Correlation between copy number variation genes (focal events) and molecular subtypes
Brain Lower Grade Glioma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C14B30RR
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C14B30RR
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 49 focal events and 12 molecular subtypes across 513 patients, 358 significant findings detected with P value < 0.05 and Q value < 0.25.

  • amp_1q22 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_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',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_3q26.33 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_4q12 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', 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_CNMF',  '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',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_9q34.3 cnv correlated to 'CN_CNMF',  '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',  'MIRSEQ_MATURE_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',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 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', and 'MRNASEQ_CHIERARCHICAL'.

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

  • amp_17q25.1 cnv correlated to 'CN_CNMF',  'RPPA_CHIERARCHICAL', and 'MRNASEQ_CNMF'.

  • 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_xp11.22 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

  • del_5p15.33 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_5q34 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 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_6q26 cnv correlated to 'MRNA_CNMF',  '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',  'MIRSEQ_MATURE_CNMF', 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',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

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

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

  • del_14q24.3 cnv correlated to 'CN_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 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 49 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, 358 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 0.00062
(0.0018) 		0.00019
(0.000614) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		0.00067
(0.00189) 		0.00045
(0.00135) 		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 0.0283
(0.0509) 		0.00019
(0.000614) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		0.00164
(0.00417) 		0.00061
(0.00178) 		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 0.0347
(0.0603) 		0.021
(0.039) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		0.0064
(0.0138) 		0.021
(0.039) 		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 0.253
(0.323) 		0.0425
(0.0721) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		0.00089
(0.00243) 		0.0429
(0.0725) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		0.05
(0.0821) 		1e-05
(4.49e-05) 		4e-05
(0.000154) 		7e-05
(0.000251)
amp 4q12 30 (6%) 483 1
(1.00) 		0.042
(0.0718) 		8e-05
(0.000282) 		1e-05
(4.49e-05) 		0.00015
(0.000504) 		0.336
(0.415) 		5e-05
(0.000187) 		1e-05
(4.49e-05) 		0.00303
(0.00721) 		0.00012
(0.000418) 		0.00251
(0.00615) 		0.00066
(0.00188)
amp 7p11 2 127 (25%) 386 0.864
(0.932) 		0.782
(0.851) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		0.0015
(0.00387) 		0.00326
(0.00764) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		0.00015
(0.000504) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05)
del 2q37 3 77 (15%) 436 0.367
(0.444) 		0.0134
(0.0265) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		0.00109
(0.00289) 		0.0149
(0.0288) 		0.00019
(0.000614) 		1e-05
(4.49e-05) 		0.0264
(0.0477) 		0.141
(0.197) 		0.0151
(0.029) 		1e-05
(4.49e-05)
del 10q26 3 151 (29%) 362 0.0821
(0.126) 		0.707
(0.778) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		0.00156
(0.00401) 		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 11p15 1 72 (14%) 441 1
(1.00) 		0.0301
(0.0535) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		0.00143
(0.00372) 		0.613
(0.694) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		3e-05
(0.000119) 		7e-05
(0.000251) 		0.00081
(0.00225) 		1e-05
(4.49e-05)
amp 3q26 33 21 (4%) 492 1
(1.00) 		0.581
(0.664) 		1e-05
(4.49e-05) 		0.00895
(0.0186) 		0.0238
(0.0433) 		0.287
(0.361) 		0.00067
(0.00189) 		0.00124
(0.00325) 		0.00049
(0.00146) 		0.0189
(0.0358) 		0.00101
(0.00271) 		0.00369
(0.00843)
amp 10p15 3 71 (14%) 442 0.525
(0.608) 		0.0847
(0.129) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		0.00824
(0.0174) 		0.00135
(0.00353) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		0.00033
(0.00104) 		0.076
(0.118) 		0.00237
(0.00588) 		1e-05
(4.49e-05)
amp 12p13 32 72 (14%) 441 0.863
(0.932) 		0.0967
(0.144) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		0.00499
(0.011) 		0.143
(0.2) 		0.00012
(0.000418) 		1e-05
(4.49e-05) 		0.0111
(0.0223) 		0.00709
(0.0151) 		0.00144
(0.00373) 		1e-05
(4.49e-05)
amp 12q14 1 37 (7%) 476 1e-05
(4.49e-05) 		2e-05
(8.4e-05) 		0.0145
(0.0285) 		0.346
(0.424) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		0.00366
(0.00841) 		1e-05
(4.49e-05) 		2e-05
(8.4e-05) 		6e-05
(0.000222)
del 3p21 31 49 (10%) 464 1
(1.00) 		0.00663
(0.0142) 		0.00093
(0.00251) 		0.00353
(0.00814) 		7e-05
(0.000251) 		0.0437
(0.0734) 		0.0585
(0.0945) 		0.00093
(0.00251) 		0.00161
(0.00412) 		0.00242
(0.00598) 		0.393
(0.472) 		0.00975
(0.0199)
del 6q26 82 (16%) 431 0.0471
(0.0782) 		0.58
(0.664) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		0.111
(0.161) 		0.00914
(0.0189) 		0.00041
(0.00126) 		0.00014
(0.000476) 		3e-05
(0.000119) 		0.161
(0.217) 		0.00333
(0.00771) 		0.00031
(0.00098)
del 9p21 3 176 (34%) 337 0.334
(0.414) 		0.0645
(0.102) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		2e-05
(8.4e-05) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		0.359
(0.437) 		1e-05
(4.49e-05) 		0.00084
(0.00232) 		1e-05
(4.49e-05)
del 11p15 5 104 (20%) 409 0.646
(0.725) 		0.00043
(0.0013) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		0.0562
(0.0912) 		0.898
(0.962) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		2e-05
(8.4e-05) 		0.00476
(0.0106) 		0.00675
(0.0144) 		1e-05
(4.49e-05)
del 13q14 2 144 (28%) 369 0.182
(0.243) 		7e-05
(0.000251) 		1e-05
(4.49e-05) 		0.00019
(0.000614) 		0.0294
(0.0526) 		0.785
(0.853) 		0.00013
(0.000447) 		1e-05
(4.49e-05) 		0.0358
(0.0617) 		0.00393
(0.00885) 		0.216
(0.283) 		0.0113
(0.0226)
del 14q24 3 122 (24%) 391 0.303
(0.38) 		0.0966
(0.144) 		1e-05
(4.49e-05) 		0.059
(0.0951) 		0.00073
(0.00204) 		0.0218
(0.04) 		0.00052
(0.00154) 		0.00058
(0.0017) 		0.0004
(0.00124) 		0.00416
(0.00934) 		0.0062
(0.0135) 		0.00174
(0.00441)
del xq21 1 78 (15%) 435 0.839
(0.908) 		0.265
(0.337) 		0.0117
(0.0234) 		3e-05
(0.000119) 		0.00108
(0.00287) 		0.015
(0.029) 		0.0121
(0.0241) 		3e-05
(0.000119) 		0.00049
(0.00146) 		0.36
(0.438) 		0.00016
(0.000532) 		8e-05
(0.000282)
amp 7q31 2 173 (34%) 340 1
(1.00) 		0.938
(0.999) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		0.102
(0.151) 		0.154
(0.212) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		0.0108
(0.0219) 		1e-05
(4.49e-05) 		0.00066
(0.00188) 		1e-05
(4.49e-05)
amp 7q32 3 181 (35%) 332 1
(1.00) 		1
(1.00) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		0.147
(0.204) 		0.138
(0.194) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		0.0335
(0.0587) 		1e-05
(4.49e-05) 		0.00092
(0.0025) 		1e-05
(4.49e-05)
amp 8q24 13 99 (19%) 414 0.369
(0.446) 		0.236
(0.307) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		0.25
(0.322) 		0.328
(0.408) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		0.00835
(0.0175) 		0.00043
(0.0013) 		0.0147
(0.0288) 		1e-05
(4.49e-05)
amp 19p13 3 129 (25%) 384 0.0737
(0.114) 		0.149
(0.207) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		0.249
(0.322) 		0.00494
(0.0109) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		0.00054
(0.00159) 		0.154
(0.212) 		2e-05
(8.4e-05) 		1e-05
(4.49e-05)
del 6q22 31 78 (15%) 435 0.617
(0.695) 		0.583
(0.664) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		0.0612
(0.0975) 		0.0148
(0.0288) 		0.0037
(0.00843) 		0.00115
(0.00303) 		0.00072
(0.00203) 		0.123
(0.176) 		0.00276
(0.00665) 		0.00325
(0.00764)
del 8q24 3 29 (6%) 484 1e-05
(4.49e-05) 		0.00014
(0.000476) 		0.339
(0.417) 		0.119
(0.172) 		0.0059
(0.0129) 		0.00637
(0.0138) 		0.0433
(0.073) 		0.00333
(0.00771) 		0.0334
(0.0586) 		0.029
(0.0519)
del 13q34 110 (21%) 403 0.506
(0.588) 		0.152
(0.21) 		1e-05
(4.49e-05) 		0.026
(0.0472) 		0.0216
(0.0397) 		0.383
(0.461) 		0.0137
(0.0269) 		0.00105
(0.00281) 		0.0467
(0.0778) 		0.00276
(0.00665) 		0.704
(0.778) 		0.0298
(0.0532)
amp 1q32 1 43 (8%) 470 1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		0.292
(0.367) 		0.445
(0.527) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		0.136
(0.193) 		2e-05
(8.4e-05) 		0.00328
(0.00765) 		3e-05
(0.000119)
amp xp11 22 63 (12%) 450 0.655
(0.731) 		1
(1.00) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		0.145
(0.202) 		0.104
(0.153) 		5e-05
(0.000187) 		1e-05
(4.49e-05) 		0.00065
(0.00187) 		0.352
(0.43) 		0.00013
(0.000447) 		0.00027
(0.000858)
del 5p15 33 50 (10%) 463 1
(1.00) 		0.0665
(0.105) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		0.777
(0.848) 		0.654
(0.731) 		0.00087
(0.00239) 		5e-05
(0.000187) 		0.00451
(0.01) 		0.206
(0.271) 		0.00373
(0.00847) 		3e-05
(0.000119)
del 5q34 64 (12%) 449 0.445
(0.527) 		0.236
(0.307) 		1e-05
(4.49e-05) 		1e-05
(4.49e-05) 		0.0595
(0.0953) 		0.0773
(0.119) 		7e-05
(0.000251) 		1e-05
(4.49e-05) 		5e-05
(0.000187) 		0.134
(0.191) 		0.00817
(0.0173) 		1e-05
(4.49e-05)
del 9p23 150 (29%) 363 0.445
(0.527) 		0.658
(0.733) 		1e-05
(4.49e-05) 		4e-05
(0.000154) 		0.00597
(0.013) 		4e-05
(0.000154) 		0.0207
(0.0386) 		0.00016
(0.000532) 		0.924
(0.988) 		0.113
(0.164) 		0.345
(0.424) 		0.0322
(0.0567)
amp 2p24 3 24 (5%) 489 0.618
(0.695) 		0.584
(0.664) 		0.00279
(0.00669) 		0.252
(0.323) 		0.0891
(0.134) 		0.0888
(0.134) 		0.0312
(0.0553) 		0.00253
(0.00617) 		0.743
(0.815) 		0.0354
(0.0613) 		0.00041
(0.00126) 		0.0314
(0.0554)
amp xp11 22 48 (9%) 465 0.651
(0.729) 		1
(1.00) 		2e-05
(8.4e-05) 		1e-05
(4.49e-05) 		0.45
(0.531) 		0.166
(0.222) 		0.0028
(0.00669) 		3e-05
(0.000119) 		0.0604
(0.0966) 		0.6
(0.681) 		0.0149
(0.0289) 		0.00195
(0.0049)
del 1q43 36 (7%) 477 0.0198
(0.037) 		0.00206
(0.00515) 		0.159
(0.216) 		0.192
(0.255) 		0.0152
(0.0291) 		0.0158
(0.0302) 		0.126
(0.179) 		0.19
(0.252) 		0.0195
(0.0367) 		0.0485
(0.0801)
del 3q13 31 39 (8%) 474 0.175
(0.234) 		0.882
(0.947) 		0.00185
(0.00467) 		0.00932
(0.0192) 		0.00967
(0.0198) 		0.0192
(0.0363) 		0.251
(0.322) 		0.0133
(0.0263) 		0.155
(0.213) 		0.00044
(0.00133) 		0.194
(0.257) 		0.124
(0.177)
del 4q34 3 137 (27%) 376 1
(1.00) 		0.356
(0.434) 		0.0986
(0.146) 		1e-05
(4.49e-05) 		0.0421
(0.0718) 		0.376
(0.453) 		0.0705
(0.11) 		8e-05
(0.000282) 		0.0279
(0.0504) 		0.0455
(0.0761) 		0.685
(0.76) 		4e-05
(0.000154)
del 12p13 1 38 (7%) 475 0.0109
(0.0221) 		3e-05
(0.000119) 		0.231
(0.301) 		0.581
(0.664) 		0.00221
(0.00551) 		0.00693
(0.0148) 		0.0221
(0.0404) 		0.0449
(0.0752) 		0.0947
(0.142) 		0.0967
(0.144)
del 12q12 72 (14%) 441 1
(1.00) 		0.151
(0.209) 		2e-05
(8.4e-05) 		1e-05
(4.49e-05) 		0.428
(0.51) 		0.983
(1.00) 		0.00312
(0.0074) 		1e-05
(4.49e-05) 		0.00567
(0.0124) 		0.496
(0.58) 		0.4
(0.478) 		0.00036
(0.00112)
amp 15q26 3 19 (4%) 494 1
(1.00) 		0.0422
(0.0718) 		0.00075
(0.00209) 		0.00024
(0.000771) 		0.165
(0.222) 		0.195
(0.258) 		0.0359
(0.0617) 		0.0618
(0.0981) 		0.48
(0.562) 		0.284
(0.358) 		0.0846
(0.129) 		0.0359
(0.0617)
del 3q29 47 (9%) 466 0.174
(0.233) 		0.883
(0.947) 		0.00035
(0.00109) 		2e-05
(8.4e-05) 		0.439
(0.522) 		0.604
(0.684) 		0.00934
(0.0192) 		6e-05
(0.000222) 		0.138
(0.194) 		0.00439
(0.00981) 		0.135
(0.191) 		0.0684
(0.108)
amp 9q34 3 46 (9%) 467 0.506
(0.588) 		0.882
(0.947) 		0.0216
(0.0397) 		0.0105
(0.0215) 		0.0182
(0.0346) 		1
(1.00) 		0.111
(0.162) 		0.00019
(0.000614) 		0.208
(0.274) 		0.0862
(0.131) 		0.926
(0.988) 		0.156
(0.214)
amp 1q22 42 (8%) 471 0.00026
(0.000831) 		0.104
(0.153) 		0.0841
(0.129) 		0.708
(0.778) 		0.00257
(0.00624) 		0.0574
(0.0929) 		0.364
(0.441) 		0.0899
(0.135) 		0.00248
(0.0061) 		0.75
(0.821)
amp 11q24 1 87 (17%) 426 0.0711
(0.111) 		0.122
(0.176) 		0.222
(0.291) 		0.00883
(0.0184) 		0.243
(0.315) 		0.0473
(0.0784) 		0.0526
(0.0856) 		0.157
(0.214) 		0.681
(0.757) 		0.113
(0.164) 		0.499
(0.582) 		0.00858
(0.018)
amp 13q34 22 (4%) 491 0.00314
(0.00741) 		0.00378
(0.00855) 		0.136
(0.193) 		0.769
(0.841) 		0.0505
(0.0827) 		0.0216
(0.0397) 		0.109
(0.16) 		0.691
(0.766) 		0.281
(0.356) 		0.11
(0.16)
amp 17q25 1 44 (9%) 469 0.0393
(0.0674) 		0.58
(0.664) 		0.0619
(0.0981) 		0.0486
(0.0801) 		0.0336
(0.0587) 		0.0518
(0.0846) 		0.165
(0.222) 		0.565
(0.651) 		0.081
(0.125) 		0.34
(0.418)
del 6p25 3 50 (10%) 463 4e-05
(0.000154) 		0.013
(0.0258) 		0.266
(0.338) 		0.329
(0.408) 		0.162
(0.219) 		0.0707
(0.11) 		0.458
(0.539) 		0.253
(0.323) 		0.283
(0.358) 		0.0866
(0.131)
del 7p22 3 23 (4%) 490 0.0197
(0.037) 		0.0691
(0.108) 		0.313
(0.392) 		0.158
(0.216) 		0.535
(0.617) 		0.707
(0.778) 		0.521
(0.604) 		0.0977
(0.145) 		0.529
(0.612) 		0.396
(0.474)
del 18q23 78 (15%) 435 0.323
(0.403) 		0.328
(0.408) 		0.115
(0.167) 		0.0593
(0.0952) 		0.982
(1.00) 		0.265
(0.337) 		0.458
(0.539) 		0.227
(0.297) 		0.138
(0.194) 		0.617
(0.695) 		0.461
(0.541) 		0.792
(0.86)
'amp_1q22' versus 'CN_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.00083

