Correlation between copy number variation genes (focal events) and molecular subtypes
Esophageal Carcinoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1HH6J34
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1HH6J34
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 85 focal events and 10 molecular subtypes across 184 patients, 363 significant findings detected with P value < 0.05 and Q value < 0.25.

  • amp_1q23.3 cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.

  • amp_1q42.3 cnv correlated to 'CN_CNMF'.

  • amp_2q14.2 cnv correlated to 'RPPA_CNMF'.

  • amp_2q31.1 cnv correlated to 'CN_CNMF',  'RPPA_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • amp_3q26.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_4q21.1 cnv correlated to 'RPPA_CNMF'.

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

  • amp_6p21.1 cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_6q23.3 cnv correlated to 'CN_CNMF',  'RPPA_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • amp_7q21.2 cnv correlated to 'RPPA_CNMF'.

  • amp_8p23.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

  • amp_12p12.1 cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

  • amp_14q21.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_15q26.1 cnv correlated to 'CN_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • amp_18p11.32 cnv correlated to 'MIRSEQ_CNMF'.

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

  • amp_19q12 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.

  • amp_xq28 cnv correlated to 'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • del_1p13.2 cnv correlated to 'CN_CNMF'.

  • del_2q22.1 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_2q33.3 cnv correlated to 'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • del_3p14.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • del_3q26.31 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_4p15.2 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.

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

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

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

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

  • del_7q31.1 cnv correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_8p23.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • del_8p12 cnv correlated to 'CN_CNMF'.

  • del_9p23 cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

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

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

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

  • del_10q21.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • del_11p15.4 cnv correlated to 'METHLYATION_CNMF'.

  • del_11q25 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_12q23.1 cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_13q12.11 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • del_13q21.31 cnv correlated to 'CN_CNMF'.

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

  • del_15q11.2 cnv correlated to 'MRNASEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

  • del_17q25.3 cnv correlated to 'MIRSEQ_MATURE_CNMF'.

  • del_18p11.23 cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_18q12.2 cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_18q21.2 cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_18q22.3 cnv correlated to 'METHLYATION_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_19p13.3 cnv correlated to 'CN_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_19q11 cnv correlated to 'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_20p12.1 cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_21q11.2 cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.

  • del_21q21.1 cnv correlated to 'METHLYATION_CNMF'.

  • del_21q22.12 cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.

