 4(2Q37.3) WILD-TYPE 81 69 106 106

Figure S160.  Get High-res Image Gene #25: 'del_2q37.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_2q37.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0146 (Fisher's exact test), Q value = 0.031

Table S161.  Gene #25: 'del_2q37.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 158 185
DEL PEAK 4(2Q37.3) MUTATED 11 15 38
DEL PEAK 4(2Q37.3) WILD-TYPE 72 143 147

Figure S161.  Get High-res Image Gene #25: 'del_2q37.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_2q37.3' versus 'MRNASEQ_CNMF'

P value = 0.00094 (Fisher's exact test), Q value = 0.0028

Table S162.  Gene #25: 'del_2q37.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 134 109 108 132 30
DEL PEAK 4(2Q37.3) MUTATED 33 20 8 13 3
DEL PEAK 4(2Q37.3) WILD-TYPE 101 89 100 119 27

Figure S162.  Get High-res Image Gene #25: 'del_2q37.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_2q37.3' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S163.  Gene #25: 'del_2q37.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
DEL PEAK 4(2Q37.3) MUTATED 31 2 1 16 5 21 1
DEL PEAK 4(2Q37.3) WILD-TYPE 104 69 35 52 85 20 71

Figure S163.  Get High-res Image Gene #25: 'del_2q37.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_2q37.3' versus 'MIRSEQ_CNMF'

P value = 0.0149 (Fisher's exact test), Q value = 0.031

Table S164.  Gene #25: 'del_2q37.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 107 183 82
DEL PEAK 4(2Q37.3) MUTATED 25 24 19 8
DEL PEAK 4(2Q37.3) WILD-TYPE 112 83 164 74

Figure S164.  Get High-res Image Gene #25: 'del_2q37.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3p21.31' versus 'MRNA_CHIERARCHICAL'

P value = 0.00731 (Fisher's exact test), Q value = 0.017

Table S165.  Gene #26: 'del_3p21.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 7 7 6
DEL PEAK 5(3P21.31) MUTATED 0 4 0 0
DEL PEAK 5(3P21.31) WILD-TYPE 7 3 7 6

Figure S165.  Get High-res Image Gene #26: 'del_3p21.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_3p21.31' versus 'CN_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00037

Table S166.  Gene #26: 'del_3p21.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
DEL PEAK 5(3P21.31) MUTATED 26 15 8
DEL PEAK 5(3P21.31) WILD-TYPE 146 105 213

Figure S166.  Get High-res Image Gene #26: 'del_3p21.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p21.31' versus 'METHLYATION_CNMF'

P value = 0.00229 (Fisher's exact test), Q value = 0.0059

Table S167.  Gene #26: 'del_3p21.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
DEL PEAK 5(3P21.31) MUTATED 32 9 6 2
DEL PEAK 5(3P21.31) WILD-TYPE 193 72 161 38

Figure S167.  Get High-res Image Gene #26: 'del_3p21.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3p21.31' versus 'RPPA_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00023

Table S168.  Gene #26: 'del_3p21.31' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 95 125 115
DEL PEAK 5(3P21.31) MUTATED 5 22 10 5
DEL PEAK 5(3P21.31) WILD-TYPE 86 73 115 110

Figure S168.  Get High-res Image Gene #26: 'del_3p21.31' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_3p21.31' versus 'RPPA_CHIERARCHICAL'

P value = 0.0433 (Fisher's exact test), Q value = 0.077

Table S169.  Gene #26: 'del_3p21.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 158 185
DEL PEAK 5(3P21.31) MUTATED 5 11 26
DEL PEAK 5(3P21.31) WILD-TYPE 78 147 159

Figure S169.  Get High-res Image Gene #26: 'del_3p21.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_3p21.31' versus 'MRNASEQ_CNMF'

P value = 0.0426 (Fisher's exact test), Q value = 0.077

Table S170.  Gene #26: 'del_3p21.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 134 109 108 132 30
DEL PEAK 5(3P21.31) MUTATED 16 16 6 11 0
DEL PEAK 5(3P21.31) WILD-TYPE 118 93 102 121 30

Figure S170.  Get High-res Image Gene #26: 'del_3p21.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3p21.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00106 (Fisher's exact test), Q value = 0.003

Table S171.  Gene #26: 'del_3p21.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
DEL PEAK 5(3P21.31) MUTATED 15 7 2 7 3 12 3
DEL PEAK 5(3P21.31) WILD-TYPE 120 64 34 61 87 29 69

Figure S171.  Get High-res Image Gene #26: 'del_3p21.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p21.31' versus 'MIRSEQ_CNMF'

P value = 0.00059 (Fisher's exact test), Q value = 0.0019

Table S172.  Gene #26: 'del_3p21.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 107 183 82
DEL PEAK 5(3P21.31) MUTATED 12 21 8 8
DEL PEAK 5(3P21.31) WILD-TYPE 125 86 175 74

Figure S172.  Get High-res Image Gene #26: 'del_3p21.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3p21.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00218 (Fisher's exact test), Q value = 0.0057

Table S173.  Gene #26: 'del_3p21.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
DEL PEAK 5(3P21.31) MUTATED 24 8 17
DEL PEAK 5(3P21.31) WILD-TYPE 198 176 86

Figure S173.  Get High-res Image Gene #26: 'del_3p21.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3q13.31' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00016

Table S174.  Gene #27: 'del_3q13.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
DEL PEAK 6(3Q13.31) MUTATED 25 8 6
DEL PEAK 6(3Q13.31) WILD-TYPE 147 112 215

Figure S174.  Get High-res Image Gene #27: 'del_3q13.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_3q13.31' versus 'METHLYATION_CNMF'

P value = 0.00401 (Fisher's exact test), Q value = 0.0098

Table S175.  Gene #27: 'del_3q13.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
DEL PEAK 6(3Q13.31) MUTATED 26 7 4 2
DEL PEAK 6(3Q13.31) WILD-TYPE 199 74 163 38

Figure S175.  Get High-res Image Gene #27: 'del_3q13.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3q13.31' versus 'RPPA_CNMF'

P value = 0.0097 (Fisher's exact test), Q value = 0.021

Table S176.  Gene #27: 'del_3q13.31' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 95 125 115
DEL PEAK 6(3Q13.31) MUTATED 2 11 17 7
DEL PEAK 6(3Q13.31) WILD-TYPE 89 84 108 108

Figure S176.  Get High-res Image Gene #27: 'del_3q13.31' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_3q13.31' versus 'RPPA_CHIERARCHICAL'

P value = 0.0194 (Fisher's exact test), Q value = 0.04

Table S177.  Gene #27: 'del_3q13.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 158 185
DEL PEAK 6(3Q13.31) MUTATED 3 10 24
DEL PEAK 6(3Q13.31) WILD-TYPE 80 148 161

Figure S177.  Get High-res Image Gene #27: 'del_3q13.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_3q13.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0125 (Fisher's exact test), Q value = 0.027

Table S178.  Gene #27: 'del_3q13.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
DEL PEAK 6(3Q13.31) MUTATED 14 4 1 7 2 8 3
DEL PEAK 6(3Q13.31) WILD-TYPE 121 67 35 61 88 33 69

Figure S178.  Get High-res Image Gene #27: 'del_3q13.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3q13.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-04 (Fisher's exact test), Q value = 0.0016

Table S179.  Gene #27: 'del_3q13.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
DEL PEAK 6(3Q13.31) MUTATED 16 6 17
DEL PEAK 6(3Q13.31) WILD-TYPE 206 178 86

Figure S179.  Get High-res Image Gene #27: 'del_3q13.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3q29' versus 'CN_CNMF'

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

Table S180.  Gene #28: 'del_3q29' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
DEL PEAK 7(3Q29) MUTATED 33 10 4
DEL PEAK 7(3Q29) WILD-TYPE 139 110 217

Figure S180.  Get High-res Image Gene #28: 'del_3q29' versus Molecular Subtype #3: 'CN_CNMF'

'del_3q29' versus 'METHLYATION_CNMF'

P value = 0.00051 (Fisher's exact test), Q value = 0.0017

Table S181.  Gene #28: 'del_3q29' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
DEL PEAK 7(3Q29) MUTATED 31 8 4 4
DEL PEAK 7(3Q29) WILD-TYPE 194 73 163 36

Figure S181.  Get High-res Image Gene #28: 'del_3q29' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3q29' versus 'MRNASEQ_CNMF'

P value = 0.016 (Fisher's exact test), Q value = 0.033

Table S182.  Gene #28: 'del_3q29' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 134 109 108 132 30
DEL PEAK 7(3Q29) MUTATED 17 15 3 11 1
DEL PEAK 7(3Q29) WILD-TYPE 117 94 105 121 29

Figure S182.  Get High-res Image Gene #28: 'del_3q29' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3q29' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00016

Table S183.  Gene #28: 'del_3q29' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
DEL PEAK 7(3Q29) MUTATED 16 5 1 6 2 13 4
DEL PEAK 7(3Q29) WILD-TYPE 119 66 35 62 88 28 68

Figure S183.  Get High-res Image Gene #28: 'del_3q29' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3q29' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00462 (Fisher's exact test), Q value = 0.011

