Correlation between copy number variation genes (focal events) and molecular subtypes
Bladder Urothelial Carcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C14X573R
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/C14X573R
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 73 focal events and 10 molecular subtypes across 408 patients, 331 significant findings detected with P value < 0.05 and Q value < 0.25.

  • amp_1p34.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

  • amp_1q23.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_2p25.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_3p25.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • amp_4p16.3 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'.

  • amp_4q13.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • amp_6p22.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF', and 'MRNASEQ_CNMF'.

  • amp_6q21 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • amp_6q23.3 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_7p21.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • amp_7p11.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'RPPA_CNMF'.

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

  • amp_8p11.21 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_8q22.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

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

  • amp_9p24.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_10p14 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • amp_11p13 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_11q13.3 cnv correlated to 'CN_CNMF'.

  • amp_11q22.2 cnv correlated to 'CN_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_12p12.1 cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_12q15 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_13q22.1 cnv correlated to 'CN_CNMF'.

  • amp_16p13.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • amp_16p11.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • amp_16q22.1 cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • amp_17p11.2 cnv correlated to 'CN_CNMF'.

  • amp_17q11.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_17q12 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_17q23.3 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • amp_19q12 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_19q13.43 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • amp_20q11.21 cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_22q12.2 cnv correlated to 'CN_CNMF'.

  • del_1p36.11 cnv correlated to 'METHLYATION_CNMF'.

  • del_1q32.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

  • del_2q34 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF', and 'MRNASEQ_CNMF'.

  • del_2q37.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF', and 'MRNASEQ_CNMF'.

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

  • del_4q22.1 cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_4q34.2 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

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

  • del_6p25.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_6q21 cnv correlated to 'CN_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_6q27 cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_7q36.3 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • del_8p21.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  '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',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • del_9q22.33 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_10p11.21 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • del_10q23.31 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

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

  • del_11q23.3 cnv correlated to 'CN_CNMF'.

  • del_11q25 cnv correlated to 'CN_CNMF'.

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

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

  • del_13q14.2 cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_14q24.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_15q13.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • del_16p13.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF', and 'MRNASEQ_CNMF'.

  • del_16q23.1 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.

  • del_17p12 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_18q23 cnv correlated to 'CN_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • del_22q13.32 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 73 focal events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 331 significant findings detected.

Clinical
Features 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
amp 4p16 3 74 (18%) 334 0.0283
(0.0714) 		0.03
(0.0738) 		0.00373
(0.015) 		0.0002
(0.00142) 		0.0179
(0.0501) 		6e-05
(0.000487) 		0.00026
(0.00177) 		0.00124
(0.00612) 		0.0217
(0.0582) 		0.00202
(0.00888)
amp 3p25 2 190 (47%) 218 1e-05
(9.73e-05) 		1e-05
(9.73e-05) 		0.224
(0.334) 		0.0265
(0.0681) 		1e-05
(9.73e-05) 		1e-05
(9.73e-05) 		0.00012
(0.000903) 		0.00012
(0.000903) 		1e-05
(9.73e-05) 		1e-05
(9.73e-05)
amp 9p24 1 88 (22%) 320 1e-05
(9.73e-05) 		0.00406
(0.0162) 		0.0309
(0.0751) 		0.00909
(0.0299) 		0.0237
(0.062) 		0.00167
(0.00767) 		0.00792
(0.0275) 		0.495
(0.585) 		0.00015
(0.00109) 		0.00098
(0.005)
amp 11p13 51 (12%) 357 1e-05
(9.73e-05) 		0.00361
(0.0147) 		0.00147
(0.00697) 		0.0363
(0.0855) 		0.025
(0.0652) 		0.00084
(0.00451) 		0.00079
(0.00434) 		0.713
(0.775) 		0.0308
(0.0751) 		0.00031
(0.00199)
del 3p14 2 117 (29%) 291 9e-05
(0.000692) 		0.0278
(0.0708) 		0.00015
(0.00109) 		0.0104
(0.033) 		1e-05
(9.73e-05) 		4e-05
(0.000348) 		0.00094
(0.0049) 		0.217
(0.33) 		0.00028
(0.00186) 		0.0002
(0.00142)
del 9p23 177 (43%) 231 1e-05
(9.73e-05) 		0.00098
(0.005) 		0.0216
(0.0582) 		0.00463
(0.0177) 		0.00046
(0.00275) 		0.00024
(0.00167) 		0.00272
(0.0115) 		0.0905
(0.169) 		3e-05
(0.000264) 		0.00286
(0.012)
del 9q22 33 178 (44%) 230 2e-05
(0.000182) 		2e-05
(0.000182) 		0.00036
(0.00223) 		1e-05
(9.73e-05) 		1e-05
(9.73e-05) 		1e-05
(9.73e-05) 		1e-05
(9.73e-05) 		0.329
(0.438) 		1e-05
(9.73e-05) 		1e-05
(9.73e-05)
del 11p15 5 211 (52%) 197 1e-05
(9.73e-05) 		0.00067
(0.00382) 		0.609
(0.682) 		0.00023
(0.00161) 		0.00293
(0.0122) 		1e-05
(9.73e-05) 		0.00018
(0.0013) 		0.0182
(0.0506) 		0.00081
(0.00438) 		0.00188
(0.00837)
del 22q13 32 188 (46%) 220 1e-05
(9.73e-05) 		0.00199
(0.0088) 		0.0297
(0.0738) 		0.00109
(0.00549) 		0.00076
(0.0042) 		0.00126
(0.00613) 		0.0427
(0.0968) 		0.589
(0.664) 		0.0018
(0.00811) 		0.0166
(0.047)
amp 1q23 3 216 (53%) 192 1e-05
(9.73e-05) 		0.0409
(0.094) 		0.0605
(0.128) 		0.858
(0.893) 		0.0285
(0.0716) 		0.0252
(0.0654) 		0.00156
(0.00735) 		0.0008
(0.00436) 		0.0447
(0.101) 		0.0108
(0.0336)
amp 2p25 1 152 (37%) 256 1e-05
(9.73e-05) 		2e-05
(0.000182) 		0.219
(0.331) 		0.624
(0.697) 		0.00034
(0.00214) 		2e-05
(0.000182) 		0.00521
(0.0193) 		0.00802
(0.0276) 		0.0379
(0.0884) 		0.00054
(0.00313)
amp 5p15 33 206 (50%) 202 1e-05
(9.73e-05) 		0.0611
(0.128) 		0.00054
(0.00313) 		0.014
(0.0416) 		0.00815
(0.0279) 		0.0195
(0.0536) 		0.00472
(0.0178) 		0.0167
(0.0472) 		0.0841
(0.162) 		0.00463
(0.0177)
del 8p21 3 252 (62%) 156 1e-05
(9.73e-05) 		1e-05
(9.73e-05) 		0.118
(0.206) 		0.0336
(0.0804) 		0.00091
(0.00478) 		0.00865
(0.0291) 		0.0694
(0.14) 		0.00448
(0.0175) 		0.0497
(0.11) 		0.0419
(0.0955)
del 13q14 2 156 (38%) 252 1e-05
(9.73e-05) 		0.279
(0.389) 		3e-05
(0.000264) 		0.0163
(0.0466) 		0.0161
(0.0462) 		0.00977
(0.0318) 		0.00104
(0.00527) 		0.354
(0.464) 		0.00721
(0.0257) 		0.00215
(0.0094)
del 14q24 1 137 (34%) 271 1e-05
(9.73e-05) 		1e-05
(9.73e-05) 		0.947
(0.956) 		0.0814
(0.158) 		0.00145
(0.00692) 		1e-05
(9.73e-05) 		0.00369
(0.015) 		0.00416
(0.0164) 		0.00161
(0.00748) 		0.00029
(0.00189)
amp 12q15 118 (29%) 290 7e-05
(0.000562) 		0.378
(0.487) 		0.885
(0.915) 		0.578
(0.653) 		0.0255
(0.0658) 		0.0091
(0.0299) 		0.00397
(0.0159) 		0.0363
(0.0855) 		0.0026
(0.0111) 		8e-05
(0.000621)
del 4q22 1 161 (39%) 247 1e-05
(9.73e-05) 		0.0996
(0.18) 		0.00112
(0.0056) 		0.0105
(0.0331) 		0.0179
(0.0501) 		0.00122
(0.00606) 		0.0133
(0.0399) 		0.82
(0.867) 		0.077
(0.15) 		0.0284
(0.0714)
amp 17q11 2 174 (43%) 234 1e-05
(9.73e-05) 		1e-05
(9.73e-05) 		0.106
(0.188) 		0.164
(0.267) 		0.00052
(0.00306) 		0.00031
(0.00199) 		0.063
(0.131) 		0.538
(0.619) 		0.00248
(0.0106) 		0.01
(0.0322)
amp 17q12 165 (40%) 243 1e-05
(9.73e-05) 		0.0325
(0.0783) 		0.206
(0.318) 		0.148
(0.251) 		0.0941
(0.173) 		0.0352
(0.0835) 		0.0371
(0.0868) 		0.106
(0.188) 		0.00909
(0.0299) 		0.00909
(0.0299)
del 8p23 3 243 (60%) 165 1e-05
(9.73e-05) 		1e-05
(9.73e-05) 		0.123
(0.212) 		0.00841
(0.0285) 		6e-05
(0.000487) 		0.00013
(0.000968) 		0.213
(0.324) 		0.00979
(0.0318) 		0.155
(0.258) 		0.195
(0.306)
del 9p21 3 239 (59%) 169 1e-05
(9.73e-05) 		0.194
(0.305) 		0.0539
(0.116) 		0.00591
(0.0215) 		0.00037
(0.00225) 		0.0223
(0.0595) 		0.238
(0.347) 		0.0913
(0.17) 		0.00414
(0.0164) 		0.0119
(0.0365)
del 12p13 1 68 (17%) 340 0.0154
(0.0445) 		0.00514
(0.0192) 		0.838
(0.879) 		0.221
(0.333) 		1e-05
(9.73e-05) 		5e-05
(0.00042) 		0.00994
(0.0321) 		0.485
(0.579) 		0.0118
(0.0365) 		0.208
(0.32)
del 15q13 1 160 (39%) 248 1e-05
(9.73e-05) 		0.00226
(0.00982) 		0.0934
(0.172) 		0.541
(0.621) 		0.00899
(0.0299) 		0.357
(0.466) 		0.0397
(0.0916) 		0.0104
(0.033) 		0.019
(0.0524) 		0.0584
(0.124)
amp 1q21 3 202 (50%) 206 1e-05
(9.73e-05) 		0.00589
(0.0215) 		0.337
(0.445) 		0.635
(0.705) 		0.0093
(0.0304) 		0.116
(0.204) 		0.0133
(0.0399) 		0.0909
(0.169) 		0.692
(0.759) 		0.0351
(0.0835)
amp 7p21 1 201 (49%) 207 1e-05
(9.73e-05) 		0.00359
(0.0147) 		0.0218
(0.0582) 		0.0932
(0.172) 		0.0133
(0.0399) 		0.0231
(0.061) 		0.0601
(0.127) 		0.312
(0.422) 		0.151
(0.255) 		0.154
(0.258)
amp 8q22 3 264 (65%) 144 1e-05
(9.73e-05) 		8e-05
(0.000621) 		0.0124
(0.0375) 		0.834
(0.876) 		0.447
(0.546) 		0.254
(0.363) 		0.0992
(0.179) 		0.0337
(0.0804) 		0.0327
(0.0784) 		0.186
(0.294)
amp 8q24 21 254 (62%) 154 1e-05
(9.73e-05) 		0.00125
(0.00612) 		0.00034
(0.00214) 		0.172
(0.277) 		0.386
(0.493) 		0.719
(0.78) 		0.0492
(0.109) 		0.0142
(0.0419) 		0.201
(0.312) 		0.24
(0.348)
amp 11q22 2 71 (17%) 337 2e-05
(0.000182) 		0.391
(0.495) 		0.888
(0.915) 		0.413
(0.515) 		0.212
(0.324) 		0.164
(0.267) 		0.00091
(0.00478) 		0.0199
(0.0543) 		0.00026
(0.00177) 		0.0141
(0.0416)
del 5q12 1 202 (50%) 206 1e-05
(9.73e-05) 		0.00141
(0.00677) 		0.0747
(0.148) 		0.269
(0.38) 		0.488
(0.581) 		0.00456
(0.0176) 		0.00182
(0.00815) 		0.0121
(0.0368) 		0.157
(0.259) 		0.0533
(0.116)
del 6q27 190 (47%) 218 1e-05
(9.73e-05) 		0.0541
(0.116) 		0.213
(0.324) 		0.0816
(0.158) 		0.735
(0.792) 		0.0107
(0.0336) 		0.0137
(0.0409) 		0.0108
(0.0336) 		0.254
(0.363) 		0.00281
(0.0119)
del 18q23 179 (44%) 229 1e-05
(9.73e-05) 		0.46
(0.559) 		0.829
(0.873) 		0.792
(0.845) 		0.929
(0.947) 		0.153
(0.257) 		0.00027
(0.00182) 		1e-05
(9.73e-05) 		0.00307
(0.0127) 		0.00439
(0.0172)
amp 3q26 33 218 (53%) 190 1e-05
(9.73e-05) 		0.894
(0.92) 		0.0018
(0.00811) 		0.187
(0.294) 		0.159
(0.261) 		0.0226
(0.0599) 		0.0103
(0.0329) 		0.178
(0.284) 		0.282
(0.391) 		0.0769
(0.15)
amp 6p22 3 171 (42%) 237 1e-05
(9.73e-05) 		5e-05
(0.00042) 		0.0459
(0.103) 		0.913
(0.936) 		0.00158
(0.00739) 		0.549
(0.626) 		0.274
(0.384) 		0.395
(0.498) 		0.332
(0.44) 		0.275
(0.385)
amp 10p14 182 (45%) 226 1e-05
(9.73e-05) 		1e-05
(9.73e-05) 		0.252
(0.362) 		0.164
(0.267) 		0.00451
(0.0175) 		5e-05
(0.00042) 		0.154
(0.258) 		0.0679
(0.138) 		0.38
(0.489) 		0.168
(0.272)
amp 16q22 1 108 (26%) 300 1e-05
(9.73e-05) 		0.563
(0.639) 		0.326
(0.436) 		0.27
(0.381) 		0.475
(0.573) 		0.00466
(0.0177) 		0.0517
(0.113) 		0.0147
(0.0429) 		0.0292
(0.0729) 		0.17
(0.275)
del 2q34 174 (43%) 234 1e-05
(9.73e-05) 		0.00098
(0.005) 		0.00662
(0.0237) 		0.485
(0.579) 		0.00767
(0.0269) 		0.108
(0.193) 		0.503
(0.589) 		0.348
(0.457) 		0.525
(0.606) 		0.927
(0.946)
del 2q37 1 207 (51%) 201 1e-05
(9.73e-05) 		0.00029
(0.00189) 		0.0434
(0.0981) 		0.602
(0.676) 		0.0255
(0.0658) 		0.0659
(0.135) 		0.236
(0.344) 		0.0725
(0.145) 		0.289
(0.397) 		0.335
(0.444)
del 6p25 3 106 (26%) 302 1e-05
(9.73e-05) 		0.00037
(0.00225) 		0.0391
(0.0907) 		0.898
(0.922) 		0.0507
(0.111) 		0.0148
(0.0429) 		0.475
(0.573) 		0.405
(0.509) 		0.358
(0.466) 		0.845
(0.885)
del 6q21 190 (47%) 218 1e-05
(9.73e-05) 		0.238
(0.347) 		0.145
(0.246) 		0.465
(0.564) 		0.886
(0.915) 		0.235
(0.344) 		0.00299
(0.0124) 		0.0147
(0.0429) 		0.256
(0.365) 		0.00625
(0.0226)
del 7q36 3 60 (15%) 348 0.00051
(0.00303) 		0.521
(0.603) 		0.119
(0.208) 		0.0976
(0.178) 		0.0325
(0.0783) 		0.482
(0.577) 		0.537
(0.619) 		0.0539
(0.116) 		0.0208
(0.0566) 		0.0297
(0.0738)
del 16p13 3 174 (43%) 234 1e-05
(9.73e-05) 		0.0186
(0.0518) 		0.00575
(0.0211) 		0.441
(0.543) 		0.00794
(0.0275) 		0.262
(0.373) 		0.946
(0.956) 		0.977
(0.98) 		0.411
(0.515) 		0.512
(0.595)
del 19p13 3 145 (36%) 263 1e-05
(9.73e-05) 		0.488
(0.581) 		0.265
(0.375) 		0.155
(0.258) 		0.0203
(0.0552) 		0.00089
(0.00474) 		0.0385
(0.0896) 		0.11
(0.194) 		0.352
(0.461) 		0.102
(0.183)
amp 1p34 2 101 (25%) 307 1e-05
(9.73e-05) 		0.00741
(0.0261) 		0.287
(0.396) 		0.652
(0.719) 		0.184
(0.291) 		0.0981
(0.178) 		0.065
(0.134) 		0.0237
(0.062) 		0.283
(0.393) 		0.0958
(0.176)
amp 4q13 3 62 (15%) 346 1e-05
(9.73e-05) 		0.0299
(0.0738) 		0.281
(0.391) 		0.66
(0.725) 		0.393
(0.496) 		0.447
(0.546) 		0.085
(0.162) 		0.0918
(0.17) 		0.118
(0.206) 		0.00162
(0.00748)
amp 6q23 3 46 (11%) 362 0.00518
(0.0193) 		0.624
(0.697) 		0.467
(0.565) 		0.224
(0.334) 		0.011
(0.0342) 		0.829
(0.873) 		0.205
(0.318) 		0.0299
(0.0738) 		0.178
(0.284) 		0.161
(0.263)
amp 7p11 2 190 (47%) 218 1e-05
(9.73e-05) 		0.00844
(0.0285) 		0.00173
(0.00789) 		0.218
(0.33) 		0.0613
(0.128) 		0.256
(0.365) 		0.0881
(0.166) 		0.645
(0.713) 		0.0737
(0.147) 		0.0895
(0.168)
amp 8p11 21 140 (34%) 268 1e-05
(9.73e-05) 		0.00071
(0.00396) 		0.0873
(0.165) 		0.611
(0.684) 		0.285
(0.394) 		0.313
(0.423) 		0.773
(0.829) 		0.0367
(0.0861) 		0.555
(0.632) 		0.482
(0.577)
amp 16p13 2 87 (21%) 321 1e-05
(9.73e-05) 		0.00044
(0.00265) 		0.986
(0.987) 		0.782
(0.837) 		0.00818
(0.0279) 		0.0849
(0.162) 		0.206
(0.318) 		0.284
(0.394) 		0.507
(0.593) 		0.408
(0.512)
amp 19q12 164 (40%) 244 1e-05
(9.73e-05) 		0.00235
(0.0102) 		0.236
(0.344) 		0.796
(0.847) 		0.23
(0.34) 		0.115
(0.203) 		0.156
(0.258) 		0.0427
(0.0968) 		0.247
(0.355) 		0.176
(0.281)
amp 19q13 43 155 (38%) 253 1e-05
(9.73e-05) 		0.00636
(0.0229) 		0.0897
(0.168) 		0.652
(0.719) 		0.344
(0.453) 		0.547
(0.625) 		0.103
(0.185) 		0.296
(0.407) 		0.0472
(0.105) 		0.083
(0.16)
amp 20q11 21 263 (64%) 145 1e-05
(9.73e-05) 		0.0692
(0.139) 		0.141
(0.241) 		0.508
(0.594) 		0.23
(0.34) 		0.0267
(0.0685) 		0.211
(0.324) 		0.156
(0.258) 		0.0661
(0.135) 		0.0469
(0.105)
del 1q32 1 72 (18%) 336 0.00028
(0.00186) 		0.0279
(0.0708) 		0.597
(0.671) 		0.195
(0.306) 		0.459
(0.559) 		0.0447
(0.101) 		0.431
(0.533) 		0.734
(0.792) 		0.559
(0.635) 		0.641
(0.71)
del 2q22 1 134 (33%) 274 0.00127
(0.00614) 		0.0077
(0.0269) 		0.492
(0.583) 		0.976
(0.98) 		0.00036
(0.00223) 		0.16
(0.262) 		0.173
(0.278) 		0.382
(0.49) 		0.072
(0.144) 		0.698
(0.764)
del 16q23 1 119 (29%) 289 1e-05
(9.73e-05) 		0.079
(0.153) 		0.077
(0.15) 		0.101
(0.182) 		0.00735
(0.026) 		0.0654
(0.134) 		0.00534
(0.0197) 		0.201
(0.312) 		0.0645
(0.133) 		0.0616
(0.128)
del 17p12 208 (51%) 200 1e-05
(9.73e-05) 		0.00056
(0.00322) 		0.33
(0.439) 		0.39
(0.495) 		0.224
(0.334) 		0.016
(0.0461) 		0.759
(0.815) 		0.806
(0.856) 		0.234
(0.344) 		0.715
(0.777)
del xq21 33 84 (21%) 324 0.234
(0.344) 		0.0416
(0.0952) 		0.328
(0.438) 		0.252
(0.362) 		0.0118
(0.0364) 		0.0966
(0.177) 		0.156
(0.258) 		0.0495
(0.109) 		0.0508
(0.111) 		0.181
(0.287)
amp 6q21 35 (9%) 373 0.00069
(0.0039) 		0.0617
(0.128) 		0.221
(0.333) 		0.389
(0.495) 		0.00071
(0.00396) 		0.0585
(0.124) 		0.581
(0.655) 		0.898
(0.922) 		0.271
(0.381) 		0.711
(0.775)
amp 8p11 23 124 (30%) 284 1e-05
(9.73e-05) 		0.0179
(0.0501) 		0.534
(0.615) 		0.344
(0.453) 		0.279
(0.389) 		0.213
(0.324) 		0.264
(0.375) 		0.476
(0.573) 		0.866
(0.898) 		0.849
(0.887)
amp 12p12 1 132 (32%) 276 6e-05
(0.000487) 		0.0652
(0.134) 		0.0888
(0.167) 		0.869
(0.9) 		0.218
(0.33) 		0.63
(0.7) 		0.304
(0.414) 		0.421
(0.525) 		0.232
(0.343) 		0.0235
(0.062)
amp 16p11 2 98 (24%) 310 1e-05
(9.73e-05) 		0.019
(0.0524) 		0.724
(0.784) 		0.512
(0.595) 		0.429
(0.532) 		0.39
(0.495) 		0.545
(0.624) 		0.378
(0.487) 		0.938
(0.951) 		0.83
(0.873)
amp 17q23 3 194 (48%) 214 1e-05
(9.73e-05) 		0.0321
(0.0778) 		0.117
(0.205) 		0.856
(0.892) 		0.429
(0.532) 		0.362
(0.47) 		0.435
(0.536) 		0.286
(0.395) 		0.131
(0.226) 		0.356
(0.465)
del 4q34 2 177 (43%) 231 1e-05
(9.73e-05) 		0.0582
(0.124) 		0.0668
(0.136) 		0.076
(0.15) 		0.143
(0.244) 		0.041
(0.094) 		0.169
(0.274) 		0.63
(0.7) 		0.499
(0.588) 		0.12
(0.208)
del 10p11 21 74 (18%) 334 0.012
(0.0366) 		0.916
(0.937) 		0.152
(0.256) 		0.512
(0.595) 		0.0308
(0.0751) 		0.0685
(0.139) 		0.499
(0.588) 		0.502
(0.589) 		0.218
(0.33) 		0.0847
(0.162)
del 10q23 31 168 (41%) 240 1e-05
(9.73e-05) 		0.0275
(0.0701) 		0.132
(0.228) 		0.0744
(0.148) 		0.179
(0.284) 		0.567
(0.643) 		0.806
(0.856) 		0.492
(0.583) 		0.244
(0.353) 		0.727
(0.785)
del 12q24 33 88 (22%) 320 1e-05
(9.73e-05) 		0.495
(0.585) 		0.299
(0.408) 		0.334
(0.443) 		0.0218
(0.0582) 		0.385
(0.493) 		0.788
(0.841) 		0.517
(0.599) 		0.94
(0.952) 		0.964
(0.971)
amp 11q13 3 135 (33%) 273 3e-05
(0.000264) 		0.133
(0.229) 		0.816
(0.864) 		0.0854
(0.162) 		0.0573
(0.123) 		0.325
(0.436) 		0.109
(0.193) 		0.434
(0.536) 		0.197
(0.309) 		0.118
(0.206)
amp 13q22 1 128 (31%) 280 1e-05
(9.73e-05) 		0.933
(0.949) 		0.319
(0.43) 		0.821
(0.867) 		0.97
(0.975) 		0.371
(0.48) 		0.377
(0.487) 		0.727
(0.785) 		0.863
(0.897) 		0.994
(0.994)
amp 17p11 2 88 (22%) 320 0.00468
(0.0177) 		0.152
(0.256) 		0.654
(0.721) 		0.937
(0.951) 		0.233
(0.343) 		0.626
(0.698) 		0.388
(0.495) 		0.224
(0.334) 		0.31
(0.42) 		0.478
(0.574)
amp 22q12 2 87 (21%) 321 8e-05
(0.000621) 		0.0533
(0.116) 		0.784
(0.838) 		0.752
(0.808) 		0.173
(0.278) 		0.0616
(0.128) 		0.098
(0.178) 		0.857
(0.892) 		0.442
(0.543) 		0.923
(0.944)
del 1p36 11 91 (22%) 317 0.141
(0.241) 		0.016
(0.0461) 		0.0969
(0.177) 		0.326
(0.436) 		0.0759
(0.15) 		0.952
(0.96) 		0.363
(0.47) 		0.056
(0.12) 		0.456
(0.556) 		0.7
(0.765)
del 11q23 3 153 (38%) 255 1e-05
(9.73e-05) 		0.297
(0.407) 		0.39
(0.495) 		0.71
(0.774) 		0.517
(0.599) 		0.2
(0.312) 		0.399
(0.502) 		0.0862
(0.163) 		0.412
(0.515) 		0.228
(0.339)
del 11q25 144 (35%) 264 1e-05
(9.73e-05) 		0.243
(0.352) 		0.482
(0.577) 		0.424
(0.528) 		0.545
(0.624) 		0.246
(0.355) 		0.501
(0.589) 		0.0789
(0.153) 		0.299
(0.408) 		0.307
(0.418)
del xp11 3 91 (22%) 317 0.437
(0.538) 		0.0763
(0.15) 		0.933
(0.949) 		0.85
(0.887) 		0.321
(0.431) 		0.572
(0.647) 		0.693
(0.759) 		0.148
(0.251) 		0.449
(0.548) 		0.318
(0.429)
'amp_1p34.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S1.  Gene #1: 'amp_1p34.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
AMP PEAK 1(1P34.2) MUTATED 23 58 5 14 1
AMP PEAK 1(1P34.2) WILD-TYPE 55 88 116 47 1