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
AMP PEAK 1(1Q22) MUTATED 15 20 7
AMP PEAK 1(1Q22) WILD-TYPE 212 91 168

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

'amp_1q22' versus 'MRNASEQ_CNMF'

P value = 0.00257 (Fisher's exact test), Q value = 0.0062

Table S2.  Gene #1: 'amp_1q22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
AMP PEAK 1(1Q22) MUTATED 8 20 3 9 2
AMP PEAK 1(1Q22) WILD-TYPE 122 95 102 124 28

Figure S2.  Get High-res Image Gene #1: 'amp_1q22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_1q22' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00248 (Fisher's exact test), Q value = 0.0061

Table S3.  Gene #1: 'amp_1q22' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
AMP PEAK 1(1Q22) MUTATED 11 16 1 14
AMP PEAK 1(1Q22) WILD-TYPE 116 103 104 140

Figure S3.  Get High-res Image Gene #1: 'amp_1q22' versus Molecular Subtype #11: 'MIRSEQ_MATURE_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 227 111 175
AMP PEAK 2(1Q32.1) MUTATED 12 26 5
AMP PEAK 2(1Q32.1) WILD-TYPE 215 85 170

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 209 134 157 13
AMP PEAK 2(1Q32.1) MUTATED 8 27 6 2
AMP PEAK 2(1Q32.1) WILD-TYPE 201 107 151 11

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 130 115 105 133 30
AMP PEAK 2(1Q32.1) MUTATED 2 26 1 12 2
AMP PEAK 2(1Q32.1) WILD-TYPE 128 89 104 121 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 = 2e-05 (Fisher's exact test), Q value = 8.4e-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 = 0.00328 (Fisher's exact test), Q value = 0.0077

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
AMP PEAK 2(1Q32.1) MUTATED 9 18 2 14
AMP PEAK 2(1Q32.1) WILD-TYPE 118 101 103 140

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
AMP PEAK 2(1Q32.1) MUTATED 5 3 10 1 18 6
AMP PEAK 2(1Q32.1) WILD-TYPE 94 74 108 55 45 86

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 = 0.00279 (Fisher's exact test), Q value = 0.0067

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
AMP PEAK 3(2P24.3) MUTATED 9 12 3
AMP PEAK 3(2P24.3) WILD-TYPE 218 99 172

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

'amp_2p24.3' versus 'MRNASEQ_CNMF'

P value = 0.0312 (Fisher's exact test), Q value = 0.055

Table S12.  Gene #3: 'amp_2p24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
AMP PEAK 3(2P24.3) MUTATED 4 12 2 6 0
AMP PEAK 3(2P24.3) WILD-TYPE 126 103 103 127 30

Figure S12.  Get High-res Image Gene #3: 'amp_2p24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_2p24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00253 (Fisher's exact test), Q value = 0.0062

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 = 0.0354 (Fisher's exact test), Q value = 0.061

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_2p24.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.0013

Table S15.  Gene #3: 'amp_2p24.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
AMP PEAK 3(2P24.3) MUTATED 3 15 1 5
AMP PEAK 3(2P24.3) WILD-TYPE 124 104 104 149

Figure S15.  Get High-res Image Gene #3: 'amp_2p24.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_2p24.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0314 (Fisher's exact test), Q value = 0.055

Table S16.  Gene #3: 'amp_2p24.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
AMP PEAK 3(2P24.3) MUTATED 4 7 2 1 7 3
AMP PEAK 3(2P24.3) WILD-TYPE 95 70 116 55 56 89

Figure S16.  Get High-res Image Gene #3: 'amp_2p24.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_3q26.33' versus 'CN_CNMF'

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

Table S17.  Gene #4: 'amp_3q26.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
AMP PEAK 4(3Q26.33) MUTATED 2 19 0
AMP PEAK 4(3Q26.33) WILD-TYPE 225 92 175

Figure S17.  Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #3: 'CN_CNMF'

'amp_3q26.33' versus 'METHLYATION_CNMF'

P value = 0.00895 (Fisher's exact test), Q value = 0.019

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
AMP PEAK 4(3Q26.33) MUTATED 7 10 2 2
AMP PEAK 4(3Q26.33) WILD-TYPE 202 124 155 11

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

'amp_3q26.33' versus 'RPPA_CNMF'

P value = 0.0238 (Fisher's exact test), Q value = 0.043

Table S19.  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 S19.  Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_3q26.33' versus 'MRNASEQ_CNMF'

P value = 0.00067 (Fisher's exact test), Q value = 0.0019

Table S20.  Gene #4: 'amp_3q26.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
AMP PEAK 4(3Q26.33) MUTATED 5 13 2 1 0
AMP PEAK 4(3Q26.33) WILD-TYPE 125 102 103 132 30

Figure S20.  Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_3q26.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00124 (Fisher's exact test), Q value = 0.0033

Table S21.  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 S21.  Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_3q26.33' versus 'MIRSEQ_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.0015

Table S22.  Gene #4: 'amp_3q26.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
AMP PEAK 4(3Q26.33) MUTATED 11 8 1 1
AMP PEAK 4(3Q26.33) WILD-TYPE 129 99 81 179

Figure S22.  Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_3q26.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0189 (Fisher's exact test), Q value = 0.036

Table S23.  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 S23.  Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_3q26.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00101 (Fisher's exact test), Q value = 0.0027

Table S24.  Gene #4: 'amp_3q26.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
AMP PEAK 4(3Q26.33) MUTATED 4 13 1 3
AMP PEAK 4(3Q26.33) WILD-TYPE 123 106 104 151

Figure S24.  Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_3q26.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00369 (Fisher's exact test), Q value = 0.0084

Table S25.  Gene #4: 'amp_3q26.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
AMP PEAK 4(3Q26.33) MUTATED 6 3 1 0 8 3
AMP PEAK 4(3Q26.33) WILD-TYPE 93 74 117 56 55 89

Figure S25.  Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_4q12' versus 'MRNA_CHIERARCHICAL'

P value = 0.042 (Fisher's exact test), Q value = 0.072

Table S26.  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 S26.  Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_4q12' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00028

Table S27.  Gene #5: 'amp_4q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
AMP PEAK 5(4Q12) MUTATED 13 15 2
AMP PEAK 5(4Q12) WILD-TYPE 214 96 173

Figure S27.  Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_4q12' versus 'METHLYATION_CNMF'

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

Table S28.  Gene #5: 'amp_4q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
AMP PEAK 5(4Q12) MUTATED 13 10 1 6
AMP PEAK 5(4Q12) WILD-TYPE 196 124 156 7

Figure S28.  Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_4q12' versus 'RPPA_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 5e-04

Table S29.  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 S29.  Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_4q12' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00019

Table S30.  Gene #5: 'amp_4q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
AMP PEAK 5(4Q12) MUTATED 5 18 0 6 1
AMP PEAK 5(4Q12) WILD-TYPE 125 97 105 127 29

Figure S30.  Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_4q12' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S31.  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 S31.  Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_4q12' versus 'MIRSEQ_CNMF'

P value = 0.00303 (Fisher's exact test), Q value = 0.0072

Table S32.  Gene #5: 'amp_4q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
AMP PEAK 5(4Q12) MUTATED 6 15 2 7
AMP PEAK 5(4Q12) WILD-TYPE 134 92 80 173

Figure S32.  Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_4q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.00042

Table S33.  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 S33.  Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_4q12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00251 (Fisher's exact test), Q value = 0.0061

Table S34.  Gene #5: 'amp_4q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
AMP PEAK 5(4Q12) MUTATED 5 16 2 7
AMP PEAK 5(4Q12) WILD-TYPE 122 103 103 147

Figure S34.  Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_4q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00066 (Fisher's exact test), Q value = 0.0019

Table S35.  Gene #5: 'amp_4q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
AMP PEAK 5(4Q12) MUTATED 3 12 5 0 7 3
AMP PEAK 5(4Q12) WILD-TYPE 96 65 113 56 56 89

Figure S35.  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 S36.  Gene #6: 'amp_7p11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
AMP PEAK 6(7P11.2) MUTATED 46 72 9
AMP PEAK 6(7P11.2) WILD-TYPE 181 39 166

Figure S36.  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 S37.  Gene #6: 'amp_7p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
AMP PEAK 6(7P11.2) MUTATED 39 72 14 2
AMP PEAK 6(7P11.2) WILD-TYPE 170 62 143 11

Figure S37.  Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_7p11.2' versus 'RPPA_CNMF'

P value = 0.0015 (Fisher's exact test), Q value = 0.0039

Table S38.  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 36 20 22
AMP PEAK 6(7P11.2) WILD-TYPE 68 59 105 93

Figure S38.  Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_7p11.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00326 (Fisher's exact test), Q value = 0.0076

Table S39.  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 58
AMP PEAK 6(7P11.2) WILD-TYPE 71 127 127

Figure S39.  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 S40.  Gene #6: 'amp_7p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
AMP PEAK 6(7P11.2) MUTATED 22 66 9 25 5
AMP PEAK 6(7P11.2) WILD-TYPE 108 49 96 108 25

Figure S40.  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 S41.  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 26 7 9 6
AMP PEAK 6(7P11.2) WILD-TYPE 116 14 33 42 83 32 66

Figure S41.  Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_7p11.2' versus 'MIRSEQ_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 5e-04

Table S42.  Gene #6: 'amp_7p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
AMP PEAK 6(7P11.2) MUTATED 45 37 11 32
AMP PEAK 6(7P11.2) WILD-TYPE 95 70 71 148

Figure S42.  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 S43.  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 36 28 61
AMP PEAK 6(7P11.2) WILD-TYPE 186 156 42

Figure S43.  Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_7p11.2' versus 'MIRSEQ_MATURE_CNMF'

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

Table S44.  Gene #6: 'amp_7p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
AMP PEAK 6(7P11.2) MUTATED 33 50 9 32
AMP PEAK 6(7P11.2) WILD-TYPE 94 69 96 122

Figure S44.  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 S45.  Gene #6: 'amp_7p11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
AMP PEAK 6(7P11.2) MUTATED 15 12 20 7 53 17
AMP PEAK 6(7P11.2) WILD-TYPE 84 65 98 49 10 75

Figure S45.  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 S46.  Gene #7: 'amp_7q31.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
AMP PEAK 7(7Q31.2) MUTATED 69 79 25
AMP PEAK 7(7Q31.2) WILD-TYPE 158 32 150

Figure S46.  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 S47.  Gene #7: 'amp_7q31.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
AMP PEAK 7(7Q31.2) MUTATED 74 68 28 3
AMP PEAK 7(7Q31.2) WILD-TYPE 135 66 129 10

Figure S47.  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 S48.  Gene #7: 'amp_7q31.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
AMP PEAK 7(7Q31.2) MUTATED 47 64 15 39 8
AMP PEAK 7(7Q31.2) WILD-TYPE 83 51 90 94 22

Figure S48.  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 S49.  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 32 14 9 15
AMP PEAK 7(7Q31.2) WILD-TYPE 91 18 30 36 76 32 57

Figure S49.  Get High-res Image Gene #7: 'amp_7q31.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_7q31.2' versus 'MIRSEQ_CNMF'

P value = 0.0108 (Fisher's exact test), Q value = 0.022

Table S50.  Gene #7: 'amp_7q31.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
AMP PEAK 7(7Q31.2) MUTATED 56 44 19 52
AMP PEAK 7(7Q31.2) WILD-TYPE 84 63 63 128

Figure S50.  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 S51.  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 64 48 59
AMP PEAK 7(7Q31.2) WILD-TYPE 158 136 44

Figure S51.  Get High-res Image Gene #7: 'amp_7q31.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_7q31.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00066 (Fisher's exact test), Q value = 0.0019

Table S52.  Gene #7: 'amp_7q31.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
AMP PEAK 7(7Q31.2) MUTATED 43 55 21 51
AMP PEAK 7(7Q31.2) WILD-TYPE 84 64 84 103