  • del_22q11.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_xp21.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • del_xp11.3 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_xq21.33 cnv correlated to 'MIRSEQ_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 85 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, 363 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 3q26 2 128 (70%) 56 1e-05
(0.000155) 		1e-05
(0.000155) 		0.0106
(0.0419) 		0.00061
(0.00476) 		1e-05
(0.000155) 		1e-05
(0.000155) 		3e-05
(0.000386) 		2e-05
(0.000266) 		1e-05
(0.000155) 		6e-05
(0.00068)
del 3q26 31 16 (9%) 168 0.00235
(0.0134) 		2e-05
(0.000266) 		0.0399
(0.099) 		0.00921
(0.038) 		0.0014
(0.00922) 		0.0001
(0.00101) 		0.00035
(0.00304) 		0.00041
(0.00338) 		0.00216
(0.0127) 		0.0001
(0.00101)
del 10p11 21 52 (28%) 132 1e-05
(0.000155) 		5e-05
(0.000599) 		0.036
(0.093) 		0.0297
(0.0823) 		1e-05
(0.000155) 		2e-05
(0.000266) 		1e-05
(0.000155) 		4e-05
(0.000493) 		0.00046
(0.00376) 		3e-05
(0.000386)
del 13q12 11 76 (41%) 108 0.00036
(0.00306) 		0.0149
(0.0541) 		0.0308
(0.0842) 		0.0383
(0.0962) 		0.00874
(0.0366) 		0.00368
(0.0187) 		0.00813
(0.0348) 		0.00947
(0.0384) 		0.013
(0.0488) 		0.0159
(0.0558)
del 16q23 1 84 (46%) 100 1e-05
(0.000155) 		1e-05
(0.000155) 		0.0391
(0.0974) 		0.0384
(0.0964) 		1e-05
(0.000155) 		1e-05
(0.000155) 		1e-05
(0.000155) 		1e-05
(0.000155) 		1e-05
(0.000155) 		1e-05
(0.000155)
del 22q11 1 79 (43%) 105 1e-05
(0.000155) 		1e-05
(0.000155) 		0.0222
(0.0704) 		0.00448
(0.0219) 		4e-05
(0.000493) 		1e-05
(0.000155) 		1e-05
(0.000155) 		1e-05
(0.000155) 		1e-05
(0.000155) 		1e-05
(0.000155)
amp 11q13 3 104 (57%) 80 1e-05
(0.000155) 		0.00328
(0.0173) 		0.0477
(0.114) 		0.0131
(0.0488) 		0.00036
(0.00306) 		0.00105
(0.00732) 		0.00115
(0.00788) 		0.00135
(0.00896) 		0.0908
(0.184) 		0.00132
(0.00883)
del 2q22 1 59 (32%) 125 1e-05
(0.000155) 		1e-05
(0.000155) 		0.0556
(0.126) 		0.00248
(0.014) 		1e-05
(0.000155) 		1e-05
(0.000155) 		1e-05
(0.000155) 		1e-05
(0.000155) 		0.00012
(0.0012) 		1e-05
(0.000155)
del 3p26 2 111 (60%) 73 1e-05
(0.000155) 		7e-05
(0.000763) 		0.0319
(0.086) 		0.0519
(0.121) 		5e-05
(0.000599) 		4e-05
(0.000493) 		0.00019
(0.00186) 		0.0002
(0.00191) 		0.0131
(0.0488) 		0.00021
(0.00198)
amp 5p15 33 98 (53%) 86 1e-05
(0.000155) 		0.0157
(0.0558) 		0.434
(0.548) 		0.283
(0.406) 		0.00219
(0.0128) 		0.00074
(0.00547) 		0.00025
(0.00228) 		0.00417
(0.0211) 		0.0109
(0.0424) 		0.00189
(0.0121)
amp 6p21 1 69 (38%) 115 0.00282
(0.0157) 		0.125
(0.226) 		0.0397
(0.0988) 		0.205
(0.32) 		0.0434
(0.105) 		0.0304
(0.0837) 		0.0034
(0.0177) 		0.00206
(0.0125) 		0.0065
(0.0292) 		0.00131
(0.00883)
amp 8p23 1 52 (28%) 132 2e-05
(0.000266) 		0.00213
(0.0127) 		0.28
(0.404) 		0.176
(0.284) 		0.00437
(0.0216) 		6e-05
(0.00068) 		0.00429
(0.0213) 		0.0151
(0.0542) 		0.00038
(0.00317) 		0.00202
(0.0124)
amp 13q22 1 65 (35%) 119 0.00191
(0.0121) 		0.00674
(0.0298) 		0.121
(0.221) 		0.189
(0.301) 		0.00692
(0.0303) 		0.00127
(0.00864) 		0.00014
(0.00138) 		0.00236
(0.0134) 		0.0128
(0.0485) 		0.00025
(0.00228)
amp 15q26 1 58 (32%) 126 0.00806
(0.0348) 		0.0726
(0.154) 		0.159
(0.264) 		0.0452
(0.108) 		0.0169
(0.0583) 		0.0158
(0.0558) 		0.00728
(0.0317) 		0.0432
(0.105) 		0.036
(0.093) 		0.0152
(0.0546)
amp 17q12 75 (41%) 109 0.00451
(0.0219) 		0.00425
(0.0212) 		0.569
(0.673) 		0.537
(0.647) 		0.00556
(0.0258) 		0.00278
(0.0155) 		0.00233
(0.0134) 		0.0191
(0.0633) 		0.0237
(0.0724) 		0.00145
(0.00948)
amp 18q11 2 59 (32%) 125 0.0127
(0.0483) 		0.00971
(0.0391) 		0.245
(0.367) 		0.141
(0.242) 		0.00566
(0.0261) 		0.00498
(0.0238) 		0.00035
(0.00304) 		0.00879
(0.0366) 		0.015
(0.0541) 		0.0006
(0.00472)
del 1p36 11 75 (41%) 109 0.0106
(0.0419) 		0.00979
(0.0393) 		0.298
(0.419) 		0.926
(0.943) 		0.0167
(0.0581) 		0.0251
(0.0741) 		0.00284
(0.0157) 		0.0231
(0.0718) 		0.0418
(0.103) 		0.0386
(0.0965)
del 3p14 3 126 (68%) 58 1e-05
(0.000155) 		1e-05
(0.000155) 		0.0958
(0.192) 		0.0593
(0.13) 		1e-05
(0.000155) 		1e-05
(0.000155) 		1e-05
(0.000155) 		1e-05
(0.000155) 		1e-05
(0.000155) 		1e-05
(0.000155)
del 3p14 2 125 (68%) 59 1e-05
(0.000155) 		1e-05
(0.000155) 		0.284
(0.407) 		0.102
(0.199) 		1e-05
(0.000155) 		1e-05
(0.000155) 		1e-05
(0.000155) 		1e-05
(0.000155) 		0.0001
(0.00101) 		2e-05
(0.000266)
del 4q34 3 99 (54%) 85 0.00049
(0.00389) 		0.00656
(0.0292) 		0.887
(0.918) 		0.885
(0.918) 		0.00515
(0.0243) 		0.00109
(0.00753) 		0.00087
(0.00627) 		0.00323
(0.0172) 		0.02
(0.0651) 		0.00215
(0.0127)
del 13q14 2 74 (40%) 110 0.00172
(0.0112) 		0.00482
(0.0231) 		0.204
(0.32) 		0.131
(0.231) 		0.0198
(0.0647) 		0.0216
(0.0697) 		0.0172
(0.059) 		0.0243
(0.0733) 		0.0228
(0.0709) 		0.0249
(0.074)
del 14q23 3 51 (28%) 133 0.00323
(0.0172) 		0.015
(0.0541) 		0.114
(0.214) 		0.0248
(0.0739) 		0.00048
(0.00385) 		0.0432
(0.105) 		0.0928
(0.187) 		0.0133
(0.049) 		0.0282
(0.0799) 		0.00215
(0.0127)
del 16p13 3 65 (35%) 119 1e-05
(0.000155) 		9e-05
(0.000956) 		0.472
(0.585) 		0.295
(0.418) 		0.0002
(0.00191) 		6e-05
(0.00068) 		2e-05
(0.000266) 		1e-05
(0.000155) 		7e-05
(0.000763) 		1e-05
(0.000155)
del 17p12 86 (47%) 98 0.0001
(0.00101) 		1e-05
(0.000155) 		0.0882
(0.18) 		0.256
(0.378) 		1e-05
(0.000155) 		2e-05
(0.000266) 		1e-05
(0.000155) 		2e-05
(0.000266) 		0.0102
(0.0406) 		1e-05
(0.000155)
amp 14q21 1 61 (33%) 123 0.00037
(0.00311) 		0.00859
(0.0363) 		0.174
(0.282) 		0.231
(0.351) 		0.00533
(0.025) 		0.00306
(0.0167) 		0.00366
(0.0187) 		0.00424
(0.0212) 		0.0574
(0.129) 		0.0131
(0.0488)
amp xq28 69 (38%) 115 0.0594
(0.13) 		0.0324
(0.087) 		0.0105
(0.0416) 		0.54
(0.649) 		0.00186
(0.012) 		0.027
(0.0784) 		0.0304
(0.0837) 		0.00192
(0.0121) 		0.364
(0.482) 		0.0035
(0.018)
del 8p23 2 90 (49%) 94 9e-05
(0.000956) 		0.0272
(0.0786) 		0.00607
(0.0276) 		0.00943
(0.0384) 		0.0527
(0.122) 		0.0482
(0.114) 		0.011
(0.0424) 		0.107
(0.205) 		0.0372
(0.0944) 		0.149
(0.253)
del 18q21 2 119 (65%) 65 0.153
(0.257) 		0.0009
(0.00643) 		0.229
(0.349) 		0.651
(0.743) 		0.00321
(0.0172) 		0.00903
(0.0374) 		0.00462
(0.0223) 		0.00202
(0.0124) 		0.0153
(0.0548) 		0.00048
(0.00385)
del xp11 3 74 (40%) 110 0.00069
(0.00514) 		0.163
(0.268) 		0.46
(0.576) 		0.886
(0.918) 		0.00511
(0.0243) 		0.0224
(0.0705) 		0.00312
(0.0169) 		0.0438
(0.106) 		0.0334
(0.0891) 		0.0174
(0.059)
amp 6q23 3 42 (23%) 142 0.0378
(0.0955) 		0.0711
(0.152) 		0.0543
(0.124) 		0.00657
(0.0292) 		0.0561
(0.127) 		0.0697
(0.15) 		0.0324
(0.087) 		0.0306
(0.0838) 		0.00938
(0.0384) 		0.00643
(0.0291)
del 10p15 3 54 (29%) 130 0.00069
(0.00514) 		0.0192
(0.0633) 		0.0617
(0.134) 		0.168
(0.275) 		0.0282
(0.0799) 		0.0256
(0.0751) 		0.00597
(0.0274) 		0.0112
(0.0431) 		0.0864
(0.178) 		0.0604
(0.132)
del 18q12 2 111 (60%) 73 0.0966
(0.192) 		0.0174
(0.059) 		0.382
(0.5) 		0.579
(0.684) 		0.0237
(0.0724) 		0.0734
(0.155) 		0.0443
(0.107) 		0.00066
(0.00501) 		0.0346
(0.0912) 		0.00026
(0.00235)
del 4q22 1 105 (57%) 79 0.00022
(0.00205) 		0.113
(0.212) 		0.739
(0.808) 		0.928
(0.943) 		0.0237
(0.0724) 		0.0297
(0.0823) 		0.003
(0.0165) 		0.143
(0.244) 		0.0525
(0.122) 		0.0362
(0.093)
del 10q21 1 46 (25%) 138 0.002
(0.0124) 		0.0219
(0.0703) 		0.601
(0.703) 		0.353
(0.473) 		0.0443
(0.107) 		0.0647
(0.14) 		0.0158
(0.0558) 		0.0562
(0.127) 		0.231
(0.351) 		0.0489
(0.115)
del 11q25 81 (44%) 103 2e-05
(0.000266) 		0.0294
(0.082) 		0.214
(0.331) 		0.26
(0.382) 		0.0671
(0.144) 		0.0498
(0.117) 		0.0594
(0.13) 		0.0829
(0.173) 		0.0262
(0.0767) 		0.0294
(0.082)
del 18p11 23 60 (33%) 124 0.315
(0.436) 		0.00608
(0.0276) 		0.85
(0.893) 		0.764
(0.824) 		0.0168
(0.0581) 		0.0311
(0.0847) 		0.0255
(0.0751) 		0.136
(0.236) 		0.139
(0.24) 		0.0483
(0.114)
del 20p12 1 33 (18%) 151 0.0335
(0.0891) 		0.161
(0.266) 		0.249
(0.371) 		0.873
(0.908) 		0.0603
(0.132) 		0.0082
(0.0348) 		0.0168
(0.0581) 		0.0496
(0.117) 		0.289
(0.413) 		0.0425
(0.104)
amp 8q24 21 145 (79%) 39 0.00229
(0.0132) 		0.0223
(0.0704) 		0.00065
(0.00498) 		0.0629
(0.136) 		0.385
(0.501) 		0.112
(0.212) 		0.00739
(0.032) 		0.0969
(0.192) 		0.355
(0.475) 		0.15
(0.253)
amp 12p12 1 79 (43%) 105 0.0338
(0.0895) 		0.128
(0.228) 		0.0278
(0.0792) 		0.562
(0.668) 		0.0192
(0.0633) 		0.0284
(0.0803) 		0.0614
(0.134) 		0.0836
(0.173) 		0.0587
(0.13) 		0.089
(0.181)
del 2q33 3 36 (20%) 148 0.295
(0.418) 		0.0668
(0.144) 		0.472
(0.585) 		0.192
(0.306) 		0.0174
(0.059) 		0.0278
(0.0792) 		0.0144
(0.0528) 		0.0705
(0.151) 		0.0738
(0.155) 		0.0273
(0.0786)
del 5q12 1 112 (61%) 72 0.00062
(0.00479) 		0.00077
(0.00564) 		0.11
(0.21) 		0.637
(0.733) 		0.256
(0.378) 		0.496
(0.605) 		0.0227
(0.0708) 		0.0237
(0.0724) 		0.433
(0.548) 		0.0581
(0.13)
del 6p25 3 74 (40%) 110 0.0162
(0.0566) 		0.0234
(0.0724) 		0.119
(0.22) 		0.43
(0.546) 		0.0192
(0.0633) 		0.33
(0.448) 		0.121
(0.221) 		0.0222
(0.0704) 		0.315
(0.436) 		0.0917
(0.185)
del 9p21 3 141 (77%) 43 1e-05
(0.000155) 		0.236
(0.357) 		0.343
(0.463) 		0.208
(0.324) 		0.00872
(0.0366) 		0.0211
(0.0682) 		0.0334
(0.0891) 		0.106
(0.204) 		0.306
(0.427) 		0.108
(0.207)
del 19p13 3 93 (51%) 91 0.00028
(0.00251) 		0.302
(0.423) 		0.678
(0.766) 		0.988
(0.992) 		0.426
(0.542) 		0.322
(0.442) 		0.0361
(0.093) 		0.0226
(0.0708) 		0.116
(0.215) 		0.00686
(0.0302)
amp 2q31 1 60 (33%) 124 0.0315
(0.0856) 		0.234
(0.354) 		0.0349
(0.0918) 		0.234
(0.355) 		0.0836
(0.173) 		0.0372
(0.0944) 		0.542
(0.65) 		0.271
(0.394) 		0.102
(0.199) 		0.655
(0.745)
amp 9q34 3 64 (35%) 120 0.025
(0.074) 		0.18
(0.289) 		0.886
(0.918) 		0.0247
(0.0739) 		0.00345
(0.0179) 		0.712
(0.788) 		0.27
(0.394) 		0.113
(0.212) 		0.119
(0.219) 		0.68
(0.766)
del 12q23 1 51 (28%) 133 0.251
(0.374) 		0.0186
(0.0626) 		0.0569
(0.128) 		0.32
(0.441) 		0.0422
(0.104) 		0.0723
(0.154) 		0.104
(0.201) 		0.133
(0.232) 		0.179
(0.289) 		0.0467
(0.111)
del 15q11 2 63 (34%) 121 0.403
(0.522) 		0.159
(0.264) 		0.329
(0.448) 		0.416
(0.534) 		0.0124
(0.0477) 		0.24
(0.361) 		0.204
(0.319) 		0.0193
(0.0633) 		0.641
(0.737) 		0.0034
(0.0177)
del 18q22 3 112 (61%) 72 0.962
(0.97) 		0.0357
(0.0929) 		0.247
(0.369) 		0.864
(0.901) 		0.0964
(0.192) 		0.133
(0.232) 		0.215
(0.333) 		0.00819
(0.0348) 		0.0511
(0.119) 		0.00086
(0.00625)
del 19q11 48 (26%) 136 0.216
(0.333) 		0.384
(0.501) 		0.114
(0.214) 		0.793
(0.849) 		0.508
(0.617) 		0.762
(0.824) 		0.352
(0.472) 		0.0145
(0.0531) 		0.00104
(0.00731) 		0.0275
(0.0789)
del 21q22 12 108 (59%) 76 0.102
(0.199) 		0.0108
(0.0423) 		0.313
(0.434) 		0.258
(0.379) 		0.0109
(0.0424) 		0.167
(0.274) 		0.0316
(0.0856) 		0.331
(0.448) 		0.0726
(0.154) 		0.201
(0.317)
del xp21 1 69 (38%) 115 0.00092
(0.00652) 		0.0371
(0.0944) 		0.132
(0.232) 		0.661
(0.751) 		0.00226
(0.0132) 		0.194
(0.307) 		0.0554
(0.126) 		0.162
(0.268) 		0.116
(0.215) 		0.152
(0.255)
amp 1q23 3 93 (51%) 91 0.00197
(0.0123) 		0.125
(0.226) 		0.674
(0.763) 		0.646
(0.74) 		0.655
(0.745) 		0.808
(0.857) 		0.17
(0.277) 		0.844
(0.888) 		0.0189
(0.0633) 		0.807
(0.857)
amp 7p11 2 126 (68%) 58 0.332
(0.449) 		0.112
(0.212) 		0.592
(0.696) 		0.75
(0.814) 		0.241
(0.362) 		0.0412
(0.102) 		0.0372
(0.0944) 		0.265
(0.387) 		0.671
(0.76) 		0.127
(0.227)
amp 19q12 54 (29%) 130 0.00439
(0.0216) 		0.158
(0.263) 		0.181
(0.29) 		0.299
(0.42) 		0.201
(0.316) 		0.115
(0.215) 		0.0383
(0.0962) 		0.275
(0.399) 		0.124
(0.225) 		0.0528
(0.122)
del 4p15 2 106 (58%) 78 0.00556
(0.0258) 		0.0999
(0.197) 		0.423
(0.54) 		0.94
(0.953) 		0.979
(0.984) 		0.473
(0.585) 		0.0482
(0.114) 		0.748
(0.814) 		0.263
(0.385) 		0.953
(0.963)
del 10q23 31 65 (35%) 119 0.0208
(0.0674) 		0.0356
(0.0929) 		0.488
(0.599) 		0.0905
(0.184) 		0.33
(0.448) 		0.292
(0.416) 		0.119
(0.22) 		0.278
(0.402) 		0.374
(0.492) 		0.457
(0.573)
del 21q11 2 107 (58%) 77 0.122
(0.222) 		0.0286
(0.0805) 		0.387
(0.504) 		0.248
(0.37) 		0.0354
(0.0928) 		0.216
(0.333) 		0.05
(0.117) 		0.168
(0.275) 		0.152
(0.255) 		0.0974
(0.193)
amp 1q42 3 96 (52%) 88 7e-05
(0.000763) 		0.312
(0.433) 		0.949
(0.961) 		0.414
(0.533) 		0.627
(0.726) 		0.737
(0.806) 		0.297
(0.419) 		0.286
(0.408) 		0.148
(0.252) 		0.263
(0.385)
amp 2q14 2 60 (33%) 124 0.352
(0.472) 		0.309
(0.43) 		0.0247
(0.0739) 		0.304
(0.424) 		0.0849
(0.175) 		0.0539
(0.123) 		0.252
(0.375) 		0.211
(0.328) 		0.271
(0.394) 		0.321
(0.441)
amp 4q21 1 34 (18%) 150 0.294
(0.418) 		0.697
(0.779) 		0.0221
(0.0704) 		0.0583
(0.13) 		0.608
(0.707) 		0.926
(0.943) 		0.954
(0.963) 		0.422
(0.54) 		0.92
(0.941) 		0.36
(0.479)
amp 7q21 2 114 (62%) 70 0.474
(0.587) 		0.158
(0.264) 		0.0268
(0.0782) 		0.917
(0.94) 		0.222
(0.34) 		0.816
(0.863) 		0.345
(0.464) 		0.606
(0.707) 		0.769
(0.828) 		0.138
(0.238)
amp 18p11 32 69 (38%) 115 0.0592
(0.13) 		0.11
(0.21) 		0.712
(0.788) 		0.466
(0.58) 		0.0592
(0.13) 		0.173
(0.282) 		0.0179
(0.0605) 		0.56
(0.666) 		0.369
(0.487) 		0.51
(0.619)
del 1p13 2 64 (35%) 120 6e-05
(0.00068) 		0.0975
(0.193) 		0.451
(0.569) 		0.569
(0.673) 		0.783
(0.841) 		0.596
(0.699) 		0.755
(0.818) 		0.105
(0.203) 		0.174
(0.283) 		0.903
(0.93)
del 7q31 1 56 (30%) 128 0.221
(0.34) 		0.0868
(0.178) 		0.694
(0.777) 		0.764
(0.824) 		0.366
(0.485) 		0.457
(0.573) 		0.401
(0.52) 		0.0969
(0.192) 		0.112
(0.212) 		0.0239
(0.0724)
del 8p12 75 (41%) 109 0.00029
(0.00257) 		0.415
(0.533) 		0.486
(0.599) 		0.481
(0.594) 		0.55
(0.658) 		0.133
(0.232) 		0.226
(0.344) 		0.805
(0.856) 		0.559
(0.666) 		0.496
(0.605)
del 9p23 108 (59%) 76 0.415
(0.533) 		0.121
(0.221) 		0.285
(0.408) 		0.712
(0.788) 		0.465
(0.58) 		0.0239
(0.0724) 		0.427
(0.543) 		0.725
(0.797) 		0.913
(0.938) 		0.698
(0.78)
del 11p15 4 79 (43%) 105 0.129
(0.228) 		0.0465
(0.111) 		0.891
(0.92) 		0.487
(0.599) 		0.368
(0.487) 		0.361
(0.479) 		0.627
(0.726) 		0.183
(0.293) 		0.804
(0.856) 		0.455
(0.573)
del 13q21 31 69 (38%) 115 0.0131
(0.0488) 		0.0531
(0.122) 		0.754
(0.817) 		0.649
(0.742) 		0.114
(0.214) 		0.116
(0.215) 		0.0883
(0.18) 		0.133
(0.232) 		0.0934
(0.188) 		0.133
(0.232)
del 17q25 3 41 (22%) 143 0.374
(0.492) 		0.821
(0.866) 		0.498
(0.606) 		0.663
(0.752) 		1
(1.00) 		1
(1.00) 		0.129
(0.228) 		0.535
(0.647) 		0.0357
(0.0929) 		0.713
(0.788)
del 21q21 1 107 (58%) 77 0.123
(0.224) 		0.00948
(0.0384) 		0.116
(0.215) 		0.128
(0.228) 		0.0537
(0.123) 		0.126
(0.227) 		0.0874
(0.179) 		0.174
(0.283) 		0.0739
(0.155) 		0.0752
(0.158)
del xq21 33 40 (22%) 144 0.161
(0.267) 		0.205
(0.32) 		0.677
(0.765) 		0.816
(0.863) 		0.157
(0.263) 		0.279
(0.403) 		0.105
(0.203) 		0.0291
(0.0817) 		0.15
(0.253) 		0.184
(0.293)
amp 1p34 2 40 (22%) 144 0.33
(0.448) 		0.63
(0.727) 		0.376
(0.494) 		0.256
(0.378) 		0.863
(0.901) 		0.681
(0.766) 		0.744
(0.811) 		0.325
(0.445) 		0.798
(0.852) 		0.55
(0.658)
amp 8p11 21 85 (46%) 99 0.491
(0.602) 		0.175
(0.283) 		0.11
(0.21) 		0.651
(0.743) 		0.851
(0.893) 		0.101
(0.199) 		0.383
(0.501) 		0.966
(0.971) 		0.731
(0.801) 		0.687
(0.77)
amp 9p13 3 40 (22%) 144 0.0827
(0.173) 		0.105
(0.203) 		0.951
(0.962) 		0.787
(0.844) 		0.864
(0.901) 		0.681
(0.766) 		0.713
(0.788) 		0.131
(0.231) 		0.532
(0.644) 		0.55
(0.658)
amp 11p13 52 (28%) 132 0.144
(0.245) 		0.457
(0.573) 		0.133
(0.232) 		0.646
(0.74) 		0.564
(0.67) 		0.33
(0.448) 		0.206
(0.321) 		0.126
(0.227) 		0.581
(0.685) 		0.25
(0.373)
amp 11p13 50 (27%) 134 0.0847
(0.175) 		0.929
(0.943) 		0.0978
(0.193) 		0.424
(0.541) 		0.411
(0.531) 		1
(1.00) 		0.965
(0.971) 		0.714
(0.788) 		0.783
(0.841) 		0.496
(0.605)
amp 12q15 51 (28%) 133 0.134
(0.233) 		0.596
(0.699) 		0.834
(0.878) 		0.809
(0.858) 		0.141
(0.241) 		0.914
(0.938) 		0.316
(0.436) 		0.598
(0.7) 		0.299
(0.42) 		0.18
(0.289)
amp 19p13 2 32 (17%) 152 0.408
(0.528) 		0.0829
(0.173) 		0.569
(0.673) 		0.415
(0.533) 		0.292
(0.415) 		0.358
(0.478) 		0.121
(0.221) 		0.393
(0.511) 		0.321
(0.441) 		0.683
(0.767)
del 1q44 17 (9%) 167 0.857
(0.898) 		0.75
(0.814) 		0.418
(0.536) 		0.305
(0.426) 		0.463
(0.579) 		0.612
(0.71) 		0.719
(0.791) 		0.644
(0.74) 		0.8
(0.854) 		0.257
(0.378)
del 3q11 1 33 (18%) 151 0.591
(0.696) 		0.625
(0.725) 		0.47
(0.585) 		0.859
(0.899) 		0.712
(0.788) 		0.819
(0.865) 		0.866
(0.902) 		0.795
(0.85) 		0.887
(0.918) 		0.629
(0.727)
del 6q16 3 55 (30%) 129 0.141
(0.242) 		0.434
(0.548) 		0.135
(0.233) 		0.554
(0.661) 		0.699
(0.78) 		0.606
(0.707) 		0.129
(0.229) 		0.508
(0.617) 		0.54
(0.649) 		0.283
(0.406)
del 6q26 50 (27%) 134 0.272
(0.395) 		0.927
(0.943) 		0.34
(0.459) 		0.297
(0.419) 		0.927
(0.943) 		0.197
(0.312) 		0.195
(0.308) 		0.731
(0.801) 		0.774
(0.833) 		0.333
(0.45)
del 7q36 3 67 (36%) 117 0.905
(0.931) 		0.71
(0.788) 		0.917
(0.94) 		0.719
(0.791) 		0.896
(0.924) 		0.225
(0.344) 		0.361
(0.479) 		0.15
(0.253) 		0.378
(0.495) 		0.164
(0.27)
del xq11 2 42 (23%) 142 0.491
(0.602) 		0.243
(0.365) 		0.484
(0.597) 		0.74
(0.808) 		0.535
(0.647) 		0.607
(0.707) 		0.128
(0.228) 		0.219
(0.336) 		0.198
(0.313) 		0.715
(0.788)
'amp_1q23.3' versus 'CN_CNMF'