Figure S1.  Get High-res Image Gene #1: 'amp_1p34.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1p34.2' versus 'METHLYATION_CNMF'

P value = 0.00741 (Fisher's exact test), Q value = 0.026

Table S2.  Gene #1: 'amp_1p34.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
AMP PEAK 1(1P34.2) MUTATED 31 45 10 15
AMP PEAK 1(1P34.2) WILD-TYPE 107 82 53 65

Figure S2.  Get High-res Image Gene #1: 'amp_1p34.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_1p34.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0237 (Fisher's exact test), Q value = 0.062

Table S3.  Gene #1: 'amp_1p34.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 266 83 56
AMP PEAK 1(1P34.2) MUTATED 55 28 18
AMP PEAK 1(1P34.2) WILD-TYPE 211 55 38

Figure S3.  Get High-res Image Gene #1: 'amp_1p34.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_1q21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S4.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
AMP PEAK 2(1Q21.3) MUTATED 50 95 21 34 2
AMP PEAK 2(1Q21.3) WILD-TYPE 28 51 100 27 0

Figure S4.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q21.3' versus 'METHLYATION_CNMF'

P value = 0.00589 (Fisher's exact test), Q value = 0.021

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
AMP PEAK 2(1Q21.3) MUTATED 60 79 26 37
AMP PEAK 2(1Q21.3) WILD-TYPE 78 48 37 43

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

'amp_1q21.3' versus 'MRNASEQ_CNMF'

P value = 0.0093 (Fisher's exact test), Q value = 0.03

Table S6.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
AMP PEAK 2(1Q21.3) MUTATED 34 65 15 47 40
AMP PEAK 2(1Q21.3) WILD-TYPE 38 70 23 56 16

Figure S6.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_1q21.3' versus 'MIRSEQ_CNMF'

P value = 0.0133 (Fisher's exact test), Q value = 0.04

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 74 114 25 87
AMP PEAK 2(1Q21.3) MUTATED 48 44 52 19 38
AMP PEAK 2(1Q21.3) WILD-TYPE 57 30 62 6 49

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

'amp_1q21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0351 (Fisher's exact test), Q value = 0.083

Table S8.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 60 41 132 74
AMP PEAK 2(1Q21.3) MUTATED 36 32 27 71 30
AMP PEAK 2(1Q21.3) WILD-TYPE 51 28 14 61 44

Figure S8.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_1q23.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S9.  Gene #3: 'amp_1q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
AMP PEAK 3(1Q23.3) MUTATED 52 105 26 31 2
AMP PEAK 3(1Q23.3) WILD-TYPE 26 41 95 30 0

Figure S9.  Get High-res Image Gene #3: 'amp_1q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q23.3' versus 'METHLYATION_CNMF'

P value = 0.0409 (Fisher's exact test), Q value = 0.094

Table S10.  Gene #3: 'amp_1q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
AMP PEAK 3(1Q23.3) MUTATED 70 80 28 38
AMP PEAK 3(1Q23.3) WILD-TYPE 68 47 35 42

Figure S10.  Get High-res Image Gene #3: 'amp_1q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_1q23.3' versus 'MRNASEQ_CNMF'

P value = 0.0285 (Fisher's exact test), Q value = 0.072

Table S11.  Gene #3: 'amp_1q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
AMP PEAK 3(1Q23.3) MUTATED 36 73 16 50 40
AMP PEAK 3(1Q23.3) WILD-TYPE 36 62 22 53 16

Figure S11.  Get High-res Image Gene #3: 'amp_1q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_1q23.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0252 (Fisher's exact test), Q value = 0.065

Table S12.  Gene #3: 'amp_1q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
AMP PEAK 3(1Q23.3) MUTATED 75 53 87
AMP PEAK 3(1Q23.3) WILD-TYPE 43 59 87

Figure S12.  Get High-res Image Gene #3: 'amp_1q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_1q23.3' versus 'MIRSEQ_CNMF'

P value = 0.00156 (Fisher's exact test), Q value = 0.0073

Table S13.  Gene #3: 'amp_1q23.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 74 114 25 87
AMP PEAK 3(1Q23.3) MUTATED 49 54 55 16 41
AMP PEAK 3(1Q23.3) WILD-TYPE 56 20 59 9 46

Figure S13.  Get High-res Image Gene #3: 'amp_1q23.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_1q23.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8e-04 (Fisher's exact test), Q value = 0.0044

Table S14.  Gene #3: 'amp_1q23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 266 83 56
AMP PEAK 3(1Q23.3) MUTATED 127 59 29
AMP PEAK 3(1Q23.3) WILD-TYPE 139 24 27

Figure S14.  Get High-res Image Gene #3: 'amp_1q23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_1q23.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0447 (Fisher's exact test), Q value = 0.1

Table S15.  Gene #3: 'amp_1q23.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 124 51 127 92
AMP PEAK 3(1Q23.3) MUTATED 66 36 65 43
AMP PEAK 3(1Q23.3) WILD-TYPE 58 15 62 49

Figure S15.  Get High-res Image Gene #3: 'amp_1q23.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_1q23.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0108 (Fisher's exact test), Q value = 0.034

Table S16.  Gene #3: 'amp_1q23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 60 41 132 74
AMP PEAK 3(1Q23.3) MUTATED 40 41 26 72 31
AMP PEAK 3(1Q23.3) WILD-TYPE 47 19 15 60 43

Figure S16.  Get High-res Image Gene #3: 'amp_1q23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_2p25.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S17.  Gene #4: 'amp_2p25.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
AMP PEAK 4(2P25.1) MUTATED 36 80 16 19 1
AMP PEAK 4(2P25.1) WILD-TYPE 42 66 105 42 1

Figure S17.  Get High-res Image Gene #4: 'amp_2p25.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_2p25.1' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00018

Table S18.  Gene #4: 'amp_2p25.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
AMP PEAK 4(2P25.1) MUTATED 41 73 15 23
AMP PEAK 4(2P25.1) WILD-TYPE 97 54 48 57

Figure S18.  Get High-res Image Gene #4: 'amp_2p25.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_2p25.1' versus 'MRNASEQ_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.0021

Table S19.  Gene #4: 'amp_2p25.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
AMP PEAK 4(2P25.1) MUTATED 25 62 5 31 28
AMP PEAK 4(2P25.1) WILD-TYPE 47 73 33 72 28

Figure S19.  Get High-res Image Gene #4: 'amp_2p25.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_2p25.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00018

Table S20.  Gene #4: 'amp_2p25.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
AMP PEAK 4(2P25.1) MUTATED 64 38 49
AMP PEAK 4(2P25.1) WILD-TYPE 54 74 125

Figure S20.  Get High-res Image Gene #4: 'amp_2p25.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_2p25.1' versus 'MIRSEQ_CNMF'

P value = 0.00521 (Fisher's exact test), Q value = 0.019

Table S21.  Gene #4: 'amp_2p25.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 74 114 25 87
AMP PEAK 4(2P25.1) MUTATED 29 39 40 13 29
AMP PEAK 4(2P25.1) WILD-TYPE 76 35 74 12 58

Figure S21.  Get High-res Image Gene #4: 'amp_2p25.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_2p25.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00802 (Fisher's exact test), Q value = 0.028

Table S22.  Gene #4: 'amp_2p25.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 266 83 56
AMP PEAK 4(2P25.1) MUTATED 88 43 19
AMP PEAK 4(2P25.1) WILD-TYPE 178 40 37

Figure S22.  Get High-res Image Gene #4: 'amp_2p25.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_2p25.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0379 (Fisher's exact test), Q value = 0.088

Table S23.  Gene #4: 'amp_2p25.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 124 51 127 92
AMP PEAK 4(2P25.1) MUTATED 47 27 48 26
AMP PEAK 4(2P25.1) WILD-TYPE 77 24 79 66

Figure S23.  Get High-res Image Gene #4: 'amp_2p25.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_2p25.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00054 (Fisher's exact test), Q value = 0.0031

Table S24.  Gene #4: 'amp_2p25.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 60 41 132 74
AMP PEAK 4(2P25.1) MUTATED 28 32 20 53 15
AMP PEAK 4(2P25.1) WILD-TYPE 59 28 21 79 59

Figure S24.  Get High-res Image Gene #4: 'amp_2p25.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_3p25.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S25.  Gene #5: 'amp_3p25.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
AMP PEAK 5(3P25.2) MUTATED 52 92 19 26 1
AMP PEAK 5(3P25.2) WILD-TYPE 26 54 102 35 1

Figure S25.  Get High-res Image Gene #5: 'amp_3p25.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3p25.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S26.  Gene #5: 'amp_3p25.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
AMP PEAK 5(3P25.2) MUTATED 48 87 27 28
AMP PEAK 5(3P25.2) WILD-TYPE 90 40 36 52

Figure S26.  Get High-res Image Gene #5: 'amp_3p25.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_3p25.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0265 (Fisher's exact test), Q value = 0.068

Table S27.  Gene #5: 'amp_3p25.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 121 98 31
AMP PEAK 5(3P25.2) MUTATED 42 65 35 10
AMP PEAK 5(3P25.2) WILD-TYPE 48 56 63 21