Figure S52.  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 S53.  Gene #7: 'amp_7q31.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
AMP PEAK 7(7Q31.2) MUTATED 27 18 32 9 49 35
AMP PEAK 7(7Q31.2) WILD-TYPE 72 59 86 47 14 57

Figure S53.  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 S54.  Gene #8: 'amp_7q32.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
AMP PEAK 8(7Q32.3) MUTATED 75 80 26
AMP PEAK 8(7Q32.3) WILD-TYPE 152 31 149

Figure S54.  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 S55.  Gene #8: 'amp_7q32.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
AMP PEAK 8(7Q32.3) MUTATED 80 69 29 3
AMP PEAK 8(7Q32.3) WILD-TYPE 129 65 128 10

Figure S55.  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 S56.  Gene #8: 'amp_7q32.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
AMP PEAK 8(7Q32.3) MUTATED 51 64 16 42 8
AMP PEAK 8(7Q32.3) WILD-TYPE 79 51 89 91 22

Figure S56.  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 S57.  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 36 15 9 15
AMP PEAK 8(7Q32.3) WILD-TYPE 88 18 30 32 75 32 57

Figure S57.  Get High-res Image Gene #8: 'amp_7q32.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_7q32.3' versus 'MIRSEQ_CNMF'

P value = 0.0335 (Fisher's exact test), Q value = 0.059

Table S58.  Gene #8: 'amp_7q32.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
AMP PEAK 8(7Q32.3) MUTATED 58 44 21 56
AMP PEAK 8(7Q32.3) WILD-TYPE 82 63 61 124

Figure S58.  Get High-res Image Gene #8: 'amp_7q32.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_7q32.3' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S59.  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 67 52 60
AMP PEAK 8(7Q32.3) WILD-TYPE 155 132 43

Figure S59.  Get High-res Image Gene #8: 'amp_7q32.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_7q32.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00092 (Fisher's exact test), Q value = 0.0025

Table S60.  Gene #8: 'amp_7q32.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
AMP PEAK 8(7Q32.3) MUTATED 45 57 23 53
AMP PEAK 8(7Q32.3) WILD-TYPE 82 62 82 101

Figure S60.  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 S61.  Gene #8: 'amp_7q32.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
AMP PEAK 8(7Q32.3) MUTATED 31 19 34 10 49 35
AMP PEAK 8(7Q32.3) WILD-TYPE 68 58 84 46 14 57

Figure S61.  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 S62.  Gene #9: 'amp_8q24.13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
AMP PEAK 9(8Q24.13) MUTATED 65 26 8
AMP PEAK 9(8Q24.13) WILD-TYPE 162 85 167

Figure S62.  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 S63.  Gene #9: 'amp_8q24.13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
AMP PEAK 9(8Q24.13) MUTATED 79 8 10 2
AMP PEAK 9(8Q24.13) WILD-TYPE 130 126 147 11

Figure S63.  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 S64.  Gene #9: 'amp_8q24.13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
AMP PEAK 9(8Q24.13) MUTATED 46 14 5 26 8
AMP PEAK 9(8Q24.13) WILD-TYPE 84 101 100 107 22

Figure S64.  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 S65.  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 8 9
AMP PEAK 9(8Q24.13) WILD-TYPE 83 68 34 48 85 33 63

Figure S65.  Get High-res Image Gene #9: 'amp_8q24.13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.13' versus 'MIRSEQ_CNMF'

P value = 0.00835 (Fisher's exact test), Q value = 0.018

Table S66.  Gene #9: 'amp_8q24.13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
AMP PEAK 9(8Q24.13) MUTATED 35 20 6 36
AMP PEAK 9(8Q24.13) WILD-TYPE 105 87 76 144

Figure S66.  Get High-res Image Gene #9: 'amp_8q24.13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_8q24.13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00043 (Fisher's exact test), Q value = 0.0013

Table S67.  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 9
AMP PEAK 9(8Q24.13) WILD-TYPE 164 154 94

Figure S67.  Get High-res Image Gene #9: 'amp_8q24.13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_8q24.13' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0147 (Fisher's exact test), Q value = 0.029

Table S68.  Gene #9: 'amp_8q24.13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
AMP PEAK 9(8Q24.13) MUTATED 37 21 15 24
AMP PEAK 9(8Q24.13) WILD-TYPE 90 98 90 130

Figure S68.  Get High-res Image Gene #9: 'amp_8q24.13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_8q24.13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S69.  Gene #9: 'amp_8q24.13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
AMP PEAK 9(8Q24.13) MUTATED 34 15 14 2 3 29
AMP PEAK 9(8Q24.13) WILD-TYPE 65 62 104 54 60 63

Figure S69.  Get High-res Image Gene #9: 'amp_8q24.13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_9q34.3' versus 'CN_CNMF'

P value = 0.0216 (Fisher's exact test), Q value = 0.04

Table S70.  Gene #10: 'amp_9q34.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
AMP PEAK 10(9Q34.3) MUTATED 23 15 8
AMP PEAK 10(9Q34.3) WILD-TYPE 204 96 167

Figure S70.  Get High-res Image Gene #10: 'amp_9q34.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_9q34.3' versus 'METHLYATION_CNMF'

P value = 0.0105 (Fisher's exact test), Q value = 0.021

Table S71.  Gene #10: 'amp_9q34.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
AMP PEAK 10(9Q34.3) MUTATED 24 10 8 4
AMP PEAK 10(9Q34.3) WILD-TYPE 185 124 149 9

Figure S71.  Get High-res Image Gene #10: 'amp_9q34.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_9q34.3' versus 'RPPA_CNMF'

P value = 0.0182 (Fisher's exact test), Q value = 0.035

Table S72.  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 S72.  Get High-res Image Gene #10: 'amp_9q34.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_9q34.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.00061

Table S73.  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 S73.  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 S74.  Gene #11: 'amp_10p15.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
AMP PEAK 11(10P15.3) MUTATED 60 11 0
AMP PEAK 11(10P15.3) WILD-TYPE 167 100 175

Figure S74.  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 S75.  Gene #11: 'amp_10p15.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
AMP PEAK 11(10P15.3) MUTATED 59 6 0 6
AMP PEAK 11(10P15.3) WILD-TYPE 150 128 157 7

Figure S75.  Get High-res Image Gene #11: 'amp_10p15.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_10p15.3' versus 'RPPA_CNMF'

P value = 0.00824 (Fisher's exact test), Q value = 0.017

Table S76.  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 S76.  Get High-res Image Gene #11: 'amp_10p15.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_10p15.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00135 (Fisher's exact test), Q value = 0.0035

Table S77.  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 S77.  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 S78.  Gene #11: 'amp_10p15.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
AMP PEAK 11(10P15.3) MUTATED 37 15 0 16 3
AMP PEAK 11(10P15.3) WILD-TYPE 93 100 105 117 27

Figure S78.  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 S79.  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 S79.  Get High-res Image Gene #11: 'amp_10p15.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_10p15.3' versus 'MIRSEQ_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.001

Table S80.  Gene #11: 'amp_10p15.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
AMP PEAK 11(10P15.3) MUTATED 20 27 4 19
AMP PEAK 11(10P15.3) WILD-TYPE 120 80 78 161

Figure S80.  Get High-res Image Gene #11: 'amp_10p15.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_10p15.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00237 (Fisher's exact test), Q value = 0.0059

Table S81.  Gene #11: 'amp_10p15.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
AMP PEAK 11(10P15.3) MUTATED 24 24 6 16
AMP PEAK 11(10P15.3) WILD-TYPE 103 95 99 138

Figure S81.  Get High-res Image Gene #11: 'amp_10p15.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_10p15.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S82.  Gene #11: 'amp_10p15.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
AMP PEAK 11(10P15.3) MUTATED 28 16 9 0 1 16
AMP PEAK 11(10P15.3) WILD-TYPE 71 61 109 56 62 76

Figure S82.  Get High-res Image Gene #11: 'amp_10p15.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_11q24.1' versus 'METHLYATION_CNMF'

P value = 0.00883 (Fisher's exact test), Q value = 0.018

Table S83.  Gene #12: 'amp_11q24.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
AMP PEAK 12(11Q24.1) MUTATED 47 12 26 2
AMP PEAK 12(11Q24.1) WILD-TYPE 162 122 131 11

Figure S83.  Get High-res Image Gene #12: 'amp_11q24.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_11q24.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0473 (Fisher's exact test), Q value = 0.078

Table S84.  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 S84.  Get High-res Image Gene #12: 'amp_11q24.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_11q24.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00858 (Fisher's exact test), Q value = 0.018

Table S85.  Gene #12: 'amp_11q24.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
AMP PEAK 12(11Q24.1) MUTATED 22 14 18 10 2 21
AMP PEAK 12(11Q24.1) WILD-TYPE 77 63 100 46 61 71

Figure S85.  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 S86.  Gene #13: 'amp_12p13.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
AMP PEAK 13(12P13.32) MUTATED 45 24 3
AMP PEAK 13(12P13.32) WILD-TYPE 182 87 172

Figure S86.  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 S87.  Gene #13: 'amp_12p13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
AMP PEAK 13(12P13.32) MUTATED 55 10 5 2
AMP PEAK 13(12P13.32) WILD-TYPE 154 124 152 11

Figure S87.  Get High-res Image Gene #13: 'amp_12p13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_12p13.32' versus 'RPPA_CNMF'

P value = 0.00499 (Fisher's exact test), Q value = 0.011

Table S88.  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 S88.  Get High-res Image Gene #13: 'amp_12p13.32' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_12p13.32' versus 'MRNASEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00042

Table S89.  Gene #13: 'amp_12p13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
AMP PEAK 13(12P13.32) MUTATED 29 22 4 13 4
AMP PEAK 13(12P13.32) WILD-TYPE 101 93 101 120 26

Figure S89.  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 S90.  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 S90.  Get High-res Image Gene #13: 'amp_12p13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_12p13.32' versus 'MIRSEQ_CNMF'

P value = 0.0111 (Fisher's exact test), Q value = 0.022

Table S91.  Gene #13: 'amp_12p13.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
AMP PEAK 13(12P13.32) MUTATED 17 26 11 18
AMP PEAK 13(12P13.32) WILD-TYPE 123 81 71 162

Figure S91.  Get High-res Image Gene #13: 'amp_12p13.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_12p13.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00709 (Fisher's exact test), Q value = 0.015

Table S92.  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 S92.  Get High-res Image Gene #13: 'amp_12p13.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_12p13.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00144 (Fisher's exact test), Q value = 0.0037

Table S93.  Gene #13: 'amp_12p13.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
AMP PEAK 13(12P13.32) MUTATED 23 27 9 13
AMP PEAK 13(12P13.32) WILD-TYPE 104 92 96 141

Figure S93.  Get High-res Image Gene #13: 'amp_12p13.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_12p13.32' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S94.  Gene #13: 'amp_12p13.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
AMP PEAK 13(12P13.32) MUTATED 19 22 4 4 7 16
AMP PEAK 13(12P13.32) WILD-TYPE 80 55 114 52 56 76

Figure S94.  Get High-res Image Gene #13: 'amp_12p13.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12q14.1' versus 'CN_CNMF'

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

Table S95.  Gene #14: 'amp_12q14.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
AMP PEAK 14(12Q14.1) MUTATED 8 28 1
AMP PEAK 14(12Q14.1) WILD-TYPE 219 83 174

Figure S95.  Get High-res Image Gene #14: 'amp_12q14.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_12q14.1' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 8.4e-05

Table S96.  Gene #14: 'amp_12q14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
AMP PEAK 14(12Q14.1) MUTATED 8 20 4 5
AMP PEAK 14(12Q14.1) WILD-TYPE 201 114 153 8

Figure S96.  Get High-res Image Gene #14: 'amp_12q14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_12q14.1' versus 'RPPA_CNMF'

P value = 0.0145 (Fisher's exact test), Q value = 0.028

Table S97.  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 S97.  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 S98.  Gene #14: 'amp_12q14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
AMP PEAK 14(12Q14.1) MUTATED 3 27 3 3 1
AMP PEAK 14(12Q14.1) WILD-TYPE 127 88 102 130 29

Figure S98.  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 S99.  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 S99.  Get High-res Image Gene #14: 'amp_12q14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_12q14.1' versus 'MIRSEQ_CNMF'

P value = 0.00366 (Fisher's exact test), Q value = 0.0084

Table S100.  Gene #14: 'amp_12q14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
AMP PEAK 14(12Q14.1) MUTATED 13 15 3 6
AMP PEAK 14(12Q14.1) WILD-TYPE 127 92 79 174

Figure S100.  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 S101.  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 S101.  Get High-res Image Gene #14: 'amp_12q14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_12q14.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 8.4e-05

Table S102.  Gene #14: 'amp_12q14.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
AMP PEAK 14(12Q14.1) MUTATED 9 21 1 6
AMP PEAK 14(12Q14.1) WILD-TYPE 118 98 104 148

Figure S102.  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 = 6e-05 (Fisher's exact test), Q value = 0.00022

Table S103.  Gene #14: 'amp_12q14.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
AMP PEAK 14(12Q14.1) MUTATED 6 6 2 2 15 6
AMP PEAK 14(12Q14.1) WILD-TYPE 93 71 116 54 48 86

Figure S103.  Get High-res Image Gene #14: 'amp_12q14.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_13q34' versus 'CN_CNMF'

P value = 0.00314 (Fisher's exact test), Q value = 0.0074

Table S104.  Gene #15: 'amp_13q34' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
AMP PEAK 15(13Q34) MUTATED 15 6 1
AMP PEAK 15(13Q34) WILD-TYPE 212 105 174

Figure S104.  Get High-res Image Gene #15: 'amp_13q34' versus Molecular Subtype #3: 'CN_CNMF'

'amp_13q34' versus 'METHLYATION_CNMF'

P value = 0.00378 (Fisher's exact test), Q value = 0.0085

Table S105.  Gene #15: 'amp_13q34' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
AMP PEAK 15(13Q34) MUTATED 14 5 1 2
AMP PEAK 15(13Q34) WILD-TYPE 195 129 156 11

Figure S105.  Get High-res Image Gene #15: 'amp_13q34' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_13q34' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0216 (Fisher's exact test), Q value = 0.04

Table S106.  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 S106.  Get High-res Image Gene #15: 'amp_13q34' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_15q26.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.0422 (Fisher's exact test), Q value = 0.072

Table S107.  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 S107.  Get High-res Image Gene #16: 'amp_15q26.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_15q26.3' versus 'CN_CNMF'