P value = 0.00197 (Fisher's exact test), Q value = 0.012

Table S1.  Gene #2: 'amp_1q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
AMP PEAK 2(1Q23.3) MUTATED 37 12 44
AMP PEAK 2(1Q23.3) WILD-TYPE 28 32 31

Figure S1.  Get High-res Image Gene #2: 'amp_1q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q23.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0189 (Fisher's exact test), Q value = 0.063

Table S2.  Gene #2: 'amp_1q23.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 66 35 11
AMP PEAK 2(1Q23.3) MUTATED 35 40 10 5
AMP PEAK 2(1Q23.3) WILD-TYPE 31 26 25 6

Figure S2.  Get High-res Image Gene #2: 'amp_1q23.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_1q42.3' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00076

Table S3.  Gene #3: 'amp_1q42.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
AMP PEAK 3(1Q42.3) MUTATED 39 10 47
AMP PEAK 3(1Q42.3) WILD-TYPE 26 34 28

Figure S3.  Get High-res Image Gene #3: 'amp_1q42.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_2q14.2' versus 'RPPA_CNMF'

P value = 0.0247 (Fisher's exact test), Q value = 0.074

Table S4.  Gene #4: 'amp_2q14.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 24 16 17 23 17 24 5
AMP PEAK 4(2Q14.2) MUTATED 5 7 3 12 9 4 1
AMP PEAK 4(2Q14.2) WILD-TYPE 19 9 14 11 8 20 4

Figure S4.  Get High-res Image Gene #4: 'amp_2q14.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_2q31.1' versus 'CN_CNMF'

P value = 0.0315 (Fisher's exact test), Q value = 0.086

Table S5.  Gene #5: 'amp_2q31.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
AMP PEAK 5(2Q31.1) MUTATED 21 8 31
AMP PEAK 5(2Q31.1) WILD-TYPE 44 36 44

Figure S5.  Get High-res Image Gene #5: 'amp_2q31.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_2q31.1' versus 'RPPA_CNMF'

P value = 0.0349 (Fisher's exact test), Q value = 0.092

Table S6.  Gene #5: 'amp_2q31.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 24 16 17 23 17 24 5
AMP PEAK 5(2Q31.1) MUTATED 4 5 2 12 8 5 1
AMP PEAK 5(2Q31.1) WILD-TYPE 20 11 15 11 9 19 4

Figure S6.  Get High-res Image Gene #5: 'amp_2q31.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_2q31.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0372 (Fisher's exact test), Q value = 0.094

Table S7.  Gene #5: 'amp_2q31.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
AMP PEAK 5(2Q31.1) MUTATED 15 10 35
AMP PEAK 5(2Q31.1) WILD-TYPE 52 10 61

Figure S7.  Get High-res Image Gene #5: 'amp_2q31.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_3q26.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S8.  Gene #6: 'amp_3q26.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
AMP PEAK 6(3Q26.2) MUTATED 40 14 74
AMP PEAK 6(3Q26.2) WILD-TYPE 25 30 1

Figure S8.  Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3q26.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S9.  Gene #6: 'amp_3q26.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
AMP PEAK 6(3Q26.2) MUTATED 41 19 68
AMP PEAK 6(3Q26.2) WILD-TYPE 35 13 8

Figure S9.  Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_3q26.2' versus 'RPPA_CNMF'

P value = 0.0106 (Fisher's exact test), Q value = 0.042

Table S10.  Gene #6: 'amp_3q26.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 24 16 17 23 17 24 5
AMP PEAK 6(3Q26.2) MUTATED 11 11 11 21 13 21 4
AMP PEAK 6(3Q26.2) WILD-TYPE 13 5 6 2 4 3 1

Figure S10.  Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_3q26.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00061 (Fisher's exact test), Q value = 0.0048

Table S11.  Gene #6: 'amp_3q26.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
AMP PEAK 6(3Q26.2) MUTATED 12 12 14 25 29
AMP PEAK 6(3Q26.2) WILD-TYPE 11 9 8 1 5

Figure S11.  Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_3q26.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S12.  Gene #6: 'amp_3q26.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 68 31
AMP PEAK 6(3Q26.2) MUTATED 44 62 21
AMP PEAK 6(3Q26.2) WILD-TYPE 40 6 10

Figure S12.  Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_3q26.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S13.  Gene #6: 'amp_3q26.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
AMP PEAK 6(3Q26.2) MUTATED 38 7 82
AMP PEAK 6(3Q26.2) WILD-TYPE 29 13 14

Figure S13.  Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_3q26.2' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00039

Table S14.  Gene #6: 'amp_3q26.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
AMP PEAK 6(3Q26.2) MUTATED 44 75 8
AMP PEAK 6(3Q26.2) WILD-TYPE 40 12 4

Figure S14.  Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_3q26.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00027

Table S15.  Gene #6: 'amp_3q26.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
AMP PEAK 6(3Q26.2) MUTATED 33 13 56 25
AMP PEAK 6(3Q26.2) WILD-TYPE 29 13 6 8

Figure S15.  Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_3q26.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S16.  Gene #6: 'amp_3q26.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 66 35 11
AMP PEAK 6(3Q26.2) MUTATED 35 62 23 6
AMP PEAK 6(3Q26.2) WILD-TYPE 31 4 12 5

Figure S16.  Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_3q26.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00068

Table S17.  Gene #6: 'amp_3q26.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
AMP PEAK 6(3Q26.2) MUTATED 35 11 80
AMP PEAK 6(3Q26.2) WILD-TYPE 27 11 14

Figure S17.  Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_4q21.1' versus 'RPPA_CNMF'

P value = 0.0221 (Fisher's exact test), Q value = 0.07

Table S18.  Gene #7: 'amp_4q21.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 24 16 17 23 17 24 5
AMP PEAK 7(4Q21.1) MUTATED 4 3 6 4 8 1 0
AMP PEAK 7(4Q21.1) WILD-TYPE 20 13 11 19 9 23 5

Figure S18.  Get High-res Image Gene #7: 'amp_4q21.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_5p15.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S19.  Gene #8: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
AMP PEAK 8(5P15.33) MUTATED 31 11 56
AMP PEAK 8(5P15.33) WILD-TYPE 34 33 19

Figure S19.  Get High-res Image Gene #8: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5p15.33' versus 'METHLYATION_CNMF'

P value = 0.0157 (Fisher's exact test), Q value = 0.056

Table S20.  Gene #8: 'amp_5p15.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
AMP PEAK 8(5P15.33) MUTATED 33 15 50
AMP PEAK 8(5P15.33) WILD-TYPE 43 17 26

Figure S20.  Get High-res Image Gene #8: 'amp_5p15.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_5p15.33' versus 'MRNASEQ_CNMF'

P value = 0.00219 (Fisher's exact test), Q value = 0.013

Table S21.  Gene #8: 'amp_5p15.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 68 31
AMP PEAK 8(5P15.33) MUTATED 34 47 17
AMP PEAK 8(5P15.33) WILD-TYPE 50 21 14

Figure S21.  Get High-res Image Gene #8: 'amp_5p15.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_5p15.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00074 (Fisher's exact test), Q value = 0.0055

Table S22.  Gene #8: 'amp_5p15.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
AMP PEAK 8(5P15.33) MUTATED 30 5 63
AMP PEAK 8(5P15.33) WILD-TYPE 37 15 33

Figure S22.  Get High-res Image Gene #8: 'amp_5p15.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'MIRSEQ_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.0023

Table S23.  Gene #8: 'amp_5p15.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
AMP PEAK 8(5P15.33) MUTATED 34 60 4
AMP PEAK 8(5P15.33) WILD-TYPE 50 27 8

Figure S23.  Get High-res Image Gene #8: 'amp_5p15.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_5p15.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00417 (Fisher's exact test), Q value = 0.021

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
AMP PEAK 8(5P15.33) MUTATED 24 11 40 23
AMP PEAK 8(5P15.33) WILD-TYPE 38 15 22 10

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

'amp_5p15.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0109 (Fisher's exact test), Q value = 0.042

Table S25.  Gene #8: 'amp_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 66 35 11
AMP PEAK 8(5P15.33) MUTATED 27 46 19 6
AMP PEAK 8(5P15.33) WILD-TYPE 39 20 16 5

Figure S25.  Get High-res Image Gene #8: 'amp_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_5p15.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00189 (Fisher's exact test), Q value = 0.012

Table S26.  Gene #8: 'amp_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
AMP PEAK 8(5P15.33) MUTATED 24 11 63
AMP PEAK 8(5P15.33) WILD-TYPE 38 11 31

Figure S26.  Get High-res Image Gene #8: 'amp_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_6p21.1' versus 'CN_CNMF'

P value = 0.00282 (Fisher's exact test), Q value = 0.016

Table S27.  Gene #9: 'amp_6p21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
AMP PEAK 9(6P21.1) MUTATED 35 11 23
AMP PEAK 9(6P21.1) WILD-TYPE 30 33 52

Figure S27.  Get High-res Image Gene #9: 'amp_6p21.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6p21.1' versus 'RPPA_CNMF'

P value = 0.0397 (Fisher's exact test), Q value = 0.099

Table S28.  Gene #9: 'amp_6p21.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 24 16 17 23 17 24 5
AMP PEAK 9(6P21.1) MUTATED 11 9 3 12 3 6 1
AMP PEAK 9(6P21.1) WILD-TYPE 13 7 14 11 14 18 4

Figure S28.  Get High-res Image Gene #9: 'amp_6p21.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_6p21.1' versus 'MRNASEQ_CNMF'

P value = 0.0434 (Fisher's exact test), Q value = 0.11

Table S29.  Gene #9: 'amp_6p21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 68 31
AMP PEAK 9(6P21.1) MUTATED 40 20 9
AMP PEAK 9(6P21.1) WILD-TYPE 44 48 22