Table S184.  Gene #28: 'del_3q29' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
DEL PEAK 7(3Q29) MUTATED 19 10 18
DEL PEAK 7(3Q29) WILD-TYPE 203 174 85

Figure S184.  Get High-res Image Gene #28: 'del_3q29' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4q34.3' versus 'CN_CNMF'

P value = 0.0132 (Fisher's exact test), Q value = 0.028

Table S185.  Gene #29: 'del_4q34.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
DEL PEAK 8(4Q34.3) MUTATED 58 22 58
DEL PEAK 8(4Q34.3) WILD-TYPE 114 98 163

Figure S185.  Get High-res Image Gene #29: 'del_4q34.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q34.3' versus 'METHLYATION_CNMF'

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

Table S186.  Gene #29: 'del_4q34.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
DEL PEAK 8(4Q34.3) MUTATED 78 5 51 4
DEL PEAK 8(4Q34.3) WILD-TYPE 147 76 116 36

Figure S186.  Get High-res Image Gene #29: 'del_4q34.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q34.3' versus 'RPPA_CNMF'

P value = 0.0448 (Fisher's exact test), Q value = 0.079

Table S187.  Gene #29: 'del_4q34.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 95 125 115
DEL PEAK 8(4Q34.3) MUTATED 16 34 34 29
DEL PEAK 8(4Q34.3) WILD-TYPE 75 61 91 86

Figure S187.  Get High-res Image Gene #29: 'del_4q34.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_4q34.3' versus 'MRNASEQ_CNMF'

P value = 0.0238 (Fisher's exact test), Q value = 0.047

Table S188.  Gene #29: 'del_4q34.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 134 109 108 132 30
DEL PEAK 8(4Q34.3) MUTATED 39 19 35 41 4
DEL PEAK 8(4Q34.3) WILD-TYPE 95 90 73 91 26

Figure S188.  Get High-res Image Gene #29: 'del_4q34.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4q34.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00033

Table S189.  Gene #29: 'del_4q34.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
DEL PEAK 8(4Q34.3) MUTATED 36 5 17 18 25 16 21
DEL PEAK 8(4Q34.3) WILD-TYPE 99 66 19 50 65 25 51

Figure S189.  Get High-res Image Gene #29: 'del_4q34.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_CNMF'

P value = 0.0307 (Fisher's exact test), Q value = 0.059

Table S190.  Gene #29: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 107 183 82
DEL PEAK 8(4Q34.3) MUTATED 25 31 52 29
DEL PEAK 8(4Q34.3) WILD-TYPE 112 76 131 53

Figure S190.  Get High-res Image Gene #29: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_4q34.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0386 (Fisher's exact test), Q value = 0.071

Table S191.  Gene #29: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
DEL PEAK 8(4Q34.3) MUTATED 62 57 18
DEL PEAK 8(4Q34.3) WILD-TYPE 160 127 85

Figure S191.  Get High-res Image Gene #29: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00123 (Fisher's exact test), Q value = 0.0034

Table S192.  Gene #29: 'del_4q34.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 185 161 159
DEL PEAK 8(4Q34.3) MUTATED 33 55 49
DEL PEAK 8(4Q34.3) WILD-TYPE 152 106 110

Figure S192.  Get High-res Image Gene #29: 'del_4q34.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_4q34.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00618 (Fisher's exact test), Q value = 0.014

Table S193.  Gene #29: 'del_4q34.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 137 188 89
DEL PEAK 8(4Q34.3) MUTATED 24 46 55 12
DEL PEAK 8(4Q34.3) WILD-TYPE 67 91 133 77

Figure S193.  Get High-res Image Gene #29: 'del_4q34.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5p15.33' versus 'CN_CNMF'

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

Table S194.  Gene #30: 'del_5p15.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
DEL PEAK 9(5P15.33) MUTATED 33 12 5
DEL PEAK 9(5P15.33) WILD-TYPE 139 108 216

Figure S194.  Get High-res Image Gene #30: 'del_5p15.33' versus Molecular Subtype #3: 'CN_CNMF'

'del_5p15.33' versus 'METHLYATION_CNMF'

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

Table S195.  Gene #30: 'del_5p15.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
DEL PEAK 9(5P15.33) MUTATED 37 9 3 1
DEL PEAK 9(5P15.33) WILD-TYPE 188 72 164 39

Figure S195.  Get High-res Image Gene #30: 'del_5p15.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5p15.33' versus 'MRNASEQ_CNMF'

P value = 0.00057 (Fisher's exact test), Q value = 0.0018

Table S196.  Gene #30: 'del_5p15.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 134 109 108 132 30
DEL PEAK 9(5P15.33) MUTATED 15 17 1 13 4
DEL PEAK 9(5P15.33) WILD-TYPE 119 92 107 119 26

Figure S196.  Get High-res Image Gene #30: 'del_5p15.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_5p15.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00023

Table S197.  Gene #30: 'del_5p15.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
DEL PEAK 9(5P15.33) MUTATED 17 4 0 9 2 12 6
DEL PEAK 9(5P15.33) WILD-TYPE 118 67 36 59 88 29 66

Figure S197.  Get High-res Image Gene #30: 'del_5p15.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5p15.33' versus 'MIRSEQ_CNMF'

P value = 0.00212 (Fisher's exact test), Q value = 0.0055

Table S198.  Gene #30: 'del_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 107 183 82
DEL PEAK 9(5P15.33) MUTATED 11 20 17 2
DEL PEAK 9(5P15.33) WILD-TYPE 126 87 166 80

Figure S198.  Get High-res Image Gene #30: 'del_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_5q34' versus 'CN_CNMF'

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

Table S199.  Gene #31: 'del_5q34' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
DEL PEAK 10(5Q34) MUTATED 49 7 8
DEL PEAK 10(5Q34) WILD-TYPE 123 113 213

Figure S199.  Get High-res Image Gene #31: 'del_5q34' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q34' versus 'METHLYATION_CNMF'

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

Table S200.  Gene #31: 'del_5q34' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
DEL PEAK 10(5Q34) MUTATED 52 7 2 3
DEL PEAK 10(5Q34) WILD-TYPE 173 74 165 37

Figure S200.  Get High-res Image Gene #31: 'del_5q34' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5q34' versus 'RPPA_CNMF'

P value = 0.0365 (Fisher's exact test), Q value = 0.068

Table S201.  Gene #31: 'del_5q34' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 95 125 115
DEL PEAK 10(5Q34) MUTATED 11 19 13 8
DEL PEAK 10(5Q34) WILD-TYPE 80 76 112 107

Figure S201.  Get High-res Image Gene #31: 'del_5q34' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_5q34' versus 'RPPA_CHIERARCHICAL'

P value = 0.0469 (Fisher's exact test), Q value = 0.082

Table S202.  Gene #31: 'del_5q34' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 158 185
DEL PEAK 10(5Q34) MUTATED 15 12 24
DEL PEAK 10(5Q34) WILD-TYPE 68 146 161

Figure S202.  Get High-res Image Gene #31: 'del_5q34' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_5q34' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00012

Table S203.  Gene #31: 'del_5q34' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 134 109 108 132 30
DEL PEAK 10(5Q34) MUTATED 20 23 1 15 5
DEL PEAK 10(5Q34) WILD-TYPE 114 86 107 117 25

Figure S203.  Get High-res Image Gene #31: 'del_5q34' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_5q34' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S204.  Gene #31: 'del_5q34' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
DEL PEAK 10(5Q34) MUTATED 20 3 0 12 2 22 5
DEL PEAK 10(5Q34) WILD-TYPE 115 68 36 56 88 19 67

Figure S204.  Get High-res Image Gene #31: 'del_5q34' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5q34' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00016

Table S205.  Gene #31: 'del_5q34' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 107 183 82
DEL PEAK 10(5Q34) MUTATED 15 28 18 3
DEL PEAK 10(5Q34) WILD-TYPE 122 79 165 79

Figure S205.  Get High-res Image Gene #31: 'del_5q34' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_6p25.3' versus 'CN_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 5e-04

Table S206.  Gene #32: 'del_6p25.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
DEL PEAK 11(6P25.3) MUTATED 25 17 8
DEL PEAK 11(6P25.3) WILD-TYPE 147 103 213

Figure S206.  Get High-res Image Gene #32: 'del_6p25.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_6p25.3' versus 'METHLYATION_CNMF'

P value = 0.0416 (Fisher's exact test), Q value = 0.076

Table S207.  Gene #32: 'del_6p25.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
DEL PEAK 11(6P25.3) MUTATED 27 11 8 4
DEL PEAK 11(6P25.3) WILD-TYPE 198 70 159 36

Figure S207.  Get High-res Image Gene #32: 'del_6p25.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_6q22.31' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00016

Table S208.  Gene #33: 'del_6q22.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
DEL PEAK 12(6Q22.31) MUTATED 29 31 18
DEL PEAK 12(6Q22.31) WILD-TYPE 143 89 203

Figure S208.  Get High-res Image Gene #33: 'del_6q22.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_6q22.31' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 8.5e-05

Table S209.  Gene #33: 'del_6q22.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
DEL PEAK 12(6Q22.31) MUTATED 49 16 8 5
DEL PEAK 12(6Q22.31) WILD-TYPE 176 65 159 35