P value = 0.00075 (Fisher's exact test), Q value = 0.0021

Table S108.  Gene #16: 'amp_15q26.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
AMP PEAK 16(15Q26.3) MUTATED 12 7 0
AMP PEAK 16(15Q26.3) WILD-TYPE 215 104 175

Figure S108.  Get High-res Image Gene #16: 'amp_15q26.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_15q26.3' versus 'METHLYATION_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.00077

Table S109.  Gene #16: 'amp_15q26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
AMP PEAK 16(15Q26.3) MUTATED 11 5 0 3
AMP PEAK 16(15Q26.3) WILD-TYPE 198 129 157 10

Figure S109.  Get High-res Image Gene #16: 'amp_15q26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_15q26.3' versus 'MRNASEQ_CNMF'

P value = 0.0359 (Fisher's exact test), Q value = 0.062

Table S110.  Gene #16: 'amp_15q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
AMP PEAK 16(15Q26.3) MUTATED 5 8 0 4 2
AMP PEAK 16(15Q26.3) WILD-TYPE 125 107 105 129 28

Figure S110.  Get High-res Image Gene #16: 'amp_15q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_15q26.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0359 (Fisher's exact test), Q value = 0.062

Table S111.  Gene #16: 'amp_15q26.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
AMP PEAK 16(15Q26.3) MUTATED 3 8 2 0 3 3
AMP PEAK 16(15Q26.3) WILD-TYPE 96 69 116 56 60 89

Figure S111.  Get High-res Image Gene #16: 'amp_15q26.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17q25.1' versus 'CN_CNMF'

P value = 0.0393 (Fisher's exact test), Q value = 0.067

Table S112.  Gene #17: 'amp_17q25.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
AMP PEAK 17(17Q25.1) MUTATED 18 16 10
AMP PEAK 17(17Q25.1) WILD-TYPE 209 95 165

Figure S112.  Get High-res Image Gene #17: 'amp_17q25.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q25.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0486 (Fisher's exact test), Q value = 0.08

Table S113.  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 S113.  Get High-res Image Gene #17: 'amp_17q25.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_17q25.1' versus 'MRNASEQ_CNMF'

P value = 0.0336 (Fisher's exact test), Q value = 0.059

Table S114.  Gene #17: 'amp_17q25.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
AMP PEAK 17(17Q25.1) MUTATED 10 18 7 9 0
AMP PEAK 17(17Q25.1) WILD-TYPE 120 97 98 124 30

Figure S114.  Get High-res Image Gene #17: 'amp_17q25.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_19p13.3' versus 'CN_CNMF'

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

Table S115.  Gene #18: 'amp_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
AMP PEAK 18(19P13.3) MUTATED 24 29 76
AMP PEAK 18(19P13.3) WILD-TYPE 203 82 99

Figure S115.  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 S116.  Gene #18: 'amp_19p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
AMP PEAK 18(19P13.3) MUTATED 19 30 80 0
AMP PEAK 18(19P13.3) WILD-TYPE 190 104 77 13

Figure S116.  Get High-res Image Gene #18: 'amp_19p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_19p13.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00494 (Fisher's exact test), Q value = 0.011

Table S117.  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 S117.  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 S118.  Gene #18: 'amp_19p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
AMP PEAK 18(19P13.3) MUTATED 10 30 53 34 2
AMP PEAK 18(19P13.3) WILD-TYPE 120 85 52 99 28

Figure S118.  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 S119.  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 S119.  Get High-res Image Gene #18: 'amp_19p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_19p13.3' versus 'MIRSEQ_CNMF'

P value = 0.00054 (Fisher's exact test), Q value = 0.0016

Table S120.  Gene #18: 'amp_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
AMP PEAK 18(19P13.3) MUTATED 26 23 36 44
AMP PEAK 18(19P13.3) WILD-TYPE 114 84 46 136

Figure S120.  Get High-res Image Gene #18: 'amp_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_19p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 8.4e-05

Table S121.  Gene #18: 'amp_19p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
AMP PEAK 18(19P13.3) MUTATED 19 27 46 37
AMP PEAK 18(19P13.3) WILD-TYPE 108 92 59 117

Figure S121.  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 = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S122.  Gene #18: 'amp_19p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
AMP PEAK 18(19P13.3) MUTATED 12 15 30 27 23 22
AMP PEAK 18(19P13.3) WILD-TYPE 87 62 88 29 40 70

Figure S122.  Get High-res Image Gene #18: 'amp_19p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_xp11.22' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 8.4e-05

Table S123.  Gene #19: 'amp_xp11.22' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
AMP PEAK 19(XP11.22) MUTATED 33 13 2
AMP PEAK 19(XP11.22) WILD-TYPE 194 98 173

Figure S123.  Get High-res Image Gene #19: '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 S124.  Gene #19: 'amp_xp11.22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
AMP PEAK 19(XP11.22) MUTATED 38 6 1 3
AMP PEAK 19(XP11.22) WILD-TYPE 171 128 156 10

Figure S124.  Get High-res Image Gene #19: 'amp_xp11.22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_xp11.22' versus 'MRNASEQ_CNMF'

P value = 0.0028 (Fisher's exact test), Q value = 0.0067

Table S125.  Gene #19: 'amp_xp11.22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
AMP PEAK 19(XP11.22) MUTATED 18 13 1 13 3
AMP PEAK 19(XP11.22) WILD-TYPE 112 102 104 120 27

Figure S125.  Get High-res Image Gene #19: '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 S126.  Gene #19: '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 19(XP11.22) MUTATED 22 3 0 9 1 8 5
AMP PEAK 19(XP11.22) WILD-TYPE 113 68 36 59 89 33 67

Figure S126.  Get High-res Image Gene #19: 'amp_xp11.22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_xp11.22' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0149 (Fisher's exact test), Q value = 0.029

Table S127.  Gene #19: 'amp_xp11.22' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
AMP PEAK 19(XP11.22) MUTATED 17 15 3 12
AMP PEAK 19(XP11.22) WILD-TYPE 110 104 102 142

Figure S127.  Get High-res Image Gene #19: 'amp_xp11.22' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_xp11.22' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00195 (Fisher's exact test), Q value = 0.0049

Table S128.  Gene #19: 'amp_xp11.22' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
AMP PEAK 19(XP11.22) MUTATED 16 12 8 0 3 8
AMP PEAK 19(XP11.22) WILD-TYPE 83 65 110 56 60 84

Figure S128.  Get High-res Image Gene #19: 'amp_xp11.22' 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 S129.  Gene #20: 'amp_xp11.22' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
AMP PEAK 20(XP11.22) MUTATED 47 14 2
AMP PEAK 20(XP11.22) WILD-TYPE 180 97 173

Figure S129.  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 S130.  Gene #20: 'amp_xp11.22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
AMP PEAK 20(XP11.22) MUTATED 49 9 1 4
AMP PEAK 20(XP11.22) WILD-TYPE 160 125 156 9

Figure S130.  Get High-res Image Gene #20: 'amp_xp11.22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_xp11.22' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00019

Table S131.  Gene #20: 'amp_xp11.22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
AMP PEAK 20(XP11.22) MUTATED 24 19 1 15 4
AMP PEAK 20(XP11.22) WILD-TYPE 106 96 104 118 26

Figure S131.  Get High-res Image Gene #20: '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 S132.  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 30 5 0 12 1 11 4
AMP PEAK 20(XP11.22) WILD-TYPE 105 66 36 56 89 30 68

Figure S132.  Get High-res Image Gene #20: 'amp_xp11.22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_xp11.22' versus 'MIRSEQ_CNMF'

P value = 0.00065 (Fisher's exact test), Q value = 0.0019

Table S133.  Gene #20: 'amp_xp11.22' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
AMP PEAK 20(XP11.22) MUTATED 22 19 1 20
AMP PEAK 20(XP11.22) WILD-TYPE 118 88 81 160

Figure S133.  Get High-res Image Gene #20: 'amp_xp11.22' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_xp11.22' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00045

Table S134.  Gene #20: 'amp_xp11.22' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
AMP PEAK 20(XP11.22) MUTATED 26 18 3 15
AMP PEAK 20(XP11.22) WILD-TYPE 101 101 102 139

Figure S134.  Get High-res Image Gene #20: 'amp_xp11.22' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_xp11.22' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 0.00086

Table S135.  Gene #20: 'amp_xp11.22' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
AMP PEAK 20(XP11.22) MUTATED 22 13 11 0 4 12
AMP PEAK 20(XP11.22) WILD-TYPE 77 64 107 56 59 80

Figure S135.  Get High-res Image Gene #20: 'amp_xp11.22' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p36.32' versus 'MRNA_CNMF'

P value = 0.00062 (Fisher's exact test), Q value = 0.0018

Table S136.  Gene #21: '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 S136.  Get High-res Image Gene #21: 'del_1p36.32' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_1p36.32' versus 'MRNA_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.00061

Table S137.  Gene #21: '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 S137.  Get High-res Image Gene #21: '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 S138.  Gene #21: 'del_1p36.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
DEL PEAK 1(1P36.32) MUTATED 13 24 169
DEL PEAK 1(1P36.32) WILD-TYPE 214 87 6

Figure S138.  Get High-res Image Gene #21: '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 S139.  Gene #21: 'del_1p36.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
DEL PEAK 1(1P36.32) MUTATED 11 38 157 0
DEL PEAK 1(1P36.32) WILD-TYPE 198 96 0 13

Figure S139.  Get High-res Image Gene #21: 'del_1p36.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p36.32' versus 'RPPA_CNMF'

P value = 0.00067 (Fisher's exact test), Q value = 0.0019

Table S140.  Gene #21: '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 S140.  Get High-res Image Gene #21: 'del_1p36.32' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_1p36.32' versus 'RPPA_CHIERARCHICAL'

P value = 0.00045 (Fisher's exact test), Q value = 0.0013

Table S141.  Gene #21: '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 S141.  Get High-res Image Gene #21: '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 S142.  Gene #21: 'del_1p36.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
DEL PEAK 1(1P36.32) MUTATED 5 22 104 62 13
DEL PEAK 1(1P36.32) WILD-TYPE 125 93 1 71 17

Figure S142.  Get High-res Image Gene #21: '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 S143.  Gene #21: '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 S143.  Get High-res Image Gene #21: '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 S144.  Gene #21: 'del_1p36.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
DEL PEAK 1(1P36.32) MUTATED 35 12 69 90
DEL PEAK 1(1P36.32) WILD-TYPE 105 95 13 90

Figure S144.  Get High-res Image Gene #21: '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 S145.  Gene #21: '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 S145.  Get High-res Image Gene #21: '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 S146.  Gene #21: 'del_1p36.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
DEL PEAK 1(1P36.32) MUTATED 23 23 84 76
DEL PEAK 1(1P36.32) WILD-TYPE 104 96 21 78

Figure S146.  Get High-res Image Gene #21: '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 S147.  Gene #21: 'del_1p36.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
DEL PEAK 1(1P36.32) MUTATED 7 26 63 55 16 39
DEL PEAK 1(1P36.32) WILD-TYPE 92 51 55 1 47 53

Figure S147.  Get High-res Image Gene #21: 'del_1p36.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p32.3' versus 'MRNA_CNMF'

P value = 0.0283 (Fisher's exact test), Q value = 0.051

Table S148.  Gene #22: '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 S148.  Get High-res Image Gene #22: 'del_1p32.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_1p32.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.00061

Table S149.  Gene #22: '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 S149.  Get High-res Image Gene #22: '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 S150.  Gene #22: 'del_1p32.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
DEL PEAK 2(1P32.3) MUTATED 10 20 166
DEL PEAK 2(1P32.3) WILD-TYPE 217 91 9

Figure S150.  Get High-res Image Gene #22: '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 S151.  Gene #22: 'del_1p32.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
DEL PEAK 2(1P32.3) MUTATED 5 34 157 0
DEL PEAK 2(1P32.3) WILD-TYPE 204 100 0 13

Figure S151.  Get High-res Image Gene #22: 'del_1p32.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p32.3' versus 'RPPA_CNMF'

P value = 0.00164 (Fisher's exact test), Q value = 0.0042

Table S152.  Gene #22: '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 S152.  Get High-res Image Gene #22: '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 = 0.0018

Table S153.  Gene #22: '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 S153.  Get High-res Image Gene #22: '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 S154.  Gene #22: 'del_1p32.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
DEL PEAK 2(1P32.3) MUTATED 4 17 104 59 12
DEL PEAK 2(1P32.3) WILD-TYPE 126 98 1 74 18

Figure S154.  Get High-res Image Gene #22: '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 S155.  Gene #22: '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 S155.  Get High-res Image Gene #22: '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 S156.  Gene #22: 'del_1p32.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
DEL PEAK 2(1P32.3) MUTATED 35 9 68 84
DEL PEAK 2(1P32.3) WILD-TYPE 105 98 14 96

Figure S156.  Get High-res Image Gene #22: '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 S157.  Gene #22: '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 S157.  Get High-res Image Gene #22: '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 S158.  Gene #22: 'del_1p32.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
DEL PEAK 2(1P32.3) MUTATED 20 22 83 71
DEL PEAK 2(1P32.3) WILD-TYPE 107 97 22 83

Figure S158.  Get High-res Image Gene #22: '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 S159.  Gene #22: 'del_1p32.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
DEL PEAK 2(1P32.3) MUTATED 7 25 61 55 12 36
DEL PEAK 2(1P32.3) WILD-TYPE 92 52 57 1 51 56

Figure S159.  Get High-res Image Gene #22: 'del_1p32.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1q43' versus 'CN_CNMF'

P value = 0.0198 (Fisher's exact test), Q value = 0.037

Table S160.  Gene #23: 'del_1q43' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
DEL PEAK 3(1Q43) MUTATED 20 11 5
DEL PEAK 3(1Q43) WILD-TYPE 207 100 170

Figure S160.  Get High-res Image Gene #23: 'del_1q43' versus Molecular Subtype #3: 'CN_CNMF'

'del_1q43' versus 'METHLYATION_CNMF'

P value = 0.00206 (Fisher's exact test), Q value = 0.0052

Table S161.  Gene #23: 'del_1q43' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
DEL PEAK 3(1Q43) MUTATED 20 10 3 3
DEL PEAK 3(1Q43) WILD-TYPE 189 124 154 10

Figure S161.  Get High-res Image Gene #23: 'del_1q43' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1q43' versus 'MRNASEQ_CNMF'