Figure S27.  Get High-res Image Gene #5: 'amp_3p25.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_3p25.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S28.  Gene #5: 'amp_3p25.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
AMP PEAK 5(3P25.2) MUTATED 35 84 4 32 33
AMP PEAK 5(3P25.2) WILD-TYPE 37 51 34 71 23

Figure S28.  Get High-res Image Gene #5: 'amp_3p25.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_3p25.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S29.  Gene #5: 'amp_3p25.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
AMP PEAK 5(3P25.2) MUTATED 78 60 50
AMP PEAK 5(3P25.2) WILD-TYPE 40 52 124

Figure S29.  Get High-res Image Gene #5: 'amp_3p25.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_3p25.2' versus 'MIRSEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 9e-04

Table S30.  Gene #5: 'amp_3p25.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 74 114 25 87
AMP PEAK 5(3P25.2) MUTATED 36 51 53 13 36
AMP PEAK 5(3P25.2) WILD-TYPE 69 23 61 12 51

Figure S30.  Get High-res Image Gene #5: 'amp_3p25.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_3p25.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 9e-04

Table S31.  Gene #5: 'amp_3p25.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 266 83 56
AMP PEAK 5(3P25.2) MUTATED 105 55 29
AMP PEAK 5(3P25.2) WILD-TYPE 161 28 27

Figure S31.  Get High-res Image Gene #5: 'amp_3p25.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_3p25.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S32.  Gene #5: 'amp_3p25.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 124 51 127 92
AMP PEAK 5(3P25.2) MUTATED 55 40 62 28
AMP PEAK 5(3P25.2) WILD-TYPE 69 11 65 64

Figure S32.  Get High-res Image Gene #5: 'amp_3p25.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_3p25.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S33.  Gene #5: 'amp_3p25.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 60 41 132 74
AMP PEAK 5(3P25.2) MUTATED 39 43 15 68 20
AMP PEAK 5(3P25.2) WILD-TYPE 48 17 26 64 54

Figure S33.  Get High-res Image Gene #5: 'amp_3p25.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_3q26.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S34.  Gene #6: 'amp_3q26.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
AMP PEAK 6(3Q26.33) MUTATED 54 99 33 30 2
AMP PEAK 6(3Q26.33) WILD-TYPE 24 47 88 31 0

Figure S34.  Get High-res Image Gene #6: 'amp_3q26.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3q26.33' versus 'RPPA_CNMF'

P value = 0.0018 (Fisher's exact test), Q value = 0.0081

Table S35.  Gene #6: 'amp_3q26.33' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 114 104
AMP PEAK 6(3Q26.33) MUTATED 59 48 68
AMP PEAK 6(3Q26.33) WILD-TYPE 63 66 36

Figure S35.  Get High-res Image Gene #6: 'amp_3q26.33' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_3q26.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0226 (Fisher's exact test), Q value = 0.06

Table S36.  Gene #6: 'amp_3q26.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
AMP PEAK 6(3Q26.33) MUTATED 74 50 93
AMP PEAK 6(3Q26.33) WILD-TYPE 44 62 81

Figure S36.  Get High-res Image Gene #6: 'amp_3q26.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_3q26.33' versus 'MIRSEQ_CNMF'

P value = 0.0103 (Fisher's exact test), Q value = 0.033

Table S37.  Gene #6: 'amp_3q26.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 74 114 25 87
AMP PEAK 6(3Q26.33) MUTATED 58 49 48 17 44
AMP PEAK 6(3Q26.33) WILD-TYPE 47 25 66 8 43

Figure S37.  Get High-res Image Gene #6: 'amp_3q26.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_4p16.3' versus 'CN_CNMF'

P value = 0.0283 (Fisher's exact test), Q value = 0.071

Table S38.  Gene #7: 'amp_4p16.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
AMP PEAK 7(4P16.3) MUTATED 18 35 15 6 0
AMP PEAK 7(4P16.3) WILD-TYPE 60 111 106 55 2

Figure S38.  Get High-res Image Gene #7: 'amp_4p16.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_4p16.3' versus 'METHLYATION_CNMF'

P value = 0.03 (Fisher's exact test), Q value = 0.074

Table S39.  Gene #7: 'amp_4p16.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
AMP PEAK 7(4P16.3) MUTATED 15 30 11 18
AMP PEAK 7(4P16.3) WILD-TYPE 123 97 52 62

Figure S39.  Get High-res Image Gene #7: 'amp_4p16.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_4p16.3' versus 'RPPA_CNMF'

P value = 0.00373 (Fisher's exact test), Q value = 0.015

Table S40.  Gene #7: 'amp_4p16.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 114 104
AMP PEAK 7(4P16.3) MUTATED 12 29 23
AMP PEAK 7(4P16.3) WILD-TYPE 110 85 81

Figure S40.  Get High-res Image Gene #7: 'amp_4p16.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_4p16.3' versus 'RPPA_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.0014

Table S41.  Gene #7: 'amp_4p16.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 121 98 31
AMP PEAK 7(4P16.3) MUTATED 13 38 10 3
AMP PEAK 7(4P16.3) WILD-TYPE 77 83 88 28

Figure S41.  Get High-res Image Gene #7: 'amp_4p16.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_4p16.3' versus 'MRNASEQ_CNMF'

P value = 0.0179 (Fisher's exact test), Q value = 0.05

Table S42.  Gene #7: 'amp_4p16.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
AMP PEAK 7(4P16.3) MUTATED 7 33 11 14 8
AMP PEAK 7(4P16.3) WILD-TYPE 65 102 27 89 48

Figure S42.  Get High-res Image Gene #7: 'amp_4p16.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_4p16.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00049

Table S43.  Gene #7: 'amp_4p16.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
AMP PEAK 7(4P16.3) MUTATED 20 35 18
AMP PEAK 7(4P16.3) WILD-TYPE 98 77 156

Figure S43.  Get High-res Image Gene #7: 'amp_4p16.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_4p16.3' versus 'MIRSEQ_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.0018

Table S44.  Gene #7: 'amp_4p16.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 74 114 25 87
AMP PEAK 7(4P16.3) MUTATED 15 21 30 2 6
AMP PEAK 7(4P16.3) WILD-TYPE 90 53 84 23 81

Figure S44.  Get High-res Image Gene #7: 'amp_4p16.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_4p16.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00124 (Fisher's exact test), Q value = 0.0061

Table S45.  Gene #7: 'amp_4p16.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 266 83 56
AMP PEAK 7(4P16.3) MUTATED 47 24 3
AMP PEAK 7(4P16.3) WILD-TYPE 219 59 53

Figure S45.  Get High-res Image Gene #7: 'amp_4p16.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_4p16.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0217 (Fisher's exact test), Q value = 0.058

Table S46.  Gene #7: 'amp_4p16.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 124 51 127 92
AMP PEAK 7(4P16.3) MUTATED 15 11 33 13
AMP PEAK 7(4P16.3) WILD-TYPE 109 40 94 79

Figure S46.  Get High-res Image Gene #7: 'amp_4p16.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_4p16.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00202 (Fisher's exact test), Q value = 0.0089

Table S47.  Gene #7: 'amp_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 60 41 132 74
AMP PEAK 7(4P16.3) MUTATED 7 15 4 35 11
AMP PEAK 7(4P16.3) WILD-TYPE 80 45 37 97 63

Figure S47.  Get High-res Image Gene #7: 'amp_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_4q13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S48.  Gene #8: 'amp_4q13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
AMP PEAK 8(4Q13.3) MUTATED 12 41 5 4 0
AMP PEAK 8(4Q13.3) WILD-TYPE 66 105 116 57 2

Figure S48.  Get High-res Image Gene #8: 'amp_4q13.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_4q13.3' versus 'METHLYATION_CNMF'

P value = 0.0299 (Fisher's exact test), Q value = 0.074

Table S49.  Gene #8: 'amp_4q13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
AMP PEAK 8(4Q13.3) MUTATED 18 28 4 12
AMP PEAK 8(4Q13.3) WILD-TYPE 120 99 59 68

Figure S49.  Get High-res Image Gene #8: 'amp_4q13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_4q13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00162 (Fisher's exact test), Q value = 0.0075

Table S50.  Gene #8: 'amp_4q13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 60 41 132 74
AMP PEAK 8(4Q13.3) MUTATED 5 14 8 28 6
AMP PEAK 8(4Q13.3) WILD-TYPE 82 46 33 104 68

Figure S50.  Get High-res Image Gene #8: 'amp_4q13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_5p15.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S51.  Gene #9: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
AMP PEAK 9(5P15.33) MUTATED 50 94 20 40 2
AMP PEAK 9(5P15.33) WILD-TYPE 28 52 101 21 0

Figure S51.  Get High-res Image Gene #9: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5p15.33' versus 'RPPA_CNMF'

P value = 0.00054 (Fisher's exact test), Q value = 0.0031

Table S52.  Gene #9: 'amp_5p15.33' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 114 104
AMP PEAK 9(5P15.33) MUTATED 63 40 63
AMP PEAK 9(5P15.33) WILD-TYPE 59 74 41

Figure S52.  Get High-res Image Gene #9: 'amp_5p15.33' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_5p15.33' versus 'RPPA_CHIERARCHICAL'

P value = 0.014 (Fisher's exact test), Q value = 0.042

Table S53.  Gene #9: 'amp_5p15.33' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 121 98 31
AMP PEAK 9(5P15.33) MUTATED 41 48 58 19
AMP PEAK 9(5P15.33) WILD-TYPE 49 73 40 12

Figure S53.  Get High-res Image Gene #9: 'amp_5p15.33' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_5p15.33' versus 'MRNASEQ_CNMF'

P value = 0.00815 (Fisher's exact test), Q value = 0.028

Table S54.  Gene #9: 'amp_5p15.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
AMP PEAK 9(5P15.33) MUTATED 32 61 13 63 34
AMP PEAK 9(5P15.33) WILD-TYPE 40 74 25 40 22

Figure S54.  Get High-res Image Gene #9: 'amp_5p15.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_5p15.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0195 (Fisher's exact test), Q value = 0.054

Table S55.  Gene #9: 'amp_5p15.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
AMP PEAK 9(5P15.33) MUTATED 50 52 101
AMP PEAK 9(5P15.33) WILD-TYPE 68 60 73

Figure S55.  Get High-res Image Gene #9: 'amp_5p15.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'MIRSEQ_CNMF'

P value = 0.00472 (Fisher's exact test), Q value = 0.018

Table S56.  Gene #9: 'amp_5p15.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 74 114 25 87
AMP PEAK 9(5P15.33) MUTATED 54 47 42 15 47
AMP PEAK 9(5P15.33) WILD-TYPE 51 27 72 10 40

Figure S56.  Get High-res Image Gene #9: 'amp_5p15.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_5p15.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0167 (Fisher's exact test), Q value = 0.047

Table S57.  Gene #9: 'amp_5p15.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 266 83 56
AMP PEAK 9(5P15.33) MUTATED 121 51 33
AMP PEAK 9(5P15.33) WILD-TYPE 145 32 23

Figure S57.  Get High-res Image Gene #9: 'amp_5p15.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00463 (Fisher's exact test), Q value = 0.018

Table S58.  Gene #9: 'amp_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 60 41 132 74
AMP PEAK 9(5P15.33) MUTATED 35 35 28 59 45
AMP PEAK 9(5P15.33) WILD-TYPE 52 25 13 73 29

Figure S58.  Get High-res Image Gene #9: 'amp_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_6p22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S59.  Gene #10: 'amp_6p22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
AMP PEAK 10(6P22.3) MUTATED 37 82 10 41 1
AMP PEAK 10(6P22.3) WILD-TYPE 41 64 111 20 1

Figure S59.  Get High-res Image Gene #10: 'amp_6p22.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6p22.3' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00042

Table S60.  Gene #10: 'amp_6p22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
AMP PEAK 10(6P22.3) MUTATED 56 73 18 24
AMP PEAK 10(6P22.3) WILD-TYPE 82 54 45 56

Figure S60.  Get High-res Image Gene #10: 'amp_6p22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6p22.3' versus 'RPPA_CNMF'

P value = 0.0459 (Fisher's exact test), Q value = 0.1

Table S61.  Gene #10: 'amp_6p22.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 114 104
AMP PEAK 10(6P22.3) MUTATED 41 41 51
AMP PEAK 10(6P22.3) WILD-TYPE 81 73 53

Figure S61.  Get High-res Image Gene #10: 'amp_6p22.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_6p22.3' versus 'MRNASEQ_CNMF'

P value = 0.00158 (Fisher's exact test), Q value = 0.0074

Table S62.  Gene #10: 'amp_6p22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
AMP PEAK 10(6P22.3) MUTATED 21 60 8 48 31
AMP PEAK 10(6P22.3) WILD-TYPE 51 75 30 55 25

Figure S62.  Get High-res Image Gene #10: 'amp_6p22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_6q21' versus 'CN_CNMF'

P value = 0.00069 (Fisher's exact test), Q value = 0.0039

Table S63.  Gene #11: 'amp_6q21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
AMP PEAK 11(6Q21) MUTATED 5 15 4 9 2
AMP PEAK 11(6Q21) WILD-TYPE 73 131 117 52 0

Figure S63.  Get High-res Image Gene #11: 'amp_6q21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6q21' versus 'MRNASEQ_CNMF'

P value = 0.00071 (Fisher's exact test), Q value = 0.004

Table S64.  Gene #11: 'amp_6q21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
AMP PEAK 11(6Q21) MUTATED 4 10 2 4 14
AMP PEAK 11(6Q21) WILD-TYPE 68 125 36 99 42

Figure S64.  Get High-res Image Gene #11: 'amp_6q21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_6q23.3' versus 'CN_CNMF'

P value = 0.00518 (Fisher's exact test), Q value = 0.019

Table S65.  Gene #12: 'amp_6q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
AMP PEAK 12(6Q23.3) MUTATED 6 21 8 9 2
AMP PEAK 12(6Q23.3) WILD-TYPE 72 125 113 52 0

Figure S65.  Get High-res Image Gene #12: 'amp_6q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6q23.3' versus 'MRNASEQ_CNMF'

P value = 0.011 (Fisher's exact test), Q value = 0.034

Table S66.  Gene #12: 'amp_6q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
AMP PEAK 12(6Q23.3) MUTATED 4 16 3 8 14
AMP PEAK 12(6Q23.3) WILD-TYPE 68 119 35 95 42

Figure S66.  Get High-res Image Gene #12: 'amp_6q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_6q23.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0299 (Fisher's exact test), Q value = 0.074

Table S67.  Gene #12: 'amp_6q23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 266 83 56
AMP PEAK 12(6Q23.3) MUTATED 34 11 1
AMP PEAK 12(6Q23.3) WILD-TYPE 232 72 55

Figure S67.  Get High-res Image Gene #12: 'amp_6q23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_7p21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S68.  Gene #13: 'amp_7p21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
AMP PEAK 13(7P21.1) MUTATED 51 91 17 40 2
AMP PEAK 13(7P21.1) WILD-TYPE 27 55 104 21 0

Figure S68.  Get High-res Image Gene #13: 'amp_7p21.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7p21.1' versus 'METHLYATION_CNMF'

P value = 0.00359 (Fisher's exact test), Q value = 0.015

Table S69.  Gene #13: 'amp_7p21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
AMP PEAK 13(7P21.1) MUTATED 69 77 23 32
AMP PEAK 13(7P21.1) WILD-TYPE 69 50 40 48

Figure S69.  Get High-res Image Gene #13: 'amp_7p21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7p21.1' versus 'RPPA_CNMF'

P value = 0.0218 (Fisher's exact test), Q value = 0.058

Table S70.  Gene #13: 'amp_7p21.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 114 104
AMP PEAK 13(7P21.1) MUTATED 55 48 62
AMP PEAK 13(7P21.1) WILD-TYPE 67 66 42

Figure S70.  Get High-res Image Gene #13: 'amp_7p21.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_7p21.1' versus 'MRNASEQ_CNMF'

P value = 0.0133 (Fisher's exact test), Q value = 0.04

Table S71.  Gene #13: 'amp_7p21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
AMP PEAK 13(7P21.1) MUTATED 29 65 12 60 33
AMP PEAK 13(7P21.1) WILD-TYPE 43 70 26 43 23

Figure S71.  Get High-res Image Gene #13: 'amp_7p21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_7p21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0231 (Fisher's exact test), Q value = 0.061

Table S72.  Gene #13: 'amp_7p21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
AMP PEAK 13(7P21.1) MUTATED 65 43 91
AMP PEAK 13(7P21.1) WILD-TYPE 53 69 83

Figure S72.  Get High-res Image Gene #13: 'amp_7p21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_7p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S73.  Gene #14: 'amp_7p11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
AMP PEAK 14(7P11.2) MUTATED 56 80 16 36 2
AMP PEAK 14(7P11.2) WILD-TYPE 22 66 105 25 0

Figure S73.  Get High-res Image Gene #14: 'amp_7p11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7p11.2' versus 'METHLYATION_CNMF'

P value = 0.00844 (Fisher's exact test), Q value = 0.029

Table S74.  Gene #14: 'amp_7p11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
AMP PEAK 14(7P11.2) MUTATED 67 71 20 32
AMP PEAK 14(7P11.2) WILD-TYPE 71 56 43 48

Figure S74.  Get High-res Image Gene #14: 'amp_7p11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7p11.2' versus 'RPPA_CNMF'

P value = 0.00173 (Fisher's exact test), Q value = 0.0079

Table S75.  Gene #14: 'amp_7p11.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 114 104
AMP PEAK 14(7P11.2) MUTATED 51 43 63
AMP PEAK 14(7P11.2) WILD-TYPE 71 71 41

Figure S75.  Get High-res Image Gene #14: 'amp_7p11.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_8p11.23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S76.  Gene #15: 'amp_8p11.23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
AMP PEAK 15(8P11.23) MUTATED 62 30 20 10 2
AMP PEAK 15(8P11.23) WILD-TYPE 16 116 101 51 0

Figure S76.  Get High-res Image Gene #15: 'amp_8p11.23' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8p11.23' versus 'METHLYATION_CNMF'

P value = 0.0179 (Fisher's exact test), Q value = 0.05

Table S77.  Gene #15: 'amp_8p11.23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
AMP PEAK 15(8P11.23) MUTATED 36 43 12 33
AMP PEAK 15(8P11.23) WILD-TYPE 102 84 51 47