Figure S209.  Get High-res Image Gene #33: 'del_6q22.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_6q22.31' versus 'RPPA_CHIERARCHICAL'

P value = 0.0154 (Fisher's exact test), Q value = 0.032

Table S210.  Gene #33: 'del_6q22.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 158 185
DEL PEAK 12(6Q22.31) MUTATED 10 17 40
DEL PEAK 12(6Q22.31) WILD-TYPE 73 141 145

Figure S210.  Get High-res Image Gene #33: 'del_6q22.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_6q22.31' versus 'MRNASEQ_CNMF'

P value = 0.00461 (Fisher's exact test), Q value = 0.011

Table S211.  Gene #33: 'del_6q22.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 134 109 108 132 30
DEL PEAK 12(6Q22.31) MUTATED 26 25 7 16 4
DEL PEAK 12(6Q22.31) WILD-TYPE 108 84 101 116 26

Figure S211.  Get High-res Image Gene #33: 'del_6q22.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_6q22.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00128 (Fisher's exact test), Q value = 0.0035

Table S212.  Gene #33: 'del_6q22.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
DEL PEAK 12(6Q22.31) MUTATED 27 16 1 12 6 10 6
DEL PEAK 12(6Q22.31) WILD-TYPE 108 55 35 56 84 31 66

Figure S212.  Get High-res Image Gene #33: 'del_6q22.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_6q22.31' versus 'MIRSEQ_CNMF'

P value = 0.00079 (Fisher's exact test), Q value = 0.0024

Table S213.  Gene #33: 'del_6q22.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 107 183 82
DEL PEAK 12(6Q22.31) MUTATED 34 18 19 6
DEL PEAK 12(6Q22.31) WILD-TYPE 103 89 164 76

Figure S213.  Get High-res Image Gene #33: 'del_6q22.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_6q22.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00661 (Fisher's exact test), Q value = 0.015

Table S214.  Gene #33: 'del_6q22.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 185 161 159
DEL PEAK 12(6Q22.31) MUTATED 40 18 17
DEL PEAK 12(6Q22.31) WILD-TYPE 145 143 142

Figure S214.  Get High-res Image Gene #33: 'del_6q22.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_6q22.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S215.  Gene #33: 'del_6q22.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 137 188 89
DEL PEAK 12(6Q22.31) MUTATED 24 11 18 22
DEL PEAK 12(6Q22.31) WILD-TYPE 67 126 170 67

Figure S215.  Get High-res Image Gene #33: 'del_6q22.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q24.3' versus 'CN_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.00096

Table S216.  Gene #34: 'del_6q24.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
DEL PEAK 13(6Q24.3) MUTATED 32 30 20
DEL PEAK 13(6Q24.3) WILD-TYPE 140 90 201

Figure S216.  Get High-res Image Gene #34: 'del_6q24.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_6q24.3' versus 'METHLYATION_CNMF'

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

Table S217.  Gene #34: 'del_6q24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
DEL PEAK 13(6Q24.3) MUTATED 53 16 8 5
DEL PEAK 13(6Q24.3) WILD-TYPE 172 65 159 35

Figure S217.  Get High-res Image Gene #34: 'del_6q24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_6q24.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00965 (Fisher's exact test), Q value = 0.021

Table S218.  Gene #34: 'del_6q24.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 158 185
DEL PEAK 13(6Q24.3) MUTATED 11 17 42
DEL PEAK 13(6Q24.3) WILD-TYPE 72 141 143

Figure S218.  Get High-res Image Gene #34: 'del_6q24.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_6q24.3' versus 'MRNASEQ_CNMF'

P value = 0.00139 (Fisher's exact test), Q value = 0.0038

Table S219.  Gene #34: 'del_6q24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 134 109 108 132 30
DEL PEAK 13(6Q24.3) MUTATED 30 25 7 16 4
DEL PEAK 13(6Q24.3) WILD-TYPE 104 84 101 116 26

Figure S219.  Get High-res Image Gene #34: 'del_6q24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_6q24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00039 (Fisher's exact test), Q value = 0.0013

Table S220.  Gene #34: 'del_6q24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
DEL PEAK 13(6Q24.3) MUTATED 31 15 1 12 6 11 6
DEL PEAK 13(6Q24.3) WILD-TYPE 104 56 35 56 84 30 66

Figure S220.  Get High-res Image Gene #34: 'del_6q24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_6q24.3' versus 'MIRSEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00037

Table S221.  Gene #34: 'del_6q24.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 107 183 82
DEL PEAK 13(6Q24.3) MUTATED 36 20 20 5
DEL PEAK 13(6Q24.3) WILD-TYPE 101 87 163 77

Figure S221.  Get High-res Image Gene #34: 'del_6q24.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_6q24.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.021 (Fisher's exact test), Q value = 0.043

Table S222.  Gene #34: 'del_6q24.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 185 161 159
DEL PEAK 13(6Q24.3) MUTATED 40 21 18
DEL PEAK 13(6Q24.3) WILD-TYPE 145 140 141

Figure S222.  Get High-res Image Gene #34: 'del_6q24.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_6q24.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 8.5e-05

Table S223.  Gene #34: 'del_6q24.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 137 188 89
DEL PEAK 13(6Q24.3) MUTATED 27 12 19 21
DEL PEAK 13(6Q24.3) WILD-TYPE 64 125 169 68

Figure S223.  Get High-res Image Gene #34: 'del_6q24.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_7p22.3' versus 'CN_CNMF'

P value = 0.0255 (Fisher's exact test), Q value = 0.05

Table S224.  Gene #35: 'del_7p22.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
DEL PEAK 14(7P22.3) MUTATED 14 3 6
DEL PEAK 14(7P22.3) WILD-TYPE 158 117 215

Figure S224.  Get High-res Image Gene #35: 'del_7p22.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_8q24.3' versus 'CN_CNMF'

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

Table S225.  Gene #36: 'del_8q24.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
DEL PEAK 15(8Q24.3) MUTATED 15 13 1
DEL PEAK 15(8Q24.3) WILD-TYPE 157 107 220

Figure S225.  Get High-res Image Gene #36: 'del_8q24.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_8q24.3' versus 'METHLYATION_CNMF'

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

Table S226.  Gene #36: 'del_8q24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
DEL PEAK 15(8Q24.3) MUTATED 17 11 0 1
DEL PEAK 15(8Q24.3) WILD-TYPE 208 70 167 39

Figure S226.  Get High-res Image Gene #36: 'del_8q24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_8q24.3' versus 'MRNASEQ_CNMF'

P value = 0.00333 (Fisher's exact test), Q value = 0.0083

Table S227.  Gene #36: 'del_8q24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 134 109 108 132 30
DEL PEAK 15(8Q24.3) MUTATED 11 11 0 6 1
DEL PEAK 15(8Q24.3) WILD-TYPE 123 98 108 126 29

Figure S227.  Get High-res Image Gene #36: 'del_8q24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_8q24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00674 (Fisher's exact test), Q value = 0.015

Table S228.  Gene #36: 'del_8q24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
DEL PEAK 15(8Q24.3) MUTATED 10 9 0 4 0 3 3
DEL PEAK 15(8Q24.3) WILD-TYPE 125 62 36 64 90 38 69

Figure S228.  Get High-res Image Gene #36: 'del_8q24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_8q24.3' versus 'MIRSEQ_CNMF'

P value = 0.00476 (Fisher's exact test), Q value = 0.011

Table S229.  Gene #36: 'del_8q24.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 107 183 82
DEL PEAK 15(8Q24.3) MUTATED 13 9 7 0
DEL PEAK 15(8Q24.3) WILD-TYPE 124 98 176 82

Figure S229.  Get High-res Image Gene #36: 'del_8q24.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_8q24.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00317 (Fisher's exact test), Q value = 0.0079

Table S230.  Gene #36: 'del_8q24.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
DEL PEAK 15(8Q24.3) MUTATED 11 5 13
DEL PEAK 15(8Q24.3) WILD-TYPE 211 179 90

Figure S230.  Get High-res Image Gene #36: 'del_8q24.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_8q24.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0297 (Fisher's exact test), Q value = 0.057

Table S231.  Gene #36: 'del_8q24.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 137 188 89
DEL PEAK 15(8Q24.3) MUTATED 8 6 5 9
DEL PEAK 15(8Q24.3) WILD-TYPE 83 131 183 80

Figure S231.  Get High-res Image Gene #36: 'del_8q24.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p23' versus 'CN_CNMF'

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

Table S232.  Gene #37: 'del_9p23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
DEL PEAK 16(9P23) MUTATED 55 57 38
DEL PEAK 16(9P23) WILD-TYPE 117 63 183

Figure S232.  Get High-res Image Gene #37: 'del_9p23' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p23' versus 'METHLYATION_CNMF'

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

Table S233.  Gene #37: 'del_9p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
DEL PEAK 16(9P23) MUTATED 79 35 28 8
DEL PEAK 16(9P23) WILD-TYPE 146 46 139 32

Figure S233.  Get High-res Image Gene #37: 'del_9p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9p23' versus 'RPPA_CNMF'