P value = 0.0152 (Fisher's exact test), Q value = 0.029

Table S162.  Gene #23: 'del_1q43' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
DEL PEAK 3(1Q43) MUTATED 14 11 1 9 1
DEL PEAK 3(1Q43) WILD-TYPE 116 104 104 124 29

Figure S162.  Get High-res Image Gene #23: 'del_1q43' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1q43' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0158 (Fisher's exact test), Q value = 0.03

Table S163.  Gene #23: '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 16 5 1 2 1 5 6
DEL PEAK 3(1Q43) WILD-TYPE 119 66 35 66 89 36 66

Figure S163.  Get High-res Image Gene #23: 'del_1q43' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1q43' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0195 (Fisher's exact test), Q value = 0.037

Table S164.  Gene #23: 'del_1q43' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
DEL PEAK 3(1Q43) MUTATED 16 9 3 7
DEL PEAK 3(1Q43) WILD-TYPE 111 110 102 147

Figure S164.  Get High-res Image Gene #23: 'del_1q43' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_1q43' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0485 (Fisher's exact test), Q value = 0.08

Table S165.  Gene #23: 'del_1q43' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
DEL PEAK 3(1Q43) MUTATED 9 10 8 1 5 2
DEL PEAK 3(1Q43) WILD-TYPE 90 67 110 55 58 90

Figure S165.  Get High-res Image Gene #23: 'del_1q43' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_2q37.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.0134 (Fisher's exact test), Q value = 0.027

Table S166.  Gene #24: '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 S166.  Get High-res Image Gene #24: '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 S167.  Gene #24: 'del_2q37.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
DEL PEAK 4(2Q37.3) MUTATED 48 24 5
DEL PEAK 4(2Q37.3) WILD-TYPE 179 87 170

Figure S167.  Get High-res Image Gene #24: '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 S168.  Gene #24: 'del_2q37.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
DEL PEAK 4(2Q37.3) MUTATED 59 7 6 5
DEL PEAK 4(2Q37.3) WILD-TYPE 150 127 151 8

Figure S168.  Get High-res Image Gene #24: 'del_2q37.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_2q37.3' versus 'RPPA_CNMF'

P value = 0.00109 (Fisher's exact test), Q value = 0.0029

Table S169.  Gene #24: '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 S169.  Get High-res Image Gene #24: 'del_2q37.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_2q37.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0149 (Fisher's exact test), Q value = 0.029

Table S170.  Gene #24: '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 S170.  Get High-res Image Gene #24: 'del_2q37.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_2q37.3' versus 'MRNASEQ_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.00061

Table S171.  Gene #24: 'del_2q37.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
DEL PEAK 4(2Q37.3) MUTATED 32 23 6 13 3
DEL PEAK 4(2Q37.3) WILD-TYPE 98 92 99 120 27

Figure S171.  Get High-res Image Gene #24: '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 S172.  Gene #24: '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 S172.  Get High-res Image Gene #24: 'del_2q37.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_2q37.3' versus 'MIRSEQ_CNMF'

P value = 0.0264 (Fisher's exact test), Q value = 0.048

Table S173.  Gene #24: 'del_2q37.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
DEL PEAK 4(2Q37.3) MUTATED 27 22 8 19
DEL PEAK 4(2Q37.3) WILD-TYPE 113 85 74 161

Figure S173.  Get High-res Image Gene #24: 'del_2q37.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_2q37.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0151 (Fisher's exact test), Q value = 0.029

Table S174.  Gene #24: 'del_2q37.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
DEL PEAK 4(2Q37.3) MUTATED 27 22 9 17
DEL PEAK 4(2Q37.3) WILD-TYPE 100 97 96 137

Figure S174.  Get High-res Image Gene #24: 'del_2q37.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_2q37.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S175.  Gene #24: 'del_2q37.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
DEL PEAK 4(2Q37.3) MUTATED 22 23 10 4 1 15
DEL PEAK 4(2Q37.3) WILD-TYPE 77 54 108 52 62 77

Figure S175.  Get High-res Image Gene #24: 'del_2q37.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p21.31' versus 'MRNA_CHIERARCHICAL'

P value = 0.00663 (Fisher's exact test), Q value = 0.014

Table S176.  Gene #25: '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 S176.  Get High-res Image Gene #25: 'del_3p21.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_3p21.31' versus 'CN_CNMF'

P value = 0.00093 (Fisher's exact test), Q value = 0.0025

Table S177.  Gene #25: 'del_3p21.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
DEL PEAK 5(3P21.31) MUTATED 23 19 7
DEL PEAK 5(3P21.31) WILD-TYPE 204 92 168

Figure S177.  Get High-res Image Gene #25: 'del_3p21.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p21.31' versus 'METHLYATION_CNMF'

P value = 0.00353 (Fisher's exact test), Q value = 0.0081

Table S178.  Gene #25: 'del_3p21.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
DEL PEAK 5(3P21.31) MUTATED 28 12 6 3
DEL PEAK 5(3P21.31) WILD-TYPE 181 122 151 10

Figure S178.  Get High-res Image Gene #25: 'del_3p21.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3p21.31' versus 'RPPA_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00025

Table S179.  Gene #25: '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 S179.  Get High-res Image Gene #25: 'del_3p21.31' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_3p21.31' versus 'RPPA_CHIERARCHICAL'

P value = 0.0437 (Fisher's exact test), Q value = 0.073

Table S180.  Gene #25: '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 S180.  Get High-res Image Gene #25: 'del_3p21.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_3p21.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00093 (Fisher's exact test), Q value = 0.0025

Table S181.  Gene #25: '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 S181.  Get High-res Image Gene #25: 'del_3p21.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p21.31' versus 'MIRSEQ_CNMF'

P value = 0.00161 (Fisher's exact test), Q value = 0.0041

Table S182.  Gene #25: 'del_3p21.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
DEL PEAK 5(3P21.31) MUTATED 13 20 8 8
DEL PEAK 5(3P21.31) WILD-TYPE 127 87 74 172

Figure S182.  Get High-res Image Gene #25: 'del_3p21.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3p21.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00242 (Fisher's exact test), Q value = 0.006

Table S183.  Gene #25: '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 S183.  Get High-res Image Gene #25: 'del_3p21.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3p21.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00975 (Fisher's exact test), Q value = 0.02

Table S184.  Gene #25: 'del_3p21.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
DEL PEAK 5(3P21.31) MUTATED 12 15 5 2 5 9
DEL PEAK 5(3P21.31) WILD-TYPE 87 62 113 54 58 83

Figure S184.  Get High-res Image Gene #25: 'del_3p21.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3q13.31' versus 'CN_CNMF'

P value = 0.00185 (Fisher's exact test), Q value = 0.0047

Table S185.  Gene #26: 'del_3q13.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
DEL PEAK 6(3Q13.31) MUTATED 25 10 4
DEL PEAK 6(3Q13.31) WILD-TYPE 202 101 171

Figure S185.  Get High-res Image Gene #26: 'del_3q13.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_3q13.31' versus 'METHLYATION_CNMF'

P value = 0.00932 (Fisher's exact test), Q value = 0.019

Table S186.  Gene #26: 'del_3q13.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
DEL PEAK 6(3Q13.31) MUTATED 24 10 4 1
DEL PEAK 6(3Q13.31) WILD-TYPE 185 124 153 12

Figure S186.  Get High-res Image Gene #26: 'del_3q13.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3q13.31' versus 'RPPA_CNMF'

P value = 0.00967 (Fisher's exact test), Q value = 0.02

Table S187.  Gene #26: '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 S187.  Get High-res Image Gene #26: 'del_3q13.31' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_3q13.31' versus 'RPPA_CHIERARCHICAL'

P value = 0.0192 (Fisher's exact test), Q value = 0.036

Table S188.  Gene #26: '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 S188.  Get High-res Image Gene #26: 'del_3q13.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_3q13.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0133 (Fisher's exact test), Q value = 0.026

Table S189.  Gene #26: '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 S189.  Get High-res Image Gene #26: 'del_3q13.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3q13.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00044 (Fisher's exact test), Q value = 0.0013

Table S190.  Gene #26: '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 S190.  Get High-res Image Gene #26: 'del_3q13.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3q29' versus 'CN_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.0011

Table S191.  Gene #27: 'del_3q29' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
DEL PEAK 7(3Q29) MUTATED 27 15 5
DEL PEAK 7(3Q29) WILD-TYPE 200 96 170

Figure S191.  Get High-res Image Gene #27: 'del_3q29' versus Molecular Subtype #3: 'CN_CNMF'

'del_3q29' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 8.4e-05

Table S192.  Gene #27: 'del_3q29' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
DEL PEAK 7(3Q29) MUTATED 28 9 4 6
DEL PEAK 7(3Q29) WILD-TYPE 181 125 153 7

Figure S192.  Get High-res Image Gene #27: 'del_3q29' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3q29' versus 'MRNASEQ_CNMF'

P value = 0.00934 (Fisher's exact test), Q value = 0.019

Table S193.  Gene #27: 'del_3q29' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
DEL PEAK 7(3Q29) MUTATED 16 16 2 11 2
DEL PEAK 7(3Q29) WILD-TYPE 114 99 103 122 28

Figure S193.  Get High-res Image Gene #27: 'del_3q29' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3q29' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00022

Table S194.  Gene #27: '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 S194.  Get High-res Image Gene #27: 'del_3q29' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3q29' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00439 (Fisher's exact test), Q value = 0.0098

Table S195.  Gene #27: '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 S195.  Get High-res Image Gene #27: 'del_3q29' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4q34.3' versus 'METHLYATION_CNMF'

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

Table S196.  Gene #28: 'del_4q34.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
DEL PEAK 8(4Q34.3) MUTATED 68 14 50 5
DEL PEAK 8(4Q34.3) WILD-TYPE 141 120 107 8

Figure S196.  Get High-res Image Gene #28: 'del_4q34.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q34.3' versus 'RPPA_CNMF'

P value = 0.0421 (Fisher's exact test), Q value = 0.072

Table S197.  Gene #28: '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 28
DEL PEAK 8(4Q34.3) WILD-TYPE 75 61 91 87

Figure S197.  Get High-res Image Gene #28: 'del_4q34.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_4q34.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00028

Table S198.  Gene #28: '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 20
DEL PEAK 8(4Q34.3) WILD-TYPE 99 66 19 50 65 25 52

Figure S198.  Get High-res Image Gene #28: 'del_4q34.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_CNMF'

P value = 0.0279 (Fisher's exact test), Q value = 0.05

Table S199.  Gene #28: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
DEL PEAK 8(4Q34.3) MUTATED 26 30 30 50
DEL PEAK 8(4Q34.3) WILD-TYPE 114 77 52 130

Figure S199.  Get High-res Image Gene #28: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_4q34.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0455 (Fisher's exact test), Q value = 0.076

Table S200.  Gene #28: '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 56 18
DEL PEAK 8(4Q34.3) WILD-TYPE 160 128 85

Figure S200.  Get High-res Image Gene #28: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00015

Table S201.  Gene #28: 'del_4q34.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
DEL PEAK 8(4Q34.3) MUTATED 22 30 31 18 4 31
DEL PEAK 8(4Q34.3) WILD-TYPE 77 47 87 38 59 61

Figure S201.  Get High-res Image Gene #28: '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 S202.  Gene #29: 'del_5p15.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
DEL PEAK 9(5P15.33) MUTATED 27 20 3
DEL PEAK 9(5P15.33) WILD-TYPE 200 91 172

Figure S202.  Get High-res Image Gene #29: '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 S203.  Gene #29: 'del_5p15.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
DEL PEAK 9(5P15.33) MUTATED 34 10 3 3
DEL PEAK 9(5P15.33) WILD-TYPE 175 124 154 10

Figure S203.  Get High-res Image Gene #29: 'del_5p15.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5p15.33' versus 'MRNASEQ_CNMF'

P value = 0.00087 (Fisher's exact test), Q value = 0.0024

Table S204.  Gene #29: 'del_5p15.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
DEL PEAK 9(5P15.33) MUTATED 14 18 1 13 4
DEL PEAK 9(5P15.33) WILD-TYPE 116 97 104 120 26

Figure S204.  Get High-res Image Gene #29: 'del_5p15.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_5p15.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00019

Table S205.  Gene #29: '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 S205.  Get High-res Image Gene #29: 'del_5p15.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5p15.33' versus 'MIRSEQ_CNMF'

P value = 0.00451 (Fisher's exact test), Q value = 0.01

Table S206.  Gene #29: 'del_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
DEL PEAK 9(5P15.33) MUTATED 10 20 3 17
DEL PEAK 9(5P15.33) WILD-TYPE 130 87 79 163

Figure S206.  Get High-res Image Gene #29: 'del_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_5p15.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00373 (Fisher's exact test), Q value = 0.0085

Table S207.  Gene #29: 'del_5p15.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
DEL PEAK 9(5P15.33) MUTATED 14 20 3 13
DEL PEAK 9(5P15.33) WILD-TYPE 113 99 102 141

Figure S207.  Get High-res Image Gene #29: 'del_5p15.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_5p15.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S208.  Gene #29: 'del_5p15.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
DEL PEAK 9(5P15.33) MUTATED 7 20 9 0 4 10
DEL PEAK 9(5P15.33) WILD-TYPE 92 57 109 56 59 82

Figure S208.  Get High-res Image Gene #29: 'del_5p15.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q34' versus 'CN_CNMF'

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

Table S209.  Gene #30: 'del_5q34' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
DEL PEAK 10(5Q34) MUTATED 41 19 4
DEL PEAK 10(5Q34) WILD-TYPE 186 92 171

Figure S209.  Get High-res Image Gene #30: '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 S210.  Gene #30: 'del_5q34' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
DEL PEAK 10(5Q34) MUTATED 41 11 3 9
DEL PEAK 10(5Q34) WILD-TYPE 168 123 154 4

Figure S210.  Get High-res Image Gene #30: 'del_5q34' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5q34' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00025

Table S211.  Gene #30: 'del_5q34' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
DEL PEAK 10(5Q34) MUTATED 19 24 2 14 5
DEL PEAK 10(5Q34) WILD-TYPE 111 91 103 119 25

Figure S211.  Get High-res Image Gene #30: '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 S212.  Gene #30: '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 11 3 22 5
DEL PEAK 10(5Q34) WILD-TYPE 115 68 36 57 87 19 67

Figure S212.  Get High-res Image Gene #30: 'del_5q34' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5q34' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00019

Table S213.  Gene #30: 'del_5q34' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
DEL PEAK 10(5Q34) MUTATED 14 29 4 17
DEL PEAK 10(5Q34) WILD-TYPE 126 78 78 163