Figure S77.  Get High-res Image Gene #15: 'amp_8p11.23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8p11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S78.  Gene #16: 'amp_8p11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
AMP PEAK 16(8P11.21) MUTATED 64 41 18 16 1
AMP PEAK 16(8P11.21) WILD-TYPE 14 105 103 45 1

Figure S78.  Get High-res Image Gene #16: 'amp_8p11.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8p11.21' versus 'METHLYATION_CNMF'

P value = 0.00071 (Fisher's exact test), Q value = 0.004

Table S79.  Gene #16: 'amp_8p11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
AMP PEAK 16(8P11.21) MUTATED 40 56 11 33
AMP PEAK 16(8P11.21) WILD-TYPE 98 71 52 47

Figure S79.  Get High-res Image Gene #16: 'amp_8p11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8p11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0367 (Fisher's exact test), Q value = 0.086

Table S80.  Gene #16: 'amp_8p11.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 266 83 56
AMP PEAK 16(8P11.21) MUTATED 99 29 11
AMP PEAK 16(8P11.21) WILD-TYPE 167 54 45

Figure S80.  Get High-res Image Gene #16: 'amp_8p11.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_8q22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S81.  Gene #17: 'amp_8q22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
AMP PEAK 17(8Q22.3) MUTATED 68 111 45 39 1
AMP PEAK 17(8Q22.3) WILD-TYPE 10 35 76 22 1

Figure S81.  Get High-res Image Gene #17: 'amp_8q22.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q22.3' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00062

Table S82.  Gene #17: 'amp_8q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
AMP PEAK 17(8Q22.3) MUTATED 82 101 30 51
AMP PEAK 17(8Q22.3) WILD-TYPE 56 26 33 29

Figure S82.  Get High-res Image Gene #17: 'amp_8q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8q22.3' versus 'RPPA_CNMF'

P value = 0.0124 (Fisher's exact test), Q value = 0.037

Table S83.  Gene #17: 'amp_8q22.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 114 104
AMP PEAK 17(8Q22.3) MUTATED 75 66 79
AMP PEAK 17(8Q22.3) WILD-TYPE 47 48 25

Figure S83.  Get High-res Image Gene #17: 'amp_8q22.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_8q22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0337 (Fisher's exact test), Q value = 0.08

Table S84.  Gene #17: 'amp_8q22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 266 83 56
AMP PEAK 17(8Q22.3) MUTATED 170 62 30
AMP PEAK 17(8Q22.3) WILD-TYPE 96 21 26

Figure S84.  Get High-res Image Gene #17: 'amp_8q22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_8q22.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0327 (Fisher's exact test), Q value = 0.078

Table S85.  Gene #17: 'amp_8q22.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 124 51 127 92
AMP PEAK 17(8Q22.3) MUTATED 75 42 83 57
AMP PEAK 17(8Q22.3) WILD-TYPE 49 9 44 35

Figure S85.  Get High-res Image Gene #17: 'amp_8q22.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_8q24.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S86.  Gene #18: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
AMP PEAK 18(8Q24.21) MUTATED 65 107 43 37 2
AMP PEAK 18(8Q24.21) WILD-TYPE 13 39 78 24 0

Figure S86.  Get High-res Image Gene #18: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

P value = 0.00125 (Fisher's exact test), Q value = 0.0061

Table S87.  Gene #18: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
AMP PEAK 18(8Q24.21) MUTATED 82 93 28 51
AMP PEAK 18(8Q24.21) WILD-TYPE 56 34 35 29

Figure S87.  Get High-res Image Gene #18: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'RPPA_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.0021

Table S88.  Gene #18: 'amp_8q24.21' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 114 104
AMP PEAK 18(8Q24.21) MUTATED 71 59 80
AMP PEAK 18(8Q24.21) WILD-TYPE 51 55 24

Figure S88.  Get High-res Image Gene #18: 'amp_8q24.21' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_8q24.21' versus 'MIRSEQ_CNMF'

P value = 0.0492 (Fisher's exact test), Q value = 0.11

Table S89.  Gene #18: 'amp_8q24.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 74 114 25 87
AMP PEAK 18(8Q24.21) MUTATED 70 53 66 18 45
AMP PEAK 18(8Q24.21) WILD-TYPE 35 21 48 7 42

Figure S89.  Get High-res Image Gene #18: 'amp_8q24.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_8q24.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0142 (Fisher's exact test), Q value = 0.042

Table S90.  Gene #18: 'amp_8q24.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 266 83 56
AMP PEAK 18(8Q24.21) MUTATED 167 59 26
AMP PEAK 18(8Q24.21) WILD-TYPE 99 24 30

Figure S90.  Get High-res Image Gene #18: 'amp_8q24.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_9p24.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S91.  Gene #19: 'amp_9p24.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
AMP PEAK 19(9P24.1) MUTATED 23 20 10 34 1
AMP PEAK 19(9P24.1) WILD-TYPE 55 126 111 27 1

Figure S91.  Get High-res Image Gene #19: 'amp_9p24.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_9p24.1' versus 'METHLYATION_CNMF'

P value = 0.00406 (Fisher's exact test), Q value = 0.016

Table S92.  Gene #19: 'amp_9p24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
AMP PEAK 19(9P24.1) MUTATED 44 21 8 15
AMP PEAK 19(9P24.1) WILD-TYPE 94 106 55 65

Figure S92.  Get High-res Image Gene #19: 'amp_9p24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_9p24.1' versus 'RPPA_CNMF'

P value = 0.0309 (Fisher's exact test), Q value = 0.075

Table S93.  Gene #19: 'amp_9p24.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 114 104
AMP PEAK 19(9P24.1) MUTATED 34 16 24
AMP PEAK 19(9P24.1) WILD-TYPE 88 98 80

Figure S93.  Get High-res Image Gene #19: 'amp_9p24.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_9p24.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.00909 (Fisher's exact test), Q value = 0.03

Table S94.  Gene #19: 'amp_9p24.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 121 98 31
AMP PEAK 19(9P24.1) MUTATED 19 16 28 11
AMP PEAK 19(9P24.1) WILD-TYPE 71 105 70 20

Figure S94.  Get High-res Image Gene #19: 'amp_9p24.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_9p24.1' versus 'MRNASEQ_CNMF'

P value = 0.0237 (Fisher's exact test), Q value = 0.062

Table S95.  Gene #19: 'amp_9p24.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
AMP PEAK 19(9P24.1) MUTATED 14 24 3 32 13
AMP PEAK 19(9P24.1) WILD-TYPE 58 111 35 71 43

Figure S95.  Get High-res Image Gene #19: 'amp_9p24.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_9p24.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00167 (Fisher's exact test), Q value = 0.0077

Table S96.  Gene #19: 'amp_9p24.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
AMP PEAK 19(9P24.1) MUTATED 21 14 51
AMP PEAK 19(9P24.1) WILD-TYPE 97 98 123

Figure S96.  Get High-res Image Gene #19: 'amp_9p24.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_9p24.1' versus 'MIRSEQ_CNMF'

P value = 0.00792 (Fisher's exact test), Q value = 0.027

Table S97.  Gene #19: 'amp_9p24.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 74 114 25 87
AMP PEAK 19(9P24.1) MUTATED 36 12 17 6 17
AMP PEAK 19(9P24.1) WILD-TYPE 69 62 97 19 70

Figure S97.  Get High-res Image Gene #19: 'amp_9p24.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_9p24.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.0011

Table S98.  Gene #19: 'amp_9p24.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 124 51 127 92
AMP PEAK 19(9P24.1) MUTATED 22 9 18 36
AMP PEAK 19(9P24.1) WILD-TYPE 102 42 109 56

Figure S98.  Get High-res Image Gene #19: 'amp_9p24.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_9p24.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00098 (Fisher's exact test), Q value = 0.005

Table S99.  Gene #19: 'amp_9p24.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 60 41 132 74
AMP PEAK 19(9P24.1) MUTATED 18 10 6 21 30
AMP PEAK 19(9P24.1) WILD-TYPE 69 50 35 111 44

Figure S99.  Get High-res Image Gene #19: 'amp_9p24.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_10p14' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S100.  Gene #20: 'amp_10p14' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
AMP PEAK 20(10P14) MUTATED 45 89 12 36 0
AMP PEAK 20(10P14) WILD-TYPE 33 57 109 25 2

Figure S100.  Get High-res Image Gene #20: 'amp_10p14' versus Molecular Subtype #1: 'CN_CNMF'

'amp_10p14' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S101.  Gene #20: 'amp_10p14' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
AMP PEAK 20(10P14) MUTATED 55 81 22 24
AMP PEAK 20(10P14) WILD-TYPE 83 46 41 56

Figure S101.  Get High-res Image Gene #20: 'amp_10p14' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_10p14' versus 'MRNASEQ_CNMF'

P value = 0.00451 (Fisher's exact test), Q value = 0.018

Table S102.  Gene #20: 'amp_10p14' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
AMP PEAK 20(10P14) MUTATED 33 63 7 45 32
AMP PEAK 20(10P14) WILD-TYPE 39 72 31 58 24

Figure S102.  Get High-res Image Gene #20: 'amp_10p14' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_10p14' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00042

Table S103.  Gene #20: 'amp_10p14' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
AMP PEAK 20(10P14) MUTATED 73 39 68
AMP PEAK 20(10P14) WILD-TYPE 45 73 106

Figure S103.  Get High-res Image Gene #20: 'amp_10p14' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_11p13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S104.  Gene #21: 'amp_11p13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
AMP PEAK 21(11P13) MUTATED 12 15 3 20 1
AMP PEAK 21(11P13) WILD-TYPE 66 131 118 41 1

Figure S104.  Get High-res Image Gene #21: 'amp_11p13' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11p13' versus 'METHLYATION_CNMF'

P value = 0.00361 (Fisher's exact test), Q value = 0.015

Table S105.  Gene #21: 'amp_11p13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
AMP PEAK 21(11P13) MUTATED 25 19 4 3
AMP PEAK 21(11P13) WILD-TYPE 113 108 59 77

Figure S105.  Get High-res Image Gene #21: 'amp_11p13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_11p13' versus 'RPPA_CNMF'

P value = 0.00147 (Fisher's exact test), Q value = 0.007

Table S106.  Gene #21: 'amp_11p13' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 114 104
AMP PEAK 21(11P13) MUTATED 22 5 18
AMP PEAK 21(11P13) WILD-TYPE 100 109 86

Figure S106.  Get High-res Image Gene #21: 'amp_11p13' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_11p13' versus 'RPPA_CHIERARCHICAL'

P value = 0.0363 (Fisher's exact test), Q value = 0.085

Table S107.  Gene #21: 'amp_11p13' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 121 98 31
AMP PEAK 21(11P13) MUTATED 14 8 17 6
AMP PEAK 21(11P13) WILD-TYPE 76 113 81 25

Figure S107.  Get High-res Image Gene #21: 'amp_11p13' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_11p13' versus 'MRNASEQ_CNMF'

P value = 0.025 (Fisher's exact test), Q value = 0.065

Table S108.  Gene #21: 'amp_11p13' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
AMP PEAK 21(11P13) MUTATED 9 9 3 20 10
AMP PEAK 21(11P13) WILD-TYPE 63 126 35 83 46

Figure S108.  Get High-res Image Gene #21: 'amp_11p13' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_11p13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00084 (Fisher's exact test), Q value = 0.0045

Table S109.  Gene #21: 'amp_11p13' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
AMP PEAK 21(11P13) MUTATED 16 4 31
AMP PEAK 21(11P13) WILD-TYPE 102 108 143

Figure S109.  Get High-res Image Gene #21: 'amp_11p13' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_11p13' versus 'MIRSEQ_CNMF'

P value = 0.00079 (Fisher's exact test), Q value = 0.0043

Table S110.  Gene #21: 'amp_11p13' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 74 114 25 87
AMP PEAK 21(11P13) MUTATED 19 7 5 8 12
AMP PEAK 21(11P13) WILD-TYPE 86 67 109 17 75

Figure S110.  Get High-res Image Gene #21: 'amp_11p13' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_11p13' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0308 (Fisher's exact test), Q value = 0.075

Table S111.  Gene #21: 'amp_11p13' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 124 51 127 92
AMP PEAK 21(11P13) MUTATED 16 4 11 20
AMP PEAK 21(11P13) WILD-TYPE 108 47 116 72

Figure S111.  Get High-res Image Gene #21: 'amp_11p13' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_11p13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.002

Table S112.  Gene #21: 'amp_11p13' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 60 41 132 74
AMP PEAK 21(11P13) MUTATED 10 4 7 9 21
AMP PEAK 21(11P13) WILD-TYPE 77 56 34 123 53

Figure S112.  Get High-res Image Gene #21: 'amp_11p13' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_11q13.3' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00026

Table S113.  Gene #22: 'amp_11q13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
AMP PEAK 22(11Q13.3) MUTATED 33 62 21 18 1
AMP PEAK 22(11Q13.3) WILD-TYPE 45 84 100 43 1

Figure S113.  Get High-res Image Gene #22: 'amp_11q13.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11q22.2' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00018

Table S114.  Gene #23: 'amp_11q22.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
AMP PEAK 23(11Q22.2) MUTATED 20 33 4 14 0
AMP PEAK 23(11Q22.2) WILD-TYPE 58 113 117 47 2

Figure S114.  Get High-res Image Gene #23: 'amp_11q22.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11q22.2' versus 'MIRSEQ_CNMF'

P value = 0.00091 (Fisher's exact test), Q value = 0.0048

Table S115.  Gene #23: 'amp_11q22.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 74 114 25 87
AMP PEAK 23(11Q22.2) MUTATED 25 22 11 4 9
AMP PEAK 23(11Q22.2) WILD-TYPE 80 52 103 21 78

Figure S115.  Get High-res Image Gene #23: 'amp_11q22.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_11q22.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0199 (Fisher's exact test), Q value = 0.054

Table S116.  Gene #23: 'amp_11q22.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 266 83 56
AMP PEAK 23(11Q22.2) MUTATED 42 23 6
AMP PEAK 23(11Q22.2) WILD-TYPE 224 60 50

Figure S116.  Get High-res Image Gene #23: 'amp_11q22.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_11q22.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.0018

Table S117.  Gene #23: 'amp_11q22.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 124 51 127 92
AMP PEAK 23(11Q22.2) MUTATED 18 17 12 24
AMP PEAK 23(11Q22.2) WILD-TYPE 106 34 115 68

Figure S117.  Get High-res Image Gene #23: 'amp_11q22.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_11q22.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0141 (Fisher's exact test), Q value = 0.042

Table S118.  Gene #23: 'amp_11q22.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 60 41 132 74
AMP PEAK 23(11Q22.2) MUTATED 10 17 5 19 20
AMP PEAK 23(11Q22.2) WILD-TYPE 77 43 36 113 54

Figure S118.  Get High-res Image Gene #23: 'amp_11q22.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12p12.1' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00049

Table S119.  Gene #24: 'amp_12p12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
AMP PEAK 24(12P12.1) MUTATED 38 52 21 21 0
AMP PEAK 24(12P12.1) WILD-TYPE 40 94 100 40 2

Figure S119.  Get High-res Image Gene #24: 'amp_12p12.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12p12.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0235 (Fisher's exact test), Q value = 0.062

Table S120.  Gene #24: 'amp_12p12.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 60 41 132 74
AMP PEAK 24(12P12.1) MUTATED 17 22 17 43 30
AMP PEAK 24(12P12.1) WILD-TYPE 70 38 24 89 44

Figure S120.  Get High-res Image Gene #24: 'amp_12p12.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12q15' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00056

Table S121.  Gene #25: 'amp_12q15' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
AMP PEAK 25(12Q15) MUTATED 27 58 25 8 0
AMP PEAK 25(12Q15) WILD-TYPE 51 88 96 53 2

Figure S121.  Get High-res Image Gene #25: 'amp_12q15' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12q15' versus 'MRNASEQ_CNMF'

P value = 0.0255 (Fisher's exact test), Q value = 0.066

Table S122.  Gene #25: 'amp_12q15' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
AMP PEAK 25(12Q15) MUTATED 22 44 12 18 22
AMP PEAK 25(12Q15) WILD-TYPE 50 91 26 85 34

Figure S122.  Get High-res Image Gene #25: 'amp_12q15' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_12q15' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0091 (Fisher's exact test), Q value = 0.03

Table S123.  Gene #25: 'amp_12q15' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
AMP PEAK 25(12Q15) MUTATED 41 40 37
AMP PEAK 25(12Q15) WILD-TYPE 77 72 137

Figure S123.  Get High-res Image Gene #25: 'amp_12q15' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_12q15' versus 'MIRSEQ_CNMF'

P value = 0.00397 (Fisher's exact test), Q value = 0.016

Table S124.  Gene #25: 'amp_12q15' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 74 114 25 87
AMP PEAK 25(12Q15) MUTATED 16 28 36 9 29
AMP PEAK 25(12Q15) WILD-TYPE 89 46 78 16 58

Figure S124.  Get High-res Image Gene #25: 'amp_12q15' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_12q15' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0363 (Fisher's exact test), Q value = 0.085

Table S125.  Gene #25: 'amp_12q15' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 266 83 56
AMP PEAK 25(12Q15) MUTATED 67 33 18
AMP PEAK 25(12Q15) WILD-TYPE 199 50 38

Figure S125.  Get High-res Image Gene #25: 'amp_12q15' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_12q15' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0026 (Fisher's exact test), Q value = 0.011

Table S126.  Gene #25: 'amp_12q15' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 124 51 127 92
AMP PEAK 25(12Q15) MUTATED 43 20 40 14
AMP PEAK 25(12Q15) WILD-TYPE 81 31 87 78

Figure S126.  Get High-res Image Gene #25: 'amp_12q15' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_12q15' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00062

Table S127.  Gene #25: 'amp_12q15' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 60 41 132 74
AMP PEAK 25(12Q15) MUTATED 23 28 19 37 10
AMP PEAK 25(12Q15) WILD-TYPE 64 32 22 95 64