P value = 0.00626 (Fisher's exact test), Q value = 0.015

Table S234.  Gene #37: 'del_9p23' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 95 125 115
DEL PEAK 16(9P23) MUTATED 21 42 38 28
DEL PEAK 16(9P23) WILD-TYPE 70 53 87 87

Figure S234.  Get High-res Image Gene #37: 'del_9p23' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_9p23' versus 'RPPA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00016

Table S235.  Gene #37: 'del_9p23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 158 185
DEL PEAK 16(9P23) MUTATED 15 37 77
DEL PEAK 16(9P23) WILD-TYPE 68 121 108

Figure S235.  Get High-res Image Gene #37: 'del_9p23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_9p23' versus 'MRNASEQ_CNMF'

P value = 0.022 (Fisher's exact test), Q value = 0.044

Table S236.  Gene #37: 'del_9p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 134 109 108 132 30
DEL PEAK 16(9P23) MUTATED 35 42 21 44 8
DEL PEAK 16(9P23) WILD-TYPE 99 67 87 88 22

Figure S236.  Get High-res Image Gene #37: 'del_9p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9p23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 0.00093

Table S237.  Gene #37: 'del_9p23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
DEL PEAK 16(9P23) MUTATED 39 27 10 31 15 16 12
DEL PEAK 16(9P23) WILD-TYPE 96 44 26 37 75 25 60

Figure S237.  Get High-res Image Gene #37: 'del_9p23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00309 (Fisher's exact test), Q value = 0.0078

Table S238.  Gene #37: 'del_9p23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 137 188 89
DEL PEAK 16(9P23) MUTATED 28 27 55 38
DEL PEAK 16(9P23) WILD-TYPE 63 110 133 51

Figure S238.  Get High-res Image Gene #37: 'del_9p23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p21.3' versus 'CN_CNMF'

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

Table S239.  Gene #38: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
DEL PEAK 17(9P21.3) MUTATED 63 77 36
DEL PEAK 17(9P21.3) WILD-TYPE 109 43 185

Figure S239.  Get High-res Image Gene #38: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

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

Table S240.  Gene #38: 'del_9p21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
DEL PEAK 17(9P21.3) MUTATED 82 59 27 8
DEL PEAK 17(9P21.3) WILD-TYPE 143 22 140 32

Figure S240.  Get High-res Image Gene #38: 'del_9p21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9p21.3' versus 'RPPA_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00023

Table S241.  Gene #38: 'del_9p21.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 95 125 115
DEL PEAK 17(9P21.3) MUTATED 22 52 46 29
DEL PEAK 17(9P21.3) WILD-TYPE 69 43 79 86

Figure S241.  Get High-res Image Gene #38: 'del_9p21.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_9p21.3' versus 'RPPA_CHIERARCHICAL'

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

Table S242.  Gene #38: 'del_9p21.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 158 185
DEL PEAK 17(9P21.3) MUTATED 14 38 97
DEL PEAK 17(9P21.3) WILD-TYPE 69 120 88

Figure S242.  Get High-res Image Gene #38: 'del_9p21.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_9p21.3' versus 'MRNASEQ_CNMF'

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

Table S243.  Gene #38: 'del_9p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 134 109 108 132 30
DEL PEAK 17(9P21.3) MUTATED 40 64 19 45 8
DEL PEAK 17(9P21.3) WILD-TYPE 94 45 89 87 22

Figure S243.  Get High-res Image Gene #38: 'del_9p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S244.  Gene #38: 'del_9p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
DEL PEAK 17(9P21.3) MUTATED 44 47 10 31 13 18 13
DEL PEAK 17(9P21.3) WILD-TYPE 91 24 26 37 77 23 59

Figure S244.  Get High-res Image Gene #38: 'del_9p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S245.  Gene #38: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
DEL PEAK 17(9P21.3) MUTATED 59 56 60
DEL PEAK 17(9P21.3) WILD-TYPE 163 128 43

Figure S245.  Get High-res Image Gene #38: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00078 (Fisher's exact test), Q value = 0.0024

Table S246.  Gene #38: 'del_9p21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 185 161 159
DEL PEAK 17(9P21.3) MUTATED 82 41 51
DEL PEAK 17(9P21.3) WILD-TYPE 103 120 108

Figure S246.  Get High-res Image Gene #38: 'del_9p21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_9p21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S247.  Gene #38: 'del_9p21.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 137 188 89
DEL PEAK 17(9P21.3) MUTATED 31 28 54 61
DEL PEAK 17(9P21.3) WILD-TYPE 60 109 134 28

Figure S247.  Get High-res Image Gene #38: 'del_9p21.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q26.3' versus 'CN_CNMF'

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

Table S248.  Gene #39: 'del_10q26.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
DEL PEAK 18(10Q26.3) MUTATED 53 85 13
DEL PEAK 18(10Q26.3) WILD-TYPE 119 35 208

Figure S248.  Get High-res Image Gene #39: 'del_10q26.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q26.3' versus 'METHLYATION_CNMF'

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

Table S249.  Gene #39: 'del_10q26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
DEL PEAK 18(10Q26.3) MUTATED 64 72 8 7
DEL PEAK 18(10Q26.3) WILD-TYPE 161 9 159 33

Figure S249.  Get High-res Image Gene #39: 'del_10q26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10q26.3' versus 'RPPA_CNMF'

P value = 0.00131 (Fisher's exact test), Q value = 0.0036

Table S250.  Gene #39: 'del_10q26.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 95 125 115
DEL PEAK 18(10Q26.3) MUTATED 20 41 33 23
DEL PEAK 18(10Q26.3) WILD-TYPE 71 54 92 92

Figure S250.  Get High-res Image Gene #39: 'del_10q26.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_10q26.3' versus 'RPPA_CHIERARCHICAL'

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

Table S251.  Gene #39: 'del_10q26.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 158 185
DEL PEAK 18(10Q26.3) MUTATED 10 31 76
DEL PEAK 18(10Q26.3) WILD-TYPE 73 127 109

Figure S251.  Get High-res Image Gene #39: 'del_10q26.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_10q26.3' versus 'MRNASEQ_CNMF'

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

Table S252.  Gene #39: 'del_10q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 134 109 108 132 30
DEL PEAK 18(10Q26.3) MUTATED 33 79 6 26 7
DEL PEAK 18(10Q26.3) WILD-TYPE 101 30 102 106 23

Figure S252.  Get High-res Image Gene #39: 'del_10q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10q26.3' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S253.  Gene #39: 'del_10q26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
DEL PEAK 18(10Q26.3) MUTATED 34 60 3 24 5 22 3
DEL PEAK 18(10Q26.3) WILD-TYPE 101 11 33 44 85 19 69

Figure S253.  Get High-res Image Gene #39: 'del_10q26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10q26.3' versus 'MIRSEQ_CNMF'

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

Table S254.  Gene #39: 'del_10q26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 107 183 82
DEL PEAK 18(10Q26.3) MUTATED 55 46 39 11
DEL PEAK 18(10Q26.3) WILD-TYPE 82 61 144 71

Figure S254.  Get High-res Image Gene #39: 'del_10q26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_10q26.3' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S255.  Gene #39: 'del_10q26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
DEL PEAK 18(10Q26.3) MUTATED 49 28 74
DEL PEAK 18(10Q26.3) WILD-TYPE 173 156 29

Figure S255.  Get High-res Image Gene #39: 'del_10q26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_10q26.3' versus 'MIRSEQ_MATURE_CNMF'

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

Table S256.  Gene #39: 'del_10q26.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 185 161 159
DEL PEAK 18(10Q26.3) MUTATED 94 22 35
DEL PEAK 18(10Q26.3) WILD-TYPE 91 139 124

Figure S256.  Get High-res Image Gene #39: 'del_10q26.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_10q26.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S257.  Gene #39: 'del_10q26.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 137 188 89
DEL PEAK 18(10Q26.3) MUTATED 28 18 33 72
DEL PEAK 18(10Q26.3) WILD-TYPE 63 119 155 17

Figure S257.  Get High-res Image Gene #39: 'del_10q26.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11p15.5' versus 'MRNA_CHIERARCHICAL'

P value = 0.00061 (Fisher's exact test), Q value = 0.0019

Table S258.  Gene #40: 'del_11p15.5' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 7 7 6
DEL PEAK 19(11P15.5) MUTATED 1 6 0 0
DEL PEAK 19(11P15.5) WILD-TYPE 6 1 7 6

Figure S258.  Get High-res Image Gene #40: 'del_11p15.5' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_11p15.5' versus 'CN_CNMF'

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

Table S259.  Gene #40: 'del_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
DEL PEAK 19(11P15.5) MUTATED 74 20 10
DEL PEAK 19(11P15.5) WILD-TYPE 98 100 211

Figure S259.  Get High-res Image Gene #40: 'del_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

'del_11p15.5' versus 'METHLYATION_CNMF'

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

Table S260.  Gene #40: 'del_11p15.5' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
DEL PEAK 19(11P15.5) MUTATED 85 14 0 5
DEL PEAK 19(11P15.5) WILD-TYPE 140 67 167 35

Figure S260.  Get High-res Image Gene #40: 'del_11p15.5' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_11p15.5' versus 'MRNASEQ_CNMF'