Figure S213.  Get High-res Image Gene #30: 'del_5q34' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_5q34' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00817 (Fisher's exact test), Q value = 0.017

Table S214.  Gene #30: 'del_5q34' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
DEL PEAK 10(5Q34) MUTATED 20 23 6 15
DEL PEAK 10(5Q34) WILD-TYPE 107 96 99 139

Figure S214.  Get High-res Image Gene #30: 'del_5q34' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_5q34' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S215.  Gene #30: 'del_5q34' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
DEL PEAK 10(5Q34) MUTATED 14 23 10 0 3 14
DEL PEAK 10(5Q34) WILD-TYPE 85 54 108 56 60 78

Figure S215.  Get High-res Image Gene #30: 'del_5q34' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6p25.3' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00015

Table S216.  Gene #31: 'del_6p25.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
DEL PEAK 11(6P25.3) MUTATED 21 23 6
DEL PEAK 11(6P25.3) WILD-TYPE 206 88 169

Figure S216.  Get High-res Image Gene #31: 'del_6p25.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_6p25.3' versus 'METHLYATION_CNMF'

P value = 0.013 (Fisher's exact test), Q value = 0.026

Table S217.  Gene #31: 'del_6p25.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
DEL PEAK 11(6P25.3) MUTATED 24 14 8 4
DEL PEAK 11(6P25.3) WILD-TYPE 185 120 149 9

Figure S217.  Get High-res Image Gene #31: 'del_6p25.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_6q22.31' versus 'CN_CNMF'

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

Table S218.  Gene #32: 'del_6q22.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
DEL PEAK 12(6Q22.31) MUTATED 31 41 6
DEL PEAK 12(6Q22.31) WILD-TYPE 196 70 169

Figure S218.  Get High-res Image Gene #32: 'del_6q22.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_6q22.31' versus 'METHLYATION_CNMF'

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

Table S219.  Gene #32: 'del_6q22.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
DEL PEAK 12(6Q22.31) MUTATED 44 23 7 4
DEL PEAK 12(6Q22.31) WILD-TYPE 165 111 150 9

Figure S219.  Get High-res Image Gene #32: 'del_6q22.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_6q22.31' versus 'RPPA_CHIERARCHICAL'

P value = 0.0148 (Fisher's exact test), Q value = 0.029

Table S220.  Gene #32: '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 S220.  Get High-res Image Gene #32: 'del_6q22.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_6q22.31' versus 'MRNASEQ_CNMF'

P value = 0.0037 (Fisher's exact test), Q value = 0.0084

Table S221.  Gene #32: 'del_6q22.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
DEL PEAK 12(6Q22.31) MUTATED 25 26 6 17 4
DEL PEAK 12(6Q22.31) WILD-TYPE 105 89 99 116 26

Figure S221.  Get High-res Image Gene #32: 'del_6q22.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_6q22.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00115 (Fisher's exact test), Q value = 0.003

Table S222.  Gene #32: '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 S222.  Get High-res Image Gene #32: 'del_6q22.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_6q22.31' versus 'MIRSEQ_CNMF'

P value = 0.00072 (Fisher's exact test), Q value = 0.002

Table S223.  Gene #32: 'del_6q22.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
DEL PEAK 12(6Q22.31) MUTATED 35 17 6 19
DEL PEAK 12(6Q22.31) WILD-TYPE 105 90 76 161

Figure S223.  Get High-res Image Gene #32: 'del_6q22.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_6q22.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00276 (Fisher's exact test), Q value = 0.0067

Table S224.  Gene #32: 'del_6q22.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
DEL PEAK 12(6Q22.31) MUTATED 29 21 7 18
DEL PEAK 12(6Q22.31) WILD-TYPE 98 98 98 136

Figure S224.  Get High-res Image Gene #32: 'del_6q22.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_6q22.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00325 (Fisher's exact test), Q value = 0.0076

Table S225.  Gene #32: 'del_6q22.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
DEL PEAK 12(6Q22.31) MUTATED 24 9 13 5 16 8
DEL PEAK 12(6Q22.31) WILD-TYPE 75 68 105 51 47 84

Figure S225.  Get High-res Image Gene #32: 'del_6q22.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q26' versus 'MRNA_CNMF'

P value = 0.0471 (Fisher's exact test), Q value = 0.078

Table S226.  Gene #33: 'del_6q26' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 9 10 8
DEL PEAK 13(6Q26) MUTATED 3 0 0
DEL PEAK 13(6Q26) WILD-TYPE 6 10 8

Figure S226.  Get High-res Image Gene #33: 'del_6q26' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_6q26' versus 'CN_CNMF'

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

Table S227.  Gene #33: 'del_6q26' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
DEL PEAK 13(6Q26) MUTATED 33 42 7
DEL PEAK 13(6Q26) WILD-TYPE 194 69 168

Figure S227.  Get High-res Image Gene #33: 'del_6q26' versus Molecular Subtype #3: 'CN_CNMF'

'del_6q26' versus 'METHLYATION_CNMF'

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

Table S228.  Gene #33: 'del_6q26' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
DEL PEAK 13(6Q26) MUTATED 47 25 7 3
DEL PEAK 13(6Q26) WILD-TYPE 162 109 150 10

Figure S228.  Get High-res Image Gene #33: 'del_6q26' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_6q26' versus 'RPPA_CHIERARCHICAL'

P value = 0.00914 (Fisher's exact test), Q value = 0.019

Table S229.  Gene #33: 'del_6q26' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 158 185
DEL PEAK 13(6Q26) MUTATED 12 16 41
DEL PEAK 13(6Q26) WILD-TYPE 71 142 144

Figure S229.  Get High-res Image Gene #33: 'del_6q26' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_6q26' versus 'MRNASEQ_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.0013

Table S230.  Gene #33: 'del_6q26' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
DEL PEAK 13(6Q26) MUTATED 31 25 6 16 4
DEL PEAK 13(6Q26) WILD-TYPE 99 90 99 117 26

Figure S230.  Get High-res Image Gene #33: 'del_6q26' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_6q26' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.00048

Table S231.  Gene #33: 'del_6q26' 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(6Q26) MUTATED 33 17 1 12 6 7 6
DEL PEAK 13(6Q26) WILD-TYPE 102 54 35 56 84 34 66

Figure S231.  Get High-res Image Gene #33: 'del_6q26' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_6q26' versus 'MIRSEQ_CNMF'

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

Table S232.  Gene #33: 'del_6q26' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
DEL PEAK 13(6Q26) MUTATED 40 16 5 20
DEL PEAK 13(6Q26) WILD-TYPE 100 91 77 160

Figure S232.  Get High-res Image Gene #33: 'del_6q26' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_6q26' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00333 (Fisher's exact test), Q value = 0.0077

Table S233.  Gene #33: 'del_6q26' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
DEL PEAK 13(6Q26) MUTATED 29 22 7 20
DEL PEAK 13(6Q26) WILD-TYPE 98 97 98 134

Figure S233.  Get High-res Image Gene #33: 'del_6q26' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_6q26' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.00098

Table S234.  Gene #33: 'del_6q26' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
DEL PEAK 13(6Q26) MUTATED 27 7 13 5 17 9
DEL PEAK 13(6Q26) WILD-TYPE 72 70 105 51 46 83

Figure S234.  Get High-res Image Gene #33: 'del_6q26' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_7p22.3' versus 'CN_CNMF'

P value = 0.0197 (Fisher's exact test), Q value = 0.037

Table S235.  Gene #34: 'del_7p22.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
DEL PEAK 14(7P22.3) MUTATED 17 2 4
DEL PEAK 14(7P22.3) WILD-TYPE 210 109 171

Figure S235.  Get High-res Image Gene #34: '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 S236.  Gene #35: 'del_8q24.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
DEL PEAK 15(8Q24.3) MUTATED 16 13 0
DEL PEAK 15(8Q24.3) WILD-TYPE 211 98 175

Figure S236.  Get High-res Image Gene #35: 'del_8q24.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_8q24.3' versus 'METHLYATION_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00048

Table S237.  Gene #35: 'del_8q24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
DEL PEAK 15(8Q24.3) MUTATED 17 11 0 1
DEL PEAK 15(8Q24.3) WILD-TYPE 192 123 157 12

Figure S237.  Get High-res Image Gene #35: 'del_8q24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_8q24.3' versus 'MRNASEQ_CNMF'

P value = 0.0059 (Fisher's exact test), Q value = 0.013

Table S238.  Gene #35: 'del_8q24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
DEL PEAK 15(8Q24.3) MUTATED 10 11 0 6 2
DEL PEAK 15(8Q24.3) WILD-TYPE 120 104 105 127 28

Figure S238.  Get High-res Image Gene #35: 'del_8q24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_8q24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00637 (Fisher's exact test), Q value = 0.014

Table S239.  Gene #35: '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 S239.  Get High-res Image Gene #35: 'del_8q24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_8q24.3' versus 'MIRSEQ_CNMF'

P value = 0.0433 (Fisher's exact test), Q value = 0.073

Table S240.  Gene #35: 'del_8q24.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
DEL PEAK 15(8Q24.3) MUTATED 12 9 1 7
DEL PEAK 15(8Q24.3) WILD-TYPE 128 98 81 173

Figure S240.  Get High-res Image Gene #35: 'del_8q24.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_8q24.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00333 (Fisher's exact test), Q value = 0.0077

Table S241.  Gene #35: '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 S241.  Get High-res Image Gene #35: 'del_8q24.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_8q24.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0334 (Fisher's exact test), Q value = 0.059

Table S242.  Gene #35: 'del_8q24.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
DEL PEAK 15(8Q24.3) MUTATED 10 11 2 5
DEL PEAK 15(8Q24.3) WILD-TYPE 117 108 103 149

Figure S242.  Get High-res Image Gene #35: 'del_8q24.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_8q24.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.029 (Fisher's exact test), Q value = 0.052

Table S243.  Gene #35: 'del_8q24.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
DEL PEAK 15(8Q24.3) MUTATED 7 5 3 0 8 5
DEL PEAK 15(8Q24.3) WILD-TYPE 92 72 115 56 55 87

Figure S243.  Get High-res Image Gene #35: '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 S244.  Gene #36: 'del_9p23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
DEL PEAK 16(9P23) MUTATED 65 58 27
DEL PEAK 16(9P23) WILD-TYPE 162 53 148

Figure S244.  Get High-res Image Gene #36: 'del_9p23' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p23' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00015

Table S245.  Gene #36: 'del_9p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
DEL PEAK 16(9P23) MUTATED 72 42 27 9
DEL PEAK 16(9P23) WILD-TYPE 137 92 130 4

Figure S245.  Get High-res Image Gene #36: 'del_9p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9p23' versus 'RPPA_CNMF'

P value = 0.00597 (Fisher's exact test), Q value = 0.013

Table S246.  Gene #36: '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 S246.  Get High-res Image Gene #36: 'del_9p23' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_9p23' versus 'RPPA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00015

Table S247.  Gene #36: '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 S247.  Get High-res Image Gene #36: 'del_9p23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_9p23' versus 'MRNASEQ_CNMF'

P value = 0.0207 (Fisher's exact test), Q value = 0.039

Table S248.  Gene #36: 'del_9p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
DEL PEAK 16(9P23) MUTATED 34 44 20 44 8
DEL PEAK 16(9P23) WILD-TYPE 96 71 85 89 22

Figure S248.  Get High-res Image Gene #36: 'del_9p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9p23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.00053

Table S249.  Gene #36: '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 S249.  Get High-res Image Gene #36: 'del_9p23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0322 (Fisher's exact test), Q value = 0.057

Table S250.  Gene #36: 'del_9p23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
DEL PEAK 16(9P23) MUTATED 30 21 34 8 27 28
DEL PEAK 16(9P23) WILD-TYPE 69 56 84 48 36 64

Figure S250.  Get High-res Image Gene #36: '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 S251.  Gene #37: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
DEL PEAK 17(9P21.3) MUTATED 75 74 27
DEL PEAK 17(9P21.3) WILD-TYPE 152 37 148

Figure S251.  Get High-res Image Gene #37: '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 S252.  Gene #37: 'del_9p21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
DEL PEAK 17(9P21.3) MUTATED 75 65 26 10
DEL PEAK 17(9P21.3) WILD-TYPE 134 69 131 3

Figure S252.  Get High-res Image Gene #37: 'del_9p21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9p21.3' versus 'RPPA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 8.4e-05

Table S253.  Gene #37: '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 S253.  Get High-res Image Gene #37: '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 S254.  Gene #37: '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 S254.  Get High-res Image Gene #37: '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 S255.  Gene #37: 'del_9p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
DEL PEAK 17(9P21.3) MUTATED 38 67 18 45 8
DEL PEAK 17(9P21.3) WILD-TYPE 92 48 87 88 22

Figure S255.  Get High-res Image Gene #37: '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 S256.  Gene #37: '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 S256.  Get High-res Image Gene #37: '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 S257.  Gene #37: '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 S257.  Get High-res Image Gene #37: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00084 (Fisher's exact test), Q value = 0.0023

Table S258.  Gene #37: 'del_9p21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
DEL PEAK 17(9P21.3) MUTATED 49 55 23 47
DEL PEAK 17(9P21.3) WILD-TYPE 78 64 82 107

Figure S258.  Get High-res Image Gene #37: '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 S259.  Gene #37: 'del_9p21.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
DEL PEAK 17(9P21.3) MUTATED 32 26 36 8 45 27
DEL PEAK 17(9P21.3) WILD-TYPE 67 51 82 48 18 65

Figure S259.  Get High-res Image Gene #37: '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 S260.  Gene #38: 'del_10q26.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
DEL PEAK 18(10Q26.3) MUTATED 68 73 10
DEL PEAK 18(10Q26.3) WILD-TYPE 159 38 165

Figure S260.  Get High-res Image Gene #38: '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 S261.  Gene #38: 'del_10q26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
DEL PEAK 18(10Q26.3) MUTATED 55 77 8 11
DEL PEAK 18(10Q26.3) WILD-TYPE 154 57 149 2

Figure S261.  Get High-res Image Gene #38: 'del_10q26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10q26.3' versus 'RPPA_CNMF'

P value = 0.00156 (Fisher's exact test), Q value = 0.004

Table S262.  Gene #38: '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 S262.  Get High-res Image Gene #38: '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 S263.  Gene #38: '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 S263.  Get High-res Image Gene #38: '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 S264.  Gene #38: 'del_10q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
DEL PEAK 18(10Q26.3) MUTATED 32 81 4 27 7
DEL PEAK 18(10Q26.3) WILD-TYPE 98 34 101 106 23