Figure S127.  Get High-res Image Gene #25: 'amp_12q15' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_13q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S128.  Gene #26: 'amp_13q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
AMP PEAK 26(13Q22.1) MUTATED 32 56 16 24 0
AMP PEAK 26(13Q22.1) WILD-TYPE 46 90 105 37 2

Figure S128.  Get High-res Image Gene #26: 'amp_13q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_16p13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S129.  Gene #27: 'amp_16p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
AMP PEAK 27(16P13.2) MUTATED 17 49 10 9 2
AMP PEAK 27(16P13.2) WILD-TYPE 61 97 111 52 0

Figure S129.  Get High-res Image Gene #27: 'amp_16p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_16p13.2' versus 'METHLYATION_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.0027

Table S130.  Gene #27: 'amp_16p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
AMP PEAK 27(16P13.2) MUTATED 26 43 9 9
AMP PEAK 27(16P13.2) WILD-TYPE 112 84 54 71

Figure S130.  Get High-res Image Gene #27: 'amp_16p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_16p13.2' versus 'MRNASEQ_CNMF'

P value = 0.00818 (Fisher's exact test), Q value = 0.028

Table S131.  Gene #27: 'amp_16p13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
AMP PEAK 27(16P13.2) MUTATED 12 28 6 18 23
AMP PEAK 27(16P13.2) WILD-TYPE 60 107 32 85 33

Figure S131.  Get High-res Image Gene #27: 'amp_16p13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_16p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S132.  Gene #28: 'amp_16p11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
AMP PEAK 28(16P11.2) MUTATED 15 57 10 14 2
AMP PEAK 28(16P11.2) WILD-TYPE 63 89 111 47 0

Figure S132.  Get High-res Image Gene #28: 'amp_16p11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_16p11.2' versus 'METHLYATION_CNMF'

P value = 0.019 (Fisher's exact test), Q value = 0.052

Table S133.  Gene #28: 'amp_16p11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
AMP PEAK 28(16P11.2) MUTATED 32 42 12 12
AMP PEAK 28(16P11.2) WILD-TYPE 106 85 51 68

Figure S133.  Get High-res Image Gene #28: 'amp_16p11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_16q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S134.  Gene #29: 'amp_16q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
AMP PEAK 29(16Q22.1) MUTATED 13 72 11 11 1
AMP PEAK 29(16Q22.1) WILD-TYPE 65 74 110 50 1

Figure S134.  Get High-res Image Gene #29: 'amp_16q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_16q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00466 (Fisher's exact test), Q value = 0.018

Table S135.  Gene #29: 'amp_16q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
AMP PEAK 29(16Q22.1) MUTATED 41 18 48
AMP PEAK 29(16Q22.1) WILD-TYPE 77 94 126

Figure S135.  Get High-res Image Gene #29: 'amp_16q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_16q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0147 (Fisher's exact test), Q value = 0.043

Table S136.  Gene #29: 'amp_16q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 266 83 56
AMP PEAK 29(16Q22.1) MUTATED 59 31 18
AMP PEAK 29(16Q22.1) WILD-TYPE 207 52 38

Figure S136.  Get High-res Image Gene #29: 'amp_16q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_16q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0292 (Fisher's exact test), Q value = 0.073

Table S137.  Gene #29: 'amp_16q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 124 51 127 92
AMP PEAK 29(16Q22.1) MUTATED 40 18 23 26
AMP PEAK 29(16Q22.1) WILD-TYPE 84 33 104 66

Figure S137.  Get High-res Image Gene #29: 'amp_16q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_17p11.2' versus 'CN_CNMF'

P value = 0.00468 (Fisher's exact test), Q value = 0.018

Table S138.  Gene #30: 'amp_17p11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
AMP PEAK 30(17P11.2) MUTATED 19 39 13 16 1
AMP PEAK 30(17P11.2) WILD-TYPE 59 107 108 45 1

Figure S138.  Get High-res Image Gene #30: 'amp_17p11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S139.  Gene #31: 'amp_17q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
AMP PEAK 31(17Q11.2) MUTATED 54 79 22 19 0
AMP PEAK 31(17Q11.2) WILD-TYPE 24 67 99 42 2

Figure S139.  Get High-res Image Gene #31: 'amp_17q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S140.  Gene #31: 'amp_17q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
AMP PEAK 31(17Q11.2) MUTATED 37 74 26 37
AMP PEAK 31(17Q11.2) WILD-TYPE 101 53 37 43

Figure S140.  Get High-res Image Gene #31: 'amp_17q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_17q11.2' versus 'MRNASEQ_CNMF'

P value = 0.00052 (Fisher's exact test), Q value = 0.0031

Table S141.  Gene #31: 'amp_17q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
AMP PEAK 31(17Q11.2) MUTATED 27 69 15 29 33
AMP PEAK 31(17Q11.2) WILD-TYPE 45 66 23 74 23

Figure S141.  Get High-res Image Gene #31: 'amp_17q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_17q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.002

Table S142.  Gene #31: 'amp_17q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
AMP PEAK 31(17Q11.2) MUTATED 62 56 55
AMP PEAK 31(17Q11.2) WILD-TYPE 56 56 119

Figure S142.  Get High-res Image Gene #31: 'amp_17q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_17q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00248 (Fisher's exact test), Q value = 0.011

Table S143.  Gene #31: 'amp_17q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 124 51 127 92
AMP PEAK 31(17Q11.2) MUTATED 53 29 62 26
AMP PEAK 31(17Q11.2) WILD-TYPE 71 22 65 66

Figure S143.  Get High-res Image Gene #31: 'amp_17q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_17q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.01 (Fisher's exact test), Q value = 0.032

Table S144.  Gene #31: 'amp_17q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 60 41 132 74
AMP PEAK 31(17Q11.2) MUTATED 35 30 17 68 20
AMP PEAK 31(17Q11.2) WILD-TYPE 52 30 24 64 54

Figure S144.  Get High-res Image Gene #31: 'amp_17q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S145.  Gene #32: 'amp_17q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
AMP PEAK 32(17Q12) MUTATED 53 67 25 20 0
AMP PEAK 32(17Q12) WILD-TYPE 25 79 96 41 2

Figure S145.  Get High-res Image Gene #32: 'amp_17q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q12' versus 'METHLYATION_CNMF'

P value = 0.0325 (Fisher's exact test), Q value = 0.078

Table S146.  Gene #32: 'amp_17q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
AMP PEAK 32(17Q12) MUTATED 43 61 25 36
AMP PEAK 32(17Q12) WILD-TYPE 95 66 38 44

Figure S146.  Get High-res Image Gene #32: 'amp_17q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_17q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0352 (Fisher's exact test), Q value = 0.083

Table S147.  Gene #32: 'amp_17q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
AMP PEAK 32(17Q12) MUTATED 50 55 59
AMP PEAK 32(17Q12) WILD-TYPE 68 57 115

Figure S147.  Get High-res Image Gene #32: 'amp_17q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_CNMF'

P value = 0.0371 (Fisher's exact test), Q value = 0.087

Table S148.  Gene #32: 'amp_17q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 74 114 25 87
AMP PEAK 32(17Q12) MUTATED 33 38 53 10 30
AMP PEAK 32(17Q12) WILD-TYPE 72 36 61 15 57

Figure S148.  Get High-res Image Gene #32: 'amp_17q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_17q12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00909 (Fisher's exact test), Q value = 0.03

Table S149.  Gene #32: 'amp_17q12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 124 51 127 92
AMP PEAK 32(17Q12) MUTATED 45 28 60 28
AMP PEAK 32(17Q12) WILD-TYPE 79 23 67 64

Figure S149.  Get High-res Image Gene #32: 'amp_17q12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_17q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00909 (Fisher's exact test), Q value = 0.03

Table S150.  Gene #32: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 60 41 132 74
AMP PEAK 32(17Q12) MUTATED 31 33 14 62 21
AMP PEAK 32(17Q12) WILD-TYPE 56 27 27 70 53

Figure S150.  Get High-res Image Gene #32: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17q23.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S151.  Gene #33: 'amp_17q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
AMP PEAK 33(17Q23.3) MUTATED 59 80 31 23 1
AMP PEAK 33(17Q23.3) WILD-TYPE 19 66 90 38 1

Figure S151.  Get High-res Image Gene #33: 'amp_17q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q23.3' versus 'METHLYATION_CNMF'

P value = 0.0321 (Fisher's exact test), Q value = 0.078

Table S152.  Gene #33: 'amp_17q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
AMP PEAK 33(17Q23.3) MUTATED 57 73 25 39
AMP PEAK 33(17Q23.3) WILD-TYPE 81 54 38 41

Figure S152.  Get High-res Image Gene #33: 'amp_17q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_19q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S153.  Gene #34: 'amp_19q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
AMP PEAK 34(19Q12) MUTATED 37 87 17 22 1
AMP PEAK 34(19Q12) WILD-TYPE 41 59 104 39 1

Figure S153.  Get High-res Image Gene #34: 'amp_19q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19q12' versus 'METHLYATION_CNMF'

P value = 0.00235 (Fisher's exact test), Q value = 0.01

Table S154.  Gene #34: 'amp_19q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
AMP PEAK 34(19Q12) MUTATED 43 68 24 29
AMP PEAK 34(19Q12) WILD-TYPE 95 59 39 51

Figure S154.  Get High-res Image Gene #34: 'amp_19q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_19q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0427 (Fisher's exact test), Q value = 0.097

Table S155.  Gene #34: 'amp_19q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 266 83 56
AMP PEAK 34(19Q12) MUTATED 96 40 28
AMP PEAK 34(19Q12) WILD-TYPE 170 43 28

Figure S155.  Get High-res Image Gene #34: 'amp_19q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_19q13.43' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S156.  Gene #35: 'amp_19q13.43' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
AMP PEAK 35(19Q13.43) MUTATED 35 80 18 22 0
AMP PEAK 35(19Q13.43) WILD-TYPE 43 66 103 39 2

Figure S156.  Get High-res Image Gene #35: 'amp_19q13.43' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19q13.43' versus 'METHLYATION_CNMF'

P value = 0.00636 (Fisher's exact test), Q value = 0.023

Table S157.  Gene #35: 'amp_19q13.43' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
AMP PEAK 35(19Q13.43) MUTATED 39 61 21 34
AMP PEAK 35(19Q13.43) WILD-TYPE 99 66 42 46

Figure S157.  Get High-res Image Gene #35: 'amp_19q13.43' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_19q13.43' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0472 (Fisher's exact test), Q value = 0.11

Table S158.  Gene #35: 'amp_19q13.43' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 124 51 127 92
AMP PEAK 35(19Q13.43) MUTATED 42 27 53 29
AMP PEAK 35(19Q13.43) WILD-TYPE 82 24 74 63

Figure S158.  Get High-res Image Gene #35: 'amp_19q13.43' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_20q11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S159.  Gene #36: 'amp_20q11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
AMP PEAK 36(20Q11.21) MUTATED 68 112 38 44 1
AMP PEAK 36(20Q11.21) WILD-TYPE 10 34 83 17 1

Figure S159.  Get High-res Image Gene #36: 'amp_20q11.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20q11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0267 (Fisher's exact test), Q value = 0.068

Table S160.  Gene #36: 'amp_20q11.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
AMP PEAK 36(20Q11.21) MUTATED 87 64 110
AMP PEAK 36(20Q11.21) WILD-TYPE 31 48 64

Figure S160.  Get High-res Image Gene #36: 'amp_20q11.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_20q11.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0469 (Fisher's exact test), Q value = 0.1

Table S161.  Gene #36: 'amp_20q11.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 60 41 132 74
AMP PEAK 36(20Q11.21) MUTATED 57 48 30 81 43
AMP PEAK 36(20Q11.21) WILD-TYPE 30 12 11 51 31

Figure S161.  Get High-res Image Gene #36: 'amp_20q11.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_22q12.2' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00062

Table S162.  Gene #37: 'amp_22q12.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
AMP PEAK 37(22Q12.2) MUTATED 17 45 10 15 0
AMP PEAK 37(22Q12.2) WILD-TYPE 61 101 111 46 2

Figure S162.  Get High-res Image Gene #37: 'amp_22q12.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.11' versus 'METHLYATION_CNMF'

P value = 0.016 (Fisher's exact test), Q value = 0.046

Table S163.  Gene #38: 'del_1p36.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
DEL PEAK 1(1P36.11) MUTATED 35 36 11 9
DEL PEAK 1(1P36.11) WILD-TYPE 103 91 52 71

Figure S163.  Get High-res Image Gene #38: 'del_1p36.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1q32.1' versus 'CN_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.0019

Table S164.  Gene #39: 'del_1q32.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
DEL PEAK 2(1Q32.1) MUTATED 16 33 7 16 0
DEL PEAK 2(1Q32.1) WILD-TYPE 62 113 114 45 2

Figure S164.  Get High-res Image Gene #39: 'del_1q32.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_1q32.1' versus 'METHLYATION_CNMF'

P value = 0.0279 (Fisher's exact test), Q value = 0.071

Table S165.  Gene #39: 'del_1q32.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
DEL PEAK 2(1Q32.1) MUTATED 18 33 11 10
DEL PEAK 2(1Q32.1) WILD-TYPE 120 94 52 70

Figure S165.  Get High-res Image Gene #39: 'del_1q32.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1q32.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0447 (Fisher's exact test), Q value = 0.1

Table S166.  Gene #39: 'del_1q32.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
DEL PEAK 2(1Q32.1) MUTATED 28 21 22
DEL PEAK 2(1Q32.1) WILD-TYPE 90 91 152

Figure S166.  Get High-res Image Gene #39: 'del_1q32.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_2q22.1' versus 'CN_CNMF'

P value = 0.00127 (Fisher's exact test), Q value = 0.0061

Table S167.  Gene #40: 'del_2q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
DEL PEAK 3(2Q22.1) MUTATED 29 55 24 24 2
DEL PEAK 3(2Q22.1) WILD-TYPE 49 91 97 37 0

Figure S167.  Get High-res Image Gene #40: 'del_2q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q22.1' versus 'METHLYATION_CNMF'

P value = 0.0077 (Fisher's exact test), Q value = 0.027

Table S168.  Gene #40: 'del_2q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
DEL PEAK 3(2Q22.1) MUTATED 36 57 18 23
DEL PEAK 3(2Q22.1) WILD-TYPE 102 70 45 57

Figure S168.  Get High-res Image Gene #40: 'del_2q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q22.1' versus 'MRNASEQ_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.0022

Table S169.  Gene #40: 'del_2q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
DEL PEAK 3(2Q22.1) MUTATED 21 51 8 22 30
DEL PEAK 3(2Q22.1) WILD-TYPE 51 84 30 81 26

Figure S169.  Get High-res Image Gene #40: 'del_2q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2q34' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S170.  Gene #41: 'del_2q34' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
DEL PEAK 4(2Q34) MUTATED 33 85 19 36 1
DEL PEAK 4(2Q34) WILD-TYPE 45 61 102 25 1

Figure S170.  Get High-res Image Gene #41: 'del_2q34' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q34' versus 'METHLYATION_CNMF'

P value = 0.00098 (Fisher's exact test), Q value = 0.005

Table S171.  Gene #41: 'del_2q34' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
DEL PEAK 4(2Q34) MUTATED 47 72 21 34
DEL PEAK 4(2Q34) WILD-TYPE 91 55 42 46

Figure S171.  Get High-res Image Gene #41: 'del_2q34' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q34' versus 'RPPA_CNMF'

P value = 0.00662 (Fisher's exact test), Q value = 0.024

Table S172.  Gene #41: 'del_2q34' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 114 104
DEL PEAK 4(2Q34) MUTATED 45 39 56
DEL PEAK 4(2Q34) WILD-TYPE 77 75 48

Figure S172.  Get High-res Image Gene #41: 'del_2q34' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_2q34' versus 'MRNASEQ_CNMF'

P value = 0.00767 (Fisher's exact test), Q value = 0.027

Table S173.  Gene #41: 'del_2q34' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
DEL PEAK 4(2Q34) MUTATED 29 64 7 42 30
DEL PEAK 4(2Q34) WILD-TYPE 43 71 31 61 26

Figure S173.  Get High-res Image Gene #41: 'del_2q34' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2q37.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S174.  Gene #42: 'del_2q37.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
DEL PEAK 5(2Q37.1) MUTATED 40 100 28 38 1
DEL PEAK 5(2Q37.1) WILD-TYPE 38 46 93 23 1

Figure S174.  Get High-res Image Gene #42: 'del_2q37.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q37.1' versus 'METHLYATION_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.0019

Table S175.  Gene #42: 'del_2q37.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
DEL PEAK 5(2Q37.1) MUTATED 54 80 27 46
DEL PEAK 5(2Q37.1) WILD-TYPE 84 47 36 34

Figure S175.  Get High-res Image Gene #42: 'del_2q37.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q37.1' versus 'RPPA_CNMF'

P value = 0.0434 (Fisher's exact test), Q value = 0.098

Table S176.  Gene #42: 'del_2q37.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 114 104
DEL PEAK 5(2Q37.1) MUTATED 55 49 61
DEL PEAK 5(2Q37.1) WILD-TYPE 67 65 43

Figure S176.  Get High-res Image Gene #42: 'del_2q37.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_2q37.1' versus 'MRNASEQ_CNMF'

P value = 0.0255 (Fisher's exact test), Q value = 0.066

Table S177.  Gene #42: 'del_2q37.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
DEL PEAK 5(2Q37.1) MUTATED 32 79 13 47 33
DEL PEAK 5(2Q37.1) WILD-TYPE 40 56 25 56 23

Figure S177.  Get High-res Image Gene #42: 'del_2q37.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p14.2' versus 'CN_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00069

Table S178.  Gene #43: 'del_3p14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
DEL PEAK 6(3P14.2) MUTATED 23 60 18 15 1
DEL PEAK 6(3P14.2) WILD-TYPE 55 86 103 46 1

Figure S178.  Get High-res Image Gene #43: 'del_3p14.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p14.2' versus 'METHLYATION_CNMF'