Figure S29.  Get High-res Image Gene #9: 'amp_6p21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_6p21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0304 (Fisher's exact test), Q value = 0.084

Table S30.  Gene #9: 'amp_6p21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
AMP PEAK 9(6P21.1) MUTATED 30 11 28
AMP PEAK 9(6P21.1) WILD-TYPE 37 9 68

Figure S30.  Get High-res Image Gene #9: 'amp_6p21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_6p21.1' versus 'MIRSEQ_CNMF'

P value = 0.0034 (Fisher's exact test), Q value = 0.018

Table S31.  Gene #9: 'amp_6p21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
AMP PEAK 9(6P21.1) MUTATED 41 26 1
AMP PEAK 9(6P21.1) WILD-TYPE 43 61 11

Figure S31.  Get High-res Image Gene #9: 'amp_6p21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_6p21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00206 (Fisher's exact test), Q value = 0.013

Table S32.  Gene #9: 'amp_6p21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
AMP PEAK 9(6P21.1) MUTATED 35 7 16 10
AMP PEAK 9(6P21.1) WILD-TYPE 27 19 46 23

Figure S32.  Get High-res Image Gene #9: 'amp_6p21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_6p21.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0065 (Fisher's exact test), Q value = 0.029

Table S33.  Gene #9: 'amp_6p21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 66 35 11
AMP PEAK 9(6P21.1) MUTATED 36 18 10 4
AMP PEAK 9(6P21.1) WILD-TYPE 30 48 25 7

Figure S33.  Get High-res Image Gene #9: 'amp_6p21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_6p21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00131 (Fisher's exact test), Q value = 0.0088

Table S34.  Gene #9: 'amp_6p21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
AMP PEAK 9(6P21.1) MUTATED 35 7 26
AMP PEAK 9(6P21.1) WILD-TYPE 27 15 68

Figure S34.  Get High-res Image Gene #9: 'amp_6p21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_6q23.3' versus 'CN_CNMF'

P value = 0.0378 (Fisher's exact test), Q value = 0.096

Table S35.  Gene #10: 'amp_6q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
AMP PEAK 10(6Q23.3) MUTATED 22 8 12
AMP PEAK 10(6Q23.3) WILD-TYPE 43 36 63

Figure S35.  Get High-res Image Gene #10: 'amp_6q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6q23.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00657 (Fisher's exact test), Q value = 0.029

Table S36.  Gene #10: 'amp_6q23.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
AMP PEAK 10(6Q23.3) MUTATED 5 10 5 1 5
AMP PEAK 10(6Q23.3) WILD-TYPE 18 11 17 25 29

Figure S36.  Get High-res Image Gene #10: 'amp_6q23.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_6q23.3' versus 'MIRSEQ_CNMF'

P value = 0.0324 (Fisher's exact test), Q value = 0.087

Table S37.  Gene #10: 'amp_6q23.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
AMP PEAK 10(6Q23.3) MUTATED 26 14 1
AMP PEAK 10(6Q23.3) WILD-TYPE 58 73 11

Figure S37.  Get High-res Image Gene #10: 'amp_6q23.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_6q23.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0306 (Fisher's exact test), Q value = 0.084

Table S38.  Gene #10: 'amp_6q23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
AMP PEAK 10(6Q23.3) MUTATED 22 4 9 6
AMP PEAK 10(6Q23.3) WILD-TYPE 40 22 53 27

Figure S38.  Get High-res Image Gene #10: 'amp_6q23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_6q23.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00938 (Fisher's exact test), Q value = 0.038

Table S39.  Gene #10: 'amp_6q23.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 66 35 11
AMP PEAK 10(6Q23.3) MUTATED 23 10 4 4
AMP PEAK 10(6Q23.3) WILD-TYPE 43 56 31 7

Figure S39.  Get High-res Image Gene #10: 'amp_6q23.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_6q23.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00643 (Fisher's exact test), Q value = 0.029

Table S40.  Gene #10: 'amp_6q23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
AMP PEAK 10(6Q23.3) MUTATED 23 3 15
AMP PEAK 10(6Q23.3) WILD-TYPE 39 19 79

Figure S40.  Get High-res Image Gene #10: 'amp_6q23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0412 (Fisher's exact test), Q value = 0.1

Table S41.  Gene #11: 'amp_7p11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
AMP PEAK 11(7P11.2) MUTATED 48 18 60
AMP PEAK 11(7P11.2) WILD-TYPE 19 2 36

Figure S41.  Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_7p11.2' versus 'MIRSEQ_CNMF'

P value = 0.0372 (Fisher's exact test), Q value = 0.094

Table S42.  Gene #11: 'amp_7p11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
AMP PEAK 11(7P11.2) MUTATED 64 56 5
AMP PEAK 11(7P11.2) WILD-TYPE 20 31 7

Figure S42.  Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_7q21.2' versus 'RPPA_CNMF'

P value = 0.0268 (Fisher's exact test), Q value = 0.078

Table S43.  Gene #12: 'amp_7q21.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 24 16 17 23 17 24 5
AMP PEAK 12(7Q21.2) MUTATED 15 7 12 20 12 10 3
AMP PEAK 12(7Q21.2) WILD-TYPE 9 9 5 3 5 14 2

Figure S43.  Get High-res Image Gene #12: 'amp_7q21.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_8p23.1' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00027

Table S44.  Gene #13: 'amp_8p23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
AMP PEAK 13(8P23.1) MUTATED 26 18 8
AMP PEAK 13(8P23.1) WILD-TYPE 39 26 67

Figure S44.  Get High-res Image Gene #13: 'amp_8p23.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8p23.1' versus 'METHLYATION_CNMF'

P value = 0.00213 (Fisher's exact test), Q value = 0.013

Table S45.  Gene #13: 'amp_8p23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
AMP PEAK 13(8P23.1) MUTATED 32 5 15
AMP PEAK 13(8P23.1) WILD-TYPE 44 27 61

Figure S45.  Get High-res Image Gene #13: 'amp_8p23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8p23.1' versus 'MRNASEQ_CNMF'

P value = 0.00437 (Fisher's exact test), Q value = 0.022

Table S46.  Gene #13: 'amp_8p23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 68 31
AMP PEAK 13(8P23.1) MUTATED 34 12 6
AMP PEAK 13(8P23.1) WILD-TYPE 50 56 25

Figure S46.  Get High-res Image Gene #13: 'amp_8p23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_8p23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00068

Table S47.  Gene #13: 'amp_8p23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
AMP PEAK 13(8P23.1) MUTATED 32 2 18
AMP PEAK 13(8P23.1) WILD-TYPE 35 18 78

Figure S47.  Get High-res Image Gene #13: 'amp_8p23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_8p23.1' versus 'MIRSEQ_CNMF'

P value = 0.00429 (Fisher's exact test), Q value = 0.021

Table S48.  Gene #13: 'amp_8p23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
AMP PEAK 13(8P23.1) MUTATED 33 15 3
AMP PEAK 13(8P23.1) WILD-TYPE 51 72 9

Figure S48.  Get High-res Image Gene #13: 'amp_8p23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_8p23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0151 (Fisher's exact test), Q value = 0.054

Table S49.  Gene #13: 'amp_8p23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
AMP PEAK 13(8P23.1) MUTATED 25 9 10 7
AMP PEAK 13(8P23.1) WILD-TYPE 37 17 52 26

Figure S49.  Get High-res Image Gene #13: 'amp_8p23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_8p23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.0032

Table S50.  Gene #13: 'amp_8p23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 66 35 11
AMP PEAK 13(8P23.1) MUTATED 28 7 11 2
AMP PEAK 13(8P23.1) WILD-TYPE 38 59 24 9

Figure S50.  Get High-res Image Gene #13: 'amp_8p23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_8p23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00202 (Fisher's exact test), Q value = 0.012

Table S51.  Gene #13: 'amp_8p23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
AMP PEAK 13(8P23.1) MUTATED 25 8 15
AMP PEAK 13(8P23.1) WILD-TYPE 37 14 79

Figure S51.  Get High-res Image Gene #13: 'amp_8p23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8q24.21' versus 'CN_CNMF'

P value = 0.00229 (Fisher's exact test), Q value = 0.013

Table S52.  Gene #15: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
AMP PEAK 15(8Q24.21) MUTATED 56 26 63
AMP PEAK 15(8Q24.21) WILD-TYPE 9 18 12

Figure S52.  Get High-res Image Gene #15: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

P value = 0.0223 (Fisher's exact test), Q value = 0.07

Table S53.  Gene #15: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
AMP PEAK 15(8Q24.21) MUTATED 59 20 66
AMP PEAK 15(8Q24.21) WILD-TYPE 17 12 10

Figure S53.  Get High-res Image Gene #15: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'RPPA_CNMF'

P value = 0.00065 (Fisher's exact test), Q value = 0.005

Table S54.  Gene #15: 'amp_8q24.21' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 24 16 17 23 17 24 5
AMP PEAK 15(8Q24.21) MUTATED 19 12 13 23 10 23 2
AMP PEAK 15(8Q24.21) WILD-TYPE 5 4 4 0 7 1 3

Figure S54.  Get High-res Image Gene #15: 'amp_8q24.21' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_8q24.21' versus 'MIRSEQ_CNMF'

P value = 0.00739 (Fisher's exact test), Q value = 0.032

Table S55.  Gene #15: 'amp_8q24.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
AMP PEAK 15(8Q24.21) MUTATED 66 73 5
AMP PEAK 15(8Q24.21) WILD-TYPE 18 14 7

Figure S55.  Get High-res Image Gene #15: 'amp_8q24.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_9q34.3' versus 'CN_CNMF'

P value = 0.025 (Fisher's exact test), Q value = 0.074

Table S56.  Gene #17: 'amp_9q34.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
AMP PEAK 17(9Q34.3) MUTATED 25 8 31
AMP PEAK 17(9Q34.3) WILD-TYPE 40 36 44

Figure S56.  Get High-res Image Gene #17: 'amp_9q34.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_9q34.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0247 (Fisher's exact test), Q value = 0.074

Table S57.  Gene #17: 'amp_9q34.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
AMP PEAK 17(9Q34.3) MUTATED 8 7 6 17 9
AMP PEAK 17(9Q34.3) WILD-TYPE 15 14 16 9 25

Figure S57.  Get High-res Image Gene #17: 'amp_9q34.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_9q34.3' versus 'MRNASEQ_CNMF'

P value = 0.00345 (Fisher's exact test), Q value = 0.018

Table S58.  Gene #17: 'amp_9q34.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 68 31
AMP PEAK 17(9Q34.3) MUTATED 25 33 5
AMP PEAK 17(9Q34.3) WILD-TYPE 59 35 26

Figure S58.  Get High-res Image Gene #17: 'amp_9q34.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_11q13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S59.  Gene #20: 'amp_11q13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
AMP PEAK 20(11Q13.3) MUTATED 28 15 61
AMP PEAK 20(11Q13.3) WILD-TYPE 37 29 14

Figure S59.  Get High-res Image Gene #20: 'amp_11q13.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11q13.3' versus 'METHLYATION_CNMF'

P value = 0.00328 (Fisher's exact test), Q value = 0.017

Table S60.  Gene #20: 'amp_11q13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
AMP PEAK 20(11Q13.3) MUTATED 32 20 52
AMP PEAK 20(11Q13.3) WILD-TYPE 44 12 24

Figure S60.  Get High-res Image Gene #20: 'amp_11q13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_11q13.3' versus 'RPPA_CNMF'

P value = 0.0477 (Fisher's exact test), Q value = 0.11

Table S61.  Gene #20: 'amp_11q13.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 24 16 17 23 17 24 5
AMP PEAK 20(11Q13.3) MUTATED 9 14 10 13 12 16 2
AMP PEAK 20(11Q13.3) WILD-TYPE 15 2 7 10 5 8 3

Figure S61.  Get High-res Image Gene #20: 'amp_11q13.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_11q13.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0131 (Fisher's exact test), Q value = 0.049

Table S62.  Gene #20: 'amp_11q13.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
AMP PEAK 20(11Q13.3) MUTATED 7 17 13 17 22
AMP PEAK 20(11Q13.3) WILD-TYPE 16 4 9 9 12

Figure S62.  Get High-res Image Gene #20: 'amp_11q13.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_11q13.3' versus 'MRNASEQ_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.0031

Table S63.  Gene #20: 'amp_11q13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 68 31
AMP PEAK 20(11Q13.3) MUTATED 35 50 18
AMP PEAK 20(11Q13.3) WILD-TYPE 49 18 13

Figure S63.  Get High-res Image Gene #20: 'amp_11q13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_11q13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00105 (Fisher's exact test), Q value = 0.0073

Table S64.  Gene #20: 'amp_11q13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
AMP PEAK 20(11Q13.3) MUTATED 27 10 66
AMP PEAK 20(11Q13.3) WILD-TYPE 40 10 30

Figure S64.  Get High-res Image Gene #20: 'amp_11q13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_11q13.3' versus 'MIRSEQ_CNMF'

P value = 0.00115 (Fisher's exact test), Q value = 0.0079

Table S65.  Gene #20: 'amp_11q13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
AMP PEAK 20(11Q13.3) MUTATED 36 61 6
AMP PEAK 20(11Q13.3) WILD-TYPE 48 26 6

Figure S65.  Get High-res Image Gene #20: 'amp_11q13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_11q13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00135 (Fisher's exact test), Q value = 0.009