Figure S264.  Get High-res Image Gene #38: '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 S265.  Gene #38: '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 S265.  Get High-res Image Gene #38: '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 S266.  Gene #38: 'del_10q26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
DEL PEAK 18(10Q26.3) MUTATED 55 46 11 39
DEL PEAK 18(10Q26.3) WILD-TYPE 85 61 71 141

Figure S266.  Get High-res Image Gene #38: '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 S267.  Gene #38: '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 S267.  Get High-res Image Gene #38: '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 S268.  Gene #38: 'del_10q26.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
DEL PEAK 18(10Q26.3) MUTATED 57 51 12 31
DEL PEAK 18(10Q26.3) WILD-TYPE 70 68 93 123

Figure S268.  Get High-res Image Gene #38: '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 S269.  Gene #38: 'del_10q26.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
DEL PEAK 18(10Q26.3) MUTATED 28 23 20 3 55 22
DEL PEAK 18(10Q26.3) WILD-TYPE 71 54 98 53 8 70

Figure S269.  Get High-res Image Gene #38: 'del_10q26.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11p15.5' versus 'MRNA_CHIERARCHICAL'

P value = 0.00043 (Fisher's exact test), Q value = 0.0013

Table S270.  Gene #39: '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 S270.  Get High-res Image Gene #39: '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 S271.  Gene #39: 'del_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
DEL PEAK 19(11P15.5) MUTATED 75 27 2
DEL PEAK 19(11P15.5) WILD-TYPE 152 84 173

Figure S271.  Get High-res Image Gene #39: '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 S272.  Gene #39: 'del_11p15.5' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
DEL PEAK 19(11P15.5) MUTATED 73 22 0 9
DEL PEAK 19(11P15.5) WILD-TYPE 136 112 157 4

Figure S272.  Get High-res Image Gene #39: '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 S273.  Gene #39: 'del_11p15.5' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
DEL PEAK 19(11P15.5) MUTATED 36 36 0 24 8
DEL PEAK 19(11P15.5) WILD-TYPE 94 79 105 109 22

Figure S273.  Get High-res Image Gene #39: '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 S274.  Gene #39: '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 S274.  Get High-res Image Gene #39: 'del_11p15.5' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 8.4e-05

Table S275.  Gene #39: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
DEL PEAK 19(11P15.5) MUTATED 23 41 7 33
DEL PEAK 19(11P15.5) WILD-TYPE 117 66 75 147

Figure S275.  Get High-res Image Gene #39: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_11p15.5' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00476 (Fisher's exact test), Q value = 0.011

Table S276.  Gene #39: '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 S276.  Get High-res Image Gene #39: 'del_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00675 (Fisher's exact test), Q value = 0.014

Table S277.  Gene #39: 'del_11p15.5' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
DEL PEAK 19(11P15.5) MUTATED 33 31 11 28
DEL PEAK 19(11P15.5) WILD-TYPE 94 88 94 126

Figure S277.  Get High-res Image Gene #39: 'del_11p15.5' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_11p15.5' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S278.  Gene #39: 'del_11p15.5' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
DEL PEAK 19(11P15.5) MUTATED 21 33 19 0 8 22
DEL PEAK 19(11P15.5) WILD-TYPE 78 44 99 56 55 70

Figure S278.  Get High-res Image Gene #39: 'del_11p15.5' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11p15.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.0301 (Fisher's exact test), Q value = 0.054

Table S279.  Gene #40: '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 S279.  Get High-res Image Gene #40: '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 S280.  Gene #40: 'del_11p15.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
DEL PEAK 20(11P15.1) MUTATED 47 23 2
DEL PEAK 20(11P15.1) WILD-TYPE 180 88 173

Figure S280.  Get High-res Image Gene #40: '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 S281.  Gene #40: 'del_11p15.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
DEL PEAK 20(11P15.1) MUTATED 42 20 1 9
DEL PEAK 20(11P15.1) WILD-TYPE 167 114 156 4

Figure S281.  Get High-res Image Gene #40: 'del_11p15.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_11p15.1' versus 'RPPA_CNMF'

P value = 0.00143 (Fisher's exact test), Q value = 0.0037

Table S282.  Gene #40: '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 S282.  Get High-res Image Gene #40: '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 S283.  Gene #40: 'del_11p15.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
DEL PEAK 20(11P15.1) MUTATED 16 35 1 13 7
DEL PEAK 20(11P15.1) WILD-TYPE 114 80 104 120 23

Figure S283.  Get High-res Image Gene #40: '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 S284.  Gene #40: '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 S284.  Get High-res Image Gene #40: 'del_11p15.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_11p15.1' versus 'MIRSEQ_CNMF'

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

Table S285.  Gene #40: 'del_11p15.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
DEL PEAK 20(11P15.1) MUTATED 16 32 5 19
DEL PEAK 20(11P15.1) WILD-TYPE 124 75 77 161

Figure S285.  Get High-res Image Gene #40: '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 = 0.00025

Table S286.  Gene #40: '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 S286.  Get High-res Image Gene #40: 'del_11p15.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_11p15.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00081 (Fisher's exact test), Q value = 0.0022

Table S287.  Gene #40: 'del_11p15.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
DEL PEAK 20(11P15.1) MUTATED 22 27 6 16
DEL PEAK 20(11P15.1) WILD-TYPE 105 92 99 138

Figure S287.  Get High-res Image Gene #40: 'del_11p15.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_11p15.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S288.  Gene #40: 'del_11p15.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
DEL PEAK 20(11P15.1) MUTATED 13 29 11 0 9 9
DEL PEAK 20(11P15.1) WILD-TYPE 86 48 107 56 54 83

Figure S288.  Get High-res Image Gene #40: 'del_11p15.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_12p13.1' versus 'CN_CNMF'

P value = 0.0109 (Fisher's exact test), Q value = 0.022

Table S289.  Gene #41: 'del_12p13.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
DEL PEAK 21(12P13.1) MUTATED 23 10 5
DEL PEAK 21(12P13.1) WILD-TYPE 204 101 170

Figure S289.  Get High-res Image Gene #41: 'del_12p13.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_12p13.1' versus 'METHLYATION_CNMF'

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

Table S290.  Gene #41: 'del_12p13.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
DEL PEAK 21(12P13.1) MUTATED 21 6 5 6
DEL PEAK 21(12P13.1) WILD-TYPE 188 128 152 7

Figure S290.  Get High-res Image Gene #41: 'del_12p13.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_12p13.1' versus 'MRNASEQ_CNMF'

P value = 0.00221 (Fisher's exact test), Q value = 0.0055

Table S291.  Gene #41: 'del_12p13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
DEL PEAK 21(12P13.1) MUTATED 15 13 1 9 0
DEL PEAK 21(12P13.1) WILD-TYPE 115 102 104 124 30

Figure S291.  Get High-res Image Gene #41: 'del_12p13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_12p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00693 (Fisher's exact test), Q value = 0.015

Table S292.  Gene #41: '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 S292.  Get High-res Image Gene #41: 'del_12p13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_12p13.1' versus 'MIRSEQ_CNMF'

P value = 0.0221 (Fisher's exact test), Q value = 0.04

Table S293.  Gene #41: 'del_12p13.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
DEL PEAK 21(12P13.1) MUTATED 7 16 5 10
DEL PEAK 21(12P13.1) WILD-TYPE 133 91 77 170

Figure S293.  Get High-res Image Gene #41: 'del_12p13.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_12p13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0449 (Fisher's exact test), Q value = 0.075

Table S294.  Gene #41: '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 S294.  Get High-res Image Gene #41: 'del_12p13.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_12q12' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 8.4e-05

Table S295.  Gene #42: 'del_12q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
DEL PEAK 22(12Q12) MUTATED 50 12 10
DEL PEAK 22(12Q12) WILD-TYPE 177 99 165

Figure S295.  Get High-res Image Gene #42: '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 S296.  Gene #42: 'del_12q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
DEL PEAK 22(12Q12) MUTATED 45 12 8 7
DEL PEAK 22(12Q12) WILD-TYPE 164 122 149 6

Figure S296.  Get High-res Image Gene #42: 'del_12q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_12q12' versus 'MRNASEQ_CNMF'

P value = 0.00312 (Fisher's exact test), Q value = 0.0074

Table S297.  Gene #42: 'del_12q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
DEL PEAK 22(12Q12) MUTATED 23 22 4 18 5
DEL PEAK 22(12Q12) WILD-TYPE 107 93 101 115 25

Figure S297.  Get High-res Image Gene #42: '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 S298.  Gene #42: '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 S298.  Get High-res Image Gene #42: 'del_12q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_12q12' versus 'MIRSEQ_CNMF'

P value = 0.00567 (Fisher's exact test), Q value = 0.012

Table S299.  Gene #42: 'del_12q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
DEL PEAK 22(12Q12) MUTATED 14 27 9 22
DEL PEAK 22(12Q12) WILD-TYPE 126 80 73 158

Figure S299.  Get High-res Image Gene #42: 'del_12q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_12q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00036 (Fisher's exact test), Q value = 0.0011

Table S300.  Gene #42: 'del_12q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
DEL PEAK 22(12Q12) MUTATED 16 22 13 4 2 15
DEL PEAK 22(12Q12) WILD-TYPE 83 55 105 52 61 77

Figure S300.  Get High-res Image Gene #42: 'del_12q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_13q14.2' versus 'MRNA_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00025

Table S301.  Gene #43: '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 S301.  Get High-res Image Gene #43: '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 S302.  Gene #43: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
DEL PEAK 23(13Q14.2) MUTATED 59 57 28
DEL PEAK 23(13Q14.2) WILD-TYPE 168 54 147

Figure S302.  Get High-res Image Gene #43: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_13q14.2' versus 'METHLYATION_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.00061

Table S303.  Gene #43: 'del_13q14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
DEL PEAK 23(13Q14.2) MUTATED 70 39 27 8
DEL PEAK 23(13Q14.2) WILD-TYPE 139 95 130 5

Figure S303.  Get High-res Image Gene #43: 'del_13q14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_13q14.2' versus 'RPPA_CNMF'

P value = 0.0294 (Fisher's exact test), Q value = 0.053

Table S304.  Gene #43: '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 20 38 30 32
DEL PEAK 23(13Q14.2) WILD-TYPE 71 57 95 83

Figure S304.  Get High-res Image Gene #43: 'del_13q14.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_13q14.2' versus 'MRNASEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00045

Table S305.  Gene #43: 'del_13q14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
DEL PEAK 23(13Q14.2) MUTATED 39 49 16 32 8
DEL PEAK 23(13Q14.2) WILD-TYPE 91 66 89 101 22

Figure S305.  Get High-res Image Gene #43: '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 S306.  Gene #43: '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 44 22 2 17 18 25 16
DEL PEAK 23(13Q14.2) WILD-TYPE 91 49 34 51 72 16 56

Figure S306.  Get High-res Image Gene #43: 'del_13q14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_CNMF'

P value = 0.0358 (Fisher's exact test), Q value = 0.062

Table S307.  Gene #43: 'del_13q14.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
DEL PEAK 23(13Q14.2) MUTATED 40 41 22 40
DEL PEAK 23(13Q14.2) WILD-TYPE 100 66 60 140

Figure S307.  Get High-res Image Gene #43: 'del_13q14.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_13q14.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00393 (Fisher's exact test), Q value = 0.0089

Table S308.  Gene #43: '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 67 37 39
DEL PEAK 23(13Q14.2) WILD-TYPE 155 147 64

Figure S308.  Get High-res Image Gene #43: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0113 (Fisher's exact test), Q value = 0.023

Table S309.  Gene #43: 'del_13q14.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
DEL PEAK 23(13Q14.2) MUTATED 24 31 25 10 21 32
DEL PEAK 23(13Q14.2) WILD-TYPE 75 46 93 46 42 60

Figure S309.  Get High-res Image Gene #43: 'del_13q14.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_13q34' versus 'CN_CNMF'

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

Table S310.  Gene #44: 'del_13q34' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
DEL PEAK 24(13Q34) MUTATED 34 50 26
DEL PEAK 24(13Q34) WILD-TYPE 193 61 149

Figure S310.  Get High-res Image Gene #44: 'del_13q34' versus Molecular Subtype #3: 'CN_CNMF'

'del_13q34' versus 'METHLYATION_CNMF'

P value = 0.026 (Fisher's exact test), Q value = 0.047

Table S311.  Gene #44: 'del_13q34' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
DEL PEAK 24(13Q34) MUTATED 44 35 25 6
DEL PEAK 24(13Q34) WILD-TYPE 165 99 132 7

Figure S311.  Get High-res Image Gene #44: 'del_13q34' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_13q34' versus 'RPPA_CNMF'

P value = 0.0216 (Fisher's exact test), Q value = 0.04

Table S312.  Gene #44: 'del_13q34' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 95 125 115
DEL PEAK 24(13Q34) MUTATED 14 30 20 25
DEL PEAK 24(13Q34) WILD-TYPE 77 65 105 90

Figure S312.  Get High-res Image Gene #44: 'del_13q34' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_13q34' versus 'MRNASEQ_CNMF'

P value = 0.0137 (Fisher's exact test), Q value = 0.027

Table S313.  Gene #44: 'del_13q34' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
DEL PEAK 24(13Q34) MUTATED 28 38 16 23 5
DEL PEAK 24(13Q34) WILD-TYPE 102 77 89 110 25

Figure S313.  Get High-res Image Gene #44: 'del_13q34' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_13q34' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00105 (Fisher's exact test), Q value = 0.0028

Table S314.  Gene #44: '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 24(13Q34) MUTATED 31 20 2 9 17 18 13
DEL PEAK 24(13Q34) WILD-TYPE 104 51 34 59 73 23 59

Figure S314.  Get High-res Image Gene #44: 'del_13q34' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_13q34' versus 'MIRSEQ_CNMF'

P value = 0.0467 (Fisher's exact test), Q value = 0.078

Table S315.  Gene #44: 'del_13q34' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
DEL PEAK 24(13Q34) MUTATED 28 33 18 30
DEL PEAK 24(13Q34) WILD-TYPE 112 74 64 150

Figure S315.  Get High-res Image Gene #44: 'del_13q34' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_13q34' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00276 (Fisher's exact test), Q value = 0.0067

Table S316.  Gene #44: 'del_13q34' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
DEL PEAK 24(13Q34) MUTATED 49 27 33
DEL PEAK 24(13Q34) WILD-TYPE 173 157 70