P value = 0.0278 (Fisher's exact test), Q value = 0.071

Table S179.  Gene #43: 'del_3p14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
DEL PEAK 6(3P14.2) MUTATED 50 28 13 26
DEL PEAK 6(3P14.2) WILD-TYPE 88 99 50 54

Figure S179.  Get High-res Image Gene #43: 'del_3p14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p14.2' versus 'RPPA_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.0011

Table S180.  Gene #43: 'del_3p14.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 114 104
DEL PEAK 6(3P14.2) MUTATED 37 18 42
DEL PEAK 6(3P14.2) WILD-TYPE 85 96 62

Figure S180.  Get High-res Image Gene #43: 'del_3p14.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_3p14.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0104 (Fisher's exact test), Q value = 0.033

Table S181.  Gene #43: 'del_3p14.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 121 98 31
DEL PEAK 6(3P14.2) MUTATED 28 22 35 12
DEL PEAK 6(3P14.2) WILD-TYPE 62 99 63 19

Figure S181.  Get High-res Image Gene #43: 'del_3p14.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_3p14.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S182.  Gene #43: 'del_3p14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
DEL PEAK 6(3P14.2) MUTATED 12 24 15 48 16
DEL PEAK 6(3P14.2) WILD-TYPE 60 111 23 55 40

Figure S182.  Get High-res Image Gene #43: 'del_3p14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00035

Table S183.  Gene #43: 'del_3p14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
DEL PEAK 6(3P14.2) MUTATED 27 19 69
DEL PEAK 6(3P14.2) WILD-TYPE 91 93 105

Figure S183.  Get High-res Image Gene #43: 'del_3p14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p14.2' versus 'MIRSEQ_CNMF'

P value = 0.00094 (Fisher's exact test), Q value = 0.0049

Table S184.  Gene #43: 'del_3p14.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 74 114 25 87
DEL PEAK 6(3P14.2) MUTATED 46 22 21 8 20
DEL PEAK 6(3P14.2) WILD-TYPE 59 52 93 17 67

Figure S184.  Get High-res Image Gene #43: 'del_3p14.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3p14.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.0019

Table S185.  Gene #43: 'del_3p14.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 124 51 127 92
DEL PEAK 6(3P14.2) MUTATED 29 13 29 44
DEL PEAK 6(3P14.2) WILD-TYPE 95 38 98 48

Figure S185.  Get High-res Image Gene #43: 'del_3p14.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_3p14.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.0014

Table S186.  Gene #43: 'del_3p14.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 60 41 132 74
DEL PEAK 6(3P14.2) MUTATED 16 16 16 31 36
DEL PEAK 6(3P14.2) WILD-TYPE 71 44 25 101 38

Figure S186.  Get High-res Image Gene #43: 'del_3p14.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S187.  Gene #44: 'del_4q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
DEL PEAK 7(4Q22.1) MUTATED 36 74 16 34 1
DEL PEAK 7(4Q22.1) WILD-TYPE 42 72 105 27 1

Figure S187.  Get High-res Image Gene #44: 'del_4q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q22.1' versus 'RPPA_CNMF'

P value = 0.00112 (Fisher's exact test), Q value = 0.0056

Table S188.  Gene #44: 'del_4q22.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 114 104
DEL PEAK 7(4Q22.1) MUTATED 51 27 48
DEL PEAK 7(4Q22.1) WILD-TYPE 71 87 56

Figure S188.  Get High-res Image Gene #44: 'del_4q22.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_4q22.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0105 (Fisher's exact test), Q value = 0.033

Table S189.  Gene #44: 'del_4q22.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 121 98 31
DEL PEAK 7(4Q22.1) MUTATED 43 34 41 8
DEL PEAK 7(4Q22.1) WILD-TYPE 47 87 57 23

Figure S189.  Get High-res Image Gene #44: 'del_4q22.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_4q22.1' versus 'MRNASEQ_CNMF'

P value = 0.0179 (Fisher's exact test), Q value = 0.05

Table S190.  Gene #44: 'del_4q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
DEL PEAK 7(4Q22.1) MUTATED 26 44 10 50 28
DEL PEAK 7(4Q22.1) WILD-TYPE 46 91 28 53 28

Figure S190.  Get High-res Image Gene #44: 'del_4q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00122 (Fisher's exact test), Q value = 0.0061

Table S191.  Gene #44: 'del_4q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
DEL PEAK 7(4Q22.1) MUTATED 52 28 78
DEL PEAK 7(4Q22.1) WILD-TYPE 66 84 96

Figure S191.  Get High-res Image Gene #44: 'del_4q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q22.1' versus 'MIRSEQ_CNMF'

P value = 0.0133 (Fisher's exact test), Q value = 0.04

Table S192.  Gene #44: 'del_4q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 74 114 25 87
DEL PEAK 7(4Q22.1) MUTATED 53 27 33 13 35
DEL PEAK 7(4Q22.1) WILD-TYPE 52 47 81 12 52

Figure S192.  Get High-res Image Gene #44: 'del_4q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_4q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0284 (Fisher's exact test), Q value = 0.071

Table S193.  Gene #44: 'del_4q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 60 41 132 74
DEL PEAK 7(4Q22.1) MUTATED 32 22 17 43 41
DEL PEAK 7(4Q22.1) WILD-TYPE 55 38 24 89 33

Figure S193.  Get High-res Image Gene #44: 'del_4q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q34.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S194.  Gene #45: 'del_4q34.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
DEL PEAK 8(4Q34.2) MUTATED 36 85 16 39 1
DEL PEAK 8(4Q34.2) WILD-TYPE 42 61 105 22 1

Figure S194.  Get High-res Image Gene #45: 'del_4q34.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q34.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.041 (Fisher's exact test), Q value = 0.094

Table S195.  Gene #45: 'del_4q34.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
DEL PEAK 8(4Q34.2) MUTATED 55 37 82
DEL PEAK 8(4Q34.2) WILD-TYPE 63 75 92

Figure S195.  Get High-res Image Gene #45: 'del_4q34.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_5q12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S196.  Gene #46: 'del_5q12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
DEL PEAK 9(5Q12.1) MUTATED 46 102 21 32 1
DEL PEAK 9(5Q12.1) WILD-TYPE 32 44 100 29 1

Figure S196.  Get High-res Image Gene #46: 'del_5q12.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q12.1' versus 'METHLYATION_CNMF'

P value = 0.00141 (Fisher's exact test), Q value = 0.0068

Table S197.  Gene #46: 'del_5q12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
DEL PEAK 9(5Q12.1) MUTATED 66 79 21 36
DEL PEAK 9(5Q12.1) WILD-TYPE 72 48 42 44

Figure S197.  Get High-res Image Gene #46: 'del_5q12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00456 (Fisher's exact test), Q value = 0.018

Table S198.  Gene #46: 'del_5q12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
DEL PEAK 9(5Q12.1) MUTATED 73 46 82
DEL PEAK 9(5Q12.1) WILD-TYPE 45 66 92

Figure S198.  Get High-res Image Gene #46: 'del_5q12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_5q12.1' versus 'MIRSEQ_CNMF'

P value = 0.00182 (Fisher's exact test), Q value = 0.0082

Table S199.  Gene #46: 'del_5q12.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 74 114 25 87
DEL PEAK 9(5Q12.1) MUTATED 45 49 46 17 45
DEL PEAK 9(5Q12.1) WILD-TYPE 60 25 68 8 42

Figure S199.  Get High-res Image Gene #46: 'del_5q12.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_5q12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0121 (Fisher's exact test), Q value = 0.037

Table S200.  Gene #46: 'del_5q12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 266 83 56
DEL PEAK 9(5Q12.1) MUTATED 119 52 31
DEL PEAK 9(5Q12.1) WILD-TYPE 147 31 25

Figure S200.  Get High-res Image Gene #46: 'del_5q12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_6p25.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S201.  Gene #47: 'del_6p25.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
DEL PEAK 10(6P25.3) MUTATED 36 47 7 15 1
DEL PEAK 10(6P25.3) WILD-TYPE 42 99 114 46 1

Figure S201.  Get High-res Image Gene #47: 'del_6p25.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_6p25.3' versus 'METHLYATION_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.0023

Table S202.  Gene #47: 'del_6p25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
DEL PEAK 10(6P25.3) MUTATED 25 51 14 16
DEL PEAK 10(6P25.3) WILD-TYPE 113 76 49 64

Figure S202.  Get High-res Image Gene #47: 'del_6p25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6p25.3' versus 'RPPA_CNMF'

P value = 0.0391 (Fisher's exact test), Q value = 0.091

Table S203.  Gene #47: 'del_6p25.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 114 104
DEL PEAK 10(6P25.3) MUTATED 34 24 38
DEL PEAK 10(6P25.3) WILD-TYPE 88 90 66

Figure S203.  Get High-res Image Gene #47: 'del_6p25.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_6p25.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0148 (Fisher's exact test), Q value = 0.043

Table S204.  Gene #47: 'del_6p25.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
DEL PEAK 10(6P25.3) MUTATED 42 26 36
DEL PEAK 10(6P25.3) WILD-TYPE 76 86 138

Figure S204.  Get High-res Image Gene #47: 'del_6p25.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6q21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S205.  Gene #48: 'del_6q21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
DEL PEAK 11(6Q21) MUTATED 54 99 16 21 0
DEL PEAK 11(6Q21) WILD-TYPE 24 47 105 40 2

Figure S205.  Get High-res Image Gene #48: 'del_6q21' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q21' versus 'MIRSEQ_CNMF'

P value = 0.00299 (Fisher's exact test), Q value = 0.012

Table S206.  Gene #48: 'del_6q21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 74 114 25 87
DEL PEAK 11(6Q21) MUTATED 42 48 44 10 45
DEL PEAK 11(6Q21) WILD-TYPE 63 26 70 15 42

Figure S206.  Get High-res Image Gene #48: 'del_6q21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_6q21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0147 (Fisher's exact test), Q value = 0.043

Table S207.  Gene #48: 'del_6q21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 266 83 56
DEL PEAK 11(6Q21) MUTATED 112 50 27
DEL PEAK 11(6Q21) WILD-TYPE 154 33 29

Figure S207.  Get High-res Image Gene #48: 'del_6q21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_6q21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00625 (Fisher's exact test), Q value = 0.023

Table S208.  Gene #48: 'del_6q21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 60 41 132 74
DEL PEAK 11(6Q21) MUTATED 36 37 27 58 29
DEL PEAK 11(6Q21) WILD-TYPE 51 23 14 74 45

Figure S208.  Get High-res Image Gene #48: 'del_6q21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q27' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S209.  Gene #49: 'del_6q27' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
DEL PEAK 12(6Q27) MUTATED 55 100 14 21 0
DEL PEAK 12(6Q27) WILD-TYPE 23 46 107 40 2

Figure S209.  Get High-res Image Gene #49: 'del_6q27' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q27' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0107 (Fisher's exact test), Q value = 0.034

Table S210.  Gene #49: 'del_6q27' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
DEL PEAK 12(6Q27) MUTATED 69 47 73
DEL PEAK 12(6Q27) WILD-TYPE 49 65 101

Figure S210.  Get High-res Image Gene #49: 'del_6q27' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6q27' versus 'MIRSEQ_CNMF'

P value = 0.0137 (Fisher's exact test), Q value = 0.041

Table S211.  Gene #49: 'del_6q27' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 74 114 25 87
DEL PEAK 12(6Q27) MUTATED 39 46 48 12 44
DEL PEAK 12(6Q27) WILD-TYPE 66 28 66 13 43

Figure S211.  Get High-res Image Gene #49: 'del_6q27' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_6q27' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0108 (Fisher's exact test), Q value = 0.034

Table S212.  Gene #49: 'del_6q27' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 266 83 56
DEL PEAK 12(6Q27) MUTATED 111 50 28
DEL PEAK 12(6Q27) WILD-TYPE 155 33 28

Figure S212.  Get High-res Image Gene #49: 'del_6q27' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_6q27' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00281 (Fisher's exact test), Q value = 0.012

Table S213.  Gene #49: 'del_6q27' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 60 41 132 74
DEL PEAK 12(6Q27) MUTATED 37 37 28 56 29
DEL PEAK 12(6Q27) WILD-TYPE 50 23 13 76 45

Figure S213.  Get High-res Image Gene #49: 'del_6q27' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_7q36.3' versus 'CN_CNMF'

P value = 0.00051 (Fisher's exact test), Q value = 0.003

Table S214.  Gene #50: 'del_7q36.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
DEL PEAK 13(7Q36.3) MUTATED 10 28 6 16 0
DEL PEAK 13(7Q36.3) WILD-TYPE 68 118 115 45 2

Figure S214.  Get High-res Image Gene #50: 'del_7q36.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_7q36.3' versus 'MRNASEQ_CNMF'

P value = 0.0325 (Fisher's exact test), Q value = 0.078

Table S215.  Gene #50: 'del_7q36.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
DEL PEAK 13(7Q36.3) MUTATED 7 15 3 23 12
DEL PEAK 13(7Q36.3) WILD-TYPE 65 120 35 80 44

Figure S215.  Get High-res Image Gene #50: 'del_7q36.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_7q36.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0208 (Fisher's exact test), Q value = 0.057

Table S216.  Gene #50: 'del_7q36.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 124 51 127 92
DEL PEAK 13(7Q36.3) MUTATED 11 6 21 22
DEL PEAK 13(7Q36.3) WILD-TYPE 113 45 106 70

Figure S216.  Get High-res Image Gene #50: 'del_7q36.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_7q36.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0297 (Fisher's exact test), Q value = 0.074

Table S217.  Gene #50: 'del_7q36.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 60 41 132 74
DEL PEAK 13(7Q36.3) MUTATED 5 10 5 24 16
DEL PEAK 13(7Q36.3) WILD-TYPE 82 50 36 108 58

Figure S217.  Get High-res Image Gene #50: 'del_7q36.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p23.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S218.  Gene #51: 'del_8p23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
DEL PEAK 14(8P23.3) MUTATED 30 130 34 48 1
DEL PEAK 14(8P23.3) WILD-TYPE 48 16 87 13 1

Figure S218.  Get High-res Image Gene #51: 'del_8p23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p23.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S219.  Gene #51: 'del_8p23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
DEL PEAK 14(8P23.3) MUTATED 89 93 22 39
DEL PEAK 14(8P23.3) WILD-TYPE 49 34 41 41

Figure S219.  Get High-res Image Gene #51: 'del_8p23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_8p23.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00841 (Fisher's exact test), Q value = 0.029

Table S220.  Gene #51: 'del_8p23.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 121 98 31
DEL PEAK 14(8P23.3) MUTATED 57 56 66 20
DEL PEAK 14(8P23.3) WILD-TYPE 33 65 32 11

Figure S220.  Get High-res Image Gene #51: 'del_8p23.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_8p23.3' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00049

Table S221.  Gene #51: 'del_8p23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
DEL PEAK 14(8P23.3) MUTATED 46 74 11 70 41
DEL PEAK 14(8P23.3) WILD-TYPE 26 61 27 33 15

Figure S221.  Get High-res Image Gene #51: 'del_8p23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_8p23.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.00097

Table S222.  Gene #51: 'del_8p23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
DEL PEAK 14(8P23.3) MUTATED 85 51 106
DEL PEAK 14(8P23.3) WILD-TYPE 33 61 68

Figure S222.  Get High-res Image Gene #51: 'del_8p23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00979 (Fisher's exact test), Q value = 0.032

Table S223.  Gene #51: 'del_8p23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 266 83 56
DEL PEAK 14(8P23.3) MUTATED 144 58 39
DEL PEAK 14(8P23.3) WILD-TYPE 122 25 17

Figure S223.  Get High-res Image Gene #51: 'del_8p23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_8p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S224.  Gene #52: 'del_8p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
DEL PEAK 15(8P21.3) MUTATED 33 135 34 49 1
DEL PEAK 15(8P21.3) WILD-TYPE 45 11 87 12 1

Figure S224.  Get High-res Image Gene #52: 'del_8p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p21.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S225.  Gene #52: 'del_8p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
DEL PEAK 15(8P21.3) MUTATED 90 95 25 42
DEL PEAK 15(8P21.3) WILD-TYPE 48 32 38 38

Figure S225.  Get High-res Image Gene #52: 'del_8p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_8p21.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0336 (Fisher's exact test), Q value = 0.08

Table S226.  Gene #52: 'del_8p21.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 121 98 31
DEL PEAK 15(8P21.3) MUTATED 60 62 67 21
DEL PEAK 15(8P21.3) WILD-TYPE 30 59 31 10

Figure S226.  Get High-res Image Gene #52: 'del_8p21.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_8p21.3' versus 'MRNASEQ_CNMF'

P value = 0.00091 (Fisher's exact test), Q value = 0.0048

Table S227.  Gene #52: 'del_8p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
DEL PEAK 15(8P21.3) MUTATED 46 80 13 76 36
DEL PEAK 15(8P21.3) WILD-TYPE 26 55 25 27 20

Figure S227.  Get High-res Image Gene #52: 'del_8p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_8p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00865 (Fisher's exact test), Q value = 0.029

Table S228.  Gene #52: 'del_8p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
DEL PEAK 15(8P21.3) MUTATED 83 57 111
DEL PEAK 15(8P21.3) WILD-TYPE 35 55 63

Figure S228.  Get High-res Image Gene #52: 'del_8p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_8p21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00448 (Fisher's exact test), Q value = 0.017

Table S229.  Gene #52: 'del_8p21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 266 83 56
DEL PEAK 15(8P21.3) MUTATED 150 63 37
DEL PEAK 15(8P21.3) WILD-TYPE 116 20 19

Figure S229.  Get High-res Image Gene #52: 'del_8p21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_8p21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0497 (Fisher's exact test), Q value = 0.11

Table S230.  Gene #52: 'del_8p21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 124 51 127 92
DEL PEAK 15(8P21.3) MUTATED 75 36 69 65
DEL PEAK 15(8P21.3) WILD-TYPE 49 15 58 27

Figure S230.  Get High-res Image Gene #52: 'del_8p21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_8p21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0419 (Fisher's exact test), Q value = 0.096