Table S66.  Gene #20: 'amp_11q13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
AMP PEAK 20(11Q13.3) MUTATED 29 8 43 23
AMP PEAK 20(11Q13.3) WILD-TYPE 33 18 19 10

Figure S66.  Get High-res Image Gene #20: 'amp_11q13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_11q13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00132 (Fisher's exact test), Q value = 0.0088

Table S67.  Gene #20: 'amp_11q13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
AMP PEAK 20(11Q13.3) MUTATED 30 7 65
AMP PEAK 20(11Q13.3) WILD-TYPE 32 15 29

Figure S67.  Get High-res Image Gene #20: 'amp_11q13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12p12.1' versus 'CN_CNMF'

P value = 0.0338 (Fisher's exact test), Q value = 0.09

Table S68.  Gene #21: 'amp_12p12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
AMP PEAK 21(12P12.1) MUTATED 26 13 40
AMP PEAK 21(12P12.1) WILD-TYPE 39 31 35

Figure S68.  Get High-res Image Gene #21: 'amp_12p12.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12p12.1' versus 'RPPA_CNMF'

P value = 0.0278 (Fisher's exact test), Q value = 0.079

Table S69.  Gene #21: 'amp_12p12.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 24 16 17 23 17 24 5
AMP PEAK 21(12P12.1) MUTATED 9 6 8 17 5 8 4
AMP PEAK 21(12P12.1) WILD-TYPE 15 10 9 6 12 16 1

Figure S69.  Get High-res Image Gene #21: 'amp_12p12.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_12p12.1' versus 'MRNASEQ_CNMF'

P value = 0.0192 (Fisher's exact test), Q value = 0.063

Table S70.  Gene #21: 'amp_12p12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 68 31
AMP PEAK 21(12P12.1) MUTATED 27 35 17
AMP PEAK 21(12P12.1) WILD-TYPE 57 33 14

Figure S70.  Get High-res Image Gene #21: 'amp_12p12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_12p12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0284 (Fisher's exact test), Q value = 0.08

Table S71.  Gene #21: 'amp_12p12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
AMP PEAK 21(12P12.1) MUTATED 21 8 50
AMP PEAK 21(12P12.1) WILD-TYPE 46 12 46

Figure S71.  Get High-res Image Gene #21: 'amp_12p12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_13q22.1' versus 'CN_CNMF'

P value = 0.00191 (Fisher's exact test), Q value = 0.012

Table S72.  Gene #23: 'amp_13q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
AMP PEAK 23(13Q22.1) MUTATED 34 13 18
AMP PEAK 23(13Q22.1) WILD-TYPE 31 31 57

Figure S72.  Get High-res Image Gene #23: 'amp_13q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_13q22.1' versus 'METHLYATION_CNMF'

P value = 0.00674 (Fisher's exact test), Q value = 0.03

Table S73.  Gene #23: 'amp_13q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
AMP PEAK 23(13Q22.1) MUTATED 37 8 20
AMP PEAK 23(13Q22.1) WILD-TYPE 39 24 56

Figure S73.  Get High-res Image Gene #23: 'amp_13q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_13q22.1' versus 'MRNASEQ_CNMF'

P value = 0.00692 (Fisher's exact test), Q value = 0.03

Table S74.  Gene #23: 'amp_13q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 68 31
AMP PEAK 23(13Q22.1) MUTATED 40 18 7
AMP PEAK 23(13Q22.1) WILD-TYPE 44 50 24

Figure S74.  Get High-res Image Gene #23: 'amp_13q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_13q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00127 (Fisher's exact test), Q value = 0.0086

Table S75.  Gene #23: 'amp_13q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
AMP PEAK 23(13Q22.1) MUTATED 30 12 23
AMP PEAK 23(13Q22.1) WILD-TYPE 37 8 73

Figure S75.  Get High-res Image Gene #23: 'amp_13q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_13q22.1' versus 'MIRSEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.0014

Table S76.  Gene #23: 'amp_13q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
AMP PEAK 23(13Q22.1) MUTATED 42 21 1
AMP PEAK 23(13Q22.1) WILD-TYPE 42 66 11

Figure S76.  Get High-res Image Gene #23: 'amp_13q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_13q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00236 (Fisher's exact test), Q value = 0.013

Table S77.  Gene #23: 'amp_13q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
AMP PEAK 23(13Q22.1) MUTATED 31 12 14 7
AMP PEAK 23(13Q22.1) WILD-TYPE 31 14 48 26

Figure S77.  Get High-res Image Gene #23: 'amp_13q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_13q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0128 (Fisher's exact test), Q value = 0.049

Table S78.  Gene #23: 'amp_13q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 66 35 11
AMP PEAK 23(13Q22.1) MUTATED 34 18 9 3
AMP PEAK 23(13Q22.1) WILD-TYPE 32 48 26 8

Figure S78.  Get High-res Image Gene #23: 'amp_13q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_13q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00025 (Fisher's exact test), Q value = 0.0023

Table S79.  Gene #23: 'amp_13q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
AMP PEAK 23(13Q22.1) MUTATED 33 10 21
AMP PEAK 23(13Q22.1) WILD-TYPE 29 12 73

Figure S79.  Get High-res Image Gene #23: 'amp_13q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_14q21.1' versus 'CN_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.0031

Table S80.  Gene #24: 'amp_14q21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
AMP PEAK 24(14Q21.1) MUTATED 19 6 36
AMP PEAK 24(14Q21.1) WILD-TYPE 46 38 39

Figure S80.  Get High-res Image Gene #24: 'amp_14q21.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_14q21.1' versus 'METHLYATION_CNMF'

P value = 0.00859 (Fisher's exact test), Q value = 0.036

Table S81.  Gene #24: 'amp_14q21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
AMP PEAK 24(14Q21.1) MUTATED 18 8 35
AMP PEAK 24(14Q21.1) WILD-TYPE 58 24 41

Figure S81.  Get High-res Image Gene #24: 'amp_14q21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_14q21.1' versus 'MRNASEQ_CNMF'

P value = 0.00533 (Fisher's exact test), Q value = 0.025

Table S82.  Gene #24: 'amp_14q21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 68 31
AMP PEAK 24(14Q21.1) MUTATED 18 31 12
AMP PEAK 24(14Q21.1) WILD-TYPE 66 37 19

Figure S82.  Get High-res Image Gene #24: 'amp_14q21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_14q21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00306 (Fisher's exact test), Q value = 0.017

Table S83.  Gene #24: 'amp_14q21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
AMP PEAK 24(14Q21.1) MUTATED 17 2 42
AMP PEAK 24(14Q21.1) WILD-TYPE 50 18 54

Figure S83.  Get High-res Image Gene #24: 'amp_14q21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_14q21.1' versus 'MIRSEQ_CNMF'

P value = 0.00366 (Fisher's exact test), Q value = 0.019

Table S84.  Gene #24: 'amp_14q21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
AMP PEAK 24(14Q21.1) MUTATED 19 39 2
AMP PEAK 24(14Q21.1) WILD-TYPE 65 48 10

Figure S84.  Get High-res Image Gene #24: 'amp_14q21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_14q21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00424 (Fisher's exact test), Q value = 0.021

Table S85.  Gene #24: 'amp_14q21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
AMP PEAK 24(14Q21.1) MUTATED 14 5 31 10
AMP PEAK 24(14Q21.1) WILD-TYPE 48 21 31 23

Figure S85.  Get High-res Image Gene #24: 'amp_14q21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_14q21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0131 (Fisher's exact test), Q value = 0.049

Table S86.  Gene #24: 'amp_14q21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
AMP PEAK 24(14Q21.1) MUTATED 14 5 41
AMP PEAK 24(14Q21.1) WILD-TYPE 48 17 53

Figure S86.  Get High-res Image Gene #24: 'amp_14q21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_15q26.1' versus 'CN_CNMF'

P value = 0.00806 (Fisher's exact test), Q value = 0.035

Table S87.  Gene #25: 'amp_15q26.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
AMP PEAK 25(15Q26.1) MUTATED 30 10 18
AMP PEAK 25(15Q26.1) WILD-TYPE 35 34 57

Figure S87.  Get High-res Image Gene #25: 'amp_15q26.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_15q26.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0452 (Fisher's exact test), Q value = 0.11

Table S88.  Gene #25: 'amp_15q26.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
AMP PEAK 25(15Q26.1) MUTATED 11 10 4 5 8
AMP PEAK 25(15Q26.1) WILD-TYPE 12 11 18 21 26

Figure S88.  Get High-res Image Gene #25: 'amp_15q26.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_15q26.1' versus 'MRNASEQ_CNMF'

P value = 0.0169 (Fisher's exact test), Q value = 0.058

Table S89.  Gene #25: 'amp_15q26.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 68 31
AMP PEAK 25(15Q26.1) MUTATED 34 13 10
AMP PEAK 25(15Q26.1) WILD-TYPE 50 55 21

Figure S89.  Get High-res Image Gene #25: 'amp_15q26.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_15q26.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0158 (Fisher's exact test), Q value = 0.056

Table S90.  Gene #25: 'amp_15q26.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
AMP PEAK 25(15Q26.1) MUTATED 27 9 21
AMP PEAK 25(15Q26.1) WILD-TYPE 40 11 75

Figure S90.  Get High-res Image Gene #25: 'amp_15q26.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_15q26.1' versus 'MIRSEQ_CNMF'

P value = 0.00728 (Fisher's exact test), Q value = 0.032

Table S91.  Gene #25: 'amp_15q26.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
AMP PEAK 25(15Q26.1) MUTATED 36 21 1
AMP PEAK 25(15Q26.1) WILD-TYPE 48 66 11

Figure S91.  Get High-res Image Gene #25: 'amp_15q26.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_15q26.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0432 (Fisher's exact test), Q value = 0.11

Table S92.  Gene #25: 'amp_15q26.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
AMP PEAK 25(15Q26.1) MUTATED 28 8 14 8
AMP PEAK 25(15Q26.1) WILD-TYPE 34 18 48 25

Figure S92.  Get High-res Image Gene #25: 'amp_15q26.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_15q26.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.036 (Fisher's exact test), Q value = 0.093

Table S93.  Gene #25: 'amp_15q26.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 66 35 11
AMP PEAK 25(15Q26.1) MUTATED 30 16 8 4
AMP PEAK 25(15Q26.1) WILD-TYPE 36 50 27 7

Figure S93.  Get High-res Image Gene #25: 'amp_15q26.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_15q26.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0152 (Fisher's exact test), Q value = 0.055

Table S94.  Gene #25: 'amp_15q26.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
AMP PEAK 25(15Q26.1) MUTATED 28 8 22
AMP PEAK 25(15Q26.1) WILD-TYPE 34 14 72

Figure S94.  Get High-res Image Gene #25: 'amp_15q26.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17q12' versus 'CN_CNMF'

P value = 0.00451 (Fisher's exact test), Q value = 0.022

Table S95.  Gene #26: 'amp_17q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
AMP PEAK 26(17Q12) MUTATED 37 15 23
AMP PEAK 26(17Q12) WILD-TYPE 28 29 52

Figure S95.  Get High-res Image Gene #26: 'amp_17q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q12' versus 'METHLYATION_CNMF'

P value = 0.00425 (Fisher's exact test), Q value = 0.021

Table S96.  Gene #26: 'amp_17q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
AMP PEAK 26(17Q12) MUTATED 41 7 27
AMP PEAK 26(17Q12) WILD-TYPE 35 25 49

Figure S96.  Get High-res Image Gene #26: 'amp_17q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_17q12' versus 'MRNASEQ_CNMF'

P value = 0.00556 (Fisher's exact test), Q value = 0.026

Table S97.  Gene #26: 'amp_17q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 68 31
AMP PEAK 26(17Q12) MUTATED 45 22 8
AMP PEAK 26(17Q12) WILD-TYPE 39 46 23

Figure S97.  Get High-res Image Gene #26: 'amp_17q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_17q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00278 (Fisher's exact test), Q value = 0.016

Table S98.  Gene #26: 'amp_17q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
AMP PEAK 26(17Q12) MUTATED 38 8 29
AMP PEAK 26(17Q12) WILD-TYPE 29 12 67

Figure S98.  Get High-res Image Gene #26: 'amp_17q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_CNMF'

P value = 0.00233 (Fisher's exact test), Q value = 0.013

Table S99.  Gene #26: 'amp_17q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
AMP PEAK 26(17Q12) MUTATED 45 27 2
AMP PEAK 26(17Q12) WILD-TYPE 39 60 10

Figure S99.  Get High-res Image Gene #26: 'amp_17q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_17q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0191 (Fisher's exact test), Q value = 0.063

Table S100.  Gene #26: 'amp_17q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
AMP PEAK 26(17Q12) MUTATED 32 14 18 10
AMP PEAK 26(17Q12) WILD-TYPE 30 12 44 23

Figure S100.  Get High-res Image Gene #26: 'amp_17q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0237 (Fisher's exact test), Q value = 0.072

Table S101.  Gene #26: 'amp_17q12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 66 35 11
AMP PEAK 26(17Q12) MUTATED 36 20 11 4
AMP PEAK 26(17Q12) WILD-TYPE 30 46 24 7

Figure S101.  Get High-res Image Gene #26: 'amp_17q12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_17q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00145 (Fisher's exact test), Q value = 0.0095