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

Table S261.  Gene #40: 'del_11p15.5' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 134 109 108 132 30
DEL PEAK 19(11P15.5) MUTATED 38 34 1 24 7
DEL PEAK 19(11P15.5) WILD-TYPE 96 75 107 108 23

Figure S261.  Get High-res Image Gene #40: 'del_11p15.5' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_11p15.5' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S262.  Gene #40: 'del_11p15.5' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
DEL PEAK 19(11P15.5) MUTATED 38 9 0 18 0 29 10
DEL PEAK 19(11P15.5) WILD-TYPE 97 62 36 50 90 12 62

Figure S262.  Get High-res Image Gene #40: 'del_11p15.5' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00012

Table S263.  Gene #40: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 107 183 82
DEL PEAK 19(11P15.5) MUTATED 23 40 33 8
DEL PEAK 19(11P15.5) WILD-TYPE 114 67 150 74

Figure S263.  Get High-res Image Gene #40: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_11p15.5' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00447 (Fisher's exact test), Q value = 0.011

Table S264.  Gene #40: 'del_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
DEL PEAK 19(11P15.5) MUTATED 42 29 33
DEL PEAK 19(11P15.5) WILD-TYPE 180 155 70

Figure S264.  Get High-res Image Gene #40: 'del_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_11p15.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.0314 (Fisher's exact test), Q value = 0.06

Table S265.  Gene #41: 'del_11p15.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 7 7 6
DEL PEAK 20(11P15.1) MUTATED 1 4 0 0
DEL PEAK 20(11P15.1) WILD-TYPE 6 3 7 6

Figure S265.  Get High-res Image Gene #41: 'del_11p15.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_11p15.1' versus 'CN_CNMF'

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

Table S266.  Gene #41: 'del_11p15.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
DEL PEAK 20(11P15.1) MUTATED 52 15 5
DEL PEAK 20(11P15.1) WILD-TYPE 120 105 216

Figure S266.  Get High-res Image Gene #41: 'del_11p15.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_11p15.1' versus 'METHLYATION_CNMF'

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

Table S267.  Gene #41: 'del_11p15.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
DEL PEAK 20(11P15.1) MUTATED 52 14 1 5
DEL PEAK 20(11P15.1) WILD-TYPE 173 67 166 35

Figure S267.  Get High-res Image Gene #41: 'del_11p15.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_11p15.1' versus 'RPPA_CNMF'

P value = 0.00149 (Fisher's exact test), Q value = 0.004

Table S268.  Gene #41: 'del_11p15.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 95 125 115
DEL PEAK 20(11P15.1) MUTATED 16 21 7 13
DEL PEAK 20(11P15.1) WILD-TYPE 75 74 118 102

Figure S268.  Get High-res Image Gene #41: 'del_11p15.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_11p15.1' versus 'MRNASEQ_CNMF'

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

Table S269.  Gene #41: 'del_11p15.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 134 109 108 132 30
DEL PEAK 20(11P15.1) MUTATED 17 34 2 13 6
DEL PEAK 20(11P15.1) WILD-TYPE 117 75 106 119 24

Figure S269.  Get High-res Image Gene #41: 'del_11p15.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_11p15.1' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S270.  Gene #41: 'del_11p15.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
DEL PEAK 20(11P15.1) MUTATED 20 9 0 6 1 29 7
DEL PEAK 20(11P15.1) WILD-TYPE 115 62 36 62 89 12 65

Figure S270.  Get High-res Image Gene #41: 'del_11p15.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_11p15.1' versus 'MIRSEQ_CNMF'

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

Table S271.  Gene #41: 'del_11p15.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 107 183 82
DEL PEAK 20(11P15.1) MUTATED 16 32 19 5
DEL PEAK 20(11P15.1) WILD-TYPE 121 75 164 77

Figure S271.  Get High-res Image Gene #41: 'del_11p15.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_11p15.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00027

Table S272.  Gene #41: 'del_11p15.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
DEL PEAK 20(11P15.1) MUTATED 27 16 29
DEL PEAK 20(11P15.1) WILD-TYPE 195 168 74

Figure S272.  Get High-res Image Gene #41: 'del_11p15.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_11p15.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0332 (Fisher's exact test), Q value = 0.063

Table S273.  Gene #41: 'del_11p15.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 137 188 89
DEL PEAK 20(11P15.1) MUTATED 13 18 19 21
DEL PEAK 20(11P15.1) WILD-TYPE 78 119 169 68

Figure S273.  Get High-res Image Gene #41: 'del_11p15.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_12p13.1' versus 'CN_CNMF'

P value = 0.00068 (Fisher's exact test), Q value = 0.0021

Table S274.  Gene #42: 'del_12p13.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
DEL PEAK 21(12P13.1) MUTATED 23 8 7
DEL PEAK 21(12P13.1) WILD-TYPE 149 112 214

Figure S274.  Get High-res Image Gene #42: 'del_12p13.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_12p13.1' versus 'METHLYATION_CNMF'

P value = 0.00197 (Fisher's exact test), Q value = 0.0052

Table S275.  Gene #42: 'del_12p13.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
DEL PEAK 21(12P13.1) MUTATED 26 7 5 0
DEL PEAK 21(12P13.1) WILD-TYPE 199 74 162 40

Figure S275.  Get High-res Image Gene #42: 'del_12p13.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_12p13.1' versus 'MRNASEQ_CNMF'

P value = 0.0101 (Fisher's exact test), Q value = 0.022

Table S276.  Gene #42: 'del_12p13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 134 109 108 132 30
DEL PEAK 21(12P13.1) MUTATED 15 12 2 9 0
DEL PEAK 21(12P13.1) WILD-TYPE 119 97 106 123 30

Figure S276.  Get High-res Image Gene #42: 'del_12p13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_12p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00685 (Fisher's exact test), Q value = 0.016

Table S277.  Gene #42: 'del_12p13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
DEL PEAK 21(12P13.1) MUTATED 15 4 1 3 3 9 3
DEL PEAK 21(12P13.1) WILD-TYPE 120 67 35 65 87 32 69

Figure S277.  Get High-res Image Gene #42: 'del_12p13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_12p13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0445 (Fisher's exact test), Q value = 0.079

Table S278.  Gene #42: 'del_12p13.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
DEL PEAK 21(12P13.1) MUTATED 13 11 14
DEL PEAK 21(12P13.1) WILD-TYPE 209 173 89

Figure S278.  Get High-res Image Gene #42: 'del_12p13.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_12q12' versus 'CN_CNMF'

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

Table S279.  Gene #43: 'del_12q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
DEL PEAK 22(12Q12) MUTATED 53 7 12
DEL PEAK 22(12Q12) WILD-TYPE 119 113 209

Figure S279.  Get High-res Image Gene #43: 'del_12q12' versus Molecular Subtype #3: 'CN_CNMF'

'del_12q12' versus 'METHLYATION_CNMF'

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

Table S280.  Gene #43: 'del_12q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
DEL PEAK 22(12Q12) MUTATED 57 5 8 2
DEL PEAK 22(12Q12) WILD-TYPE 168 76 159 38

Figure S280.  Get High-res Image Gene #43: 'del_12q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_12q12' versus 'MRNASEQ_CNMF'

P value = 0.00188 (Fisher's exact test), Q value = 0.0049

Table S281.  Gene #43: 'del_12q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 134 109 108 132 30
DEL PEAK 22(12Q12) MUTATED 24 21 4 18 5
DEL PEAK 22(12Q12) WILD-TYPE 110 88 104 114 25

Figure S281.  Get High-res Image Gene #43: 'del_12q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_12q12' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S282.  Gene #43: 'del_12q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
DEL PEAK 22(12Q12) MUTATED 25 4 3 11 4 18 7
DEL PEAK 22(12Q12) WILD-TYPE 110 67 33 57 86 23 65

Figure S282.  Get High-res Image Gene #43: 'del_12q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_12q12' versus 'MIRSEQ_CNMF'

P value = 0.013 (Fisher's exact test), Q value = 0.028

Table S283.  Gene #43: 'del_12q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 107 183 82
DEL PEAK 22(12Q12) MUTATED 14 26 23 9
DEL PEAK 22(12Q12) WILD-TYPE 123 81 160 73

Figure S283.  Get High-res Image Gene #43: 'del_12q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_13q14.2' versus 'MRNA_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 3e-04

Table S284.  Gene #44: 'del_13q14.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 7 7 6
DEL PEAK 23(13Q14.2) MUTATED 2 7 0 0
DEL PEAK 23(13Q14.2) WILD-TYPE 5 0 7 6

Figure S284.  Get High-res Image Gene #44: 'del_13q14.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_13q14.2' versus 'CN_CNMF'

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

Table S285.  Gene #44: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
DEL PEAK 23(13Q14.2) MUTATED 73 36 33
DEL PEAK 23(13Q14.2) WILD-TYPE 99 84 188

Figure S285.  Get High-res Image Gene #44: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_13q14.2' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00016

Table S286.  Gene #44: 'del_13q14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
DEL PEAK 23(13Q14.2) MUTATED 80 28 27 7
DEL PEAK 23(13Q14.2) WILD-TYPE 145 53 140 33

Figure S286.  Get High-res Image Gene #44: 'del_13q14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_13q14.2' versus 'RPPA_CNMF'