Table S231.  Gene #52: 'del_8p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 60 41 132 74
DEL PEAK 15(8P21.3) MUTATED 47 46 27 76 49
DEL PEAK 15(8P21.3) WILD-TYPE 40 14 14 56 25

Figure S231.  Get High-res Image Gene #52: 'del_8p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S232.  Gene #53: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
DEL PEAK 16(9P23) MUTATED 32 89 52 3 1
DEL PEAK 16(9P23) WILD-TYPE 46 57 69 58 1

Figure S232.  Get High-res Image Gene #53: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p23' versus 'METHLYATION_CNMF'

P value = 0.00098 (Fisher's exact test), Q value = 0.005

Table S233.  Gene #53: 'del_9p23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
DEL PEAK 16(9P23) MUTATED 41 65 31 40
DEL PEAK 16(9P23) WILD-TYPE 97 62 32 40

Figure S233.  Get High-res Image Gene #53: 'del_9p23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p23' versus 'RPPA_CNMF'

P value = 0.0216 (Fisher's exact test), Q value = 0.058

Table S234.  Gene #53: 'del_9p23' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 114 104
DEL PEAK 16(9P23) MUTATED 44 61 42
DEL PEAK 16(9P23) WILD-TYPE 78 53 62

Figure S234.  Get High-res Image Gene #53: 'del_9p23' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_9p23' versus 'RPPA_CHIERARCHICAL'

P value = 0.00463 (Fisher's exact test), Q value = 0.018

Table S235.  Gene #53: 'del_9p23' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 121 98 31
DEL PEAK 16(9P23) MUTATED 39 66 30 12
DEL PEAK 16(9P23) WILD-TYPE 51 55 68 19

Figure S235.  Get High-res Image Gene #53: 'del_9p23' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_9p23' versus 'MRNASEQ_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.0028

Table S236.  Gene #53: 'del_9p23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
DEL PEAK 16(9P23) MUTATED 31 66 26 30 24
DEL PEAK 16(9P23) WILD-TYPE 41 69 12 73 32

Figure S236.  Get High-res Image Gene #53: 'del_9p23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9p23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.0017

Table S237.  Gene #53: 'del_9p23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
DEL PEAK 16(9P23) MUTATED 61 60 56
DEL PEAK 16(9P23) WILD-TYPE 57 52 118

Figure S237.  Get High-res Image Gene #53: 'del_9p23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_CNMF'

P value = 0.00272 (Fisher's exact test), Q value = 0.012

Table S238.  Gene #53: 'del_9p23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 74 114 25 87
DEL PEAK 16(9P23) MUTATED 29 39 57 12 39
DEL PEAK 16(9P23) WILD-TYPE 76 35 57 13 48

Figure S238.  Get High-res Image Gene #53: 'del_9p23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_9p23' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00026

Table S239.  Gene #53: 'del_9p23' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 124 51 127 92
DEL PEAK 16(9P23) MUTATED 57 28 66 21
DEL PEAK 16(9P23) WILD-TYPE 67 23 61 71

Figure S239.  Get High-res Image Gene #53: 'del_9p23' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_9p23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00286 (Fisher's exact test), Q value = 0.012

Table S240.  Gene #53: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 60 41 132 74
DEL PEAK 16(9P23) MUTATED 35 33 22 63 19
DEL PEAK 16(9P23) WILD-TYPE 52 27 19 69 55

Figure S240.  Get High-res Image Gene #53: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S241.  Gene #54: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
DEL PEAK 17(9P21.3) MUTATED 47 105 77 9 1
DEL PEAK 17(9P21.3) WILD-TYPE 31 41 44 52 1

Figure S241.  Get High-res Image Gene #54: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00591 (Fisher's exact test), Q value = 0.021

Table S242.  Gene #54: 'del_9p21.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 121 98 31
DEL PEAK 17(9P21.3) MUTATED 48 83 47 22
DEL PEAK 17(9P21.3) WILD-TYPE 42 38 51 9

Figure S242.  Get High-res Image Gene #54: 'del_9p21.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.0023

Table S243.  Gene #54: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
DEL PEAK 17(9P21.3) MUTATED 36 85 33 51 33
DEL PEAK 17(9P21.3) WILD-TYPE 36 50 5 52 23

Figure S243.  Get High-res Image Gene #54: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0223 (Fisher's exact test), Q value = 0.059

Table S244.  Gene #54: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
DEL PEAK 17(9P21.3) MUTATED 75 74 89
DEL PEAK 17(9P21.3) WILD-TYPE 43 38 85

Figure S244.  Get High-res Image Gene #54: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00414 (Fisher's exact test), Q value = 0.016

Table S245.  Gene #54: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 124 51 127 92
DEL PEAK 17(9P21.3) MUTATED 74 35 83 40
DEL PEAK 17(9P21.3) WILD-TYPE 50 16 44 52

Figure S245.  Get High-res Image Gene #54: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_9p21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0119 (Fisher's exact test), Q value = 0.036

Table S246.  Gene #54: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 60 41 132 74
DEL PEAK 17(9P21.3) MUTATED 44 41 31 80 36
DEL PEAK 17(9P21.3) WILD-TYPE 43 19 10 52 38

Figure S246.  Get High-res Image Gene #54: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9q22.33' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00018

Table S247.  Gene #55: 'del_9q22.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
DEL PEAK 18(9Q22.33) MUTATED 39 77 53 9 0
DEL PEAK 18(9Q22.33) WILD-TYPE 39 69 68 52 2

Figure S247.  Get High-res Image Gene #55: 'del_9q22.33' versus Molecular Subtype #1: 'CN_CNMF'

'del_9q22.33' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00018

Table S248.  Gene #55: 'del_9q22.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
DEL PEAK 18(9Q22.33) MUTATED 36 67 33 42
DEL PEAK 18(9Q22.33) WILD-TYPE 102 60 30 38

Figure S248.  Get High-res Image Gene #55: 'del_9q22.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9q22.33' versus 'RPPA_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.0022

Table S249.  Gene #55: 'del_9q22.33' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 114 104
DEL PEAK 18(9Q22.33) MUTATED 44 66 35
DEL PEAK 18(9Q22.33) WILD-TYPE 78 48 69

Figure S249.  Get High-res Image Gene #55: 'del_9q22.33' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_9q22.33' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S250.  Gene #55: 'del_9q22.33' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 121 98 31
DEL PEAK 18(9Q22.33) MUTATED 40 76 21 8
DEL PEAK 18(9Q22.33) WILD-TYPE 50 45 77 23

Figure S250.  Get High-res Image Gene #55: 'del_9q22.33' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_9q22.33' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S251.  Gene #55: 'del_9q22.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
DEL PEAK 18(9Q22.33) MUTATED 30 75 26 21 26
DEL PEAK 18(9Q22.33) WILD-TYPE 42 60 12 82 30

Figure S251.  Get High-res Image Gene #55: 'del_9q22.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9q22.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S252.  Gene #55: 'del_9q22.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
DEL PEAK 18(9Q22.33) MUTATED 64 68 46
DEL PEAK 18(9Q22.33) WILD-TYPE 54 44 128

Figure S252.  Get High-res Image Gene #55: 'del_9q22.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9q22.33' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S253.  Gene #55: 'del_9q22.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 74 114 25 87
DEL PEAK 18(9Q22.33) MUTATED 25 35 70 11 36
DEL PEAK 18(9Q22.33) WILD-TYPE 80 39 44 14 51

Figure S253.  Get High-res Image Gene #55: 'del_9q22.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_9q22.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S254.  Gene #55: 'del_9q22.33' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 124 51 127 92
DEL PEAK 18(9Q22.33) MUTATED 52 29 77 15
DEL PEAK 18(9Q22.33) WILD-TYPE 72 22 50 77

Figure S254.  Get High-res Image Gene #55: 'del_9q22.33' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_9q22.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S255.  Gene #55: 'del_9q22.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 60 41 132 74
DEL PEAK 18(9Q22.33) MUTATED 34 34 20 73 12
DEL PEAK 18(9Q22.33) WILD-TYPE 53 26 21 59 62

Figure S255.  Get High-res Image Gene #55: 'del_9q22.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10p11.21' versus 'CN_CNMF'

P value = 0.012 (Fisher's exact test), Q value = 0.037

Table S256.  Gene #56: 'del_10p11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
DEL PEAK 19(10P11.21) MUTATED 15 33 11 14 1
DEL PEAK 19(10P11.21) WILD-TYPE 63 113 110 47 1

Figure S256.  Get High-res Image Gene #56: 'del_10p11.21' versus Molecular Subtype #1: 'CN_CNMF'

'del_10p11.21' versus 'MRNASEQ_CNMF'

P value = 0.0308 (Fisher's exact test), Q value = 0.075

Table S257.  Gene #56: 'del_10p11.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
DEL PEAK 19(10P11.21) MUTATED 7 18 10 25 12
DEL PEAK 19(10P11.21) WILD-TYPE 65 117 28 78 44

Figure S257.  Get High-res Image Gene #56: 'del_10p11.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S258.  Gene #57: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
DEL PEAK 20(10Q23.31) MUTATED 46 71 18 33 0
DEL PEAK 20(10Q23.31) WILD-TYPE 32 75 103 28 2

Figure S258.  Get High-res Image Gene #57: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q23.31' versus 'METHLYATION_CNMF'

P value = 0.0275 (Fisher's exact test), Q value = 0.07

Table S259.  Gene #57: 'del_10q23.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
DEL PEAK 20(10Q23.31) MUTATED 48 66 23 31
DEL PEAK 20(10Q23.31) WILD-TYPE 90 61 40 49

Figure S259.  Get High-res Image Gene #57: 'del_10q23.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11p15.5' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S260.  Gene #58: 'del_11p15.5' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
DEL PEAK 21(11P15.5) MUTATED 46 113 35 16 1
DEL PEAK 21(11P15.5) WILD-TYPE 32 33 86 45 1

Figure S260.  Get High-res Image Gene #58: 'del_11p15.5' versus Molecular Subtype #1: 'CN_CNMF'

'del_11p15.5' versus 'METHLYATION_CNMF'

P value = 0.00067 (Fisher's exact test), Q value = 0.0038

Table S261.  Gene #58: 'del_11p15.5' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
DEL PEAK 21(11P15.5) MUTATED 52 77 38 44
DEL PEAK 21(11P15.5) WILD-TYPE 86 50 25 36

Figure S261.  Get High-res Image Gene #58: 'del_11p15.5' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11p15.5' versus 'RPPA_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.0016

Table S262.  Gene #58: 'del_11p15.5' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 121 98 31
DEL PEAK 21(11P15.5) MUTATED 56 72 37 10
DEL PEAK 21(11P15.5) WILD-TYPE 34 49 61 21

Figure S262.  Get High-res Image Gene #58: 'del_11p15.5' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_11p15.5' versus 'MRNASEQ_CNMF'

P value = 0.00293 (Fisher's exact test), Q value = 0.012

Table S263.  Gene #58: 'del_11p15.5' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
DEL PEAK 21(11P15.5) MUTATED 36 86 21 40 25
DEL PEAK 21(11P15.5) WILD-TYPE 36 49 17 63 31

Figure S263.  Get High-res Image Gene #58: 'del_11p15.5' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_11p15.5' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S264.  Gene #58: 'del_11p15.5' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
DEL PEAK 21(11P15.5) MUTATED 76 66 66
DEL PEAK 21(11P15.5) WILD-TYPE 42 46 108

Figure S264.  Get High-res Image Gene #58: 'del_11p15.5' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.0013

Table S265.  Gene #58: 'del_11p15.5' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 74 114 25 87
DEL PEAK 21(11P15.5) MUTATED 35 48 69 13 45
DEL PEAK 21(11P15.5) WILD-TYPE 70 26 45 12 42

Figure S265.  Get High-res Image Gene #58: 'del_11p15.5' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_11p15.5' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0182 (Fisher's exact test), Q value = 0.051

Table S266.  Gene #58: 'del_11p15.5' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 266 83 56
DEL PEAK 21(11P15.5) MUTATED 126 54 30
DEL PEAK 21(11P15.5) WILD-TYPE 140 29 26

Figure S266.  Get High-res Image Gene #58: 'del_11p15.5' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00081 (Fisher's exact test), Q value = 0.0044

Table S267.  Gene #58: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 124 51 127 92
DEL PEAK 21(11P15.5) MUTATED 72 31 71 31
DEL PEAK 21(11P15.5) WILD-TYPE 52 20 56 61

Figure S267.  Get High-res Image Gene #58: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_11p15.5' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00188 (Fisher's exact test), Q value = 0.0084

Table S268.  Gene #58: 'del_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 60 41 132 74
DEL PEAK 21(11P15.5) MUTATED 45 41 24 70 25
DEL PEAK 21(11P15.5) WILD-TYPE 42 19 17 62 49

Figure S268.  Get High-res Image Gene #58: 'del_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11q23.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S269.  Gene #59: 'del_11q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
DEL PEAK 22(11Q23.3) MUTATED 39 70 24 19 1
DEL PEAK 22(11Q23.3) WILD-TYPE 39 76 97 42 1

Figure S269.  Get High-res Image Gene #59: 'del_11q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q25' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S270.  Gene #60: 'del_11q25' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
DEL PEAK 23(11Q25) MUTATED 34 71 20 17 2
DEL PEAK 23(11Q25) WILD-TYPE 44 75 101 44 0

Figure S270.  Get High-res Image Gene #60: 'del_11q25' versus Molecular Subtype #1: 'CN_CNMF'

'del_12p13.1' versus 'CN_CNMF'

P value = 0.0154 (Fisher's exact test), Q value = 0.045

Table S271.  Gene #61: 'del_12p13.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
DEL PEAK 24(12P13.1) MUTATED 12 34 11 10 1
DEL PEAK 24(12P13.1) WILD-TYPE 66 112 110 51 1

Figure S271.  Get High-res Image Gene #61: 'del_12p13.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_12p13.1' versus 'METHLYATION_CNMF'

P value = 0.00514 (Fisher's exact test), Q value = 0.019

Table S272.  Gene #61: 'del_12p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
DEL PEAK 24(12P13.1) MUTATED 14 33 11 10
DEL PEAK 24(12P13.1) WILD-TYPE 124 94 52 70

Figure S272.  Get High-res Image Gene #61: 'del_12p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_12p13.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S273.  Gene #61: 'del_12p13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
DEL PEAK 24(12P13.1) MUTATED 16 36 4 5 6
DEL PEAK 24(12P13.1) WILD-TYPE 56 99 34 98 50

Figure S273.  Get High-res Image Gene #61: 'del_12p13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_12p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00042

Table S274.  Gene #61: 'del_12p13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
DEL PEAK 24(12P13.1) MUTATED 34 18 15
DEL PEAK 24(12P13.1) WILD-TYPE 84 94 159

Figure S274.  Get High-res Image Gene #61: 'del_12p13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_12p13.1' versus 'MIRSEQ_CNMF'

P value = 0.00994 (Fisher's exact test), Q value = 0.032

Table S275.  Gene #61: 'del_12p13.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 74 114 25 87
DEL PEAK 24(12P13.1) MUTATED 7 15 24 3 19
DEL PEAK 24(12P13.1) WILD-TYPE 98 59 90 22 68

Figure S275.  Get High-res Image Gene #61: 'del_12p13.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_12p13.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0118 (Fisher's exact test), Q value = 0.036

Table S276.  Gene #61: 'del_12p13.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 124 51 127 92
DEL PEAK 24(12P13.1) MUTATED 26 11 24 6
DEL PEAK 24(12P13.1) WILD-TYPE 98 40 103 86

Figure S276.  Get High-res Image Gene #61: 'del_12p13.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_12q24.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S277.  Gene #62: 'del_12q24.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
DEL PEAK 25(12Q24.33) MUTATED 14 42 9 22 1
DEL PEAK 25(12Q24.33) WILD-TYPE 64 104 112 39 1

Figure S277.  Get High-res Image Gene #62: 'del_12q24.33' versus Molecular Subtype #1: 'CN_CNMF'

'del_12q24.33' versus 'MRNASEQ_CNMF'

P value = 0.0218 (Fisher's exact test), Q value = 0.058

Table S278.  Gene #62: 'del_12q24.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
DEL PEAK 25(12Q24.33) MUTATED 19 35 3 24 6
DEL PEAK 25(12Q24.33) WILD-TYPE 53 100 35 79 50

Figure S278.  Get High-res Image Gene #62: 'del_12q24.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_13q14.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S279.  Gene #63: 'del_13q14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
DEL PEAK 26(13Q14.2) MUTATED 45 53 13 43 2
DEL PEAK 26(13Q14.2) WILD-TYPE 33 93 108 18 0

Figure S279.  Get High-res Image Gene #63: 'del_13q14.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q14.2' versus 'RPPA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00026

Table S280.  Gene #63: 'del_13q14.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 114 104
DEL PEAK 26(13Q14.2) MUTATED 43 30 59
DEL PEAK 26(13Q14.2) WILD-TYPE 79 84 45

Figure S280.  Get High-res Image Gene #63: 'del_13q14.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_13q14.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0163 (Fisher's exact test), Q value = 0.047

Table S281.  Gene #63: 'del_13q14.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 121 98 31
DEL PEAK 26(13Q14.2) MUTATED 36 40 49 7
DEL PEAK 26(13Q14.2) WILD-TYPE 54 81 49 24

Figure S281.  Get High-res Image Gene #63: 'del_13q14.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_13q14.2' versus 'MRNASEQ_CNMF'

P value = 0.0161 (Fisher's exact test), Q value = 0.046

Table S282.  Gene #63: 'del_13q14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
DEL PEAK 26(13Q14.2) MUTATED 26 41 10 50 26
DEL PEAK 26(13Q14.2) WILD-TYPE 46 94 28 53 30

Figure S282.  Get High-res Image Gene #63: 'del_13q14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_13q14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00977 (Fisher's exact test), Q value = 0.032

Table S283.  Gene #63: 'del_13q14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
DEL PEAK 26(13Q14.2) MUTATED 43 31 79
DEL PEAK 26(13Q14.2) WILD-TYPE 75 81 95

Figure S283.  Get High-res Image Gene #63: 'del_13q14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_CNMF'