Table S102.  Gene #26: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
AMP PEAK 26(17Q12) MUTATED 32 13 26
AMP PEAK 26(17Q12) WILD-TYPE 30 9 68

Figure S102.  Get High-res Image Gene #26: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_18p11.32' versus 'MIRSEQ_CNMF'

P value = 0.0179 (Fisher's exact test), Q value = 0.061

Table S103.  Gene #27: 'amp_18p11.32' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
AMP PEAK 27(18P11.32) MUTATED 27 40 1
AMP PEAK 27(18P11.32) WILD-TYPE 57 47 11

Figure S103.  Get High-res Image Gene #27: 'amp_18p11.32' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_18q11.2' versus 'CN_CNMF'

P value = 0.0127 (Fisher's exact test), Q value = 0.048

Table S104.  Gene #28: 'amp_18q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
AMP PEAK 28(18Q11.2) MUTATED 30 11 18
AMP PEAK 28(18Q11.2) WILD-TYPE 35 33 57

Figure S104.  Get High-res Image Gene #28: 'amp_18q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_18q11.2' versus 'METHLYATION_CNMF'

P value = 0.00971 (Fisher's exact test), Q value = 0.039

Table S105.  Gene #28: 'amp_18q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
AMP PEAK 28(18Q11.2) MUTATED 34 8 17
AMP PEAK 28(18Q11.2) WILD-TYPE 42 24 59

Figure S105.  Get High-res Image Gene #28: 'amp_18q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_18q11.2' versus 'MRNASEQ_CNMF'

P value = 0.00566 (Fisher's exact test), Q value = 0.026

Table S106.  Gene #28: 'amp_18q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 68 31
AMP PEAK 28(18Q11.2) MUTATED 36 19 4
AMP PEAK 28(18Q11.2) WILD-TYPE 48 49 27

Figure S106.  Get High-res Image Gene #28: 'amp_18q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_18q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00498 (Fisher's exact test), Q value = 0.024

Table S107.  Gene #28: 'amp_18q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
AMP PEAK 28(18Q11.2) MUTATED 28 10 21
AMP PEAK 28(18Q11.2) WILD-TYPE 39 10 75

Figure S107.  Get High-res Image Gene #28: 'amp_18q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_18q11.2' versus 'MIRSEQ_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.003

Table S108.  Gene #28: 'amp_18q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
AMP PEAK 28(18Q11.2) MUTATED 38 21 0
AMP PEAK 28(18Q11.2) WILD-TYPE 46 66 12

Figure S108.  Get High-res Image Gene #28: 'amp_18q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_18q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00879 (Fisher's exact test), Q value = 0.037

Table S109.  Gene #28: 'amp_18q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
AMP PEAK 28(18Q11.2) MUTATED 28 11 14 6
AMP PEAK 28(18Q11.2) WILD-TYPE 34 15 48 27

Figure S109.  Get High-res Image Gene #28: 'amp_18q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_18q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.015 (Fisher's exact test), Q value = 0.054

Table S110.  Gene #28: 'amp_18q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 66 35 11
AMP PEAK 28(18Q11.2) MUTATED 31 14 10 3
AMP PEAK 28(18Q11.2) WILD-TYPE 35 52 25 8

Figure S110.  Get High-res Image Gene #28: 'amp_18q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_18q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6e-04 (Fisher's exact test), Q value = 0.0047

Table S111.  Gene #28: 'amp_18q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
AMP PEAK 28(18Q11.2) MUTATED 28 11 19
AMP PEAK 28(18Q11.2) WILD-TYPE 34 11 75

Figure S111.  Get High-res Image Gene #28: 'amp_18q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19q12' versus 'CN_CNMF'

P value = 0.00439 (Fisher's exact test), Q value = 0.022

Table S112.  Gene #30: 'amp_19q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
AMP PEAK 30(19Q12) MUTATED 29 9 16
AMP PEAK 30(19Q12) WILD-TYPE 36 35 59

Figure S112.  Get High-res Image Gene #30: 'amp_19q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19q12' versus 'MIRSEQ_CNMF'

P value = 0.0383 (Fisher's exact test), Q value = 0.096

Table S113.  Gene #30: 'amp_19q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
AMP PEAK 30(19Q12) MUTATED 32 21 1
AMP PEAK 30(19Q12) WILD-TYPE 52 66 11

Figure S113.  Get High-res Image Gene #30: 'amp_19q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_xq28' versus 'METHLYATION_CNMF'

P value = 0.0324 (Fisher's exact test), Q value = 0.087

Table S114.  Gene #31: 'amp_xq28' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
AMP PEAK 31(XQ28) MUTATED 22 10 37
AMP PEAK 31(XQ28) WILD-TYPE 54 22 39

Figure S114.  Get High-res Image Gene #31: 'amp_xq28' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_xq28' versus 'RPPA_CNMF'

P value = 0.0105 (Fisher's exact test), Q value = 0.042

Table S115.  Gene #31: 'amp_xq28' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 24 16 17 23 17 24 5
AMP PEAK 31(XQ28) MUTATED 8 5 5 17 5 10 0
AMP PEAK 31(XQ28) WILD-TYPE 16 11 12 6 12 14 5

Figure S115.  Get High-res Image Gene #31: 'amp_xq28' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_xq28' versus 'MRNASEQ_CNMF'

P value = 0.00186 (Fisher's exact test), Q value = 0.012

Table S116.  Gene #31: 'amp_xq28' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 68 31
AMP PEAK 31(XQ28) MUTATED 24 37 8
AMP PEAK 31(XQ28) WILD-TYPE 60 31 23

Figure S116.  Get High-res Image Gene #31: 'amp_xq28' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_xq28' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.027 (Fisher's exact test), Q value = 0.078

Table S117.  Gene #31: 'amp_xq28' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
AMP PEAK 31(XQ28) MUTATED 18 6 45
AMP PEAK 31(XQ28) WILD-TYPE 49 14 51

Figure S117.  Get High-res Image Gene #31: 'amp_xq28' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_xq28' versus 'MIRSEQ_CNMF'

P value = 0.0304 (Fisher's exact test), Q value = 0.084

Table S118.  Gene #31: 'amp_xq28' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
AMP PEAK 31(XQ28) MUTATED 24 41 3
AMP PEAK 31(XQ28) WILD-TYPE 60 46 9

Figure S118.  Get High-res Image Gene #31: 'amp_xq28' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_xq28' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00192 (Fisher's exact test), Q value = 0.012

Table S119.  Gene #31: 'amp_xq28' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
AMP PEAK 31(XQ28) MUTATED 22 2 29 15
AMP PEAK 31(XQ28) WILD-TYPE 40 24 33 18

Figure S119.  Get High-res Image Gene #31: 'amp_xq28' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_xq28' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0035 (Fisher's exact test), Q value = 0.018

Table S120.  Gene #31: 'amp_xq28' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
AMP PEAK 31(XQ28) MUTATED 22 2 43
AMP PEAK 31(XQ28) WILD-TYPE 40 20 51

Figure S120.  Get High-res Image Gene #31: 'amp_xq28' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p36.11' versus 'CN_CNMF'

P value = 0.0106 (Fisher's exact test), Q value = 0.042

Table S121.  Gene #32: 'del_1p36.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
DEL PEAK 1(1P36.11) MUTATED 36 13 26
DEL PEAK 1(1P36.11) WILD-TYPE 29 31 49

Figure S121.  Get High-res Image Gene #32: 'del_1p36.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.11' versus 'METHLYATION_CNMF'

P value = 0.00979 (Fisher's exact test), Q value = 0.039

Table S122.  Gene #32: 'del_1p36.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
DEL PEAK 1(1P36.11) MUTATED 41 9 25
DEL PEAK 1(1P36.11) WILD-TYPE 35 23 51

Figure S122.  Get High-res Image Gene #32: 'del_1p36.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p36.11' versus 'MRNASEQ_CNMF'

P value = 0.0167 (Fisher's exact test), Q value = 0.058

Table S123.  Gene #32: 'del_1p36.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 68 31
DEL PEAK 1(1P36.11) MUTATED 44 21 10
DEL PEAK 1(1P36.11) WILD-TYPE 40 47 21

Figure S123.  Get High-res Image Gene #32: 'del_1p36.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_1p36.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0251 (Fisher's exact test), Q value = 0.074

Table S124.  Gene #32: 'del_1p36.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
DEL PEAK 1(1P36.11) MUTATED 36 8 31
DEL PEAK 1(1P36.11) WILD-TYPE 31 12 65

Figure S124.  Get High-res Image Gene #32: 'del_1p36.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.11' versus 'MIRSEQ_CNMF'

P value = 0.00284 (Fisher's exact test), Q value = 0.016

Table S125.  Gene #32: 'del_1p36.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
DEL PEAK 1(1P36.11) MUTATED 44 30 1
DEL PEAK 1(1P36.11) WILD-TYPE 40 57 11

Figure S125.  Get High-res Image Gene #32: 'del_1p36.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_1p36.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0231 (Fisher's exact test), Q value = 0.072

Table S126.  Gene #32: 'del_1p36.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
DEL PEAK 1(1P36.11) MUTATED 33 11 24 7
DEL PEAK 1(1P36.11) WILD-TYPE 29 15 38 26

Figure S126.  Get High-res Image Gene #32: 'del_1p36.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.11' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0418 (Fisher's exact test), Q value = 0.1

Table S127.  Gene #32: 'del_1p36.11' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 66 35 11
DEL PEAK 1(1P36.11) MUTATED 36 25 10 3
DEL PEAK 1(1P36.11) WILD-TYPE 30 41 25 8

Figure S127.  Get High-res Image Gene #32: 'del_1p36.11' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_1p36.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0386 (Fisher's exact test), Q value = 0.097

Table S128.  Gene #32: 'del_1p36.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
DEL PEAK 1(1P36.11) MUTATED 33 10 31
DEL PEAK 1(1P36.11) WILD-TYPE 29 12 63

Figure S128.  Get High-res Image Gene #32: 'del_1p36.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p13.2' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00068

Table S129.  Gene #33: 'del_1p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
DEL PEAK 2(1P13.2) MUTATED 29 4 31
DEL PEAK 2(1P13.2) WILD-TYPE 36 40 44

Figure S129.  Get High-res Image Gene #33: 'del_1p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S130.  Gene #35: 'del_2q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
DEL PEAK 4(2Q22.1) MUTATED 11 8 40
DEL PEAK 4(2Q22.1) WILD-TYPE 54 36 35

Figure S130.  Get High-res Image Gene #35: 'del_2q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q22.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S131.  Gene #35: 'del_2q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
DEL PEAK 4(2Q22.1) MUTATED 10 8 41
DEL PEAK 4(2Q22.1) WILD-TYPE 66 24 35

Figure S131.  Get High-res Image Gene #35: 'del_2q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q22.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.00248 (Fisher's exact test), Q value = 0.014

Table S132.  Gene #35: 'del_2q22.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
DEL PEAK 4(2Q22.1) MUTATED 3 7 4 10 20
DEL PEAK 4(2Q22.1) WILD-TYPE 20 14 18 16 14

Figure S132.  Get High-res Image Gene #35: 'del_2q22.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_2q22.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S133.  Gene #35: 'del_2q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 68 31
DEL PEAK 4(2Q22.1) MUTATED 11 32 15
DEL PEAK 4(2Q22.1) WILD-TYPE 73 36 16

Figure S133.  Get High-res Image Gene #35: 'del_2q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S134.  Gene #35: 'del_2q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
DEL PEAK 4(2Q22.1) MUTATED 6 6 46
DEL PEAK 4(2Q22.1) WILD-TYPE 61 14 50

Figure S134.  Get High-res Image Gene #35: 'del_2q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_2q22.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S135.  Gene #35: 'del_2q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
DEL PEAK 4(2Q22.1) MUTATED 12 45 2
DEL PEAK 4(2Q22.1) WILD-TYPE 72 42 10

Figure S135.  Get High-res Image Gene #35: 'del_2q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_2q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S136.  Gene #35: 'del_2q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
DEL PEAK 4(2Q22.1) MUTATED 10 3 26 20
DEL PEAK 4(2Q22.1) WILD-TYPE 52 23 36 13

Figure S136.  Get High-res Image Gene #35: 'del_2q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_2q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.0012

Table S137.  Gene #35: 'del_2q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 66 35 11
DEL PEAK 4(2Q22.1) MUTATED 11 35 10 3
DEL PEAK 4(2Q22.1) WILD-TYPE 55 31 25 8

Figure S137.  Get High-res Image Gene #35: 'del_2q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_2q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S138.  Gene #35: 'del_2q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
DEL PEAK 4(2Q22.1) MUTATED 10 3 46
DEL PEAK 4(2Q22.1) WILD-TYPE 52 19 48

Figure S138.  Get High-res Image Gene #35: 'del_2q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_2q33.3' versus 'MRNASEQ_CNMF'

P value = 0.0174 (Fisher's exact test), Q value = 0.059

Table S139.  Gene #36: 'del_2q33.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 68 31
DEL PEAK 5(2Q33.3) MUTATED 10 15 11
DEL PEAK 5(2Q33.3) WILD-TYPE 74 53 20

Figure S139.  Get High-res Image Gene #36: 'del_2q33.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2q33.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0278 (Fisher's exact test), Q value = 0.079

Table S140.  Gene #36: 'del_2q33.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
DEL PEAK 5(2Q33.3) MUTATED 7 3 26
DEL PEAK 5(2Q33.3) WILD-TYPE 60 17 70