Figure S316.  Get High-res Image Gene #44: 'del_13q34' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_13q34' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0298 (Fisher's exact test), Q value = 0.053

Table S317.  Gene #44: 'del_13q34' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
DEL PEAK 24(13Q34) MUTATED 15 20 19 9 19 27
DEL PEAK 24(13Q34) WILD-TYPE 84 57 99 47 44 65

Figure S317.  Get High-res Image Gene #44: 'del_13q34' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_14q24.3' versus 'CN_CNMF'

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

Table S318.  Gene #45: 'del_14q24.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
DEL PEAK 25(14Q24.3) MUTATED 36 53 33
DEL PEAK 25(14Q24.3) WILD-TYPE 191 58 142

Figure S318.  Get High-res Image Gene #45: 'del_14q24.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_14q24.3' versus 'RPPA_CNMF'

P value = 0.00073 (Fisher's exact test), Q value = 0.002

Table S319.  Gene #45: '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 25(14Q24.3) MUTATED 11 36 31 26
DEL PEAK 25(14Q24.3) WILD-TYPE 80 59 94 89

Figure S319.  Get High-res Image Gene #45: 'del_14q24.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_14q24.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0218 (Fisher's exact test), Q value = 0.04

Table S320.  Gene #45: 'del_14q24.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 158 185
DEL PEAK 25(14Q24.3) MUTATED 14 33 57
DEL PEAK 25(14Q24.3) WILD-TYPE 69 125 128

Figure S320.  Get High-res Image Gene #45: 'del_14q24.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_14q24.3' versus 'MRNASEQ_CNMF'

P value = 0.00052 (Fisher's exact test), Q value = 0.0015

Table S321.  Gene #45: 'del_14q24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
DEL PEAK 25(14Q24.3) MUTATED 24 45 23 22 8
DEL PEAK 25(14Q24.3) WILD-TYPE 106 70 82 111 22

Figure S321.  Get High-res Image Gene #45: 'del_14q24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_14q24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00058 (Fisher's exact test), Q value = 0.0017

Table S322.  Gene #45: '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 25(14Q24.3) MUTATED 33 27 8 12 17 17 8
DEL PEAK 25(14Q24.3) WILD-TYPE 102 44 28 56 73 24 64

Figure S322.  Get High-res Image Gene #45: 'del_14q24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_14q24.3' versus 'MIRSEQ_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.0012

Table S323.  Gene #45: 'del_14q24.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
DEL PEAK 25(14Q24.3) MUTATED 52 20 17 32
DEL PEAK 25(14Q24.3) WILD-TYPE 88 87 65 148

Figure S323.  Get High-res Image Gene #45: 'del_14q24.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_14q24.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00416 (Fisher's exact test), Q value = 0.0093

Table S324.  Gene #45: 'del_14q24.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
DEL PEAK 25(14Q24.3) MUTATED 55 31 35
DEL PEAK 25(14Q24.3) WILD-TYPE 167 153 68

Figure S324.  Get High-res Image Gene #45: 'del_14q24.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_14q24.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0062 (Fisher's exact test), Q value = 0.013

Table S325.  Gene #45: 'del_14q24.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
DEL PEAK 25(14Q24.3) MUTATED 37 37 24 23
DEL PEAK 25(14Q24.3) WILD-TYPE 90 82 81 131

Figure S325.  Get High-res Image Gene #45: 'del_14q24.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_14q24.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00174 (Fisher's exact test), Q value = 0.0044

Table S326.  Gene #45: 'del_14q24.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
DEL PEAK 25(14Q24.3) MUTATED 27 25 18 13 24 14
DEL PEAK 25(14Q24.3) WILD-TYPE 72 52 100 43 39 78

Figure S326.  Get High-res Image Gene #45: 'del_14q24.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19q13.42' versus 'MRNA_CNMF'

P value = 0.0347 (Fisher's exact test), Q value = 0.06

Table S327.  Gene #47: 'del_19q13.42' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 9 10 8
DEL PEAK 27(19Q13.42) MUTATED 7 10 4
DEL PEAK 27(19Q13.42) WILD-TYPE 2 0 4

Figure S327.  Get High-res Image Gene #47: 'del_19q13.42' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_19q13.42' versus 'MRNA_CHIERARCHICAL'

P value = 0.021 (Fisher's exact test), Q value = 0.039

Table S328.  Gene #47: '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 27(19Q13.42) MUTATED 4 7 7 3
DEL PEAK 27(19Q13.42) WILD-TYPE 3 0 0 3

Figure S328.  Get High-res Image Gene #47: '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 S329.  Gene #47: 'del_19q13.42' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
DEL PEAK 27(19Q13.42) MUTATED 63 44 171
DEL PEAK 27(19Q13.42) WILD-TYPE 164 67 4

Figure S329.  Get High-res Image Gene #47: '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 S330.  Gene #47: 'del_19q13.42' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
DEL PEAK 27(19Q13.42) MUTATED 78 35 157 8
DEL PEAK 27(19Q13.42) WILD-TYPE 131 99 0 5

Figure S330.  Get High-res Image Gene #47: 'del_19q13.42' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_19q13.42' versus 'RPPA_CNMF'

P value = 0.0064 (Fisher's exact test), Q value = 0.014

Table S331.  Gene #47: '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 27(19Q13.42) MUTATED 36 56 72 72
DEL PEAK 27(19Q13.42) WILD-TYPE 55 39 53 43

Figure S331.  Get High-res Image Gene #47: 'del_19q13.42' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_19q13.42' versus 'RPPA_CHIERARCHICAL'

P value = 0.021 (Fisher's exact test), Q value = 0.039

Table S332.  Gene #47: 'del_19q13.42' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 158 185
DEL PEAK 27(19Q13.42) MUTATED 36 98 102
DEL PEAK 27(19Q13.42) WILD-TYPE 47 60 83

Figure S332.  Get High-res Image Gene #47: '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 S333.  Gene #47: 'del_19q13.42' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
DEL PEAK 27(19Q13.42) MUTATED 46 37 105 77 13
DEL PEAK 27(19Q13.42) WILD-TYPE 84 78 0 56 17

Figure S333.  Get High-res Image Gene #47: '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 S334.  Gene #47: '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 27(19Q13.42) MUTATED 46 9 36 21 89 23 54
DEL PEAK 27(19Q13.42) WILD-TYPE 89 62 0 47 1 18 18

Figure S334.  Get High-res Image Gene #47: '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 S335.  Gene #47: 'del_19q13.42' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
DEL PEAK 27(19Q13.42) MUTATED 59 38 77 104
DEL PEAK 27(19Q13.42) WILD-TYPE 81 69 5 76

Figure S335.  Get High-res Image Gene #47: '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 S336.  Gene #47: 'del_19q13.42' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
DEL PEAK 27(19Q13.42) MUTATED 137 119 22
DEL PEAK 27(19Q13.42) WILD-TYPE 85 65 81

Figure S336.  Get High-res Image Gene #47: '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 S337.  Gene #47: 'del_19q13.42' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
DEL PEAK 27(19Q13.42) MUTATED 49 45 95 88
DEL PEAK 27(19Q13.42) WILD-TYPE 78 74 10 66

Figure S337.  Get High-res Image Gene #47: '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 S338.  Gene #47: 'del_19q13.42' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
DEL PEAK 27(19Q13.42) MUTATED 39 51 74 56 4 53
DEL PEAK 27(19Q13.42) WILD-TYPE 60 26 44 0 59 39

Figure S338.  Get High-res Image Gene #47: 'del_19q13.42' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_22q13.31' versus 'MRNA_CHIERARCHICAL'

P value = 0.0425 (Fisher's exact test), Q value = 0.072

Table S339.  Gene #48: '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 28(22Q13.31) MUTATED 2 4 0 0
DEL PEAK 28(22Q13.31) WILD-TYPE 5 3 7 6

Figure S339.  Get High-res Image Gene #48: '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 S340.  Gene #48: 'del_22q13.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
DEL PEAK 28(22Q13.31) MUTATED 36 37 4
DEL PEAK 28(22Q13.31) WILD-TYPE 191 74 171

Figure S340.  Get High-res Image Gene #48: '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 S341.  Gene #48: 'del_22q13.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
DEL PEAK 28(22Q13.31) MUTATED 36 34 4 3
DEL PEAK 28(22Q13.31) WILD-TYPE 173 100 153 10

Figure S341.  Get High-res Image Gene #48: 'del_22q13.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_22q13.31' versus 'RPPA_CNMF'

P value = 0.00089 (Fisher's exact test), Q value = 0.0024

Table S342.  Gene #48: '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 28(22Q13.31) MUTATED 10 27 13 12
DEL PEAK 28(22Q13.31) WILD-TYPE 81 68 112 103

Figure S342.  Get High-res Image Gene #48: 'del_22q13.31' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_22q13.31' versus 'RPPA_CHIERARCHICAL'

P value = 0.0429 (Fisher's exact test), Q value = 0.073

Table S343.  Gene #48: 'del_22q13.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 158 185
DEL PEAK 28(22Q13.31) MUTATED 10 16 36
DEL PEAK 28(22Q13.31) WILD-TYPE 73 142 149

Figure S343.  Get High-res Image Gene #48: '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 S344.  Gene #48: 'del_22q13.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
DEL PEAK 28(22Q13.31) MUTATED 14 40 2 15 6
DEL PEAK 28(22Q13.31) WILD-TYPE 116 75 103 118 24

Figure S344.  Get High-res Image Gene #48: '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 S345.  Gene #48: '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 28(22Q13.31) MUTATED 17 26 2 14 2 14 2
DEL PEAK 28(22Q13.31) WILD-TYPE 118 45 34 54 88 27 70

Figure S345.  Get High-res Image Gene #48: 'del_22q13.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.31' versus 'MIRSEQ_CNMF'

P value = 0.05 (Fisher's exact test), Q value = 0.082

Table S346.  Gene #48: 'del_22q13.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
DEL PEAK 28(22Q13.31) MUTATED 26 22 7 22
DEL PEAK 28(22Q13.31) WILD-TYPE 114 85 75 158

Figure S346.  Get High-res Image Gene #48: 'del_22q13.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_22q13.31' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S347.  Gene #48: 'del_22q13.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
DEL PEAK 28(22Q13.31) MUTATED 27 18 32
DEL PEAK 28(22Q13.31) WILD-TYPE 195 166 71

Figure S347.  Get High-res Image Gene #48: 'del_22q13.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_22q13.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00015

Table S348.  Gene #48: 'del_22q13.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
DEL PEAK 28(22Q13.31) MUTATED 23 32 6 15
DEL PEAK 28(22Q13.31) WILD-TYPE 104 87 99 139

Figure S348.  Get High-res Image Gene #48: 'del_22q13.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_22q13.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00025

Table S349.  Gene #48: 'del_22q13.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
DEL PEAK 28(22Q13.31) MUTATED 10 20 14 3 20 9
DEL PEAK 28(22Q13.31) WILD-TYPE 89 57 104 53 43 83

Figure S349.  Get High-res Image Gene #48: 'del_22q13.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xq21.1' versus 'CN_CNMF'

P value = 0.0117 (Fisher's exact test), Q value = 0.023

Table S350.  Gene #49: 'del_xq21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
DEL PEAK 29(XQ21.1) MUTATED 23 23 32
DEL PEAK 29(XQ21.1) WILD-TYPE 204 88 143

Figure S350.  Get High-res Image Gene #49: 'del_xq21.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_xq21.1' versus 'METHLYATION_CNMF'

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

Table S351.  Gene #49: 'del_xq21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
DEL PEAK 29(XQ21.1) MUTATED 30 10 30 8
DEL PEAK 29(XQ21.1) WILD-TYPE 179 124 127 5

Figure S351.  Get High-res Image Gene #49: 'del_xq21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_xq21.1' versus 'RPPA_CNMF'

P value = 0.00108 (Fisher's exact test), Q value = 0.0029

Table S352.  Gene #49: '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 29(XQ21.1) MUTATED 6 26 20 14
DEL PEAK 29(XQ21.1) WILD-TYPE 85 69 105 101

Figure S352.  Get High-res Image Gene #49: 'del_xq21.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_xq21.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.015 (Fisher's exact test), Q value = 0.029

Table S353.  Gene #49: 'del_xq21.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 158 185
DEL PEAK 29(XQ21.1) MUTATED 6 22 38
DEL PEAK 29(XQ21.1) WILD-TYPE 77 136 147

Figure S353.  Get High-res Image Gene #49: 'del_xq21.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_xq21.1' versus 'MRNASEQ_CNMF'

P value = 0.0121 (Fisher's exact test), Q value = 0.024

Table S354.  Gene #49: 'del_xq21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
DEL PEAK 29(XQ21.1) MUTATED 14 24 23 16 1
DEL PEAK 29(XQ21.1) WILD-TYPE 116 91 82 117 29

Figure S354.  Get High-res Image Gene #49: 'del_xq21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_xq21.1' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S355.  Gene #49: '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 29(XQ21.1) MUTATED 13 8 9 8 20 16 4
DEL PEAK 29(XQ21.1) WILD-TYPE 122 63 27 60 70 25 68

Figure S355.  Get High-res Image Gene #49: 'del_xq21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_xq21.1' versus 'MIRSEQ_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.0015

Table S356.  Gene #49: 'del_xq21.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
DEL PEAK 29(XQ21.1) MUTATED 14 18 25 21
DEL PEAK 29(XQ21.1) WILD-TYPE 126 89 57 159

Figure S356.  Get High-res Image Gene #49: 'del_xq21.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_xq21.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.00053

Table S357.  Gene #49: 'del_xq21.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
DEL PEAK 29(XQ21.1) MUTATED 20 15 30 12
DEL PEAK 29(XQ21.1) WILD-TYPE 107 104 75 142

Figure S357.  Get High-res Image Gene #49: 'del_xq21.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_xq21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00028

Table S358.  Gene #49: 'del_xq21.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
DEL PEAK 29(XQ21.1) MUTATED 12 18 6 13 6 22
DEL PEAK 29(XQ21.1) WILD-TYPE 87 59 112 43 57 70

Figure S358.  Get High-res Image Gene #49: 'del_xq21.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data
Input

  • Copy number data file = all_lesions.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LGG-TP/22533658/transformed.cor.cli.txt

  • Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LGG-TP/22553887/LGG-TP.transferedmergedcluster.txt

  • Number of patients = 513

  • Number of significantly focal cnvs = 49

  • 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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