P value = 0.00104 (Fisher's exact test), Q value = 0.0053

Table S284.  Gene #63: 'del_13q14.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 74 114 25 87
DEL PEAK 26(13Q14.2) MUTATED 53 29 33 15 26
DEL PEAK 26(13Q14.2) WILD-TYPE 52 45 81 10 61

Figure S284.  Get High-res Image Gene #63: 'del_13q14.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_13q14.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00721 (Fisher's exact test), Q value = 0.026

Table S285.  Gene #63: 'del_13q14.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 124 51 127 92
DEL PEAK 26(13Q14.2) MUTATED 38 17 50 49
DEL PEAK 26(13Q14.2) WILD-TYPE 86 34 77 43

Figure S285.  Get High-res Image Gene #63: 'del_13q14.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_13q14.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00215 (Fisher's exact test), Q value = 0.0094

Table S286.  Gene #63: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 60 41 132 74
DEL PEAK 26(13Q14.2) MUTATED 26 23 15 46 44
DEL PEAK 26(13Q14.2) WILD-TYPE 61 37 26 86 30

Figure S286.  Get High-res Image Gene #63: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_14q24.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S287.  Gene #64: 'del_14q24.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
DEL PEAK 27(14Q24.1) MUTATED 31 83 10 13 0
DEL PEAK 27(14Q24.1) WILD-TYPE 47 63 111 48 2

Figure S287.  Get High-res Image Gene #64: 'del_14q24.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q24.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S288.  Gene #64: 'del_14q24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
DEL PEAK 27(14Q24.1) MUTATED 36 66 23 12
DEL PEAK 27(14Q24.1) WILD-TYPE 102 61 40 68

Figure S288.  Get High-res Image Gene #64: 'del_14q24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_14q24.1' versus 'MRNASEQ_CNMF'

P value = 0.00145 (Fisher's exact test), Q value = 0.0069

Table S289.  Gene #64: 'del_14q24.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
DEL PEAK 27(14Q24.1) MUTATED 27 56 8 21 24
DEL PEAK 27(14Q24.1) WILD-TYPE 45 79 30 82 32

Figure S289.  Get High-res Image Gene #64: 'del_14q24.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_14q24.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S290.  Gene #64: 'del_14q24.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
DEL PEAK 27(14Q24.1) MUTATED 64 35 37
DEL PEAK 27(14Q24.1) WILD-TYPE 54 77 137

Figure S290.  Get High-res Image Gene #64: 'del_14q24.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_14q24.1' versus 'MIRSEQ_CNMF'

P value = 0.00369 (Fisher's exact test), Q value = 0.015

Table S291.  Gene #64: 'del_14q24.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 74 114 25 87
DEL PEAK 27(14Q24.1) MUTATED 23 37 38 9 29
DEL PEAK 27(14Q24.1) WILD-TYPE 82 37 76 16 58

Figure S291.  Get High-res Image Gene #64: 'del_14q24.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_14q24.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00416 (Fisher's exact test), Q value = 0.016

Table S292.  Gene #64: 'del_14q24.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 266 83 56
DEL PEAK 27(14Q24.1) MUTATED 76 40 20
DEL PEAK 27(14Q24.1) WILD-TYPE 190 43 36

Figure S292.  Get High-res Image Gene #64: 'del_14q24.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_14q24.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00161 (Fisher's exact test), Q value = 0.0075

Table S293.  Gene #64: 'del_14q24.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 124 51 127 92
DEL PEAK 27(14Q24.1) MUTATED 50 25 40 19
DEL PEAK 27(14Q24.1) WILD-TYPE 74 26 87 73

Figure S293.  Get High-res Image Gene #64: 'del_14q24.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_14q24.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.0019

Table S294.  Gene #64: 'del_14q24.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 60 41 132 74
DEL PEAK 27(14Q24.1) MUTATED 27 31 20 43 13
DEL PEAK 27(14Q24.1) WILD-TYPE 60 29 21 89 61

Figure S294.  Get High-res Image Gene #64: 'del_14q24.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_15q13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S295.  Gene #65: 'del_15q13.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
DEL PEAK 28(15Q13.1) MUTATED 38 79 9 33 1
DEL PEAK 28(15Q13.1) WILD-TYPE 40 67 112 28 1

Figure S295.  Get High-res Image Gene #65: 'del_15q13.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_15q13.1' versus 'METHLYATION_CNMF'

P value = 0.00226 (Fisher's exact test), Q value = 0.0098

Table S296.  Gene #65: 'del_15q13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
DEL PEAK 28(15Q13.1) MUTATED 56 63 14 27
DEL PEAK 28(15Q13.1) WILD-TYPE 82 64 49 53

Figure S296.  Get High-res Image Gene #65: 'del_15q13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_15q13.1' versus 'MRNASEQ_CNMF'

P value = 0.00899 (Fisher's exact test), Q value = 0.03

Table S297.  Gene #65: 'del_15q13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
DEL PEAK 28(15Q13.1) MUTATED 26 51 6 47 27
DEL PEAK 28(15Q13.1) WILD-TYPE 46 84 32 56 29

Figure S297.  Get High-res Image Gene #65: 'del_15q13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_15q13.1' versus 'MIRSEQ_CNMF'

P value = 0.0397 (Fisher's exact test), Q value = 0.092

Table S298.  Gene #65: 'del_15q13.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 74 114 25 87
DEL PEAK 28(15Q13.1) MUTATED 41 41 39 8 31
DEL PEAK 28(15Q13.1) WILD-TYPE 64 33 75 17 56

Figure S298.  Get High-res Image Gene #65: 'del_15q13.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_15q13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0104 (Fisher's exact test), Q value = 0.033

Table S299.  Gene #65: 'del_15q13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 266 83 56
DEL PEAK 28(15Q13.1) MUTATED 95 45 20
DEL PEAK 28(15Q13.1) WILD-TYPE 171 38 36

Figure S299.  Get High-res Image Gene #65: 'del_15q13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_15q13.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.019 (Fisher's exact test), Q value = 0.052

Table S300.  Gene #65: 'del_15q13.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 124 51 127 92
DEL PEAK 28(15Q13.1) MUTATED 41 29 46 41
DEL PEAK 28(15Q13.1) WILD-TYPE 83 22 81 51

Figure S300.  Get High-res Image Gene #65: 'del_15q13.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_16p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S301.  Gene #66: 'del_16p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
DEL PEAK 29(16P13.3) MUTATED 41 80 9 43 1
DEL PEAK 29(16P13.3) WILD-TYPE 37 66 112 18 1

Figure S301.  Get High-res Image Gene #66: 'del_16p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_16p13.3' versus 'METHLYATION_CNMF'

P value = 0.0186 (Fisher's exact test), Q value = 0.052

Table S302.  Gene #66: 'del_16p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
DEL PEAK 29(16P13.3) MUTATED 56 66 18 34
DEL PEAK 29(16P13.3) WILD-TYPE 82 61 45 46

Figure S302.  Get High-res Image Gene #66: 'del_16p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16p13.3' versus 'RPPA_CNMF'

P value = 0.00575 (Fisher's exact test), Q value = 0.021

Table S303.  Gene #66: 'del_16p13.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 114 104
DEL PEAK 29(16P13.3) MUTATED 54 36 55
DEL PEAK 29(16P13.3) WILD-TYPE 68 78 49

Figure S303.  Get High-res Image Gene #66: 'del_16p13.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_16p13.3' versus 'MRNASEQ_CNMF'

P value = 0.00794 (Fisher's exact test), Q value = 0.027

Table S304.  Gene #66: 'del_16p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
DEL PEAK 29(16P13.3) MUTATED 32 55 7 51 29
DEL PEAK 29(16P13.3) WILD-TYPE 40 80 31 52 27

Figure S304.  Get High-res Image Gene #66: 'del_16p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16q23.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S305.  Gene #67: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
DEL PEAK 30(16Q23.1) MUTATED 45 33 8 33 0
DEL PEAK 30(16Q23.1) WILD-TYPE 33 113 113 28 2

Figure S305.  Get High-res Image Gene #67: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.1' versus 'MRNASEQ_CNMF'

P value = 0.00735 (Fisher's exact test), Q value = 0.026

Table S306.  Gene #67: 'del_16q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
DEL PEAK 30(16Q23.1) MUTATED 14 37 7 34 26
DEL PEAK 30(16Q23.1) WILD-TYPE 58 98 31 69 30

Figure S306.  Get High-res Image Gene #67: 'del_16q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16q23.1' versus 'MIRSEQ_CNMF'

P value = 0.00534 (Fisher's exact test), Q value = 0.02

Table S307.  Gene #67: 'del_16q23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 74 114 25 87
DEL PEAK 30(16Q23.1) MUTATED 36 24 27 14 18
DEL PEAK 30(16Q23.1) WILD-TYPE 69 50 87 11 69

Figure S307.  Get High-res Image Gene #67: 'del_16q23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_17p12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S308.  Gene #68: 'del_17p12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
DEL PEAK 31(17P12) MUTATED 56 100 29 22 1
DEL PEAK 31(17P12) WILD-TYPE 22 46 92 39 1

Figure S308.  Get High-res Image Gene #68: 'del_17p12' versus Molecular Subtype #1: 'CN_CNMF'

'del_17p12' versus 'METHLYATION_CNMF'

P value = 0.00056 (Fisher's exact test), Q value = 0.0032

Table S309.  Gene #68: 'del_17p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
DEL PEAK 31(17P12) MUTATED 61 84 30 33
DEL PEAK 31(17P12) WILD-TYPE 77 43 33 47

Figure S309.  Get High-res Image Gene #68: 'del_17p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17p12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.016 (Fisher's exact test), Q value = 0.046

Table S310.  Gene #68: 'del_17p12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
DEL PEAK 31(17P12) MUTATED 73 53 79
DEL PEAK 31(17P12) WILD-TYPE 45 59 95

Figure S310.  Get High-res Image Gene #68: 'del_17p12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_18q23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S311.  Gene #69: 'del_18q23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
DEL PEAK 32(18Q23) MUTATED 38 86 23 30 2
DEL PEAK 32(18Q23) WILD-TYPE 40 60 98 31 0

Figure S311.  Get High-res Image Gene #69: 'del_18q23' versus Molecular Subtype #1: 'CN_CNMF'

'del_18q23' versus 'MIRSEQ_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.0018

Table S312.  Gene #69: 'del_18q23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 74 114 25 87
DEL PEAK 32(18Q23) MUTATED 42 50 41 8 37
DEL PEAK 32(18Q23) WILD-TYPE 63 24 73 17 50

Figure S312.  Get High-res Image Gene #69: 'del_18q23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_18q23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S313.  Gene #69: 'del_18q23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 266 83 56
DEL PEAK 32(18Q23) MUTATED 100 57 21
DEL PEAK 32(18Q23) WILD-TYPE 166 26 35

Figure S313.  Get High-res Image Gene #69: 'del_18q23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_18q23' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00307 (Fisher's exact test), Q value = 0.013

Table S314.  Gene #69: 'del_18q23' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 124 51 127 92
DEL PEAK 32(18Q23) MUTATED 54 35 49 39
DEL PEAK 32(18Q23) WILD-TYPE 70 16 78 53

Figure S314.  Get High-res Image Gene #69: 'del_18q23' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_18q23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00439 (Fisher's exact test), Q value = 0.017

Table S315.  Gene #69: 'del_18q23' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 60 41 132 74
DEL PEAK 32(18Q23) MUTATED 40 40 15 50 32
DEL PEAK 32(18Q23) WILD-TYPE 47 20 26 82 42

Figure S315.  Get High-res Image Gene #69: 'del_18q23' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S316.  Gene #70: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
DEL PEAK 33(19P13.3) MUTATED 32 72 21 19 1
DEL PEAK 33(19P13.3) WILD-TYPE 46 74 100 42 1

Figure S316.  Get High-res Image Gene #70: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_19p13.3' versus 'MRNASEQ_CNMF'

P value = 0.0203 (Fisher's exact test), Q value = 0.055

Table S317.  Gene #70: 'del_19p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
DEL PEAK 33(19P13.3) MUTATED 24 35 13 45 26
DEL PEAK 33(19P13.3) WILD-TYPE 48 100 25 58 30

Figure S317.  Get High-res Image Gene #70: 'del_19p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_19p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00089 (Fisher's exact test), Q value = 0.0047

Table S318.  Gene #70: 'del_19p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
DEL PEAK 33(19P13.3) MUTATED 49 24 70
DEL PEAK 33(19P13.3) WILD-TYPE 69 88 104

Figure S318.  Get High-res Image Gene #70: 'del_19p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_CNMF'

P value = 0.0385 (Fisher's exact test), Q value = 0.09

Table S319.  Gene #70: 'del_19p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 74 114 25 87
DEL PEAK 33(19P13.3) MUTATED 39 36 31 10 27
DEL PEAK 33(19P13.3) WILD-TYPE 66 38 83 15 60

Figure S319.  Get High-res Image Gene #70: 'del_19p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_22q13.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.7e-05

Table S320.  Gene #71: 'del_22q13.32' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 78 146 121 61 2
DEL PEAK 34(22Q13.32) MUTATED 40 89 10 49 0
DEL PEAK 34(22Q13.32) WILD-TYPE 38 57 111 12 2

Figure S320.  Get High-res Image Gene #71: 'del_22q13.32' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q13.32' versus 'METHLYATION_CNMF'

P value = 0.00199 (Fisher's exact test), Q value = 0.0088

Table S321.  Gene #71: 'del_22q13.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
DEL PEAK 34(22Q13.32) MUTATED 72 65 16 35
DEL PEAK 34(22Q13.32) WILD-TYPE 66 62 47 45

Figure S321.  Get High-res Image Gene #71: 'del_22q13.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_22q13.32' versus 'RPPA_CNMF'

P value = 0.0297 (Fisher's exact test), Q value = 0.074

Table S322.  Gene #71: 'del_22q13.32' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 114 104
DEL PEAK 34(22Q13.32) MUTATED 66 42 47
DEL PEAK 34(22Q13.32) WILD-TYPE 56 72 57

Figure S322.  Get High-res Image Gene #71: 'del_22q13.32' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_22q13.32' versus 'RPPA_CHIERARCHICAL'

P value = 0.00109 (Fisher's exact test), Q value = 0.0055

Table S323.  Gene #71: 'del_22q13.32' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 121 98 31
DEL PEAK 34(22Q13.32) MUTATED 55 41 47 12
DEL PEAK 34(22Q13.32) WILD-TYPE 35 80 51 19

Figure S323.  Get High-res Image Gene #71: 'del_22q13.32' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_22q13.32' versus 'MRNASEQ_CNMF'

P value = 0.00076 (Fisher's exact test), Q value = 0.0042

Table S324.  Gene #71: 'del_22q13.32' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
DEL PEAK 34(22Q13.32) MUTATED 32 53 9 62 28
DEL PEAK 34(22Q13.32) WILD-TYPE 40 82 29 41 28

Figure S324.  Get High-res Image Gene #71: 'del_22q13.32' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_22q13.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00126 (Fisher's exact test), Q value = 0.0061

Table S325.  Gene #71: 'del_22q13.32' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
DEL PEAK 34(22Q13.32) MUTATED 58 35 91
DEL PEAK 34(22Q13.32) WILD-TYPE 60 77 83

Figure S325.  Get High-res Image Gene #71: 'del_22q13.32' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.32' versus 'MIRSEQ_CNMF'

P value = 0.0427 (Fisher's exact test), Q value = 0.097

Table S326.  Gene #71: 'del_22q13.32' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 74 114 25 87
DEL PEAK 34(22Q13.32) MUTATED 56 38 39 12 42
DEL PEAK 34(22Q13.32) WILD-TYPE 49 36 75 13 45

Figure S326.  Get High-res Image Gene #71: 'del_22q13.32' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_22q13.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0018 (Fisher's exact test), Q value = 0.0081

Table S327.  Gene #71: 'del_22q13.32' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 124 51 127 92
DEL PEAK 34(22Q13.32) MUTATED 58 20 48 58
DEL PEAK 34(22Q13.32) WILD-TYPE 66 31 79 34

Figure S327.  Get High-res Image Gene #71: 'del_22q13.32' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_22q13.32' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0166 (Fisher's exact test), Q value = 0.047

Table S328.  Gene #71: 'del_22q13.32' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 60 41 132 74
DEL PEAK 34(22Q13.32) MUTATED 36 27 21 53 47
DEL PEAK 34(22Q13.32) WILD-TYPE 51 33 20 79 27

Figure S328.  Get High-res Image Gene #71: 'del_22q13.32' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xq21.33' versus 'METHLYATION_CNMF'

P value = 0.0416 (Fisher's exact test), Q value = 0.095

Table S329.  Gene #73: 'del_xq21.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 127 63 80
DEL PEAK 36(XQ21.33) MUTATED 19 33 11 21
DEL PEAK 36(XQ21.33) WILD-TYPE 119 94 52 59

Figure S329.  Get High-res Image Gene #73: 'del_xq21.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xq21.33' versus 'MRNASEQ_CNMF'

P value = 0.0118 (Fisher's exact test), Q value = 0.036

Table S330.  Gene #73: 'del_xq21.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 135 38 103 56
DEL PEAK 36(XQ21.33) MUTATED 7 30 12 17 17
DEL PEAK 36(XQ21.33) WILD-TYPE 65 105 26 86 39

Figure S330.  Get High-res Image Gene #73: 'del_xq21.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_xq21.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0495 (Fisher's exact test), Q value = 0.11

Table S331.  Gene #73: 'del_xq21.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 266 83 56
DEL PEAK 36(XQ21.33) MUTATED 60 19 5
DEL PEAK 36(XQ21.33) WILD-TYPE 206 64 51

Figure S331.  Get High-res Image Gene #73: 'del_xq21.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

Methods & Data
Input

  • Copy number data file = all_lesions.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/BLCA-TP/22507728/transformed.cor.cli.txt

  • Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/BLCA-TP/22541056/BLCA-TP.transferedmergedcluster.txt

  • Number of patients = 408

  • Number of significantly focal cnvs = 73

  • Number of molecular subtypes = 10

  • Exclude genes that fewer than K tumors have alterations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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