Figure S140.  Get High-res Image Gene #36: 'del_2q33.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_2q33.3' versus 'MIRSEQ_CNMF'

P value = 0.0144 (Fisher's exact test), Q value = 0.053

Table S141.  Gene #36: 'del_2q33.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
DEL PEAK 5(2Q33.3) MUTATED 9 22 4
DEL PEAK 5(2Q33.3) WILD-TYPE 75 65 8

Figure S141.  Get High-res Image Gene #36: 'del_2q33.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_2q33.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0273 (Fisher's exact test), Q value = 0.079

Table S142.  Gene #36: 'del_2q33.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
DEL PEAK 5(2Q33.3) MUTATED 6 3 25
DEL PEAK 5(2Q33.3) WILD-TYPE 56 19 69

Figure S142.  Get High-res Image Gene #36: 'del_2q33.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p26.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S143.  Gene #37: 'del_3p26.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
DEL PEAK 6(3P26.2) MUTATED 32 16 63
DEL PEAK 6(3P26.2) WILD-TYPE 33 28 12

Figure S143.  Get High-res Image Gene #37: 'del_3p26.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p26.2' versus 'METHLYATION_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00076

Table S144.  Gene #37: 'del_3p26.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
DEL PEAK 6(3P26.2) MUTATED 33 18 60
DEL PEAK 6(3P26.2) WILD-TYPE 43 14 16

Figure S144.  Get High-res Image Gene #37: 'del_3p26.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p26.2' versus 'RPPA_CNMF'

P value = 0.0319 (Fisher's exact test), Q value = 0.086

Table S145.  Gene #37: 'del_3p26.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 24 16 17 23 17 24 5
DEL PEAK 6(3P26.2) MUTATED 10 13 13 18 8 18 3
DEL PEAK 6(3P26.2) WILD-TYPE 14 3 4 5 9 6 2

Figure S145.  Get High-res Image Gene #37: 'del_3p26.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_3p26.2' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 6e-04

Table S146.  Gene #37: 'del_3p26.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 68 31
DEL PEAK 6(3P26.2) MUTATED 38 55 17
DEL PEAK 6(3P26.2) WILD-TYPE 46 13 14

Figure S146.  Get High-res Image Gene #37: 'del_3p26.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p26.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00049

Table S147.  Gene #37: 'del_3p26.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
DEL PEAK 6(3P26.2) MUTATED 27 11 72
DEL PEAK 6(3P26.2) WILD-TYPE 40 9 24

Figure S147.  Get High-res Image Gene #37: 'del_3p26.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p26.2' versus 'MIRSEQ_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.0019

Table S148.  Gene #37: 'del_3p26.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
DEL PEAK 6(3P26.2) MUTATED 38 66 7
DEL PEAK 6(3P26.2) WILD-TYPE 46 21 5

Figure S148.  Get High-res Image Gene #37: 'del_3p26.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3p26.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.0019

Table S149.  Gene #37: 'del_3p26.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
DEL PEAK 6(3P26.2) MUTATED 29 10 48 24
DEL PEAK 6(3P26.2) WILD-TYPE 33 16 14 9

Figure S149.  Get High-res Image Gene #37: 'del_3p26.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p26.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0131 (Fisher's exact test), Q value = 0.049

Table S150.  Gene #37: 'del_3p26.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 66 35 11
DEL PEAK 6(3P26.2) MUTATED 32 50 21 7
DEL PEAK 6(3P26.2) WILD-TYPE 34 16 14 4

Figure S150.  Get High-res Image Gene #37: 'del_3p26.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_3p26.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.002

Table S151.  Gene #37: 'del_3p26.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
DEL PEAK 6(3P26.2) MUTATED 29 10 71
DEL PEAK 6(3P26.2) WILD-TYPE 33 12 23

Figure S151.  Get High-res Image Gene #37: 'del_3p26.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p14.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S152.  Gene #38: 'del_3p14.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
DEL PEAK 7(3P14.3) MUTATED 37 18 71
DEL PEAK 7(3P14.3) WILD-TYPE 28 26 4

Figure S152.  Get High-res Image Gene #38: 'del_3p14.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p14.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S153.  Gene #38: 'del_3p14.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
DEL PEAK 7(3P14.3) MUTATED 37 23 66
DEL PEAK 7(3P14.3) WILD-TYPE 39 9 10

Figure S153.  Get High-res Image Gene #38: 'del_3p14.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p14.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S154.  Gene #38: 'del_3p14.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 68 31
DEL PEAK 7(3P14.3) MUTATED 43 61 21
DEL PEAK 7(3P14.3) WILD-TYPE 41 7 10

Figure S154.  Get High-res Image Gene #38: 'del_3p14.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p14.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S155.  Gene #38: 'del_3p14.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
DEL PEAK 7(3P14.3) MUTATED 32 11 82
DEL PEAK 7(3P14.3) WILD-TYPE 35 9 14

Figure S155.  Get High-res Image Gene #38: 'del_3p14.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p14.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S156.  Gene #38: 'del_3p14.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
DEL PEAK 7(3P14.3) MUTATED 43 76 7
DEL PEAK 7(3P14.3) WILD-TYPE 41 11 5

Figure S156.  Get High-res Image Gene #38: 'del_3p14.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3p14.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S157.  Gene #38: 'del_3p14.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
DEL PEAK 7(3P14.3) MUTATED 32 12 54 28
DEL PEAK 7(3P14.3) WILD-TYPE 30 14 8 5

Figure S157.  Get High-res Image Gene #38: 'del_3p14.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p14.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S158.  Gene #38: 'del_3p14.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 66 35 11
DEL PEAK 7(3P14.3) MUTATED 32 59 25 8
DEL PEAK 7(3P14.3) WILD-TYPE 34 7 10 3

Figure S158.  Get High-res Image Gene #38: 'del_3p14.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_3p14.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S159.  Gene #38: 'del_3p14.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
DEL PEAK 7(3P14.3) MUTATED 32 11 81
DEL PEAK 7(3P14.3) WILD-TYPE 30 11 13

Figure S159.  Get High-res Image Gene #38: 'del_3p14.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p14.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S160.  Gene #39: 'del_3p14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
DEL PEAK 8(3P14.2) MUTATED 38 17 70
DEL PEAK 8(3P14.2) WILD-TYPE 27 27 5

Figure S160.  Get High-res Image Gene #39: 'del_3p14.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p14.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S161.  Gene #39: 'del_3p14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
DEL PEAK 8(3P14.2) MUTATED 38 22 65
DEL PEAK 8(3P14.2) WILD-TYPE 38 10 11

Figure S161.  Get High-res Image Gene #39: 'del_3p14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p14.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S162.  Gene #39: 'del_3p14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 68 31
DEL PEAK 8(3P14.2) MUTATED 43 60 21
DEL PEAK 8(3P14.2) WILD-TYPE 41 8 10

Figure S162.  Get High-res Image Gene #39: 'del_3p14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S163.  Gene #39: 'del_3p14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
DEL PEAK 8(3P14.2) MUTATED 31 12 81
DEL PEAK 8(3P14.2) WILD-TYPE 36 8 15

Figure S163.  Get High-res Image Gene #39: 'del_3p14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p14.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S164.  Gene #39: 'del_3p14.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
DEL PEAK 8(3P14.2) MUTATED 43 75 7
DEL PEAK 8(3P14.2) WILD-TYPE 41 12 5

Figure S164.  Get High-res Image Gene #39: 'del_3p14.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3p14.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S165.  Gene #39: 'del_3p14.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
DEL PEAK 8(3P14.2) MUTATED 33 11 53 28
DEL PEAK 8(3P14.2) WILD-TYPE 29 15 9 5

Figure S165.  Get High-res Image Gene #39: 'del_3p14.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p14.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.001

Table S166.  Gene #39: 'del_3p14.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 66 35 11
DEL PEAK 8(3P14.2) MUTATED 34 58 24 7
DEL PEAK 8(3P14.2) WILD-TYPE 32 8 11 4

Figure S166.  Get High-res Image Gene #39: 'del_3p14.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_3p14.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00027

Table S167.  Gene #39: 'del_3p14.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
DEL PEAK 8(3P14.2) MUTATED 33 10 80
DEL PEAK 8(3P14.2) WILD-TYPE 29 12 14

Figure S167.  Get High-res Image Gene #39: 'del_3p14.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3q26.31' versus 'CN_CNMF'

P value = 0.00235 (Fisher's exact test), Q value = 0.013

Table S168.  Gene #41: 'del_3q26.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
DEL PEAK 10(3Q26.31) MUTATED 11 4 1
DEL PEAK 10(3Q26.31) WILD-TYPE 54 40 74

Figure S168.  Get High-res Image Gene #41: 'del_3q26.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_3q26.31' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00027

Table S169.  Gene #41: 'del_3q26.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
DEL PEAK 10(3Q26.31) MUTATED 15 0 1
DEL PEAK 10(3Q26.31) WILD-TYPE 61 32 75

Figure S169.  Get High-res Image Gene #41: 'del_3q26.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3q26.31' versus 'RPPA_CNMF'

P value = 0.0399 (Fisher's exact test), Q value = 0.099

Table S170.  Gene #41: 'del_3q26.31' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 24 16 17 23 17 24 5
DEL PEAK 10(3Q26.31) MUTATED 5 1 3 0 1 0 0
DEL PEAK 10(3Q26.31) WILD-TYPE 19 15 14 23 16 24 5

Figure S170.  Get High-res Image Gene #41: 'del_3q26.31' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_3q26.31' versus 'RPPA_CHIERARCHICAL'

P value = 0.00921 (Fisher's exact test), Q value = 0.038

Table S171.  Gene #41: 'del_3q26.31' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
DEL PEAK 10(3Q26.31) MUTATED 4 3 3 0 0
DEL PEAK 10(3Q26.31) WILD-TYPE 19 18 19 26 34

Figure S171.  Get High-res Image Gene #41: 'del_3q26.31' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_3q26.31' versus 'MRNASEQ_CNMF'

P value = 0.0014 (Fisher's exact test), Q value = 0.0092

Table S172.  Gene #41: 'del_3q26.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 68 31
DEL PEAK 10(3Q26.31) MUTATED 14 1 1
DEL PEAK 10(3Q26.31) WILD-TYPE 70 67 30

Figure S172.  Get High-res Image Gene #41: 'del_3q26.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3q26.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.001

Table S173.  Gene #41: 'del_3q26.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
DEL PEAK 10(3Q26.31) MUTATED 12 3 1
DEL PEAK 10(3Q26.31) WILD-TYPE 55 17 95

Figure S173.  Get High-res Image Gene #41: 'del_3q26.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3q26.31' versus 'MIRSEQ_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.003

Table S174.  Gene #41: 'del_3q26.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
DEL PEAK 10(3Q26.31) MUTATED 15 1 0
DEL PEAK 10(3Q26.31) WILD-TYPE 69 86 12

Figure S174.  Get High-res Image Gene #41: 'del_3q26.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3q26.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00041 (Fisher's exact test), Q value = 0.0034

Table S175.  Gene #41: 'del_3q26.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
DEL PEAK 10(3Q26.31) MUTATED 11 4 0 1
DEL PEAK 10(3Q26.31) WILD-TYPE 51 22 62 32

Figure S175.  Get High-res Image Gene #41: 'del_3q26.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3q26.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00216 (Fisher's exact test), Q value = 0.013

Table S176.  Gene #41: 'del_3q26.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 66 35 11
DEL PEAK 10(3Q26.31) MUTATED 13 1 2 0
DEL PEAK 10(3Q26.31) WILD-TYPE 53 65 33 11

Figure S176.  Get High-res Image Gene #41: 'del_3q26.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_3q26.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.001

Table S177.  Gene #41: 'del_3q26.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
DEL PEAK 10(3Q26.31) MUTATED 11 4 1
DEL PEAK 10(3Q26.31) WILD-TYPE 51 18 93

Figure S177.  Get High-res Image Gene #41: 'del_3q26.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4p15.2' versus 'CN_CNMF'

P value = 0.00556 (Fisher's exact test), Q value = 0.026

Table S178.  Gene #42: 'del_4p15.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
DEL PEAK 11(4P15.2) MUTATED 42 16 48
DEL PEAK 11(4P15.2) WILD-TYPE 23 28 27

Figure S178.  Get High-res Image Gene #42: 'del_4p15.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_4p15.2' versus 'MIRSEQ_CNMF'

P value = 0.0482 (Fisher's exact test), Q value = 0.11

Table S179.  Gene #42: 'del_4p15.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
DEL PEAK 11(4P15.2) MUTATED 48 55 3
DEL PEAK 11(4P15.2) WILD-TYPE 36 32 9

Figure S179.  Get High-res Image Gene #42: 'del_4p15.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_4q22.1' versus 'CN_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.0021

Table S180.  Gene #43: 'del_4q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
DEL PEAK 12(4Q22.1) MUTATED 49 16 40
DEL PEAK 12(4Q22.1) WILD-TYPE 16 28 35

Figure S180.  Get High-res Image Gene #43: 'del_4q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q22.1' versus 'MRNASEQ_CNMF'

P value = 0.0237 (Fisher's exact test), Q value = 0.072

Table S181.  Gene #43: 'del_4q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 68 31
DEL PEAK 12(4Q22.1) MUTATED 56 37 12
DEL PEAK 12(4Q22.1) WILD-TYPE 28 31 19

Figure S181.  Get High-res Image Gene #43: 'del_4q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0297 (Fisher's exact test), Q value = 0.082