P value = 0.0335 (Fisher's exact test), Q value = 0.063

Table S287.  Gene #44: 'del_13q14.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 95 125 115
DEL PEAK 23(13Q14.2) MUTATED 19 37 30 32
DEL PEAK 23(13Q14.2) WILD-TYPE 72 58 95 83

Figure S287.  Get High-res Image Gene #44: 'del_13q14.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_13q14.2' versus 'MRNASEQ_CNMF'

P value = 0.00708 (Fisher's exact test), Q value = 0.016

Table S288.  Gene #44: 'del_13q14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 134 109 108 132 30
DEL PEAK 23(13Q14.2) MUTATED 40 43 19 32 8
DEL PEAK 23(13Q14.2) WILD-TYPE 94 66 89 100 22

Figure S288.  Get High-res Image Gene #44: 'del_13q14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_13q14.2' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S289.  Gene #44: 'del_13q14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
DEL PEAK 23(13Q14.2) MUTATED 43 21 2 17 18 25 16
DEL PEAK 23(13Q14.2) WILD-TYPE 92 50 34 51 72 16 56

Figure S289.  Get High-res Image Gene #44: 'del_13q14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_CNMF'

P value = 0.018 (Fisher's exact test), Q value = 0.037

Table S290.  Gene #44: 'del_13q14.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 107 183 82
DEL PEAK 23(13Q14.2) MUTATED 38 42 40 21
DEL PEAK 23(13Q14.2) WILD-TYPE 99 65 143 61

Figure S290.  Get High-res Image Gene #44: 'del_13q14.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_13q14.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00612 (Fisher's exact test), Q value = 0.014

Table S291.  Gene #44: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
DEL PEAK 23(13Q14.2) MUTATED 66 37 38
DEL PEAK 23(13Q14.2) WILD-TYPE 156 147 65

Figure S291.  Get High-res Image Gene #44: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MRNA_CHIERARCHICAL'

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

Table S292.  Gene #45: 'del_13q14.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 7 7 6
DEL PEAK 24(13Q14.2) MUTATED 2 7 0 0
DEL PEAK 24(13Q14.2) WILD-TYPE 5 0 7 6

Figure S292.  Get High-res Image Gene #45: 'del_13q14.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_13q14.2' versus 'CN_CNMF'

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

Table S293.  Gene #45: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
DEL PEAK 24(13Q14.2) MUTATED 74 37 33
DEL PEAK 24(13Q14.2) WILD-TYPE 98 83 188

Figure S293.  Get High-res Image Gene #45: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_13q14.2' versus 'METHLYATION_CNMF'

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

Table S294.  Gene #45: 'del_13q14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
DEL PEAK 24(13Q14.2) MUTATED 81 29 27 7
DEL PEAK 24(13Q14.2) WILD-TYPE 144 52 140 33

Figure S294.  Get High-res Image Gene #45: 'del_13q14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_13q14.2' versus 'RPPA_CNMF'

P value = 0.0286 (Fisher's exact test), Q value = 0.055

Table S295.  Gene #45: 'del_13q14.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 95 125 115
DEL PEAK 24(13Q14.2) MUTATED 20 38 30 32
DEL PEAK 24(13Q14.2) WILD-TYPE 71 57 95 83

Figure S295.  Get High-res Image Gene #45: 'del_13q14.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_13q14.2' versus 'MRNASEQ_CNMF'

P value = 0.00363 (Fisher's exact test), Q value = 0.009

Table S296.  Gene #45: 'del_13q14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 134 109 108 132 30
DEL PEAK 24(13Q14.2) MUTATED 41 44 19 32 8
DEL PEAK 24(13Q14.2) WILD-TYPE 93 65 89 100 22

Figure S296.  Get High-res Image Gene #45: 'del_13q14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_13q14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 8.5e-05

Table S297.  Gene #45: 'del_13q14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
DEL PEAK 24(13Q14.2) MUTATED 44 22 2 17 18 25 16
DEL PEAK 24(13Q14.2) WILD-TYPE 91 49 34 51 72 16 56

Figure S297.  Get High-res Image Gene #45: 'del_13q14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_CNMF'

P value = 0.0161 (Fisher's exact test), Q value = 0.033

Table S298.  Gene #45: 'del_13q14.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 107 183 82
DEL PEAK 24(13Q14.2) MUTATED 40 42 40 21
DEL PEAK 24(13Q14.2) WILD-TYPE 97 65 143 61

Figure S298.  Get High-res Image Gene #45: 'del_13q14.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_13q14.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00381 (Fisher's exact test), Q value = 0.0093

Table S299.  Gene #45: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
DEL PEAK 24(13Q14.2) MUTATED 67 37 39
DEL PEAK 24(13Q14.2) WILD-TYPE 155 147 64

Figure S299.  Get High-res Image Gene #45: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_13q34' versus 'CN_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00033

Table S300.  Gene #46: 'del_13q34' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
DEL PEAK 25(13Q34) MUTATED 52 30 28
DEL PEAK 25(13Q34) WILD-TYPE 120 90 193

Figure S300.  Get High-res Image Gene #46: 'del_13q34' versus Molecular Subtype #3: 'CN_CNMF'

'del_13q34' versus 'METHLYATION_CNMF'

P value = 0.0112 (Fisher's exact test), Q value = 0.024

Table S301.  Gene #46: 'del_13q34' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
DEL PEAK 25(13Q34) MUTATED 51 27 26 6
DEL PEAK 25(13Q34) WILD-TYPE 174 54 141 34

Figure S301.  Get High-res Image Gene #46: 'del_13q34' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_13q34' versus 'RPPA_CNMF'

P value = 0.0219 (Fisher's exact test), Q value = 0.044

Table S302.  Gene #46: 'del_13q34' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 95 125 115
DEL PEAK 25(13Q34) MUTATED 14 30 20 25
DEL PEAK 25(13Q34) WILD-TYPE 77 65 105 90

Figure S302.  Get High-res Image Gene #46: 'del_13q34' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_13q34' versus 'MRNASEQ_CNMF'

P value = 0.0427 (Fisher's exact test), Q value = 0.077

Table S303.  Gene #46: 'del_13q34' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 134 109 108 132 30
DEL PEAK 25(13Q34) MUTATED 29 35 18 23 5
DEL PEAK 25(13Q34) WILD-TYPE 105 74 90 109 25

Figure S303.  Get High-res Image Gene #46: 'del_13q34' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_13q34' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00085 (Fisher's exact test), Q value = 0.0025

Table S304.  Gene #46: 'del_13q34' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
DEL PEAK 25(13Q34) MUTATED 31 20 2 9 17 18 13
DEL PEAK 25(13Q34) WILD-TYPE 104 51 34 59 73 23 59

Figure S304.  Get High-res Image Gene #46: 'del_13q34' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_13q34' versus 'MIRSEQ_CNMF'

P value = 0.0259 (Fisher's exact test), Q value = 0.05

Table S305.  Gene #46: 'del_13q34' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 107 183 82
DEL PEAK 25(13Q34) MUTATED 28 34 30 17
DEL PEAK 25(13Q34) WILD-TYPE 109 73 153 65

Figure S305.  Get High-res Image Gene #46: 'del_13q34' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_13q34' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00262 (Fisher's exact test), Q value = 0.0067

Table S306.  Gene #46: 'del_13q34' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
DEL PEAK 25(13Q34) MUTATED 49 27 33
DEL PEAK 25(13Q34) WILD-TYPE 173 157 70

Figure S306.  Get High-res Image Gene #46: 'del_13q34' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_14q24.3' versus 'CN_CNMF'

P value = 0.0043 (Fisher's exact test), Q value = 0.01

Table S307.  Gene #47: 'del_14q24.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
DEL PEAK 26(14Q24.3) MUTATED 36 42 43
DEL PEAK 26(14Q24.3) WILD-TYPE 136 78 178

Figure S307.  Get High-res Image Gene #47: 'del_14q24.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_14q24.3' versus 'METHLYATION_CNMF'

P value = 0.0116 (Fisher's exact test), Q value = 0.025

Table S308.  Gene #47: 'del_14q24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
DEL PEAK 26(14Q24.3) MUTATED 53 30 32 6
DEL PEAK 26(14Q24.3) WILD-TYPE 172 51 135 34

Figure S308.  Get High-res Image Gene #47: 'del_14q24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_14q24.3' versus 'RPPA_CNMF'

P value = 0.00058 (Fisher's exact test), Q value = 0.0018

Table S309.  Gene #47: 'del_14q24.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 95 125 115
DEL PEAK 26(14Q24.3) MUTATED 11 36 31 26
DEL PEAK 26(14Q24.3) WILD-TYPE 80 59 94 89

Figure S309.  Get High-res Image Gene #47: 'del_14q24.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_14q24.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0222 (Fisher's exact test), Q value = 0.044

Table S310.  Gene #47: 'del_14q24.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 158 185
DEL PEAK 26(14Q24.3) MUTATED 14 33 57
DEL PEAK 26(14Q24.3) WILD-TYPE 69 125 128

Figure S310.  Get High-res Image Gene #47: 'del_14q24.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_14q24.3' versus 'MRNASEQ_CNMF'

P value = 0.00093 (Fisher's exact test), Q value = 0.0027

Table S311.  Gene #47: 'del_14q24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 134 109 108 132 30
DEL PEAK 26(14Q24.3) MUTATED 25 42 25 21 8
DEL PEAK 26(14Q24.3) WILD-TYPE 109 67 83 111 22

Figure S311.  Get High-res Image Gene #47: 'del_14q24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_14q24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00065 (Fisher's exact test), Q value = 0.002

Table S312.  Gene #47: 'del_14q24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
DEL PEAK 26(14Q24.3) MUTATED 32 27 8 12 17 17 8
DEL PEAK 26(14Q24.3) WILD-TYPE 103 44 28 56 73 24 64

Figure S312.  Get High-res Image Gene #47: 'del_14q24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_14q24.3' versus 'MIRSEQ_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.0011

Table S313.  Gene #47: 'del_14q24.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 107 183 82
DEL PEAK 26(14Q24.3) MUTATED 51 21 32 16
DEL PEAK 26(14Q24.3) WILD-TYPE 86 86 151 66

Figure S313.  Get High-res Image Gene #47: 'del_14q24.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_14q24.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00468 (Fisher's exact test), Q value = 0.011

Table S314.  Gene #47: 'del_14q24.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
DEL PEAK 26(14Q24.3) MUTATED 54 31 35
DEL PEAK 26(14Q24.3) WILD-TYPE 168 153 68

Figure S314.  Get High-res Image Gene #47: 'del_14q24.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_14q24.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00166 (Fisher's exact test), Q value = 0.0044

Table S315.  Gene #47: 'del_14q24.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 185 161 159
DEL PEAK 26(14Q24.3) MUTATED 58 38 24
DEL PEAK 26(14Q24.3) WILD-TYPE 127 123 135

Figure S315.  Get High-res Image Gene #47: 'del_14q24.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_14q24.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00114 (Fisher's exact test), Q value = 0.0032

Table S316.  Gene #47: 'del_14q24.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 137 188 89
DEL PEAK 26(14Q24.3) MUTATED 26 33 29 32
DEL PEAK 26(14Q24.3) WILD-TYPE 65 104 159 57

Figure S316.  Get High-res Image Gene #47: 'del_14q24.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18q23' versus 'METHLYATION_CNMF'

P value = 0.00327 (Fisher's exact test), Q value = 0.0082

Table S317.  Gene #48: 'del_18q23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
DEL PEAK 27(18Q23) MUTATED 31 13 34 0
DEL PEAK 27(18Q23) WILD-TYPE 194 68 133 40

Figure S317.  Get High-res Image Gene #48: 'del_18q23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_19q13.41' versus 'MRNA_CNMF'

P value = 0.0347 (Fisher's exact test), Q value = 0.065

Table S318.  Gene #49: 'del_19q13.41' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 9 10 8
DEL PEAK 28(19Q13.41) MUTATED 6 10 4
DEL PEAK 28(19Q13.41) WILD-TYPE 3 0 4

Figure S318.  Get High-res Image Gene #49: 'del_19q13.41' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_19q13.41' versus 'MRNA_CHIERARCHICAL'

P value = 0.0102 (Fisher's exact test), Q value = 0.022

Table S319.  Gene #49: 'del_19q13.41' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 7 7 6
DEL PEAK 28(19Q13.41) MUTATED 3 7 7 3
DEL PEAK 28(19Q13.41) WILD-TYPE 4 0 0 3

Figure S319.  Get High-res Image Gene #49: 'del_19q13.41' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_19q13.41' versus 'CN_CNMF'

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

Table S320.  Gene #49: 'del_19q13.41' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
DEL PEAK 28(19Q13.41) MUTATED 40 35 192
DEL PEAK 28(19Q13.41) WILD-TYPE 132 85 29

Figure S320.  Get High-res Image Gene #49: 'del_19q13.41' versus Molecular Subtype #3: 'CN_CNMF'

'del_19q13.41' versus 'METHLYATION_CNMF'

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

Table S321.  Gene #49: 'del_19q13.41' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
DEL PEAK 28(19Q13.41) MUTATED 78 12 167 10
DEL PEAK 28(19Q13.41) WILD-TYPE 147 69 0 30

Figure S321.  Get High-res Image Gene #49: 'del_19q13.41' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_19q13.41' versus 'RPPA_CNMF'

P value = 0.00494 (Fisher's exact test), Q value = 0.012

Table S322.  Gene #49: 'del_19q13.41' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 95 125 115
DEL PEAK 28(19Q13.41) MUTATED 35 52 68 73
DEL PEAK 28(19Q13.41) WILD-TYPE 56 43 57 42

Figure S322.  Get High-res Image Gene #49: 'del_19q13.41' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_19q13.41' versus 'RPPA_CHIERARCHICAL'

P value = 0.0138 (Fisher's exact test), Q value = 0.029

Table S323.  Gene #49: 'del_19q13.41' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 158 185
DEL PEAK 28(19Q13.41) MUTATED 36 98 94
DEL PEAK 28(19Q13.41) WILD-TYPE 47 60 91

Figure S323.  Get High-res Image Gene #49: 'del_19q13.41' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_19q13.41' versus 'MRNASEQ_CNMF'

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

Table S324.  Gene #49: 'del_19q13.41' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 134 109 108 132 30
DEL PEAK 28(19Q13.41) MUTATED 41 30 107 77 12
DEL PEAK 28(19Q13.41) WILD-TYPE 93 79 1 55 18

Figure S324.  Get High-res Image Gene #49: 'del_19q13.41' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_19q13.41' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S325.  Gene #49: 'del_19q13.41' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
DEL PEAK 28(19Q13.41) MUTATED 39 7 36 19 89 23 54
DEL PEAK 28(19Q13.41) WILD-TYPE 96 64 0 49 1 18 18

Figure S325.  Get High-res Image Gene #49: 'del_19q13.41' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_19q13.41' versus 'MIRSEQ_CNMF'

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

Table S326.  Gene #49: 'del_19q13.41' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 107 183 82
DEL PEAK 28(19Q13.41) MUTATED 50 36 107 74
DEL PEAK 28(19Q13.41) WILD-TYPE 87 71 76 8

Figure S326.  Get High-res Image Gene #49: 'del_19q13.41' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_19q13.41' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S327.  Gene #49: 'del_19q13.41' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
DEL PEAK 28(19Q13.41) MUTATED 129 118 20
DEL PEAK 28(19Q13.41) WILD-TYPE 93 66 83

Figure S327.  Get High-res Image Gene #49: 'del_19q13.41' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_19q13.41' versus 'MIRSEQ_MATURE_CNMF'

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

Table S328.  Gene #49: 'del_19q13.41' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 185 161 159
DEL PEAK 28(19Q13.41) MUTATED 61 110 95
DEL PEAK 28(19Q13.41) WILD-TYPE 124 51 64

Figure S328.  Get High-res Image Gene #49: 'del_19q13.41' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_19q13.41' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S329.  Gene #49: 'del_19q13.41' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 137 188 89
DEL PEAK 28(19Q13.41) MUTATED 32 105 113 16
DEL PEAK 28(19Q13.41) WILD-TYPE 59 32 75 73

Figure S329.  Get High-res Image Gene #49: 'del_19q13.41' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19q13.42' versus 'MRNA_CNMF'

P value = 0.035 (Fisher's exact test), Q value = 0.065

Table S330.  Gene #50: 'del_19q13.42' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 9 10 8
DEL PEAK 29(19Q13.42) MUTATED 7 10 4
DEL PEAK 29(19Q13.42) WILD-TYPE 2 0 4

Figure S330.  Get High-res Image Gene #50: 'del_19q13.42' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_19q13.42' versus 'MRNA_CHIERARCHICAL'

P value = 0.0213 (Fisher's exact test), Q value = 0.043

Table S331.  Gene #50: 'del_19q13.42' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 7 7 6
DEL PEAK 29(19Q13.42) MUTATED 4 7 7 3
DEL PEAK 29(19Q13.42) WILD-TYPE 3 0 0 3

Figure S331.  Get High-res Image Gene #50: 'del_19q13.42' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_19q13.42' versus 'CN_CNMF'

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

Table S332.  Gene #50: 'del_19q13.42' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
DEL PEAK 29(19Q13.42) MUTATED 42 38 198
DEL PEAK 29(19Q13.42) WILD-TYPE 130 82 23

Figure S332.  Get High-res Image Gene #50: 'del_19q13.42' versus Molecular Subtype #3: 'CN_CNMF'

'del_19q13.42' versus 'METHLYATION_CNMF'

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

Table S333.  Gene #50: 'del_19q13.42' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
DEL PEAK 29(19Q13.42) MUTATED 88 13 167 10
DEL PEAK 29(19Q13.42) WILD-TYPE 137 68 0 30

Figure S333.  Get High-res Image Gene #50: 'del_19q13.42' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_19q13.42' versus 'RPPA_CNMF'

P value = 0.00663 (Fisher's exact test), Q value = 0.015

Table S334.  Gene #50: 'del_19q13.42' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 95 125 115
DEL PEAK 29(19Q13.42) MUTATED 36 56 72 72
DEL PEAK 29(19Q13.42) WILD-TYPE 55 39 53 43

Figure S334.  Get High-res Image Gene #50: 'del_19q13.42' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_19q13.42' versus 'RPPA_CHIERARCHICAL'

P value = 0.0224 (Fisher's exact test), Q value = 0.044

Table S335.  Gene #50: 'del_19q13.42' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 158 185
DEL PEAK 29(19Q13.42) MUTATED 36 98 102
DEL PEAK 29(19Q13.42) WILD-TYPE 47 60 83

Figure S335.  Get High-res Image Gene #50: 'del_19q13.42' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_19q13.42' versus 'MRNASEQ_CNMF'

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

Table S336.  Gene #50: 'del_19q13.42' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 134 109 108 132 30
DEL PEAK 29(19Q13.42) MUTATED 50 32 107 77 12
DEL PEAK 29(19Q13.42) WILD-TYPE 84 77 1 55 18

Figure S336.  Get High-res Image Gene #50: 'del_19q13.42' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_19q13.42' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S337.  Gene #50: 'del_19q13.42' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
DEL PEAK 29(19Q13.42) MUTATED 46 9 36 21 89 23 54
DEL PEAK 29(19Q13.42) WILD-TYPE 89 62 0 47 1 18 18

Figure S337.  Get High-res Image Gene #50: 'del_19q13.42' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_19q13.42' versus 'MIRSEQ_CNMF'

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

Table S338.  Gene #50: 'del_19q13.42' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 107 183 82
DEL PEAK 29(19Q13.42) MUTATED 56 40 106 76
DEL PEAK 29(19Q13.42) WILD-TYPE 81 67 77 6

Figure S338.  Get High-res Image Gene #50: 'del_19q13.42' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_19q13.42' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S339.  Gene #50: 'del_19q13.42' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
DEL PEAK 29(19Q13.42) MUTATED 137 119 22
DEL PEAK 29(19Q13.42) WILD-TYPE 85 65 81

Figure S339.  Get High-res Image Gene #50: 'del_19q13.42' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_19q13.42' versus 'MIRSEQ_MATURE_CNMF'

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

Table S340.  Gene #50: 'del_19q13.42' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 185 161 159
DEL PEAK 29(19Q13.42) MUTATED 69 113 95
DEL PEAK 29(19Q13.42) WILD-TYPE 116 48 64

Figure S340.  Get High-res Image Gene #50: 'del_19q13.42' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_19q13.42' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S341.  Gene #50: 'del_19q13.42' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 137 188 89
DEL PEAK 29(19Q13.42) MUTATED 36 109 115 17
DEL PEAK 29(19Q13.42) WILD-TYPE 55 28 73 72

Figure S341.  Get High-res Image Gene #50: 'del_19q13.42' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_22q13.31' versus 'MRNA_CHIERARCHICAL'

P value = 0.0421 (Fisher's exact test), Q value = 0.077

Table S342.  Gene #51: 'del_22q13.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 7 7 6
DEL PEAK 30(22Q13.31) MUTATED 2 4 0 0
DEL PEAK 30(22Q13.31) WILD-TYPE 5 3 7 6

Figure S342.  Get High-res Image Gene #51: 'del_22q13.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_22q13.31' versus 'CN_CNMF'

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

Table S343.  Gene #51: 'del_22q13.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 120 221
DEL PEAK 30(22Q13.31) MUTATED 34 35 8
DEL PEAK 30(22Q13.31) WILD-TYPE 138 85 213

Figure S343.  Get High-res Image Gene #51: 'del_22q13.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_22q13.31' versus 'METHLYATION_CNMF'

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

Table S344.  Gene #51: 'del_22q13.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 225 81 167 40
DEL PEAK 30(22Q13.31) MUTATED 39 29 4 5
DEL PEAK 30(22Q13.31) WILD-TYPE 186 52 163 35

Figure S344.  Get High-res Image Gene #51: 'del_22q13.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_22q13.31' versus 'RPPA_CNMF'

P value = 0.00079 (Fisher's exact test), Q value = 0.0024

Table S345.  Gene #51: 'del_22q13.31' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 95 125 115
DEL PEAK 30(22Q13.31) MUTATED 10 27 13 12
DEL PEAK 30(22Q13.31) WILD-TYPE 81 68 112 103

Figure S345.  Get High-res Image Gene #51: 'del_22q13.31' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_22q13.31' versus 'RPPA_CHIERARCHICAL'

P value = 0.0415 (Fisher's exact test), Q value = 0.076

Table S346.  Gene #51: 'del_22q13.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 158 185
DEL PEAK 30(22Q13.31) MUTATED 10 16 36
DEL PEAK 30(22Q13.31) WILD-TYPE 73 142 149

Figure S346.  Get High-res Image Gene #51: 'del_22q13.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_22q13.31' versus 'MRNASEQ_CNMF'

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

Table S347.  Gene #51: 'del_22q13.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 134 109 108 132 30
DEL PEAK 30(22Q13.31) MUTATED 14 39 4 14 6
DEL PEAK 30(22Q13.31) WILD-TYPE 120 70 104 118 24

Figure S347.  Get High-res Image Gene #51: 'del_22q13.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_22q13.31' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S348.  Gene #51: 'del_22q13.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
DEL PEAK 30(22Q13.31) MUTATED 17 26 2 14 2 14 2
DEL PEAK 30(22Q13.31) WILD-TYPE 118 45 34 54 88 27 70

Figure S348.  Get High-res Image Gene #51: 'del_22q13.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.31' versus 'MIRSEQ_CNMF'

P value = 0.0352 (Fisher's exact test), Q value = 0.066

Table S349.  Gene #51: 'del_22q13.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 107 183 82
DEL PEAK 30(22Q13.31) MUTATED 25 23 22 7
DEL PEAK 30(22Q13.31) WILD-TYPE 112 84 161 75

Figure S349.  Get High-res Image Gene #51: 'del_22q13.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_22q13.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 8.5e-05

Table S350.  Gene #51: 'del_22q13.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
DEL PEAK 30(22Q13.31) MUTATED 27 18 32
DEL PEAK 30(22Q13.31) WILD-TYPE 195 166 71

Figure S350.  Get High-res Image Gene #51: 'del_22q13.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_22q13.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00144 (Fisher's exact test), Q value = 0.0039

Table S351.  Gene #51: 'del_22q13.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 185 161 159
DEL PEAK 30(22Q13.31) MUTATED 42 18 16
DEL PEAK 30(22Q13.31) WILD-TYPE 143 143 143

Figure S351.  Get High-res Image Gene #51: 'del_22q13.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_22q13.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 3e-04

Table S352.  Gene #51: 'del_22q13.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 137 188 89
DEL PEAK 30(22Q13.31) MUTATED 11 18 18 29
DEL PEAK 30(22Q13.31) WILD-TYPE 80 119 170 60

Figure S352.  Get High-res Image Gene #51: 'del_22q13.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xq21.1' versus 'RPPA_CNMF'

P value = 0.00087 (Fisher's exact test), Q value = 0.0026

Table S353.  Gene #52: 'del_xq21.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 95 125 115
DEL PEAK 31(XQ21.1) MUTATED 6 26 20 14
DEL PEAK 31(XQ21.1) WILD-TYPE 85 69 105 101

Figure S353.  Get High-res Image Gene #52: 'del_xq21.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_xq21.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0144 (Fisher's exact test), Q value = 0.03

Table S354.  Gene #52: 'del_xq21.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 158 185
DEL PEAK 31(XQ21.1) MUTATED 6 22 38
DEL PEAK 31(XQ21.1) WILD-TYPE 77 136 147

Figure S354.  Get High-res Image Gene #52: 'del_xq21.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_xq21.1' versus 'MRNASEQ_CNMF'

P value = 0.00837 (Fisher's exact test), Q value = 0.019

Table S355.  Gene #52: 'del_xq21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 134 109 108 132 30
DEL PEAK 31(XQ21.1) MUTATED 14 23 24 16 1
DEL PEAK 31(XQ21.1) WILD-TYPE 120 86 84 116 29

Figure S355.  Get High-res Image Gene #52: 'del_xq21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_xq21.1' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S356.  Gene #52: 'del_xq21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
DEL PEAK 31(XQ21.1) MUTATED 13 8 9 8 20 16 4
DEL PEAK 31(XQ21.1) WILD-TYPE 122 63 27 60 70 25 68

Figure S356.  Get High-res Image Gene #52: 'del_xq21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_xq21.1' versus 'MIRSEQ_CNMF'

P value = 0.00101 (Fisher's exact test), Q value = 0.0029

Table S357.  Gene #52: 'del_xq21.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 107 183 82
DEL PEAK 31(XQ21.1) MUTATED 14 19 21 24
DEL PEAK 31(XQ21.1) WILD-TYPE 123 88 162 58

Figure S357.  Get High-res Image Gene #52: 'del_xq21.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

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/LGG-TP/19781933/transformed.cor.cli.txt

  • Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LGG-TP/20146758/LGG-TP.transferedmergedcluster.txt

  • Number of patients = 513

  • Number of significantly focal cnvs = 52

  • Number of molecular subtypes = 12

  • Exclude genes that fewer than K tumors have alterations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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