Table S182.  Gene #43: 'del_4q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
DEL PEAK 12(4Q22.1) MUTATED 47 10 48
DEL PEAK 12(4Q22.1) WILD-TYPE 20 10 48

Figure S182.  Get High-res Image Gene #43: 'del_4q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q22.1' versus 'MIRSEQ_CNMF'

P value = 0.003 (Fisher's exact test), Q value = 0.016

Table S183.  Gene #43: 'del_4q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
DEL PEAK 12(4Q22.1) MUTATED 56 47 2
DEL PEAK 12(4Q22.1) WILD-TYPE 28 40 10

Figure S183.  Get High-res Image Gene #43: 'del_4q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_4q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0362 (Fisher's exact test), Q value = 0.093

Table S184.  Gene #43: 'del_4q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
DEL PEAK 12(4Q22.1) MUTATED 43 14 46
DEL PEAK 12(4Q22.1) WILD-TYPE 19 8 48

Figure S184.  Get High-res Image Gene #43: 'del_4q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q34.3' versus 'CN_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.0039

Table S185.  Gene #44: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
DEL PEAK 13(4Q34.3) MUTATED 47 16 36
DEL PEAK 13(4Q34.3) WILD-TYPE 18 28 39

Figure S185.  Get High-res Image Gene #44: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q34.3' versus 'METHLYATION_CNMF'

P value = 0.00656 (Fisher's exact test), Q value = 0.029

Table S186.  Gene #44: 'del_4q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
DEL PEAK 13(4Q34.3) MUTATED 51 12 36
DEL PEAK 13(4Q34.3) WILD-TYPE 25 20 40

Figure S186.  Get High-res Image Gene #44: 'del_4q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q34.3' versus 'MRNASEQ_CNMF'

P value = 0.00515 (Fisher's exact test), Q value = 0.024

Table S187.  Gene #44: 'del_4q34.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 68 31
DEL PEAK 13(4Q34.3) MUTATED 56 28 15
DEL PEAK 13(4Q34.3) WILD-TYPE 28 40 16

Figure S187.  Get High-res Image Gene #44: 'del_4q34.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4q34.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00109 (Fisher's exact test), Q value = 0.0075

Table S188.  Gene #44: 'del_4q34.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
DEL PEAK 13(4Q34.3) MUTATED 48 9 42
DEL PEAK 13(4Q34.3) WILD-TYPE 19 11 54

Figure S188.  Get High-res Image Gene #44: 'del_4q34.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_CNMF'

P value = 0.00087 (Fisher's exact test), Q value = 0.0063

Table S189.  Gene #44: 'del_4q34.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
DEL PEAK 13(4Q34.3) MUTATED 56 41 2
DEL PEAK 13(4Q34.3) WILD-TYPE 28 46 10

Figure S189.  Get High-res Image Gene #44: 'del_4q34.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_4q34.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00323 (Fisher's exact test), Q value = 0.017

Table S190.  Gene #44: 'del_4q34.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
DEL PEAK 13(4Q34.3) MUTATED 44 14 30 11
DEL PEAK 13(4Q34.3) WILD-TYPE 18 12 32 22

Figure S190.  Get High-res Image Gene #44: 'del_4q34.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.02 (Fisher's exact test), Q value = 0.065

Table S191.  Gene #44: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 66 35 11
DEL PEAK 13(4Q34.3) MUTATED 44 31 14 8
DEL PEAK 13(4Q34.3) WILD-TYPE 22 35 21 3

Figure S191.  Get High-res Image Gene #44: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_4q34.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00215 (Fisher's exact test), Q value = 0.013

Table S192.  Gene #44: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
DEL PEAK 13(4Q34.3) MUTATED 44 13 40
DEL PEAK 13(4Q34.3) WILD-TYPE 18 9 54

Figure S192.  Get High-res Image Gene #44: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q12.1' versus 'CN_CNMF'

P value = 0.00062 (Fisher's exact test), Q value = 0.0048

Table S193.  Gene #45: 'del_5q12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
DEL PEAK 14(5Q12.1) MUTATED 49 17 46
DEL PEAK 14(5Q12.1) WILD-TYPE 16 27 29

Figure S193.  Get High-res Image Gene #45: 'del_5q12.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q12.1' versus 'METHLYATION_CNMF'

P value = 0.00077 (Fisher's exact test), Q value = 0.0056

Table S194.  Gene #45: 'del_5q12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
DEL PEAK 14(5Q12.1) MUTATED 53 10 49
DEL PEAK 14(5Q12.1) WILD-TYPE 23 22 27

Figure S194.  Get High-res Image Gene #45: 'del_5q12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q12.1' versus 'MIRSEQ_CNMF'

P value = 0.0227 (Fisher's exact test), Q value = 0.071

Table S195.  Gene #45: 'del_5q12.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
DEL PEAK 14(5Q12.1) MUTATED 56 52 3
DEL PEAK 14(5Q12.1) WILD-TYPE 28 35 9

Figure S195.  Get High-res Image Gene #45: 'del_5q12.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_5q12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0237 (Fisher's exact test), Q value = 0.072

Table S196.  Gene #45: 'del_5q12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
DEL PEAK 14(5Q12.1) MUTATED 46 12 32 21
DEL PEAK 14(5Q12.1) WILD-TYPE 16 14 30 12

Figure S196.  Get High-res Image Gene #45: 'del_5q12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_6p25.3' versus 'CN_CNMF'

P value = 0.0162 (Fisher's exact test), Q value = 0.057

Table S197.  Gene #46: 'del_6p25.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
DEL PEAK 15(6P25.3) MUTATED 34 11 29
DEL PEAK 15(6P25.3) WILD-TYPE 31 33 46

Figure S197.  Get High-res Image Gene #46: 'del_6p25.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_6p25.3' versus 'METHLYATION_CNMF'

P value = 0.0234 (Fisher's exact test), Q value = 0.072

Table S198.  Gene #46: 'del_6p25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
DEL PEAK 15(6P25.3) MUTATED 38 7 29
DEL PEAK 15(6P25.3) WILD-TYPE 38 25 47

Figure S198.  Get High-res Image Gene #46: 'del_6p25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6p25.3' versus 'MRNASEQ_CNMF'

P value = 0.0192 (Fisher's exact test), Q value = 0.063

Table S199.  Gene #46: 'del_6p25.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 68 31
DEL PEAK 15(6P25.3) MUTATED 40 28 6
DEL PEAK 15(6P25.3) WILD-TYPE 44 40 25

Figure S199.  Get High-res Image Gene #46: 'del_6p25.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6p25.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0222 (Fisher's exact test), Q value = 0.07

Table S200.  Gene #46: 'del_6p25.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
DEL PEAK 15(6P25.3) MUTATED 31 10 26 6
DEL PEAK 15(6P25.3) WILD-TYPE 31 16 36 27

Figure S200.  Get High-res Image Gene #46: 'del_6p25.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_7q31.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0239 (Fisher's exact test), Q value = 0.072

Table S201.  Gene #49: 'del_7q31.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
DEL PEAK 18(7Q31.1) MUTATED 27 4 24
DEL PEAK 18(7Q31.1) WILD-TYPE 35 18 70

Figure S201.  Get High-res Image Gene #49: 'del_7q31.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p23.2' versus 'CN_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00096

Table S202.  Gene #51: 'del_8p23.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
DEL PEAK 20(8P23.2) MUTATED 30 11 49
DEL PEAK 20(8P23.2) WILD-TYPE 35 33 26

Figure S202.  Get High-res Image Gene #51: 'del_8p23.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p23.2' versus 'METHLYATION_CNMF'

P value = 0.0272 (Fisher's exact test), Q value = 0.079

Table S203.  Gene #51: 'del_8p23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
DEL PEAK 20(8P23.2) MUTATED 32 12 46
DEL PEAK 20(8P23.2) WILD-TYPE 44 20 30

Figure S203.  Get High-res Image Gene #51: 'del_8p23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_8p23.2' versus 'RPPA_CNMF'

P value = 0.00607 (Fisher's exact test), Q value = 0.028

Table S204.  Gene #51: 'del_8p23.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 24 16 17 23 17 24 5
DEL PEAK 20(8P23.2) MUTATED 6 6 7 14 13 16 1
DEL PEAK 20(8P23.2) WILD-TYPE 18 10 10 9 4 8 4

Figure S204.  Get High-res Image Gene #51: 'del_8p23.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_8p23.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00943 (Fisher's exact test), Q value = 0.038

Table S205.  Gene #51: 'del_8p23.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
DEL PEAK 20(8P23.2) MUTATED 5 8 14 14 22
DEL PEAK 20(8P23.2) WILD-TYPE 18 13 8 12 12

Figure S205.  Get High-res Image Gene #51: 'del_8p23.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_8p23.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0482 (Fisher's exact test), Q value = 0.11

Table S206.  Gene #51: 'del_8p23.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
DEL PEAK 20(8P23.2) MUTATED 27 7 55
DEL PEAK 20(8P23.2) WILD-TYPE 40 13 41

Figure S206.  Get High-res Image Gene #51: 'del_8p23.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_CNMF'

P value = 0.011 (Fisher's exact test), Q value = 0.042

Table S207.  Gene #51: 'del_8p23.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
DEL PEAK 20(8P23.2) MUTATED 33 53 4
DEL PEAK 20(8P23.2) WILD-TYPE 51 34 8

Figure S207.  Get High-res Image Gene #51: 'del_8p23.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_8p23.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0372 (Fisher's exact test), Q value = 0.094

Table S208.  Gene #51: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 66 35 11
DEL PEAK 20(8P23.2) MUTATED 25 41 15 5
DEL PEAK 20(8P23.2) WILD-TYPE 41 25 20 6

Figure S208.  Get High-res Image Gene #51: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_8p12' versus 'CN_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.0026

Table S209.  Gene #52: 'del_8p12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
DEL PEAK 21(8P12) MUTATED 29 7 39
DEL PEAK 21(8P12) WILD-TYPE 36 37 36

Figure S209.  Get High-res Image Gene #52: 'del_8p12' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0239 (Fisher's exact test), Q value = 0.072

Table S210.  Gene #53: 'del_9p23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
DEL PEAK 22(9P23) MUTATED 46 7 54
DEL PEAK 22(9P23) WILD-TYPE 21 13 42

Figure S210.  Get High-res Image Gene #53: 'del_9p23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S211.  Gene #54: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
DEL PEAK 23(9P21.3) MUTATED 46 25 70
DEL PEAK 23(9P21.3) WILD-TYPE 19 19 5

Figure S211.  Get High-res Image Gene #54: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 0.00872 (Fisher's exact test), Q value = 0.037

Table S212.  Gene #54: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 68 31
DEL PEAK 23(9P21.3) MUTATED 60 60 20
DEL PEAK 23(9P21.3) WILD-TYPE 24 8 11

Figure S212.  Get High-res Image Gene #54: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0211 (Fisher's exact test), Q value = 0.068

Table S213.  Gene #54: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
DEL PEAK 23(9P21.3) MUTATED 49 11 80
DEL PEAK 23(9P21.3) WILD-TYPE 18 9 16

Figure S213.  Get High-res Image Gene #54: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_CNMF'

P value = 0.0334 (Fisher's exact test), Q value = 0.089

Table S214.  Gene #54: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
DEL PEAK 23(9P21.3) MUTATED 59 74 8
DEL PEAK 23(9P21.3) WILD-TYPE 25 13 4

Figure S214.  Get High-res Image Gene #54: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_10p15.3' versus 'CN_CNMF'

P value = 0.00069 (Fisher's exact test), Q value = 0.0051

Table S215.  Gene #55: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
DEL PEAK 24(10P15.3) MUTATED 15 6 33
DEL PEAK 24(10P15.3) WILD-TYPE 50 38 42

Figure S215.  Get High-res Image Gene #55: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10p15.3' versus 'METHLYATION_CNMF'

P value = 0.0192 (Fisher's exact test), Q value = 0.063

Table S216.  Gene #55: 'del_10p15.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
DEL PEAK 24(10P15.3) MUTATED 14 13 27
DEL PEAK 24(10P15.3) WILD-TYPE 62 19 49

Figure S216.  Get High-res Image Gene #55: 'del_10p15.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10p15.3' versus 'MRNASEQ_CNMF'

P value = 0.0282 (Fisher's exact test), Q value = 0.08

Table S217.  Gene #55: 'del_10p15.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 68 31
DEL PEAK 24(10P15.3) MUTATED 17 27 10
DEL PEAK 24(10P15.3) WILD-TYPE 67 41 21

Figure S217.  Get High-res Image Gene #55: 'del_10p15.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10p15.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0256 (Fisher's exact test), Q value = 0.075

Table S218.  Gene #55: 'del_10p15.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
DEL PEAK 24(10P15.3) MUTATED 12 6 36
DEL PEAK 24(10P15.3) WILD-TYPE 55 14 60

Figure S218.  Get High-res Image Gene #55: 'del_10p15.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10p15.3' versus 'MIRSEQ_CNMF'

P value = 0.00597 (Fisher's exact test), Q value = 0.027

Table S219.  Gene #55: 'del_10p15.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
DEL PEAK 24(10P15.3) MUTATED 18 35 1
DEL PEAK 24(10P15.3) WILD-TYPE 66 52 11

Figure S219.  Get High-res Image Gene #55: 'del_10p15.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_10p15.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0112 (Fisher's exact test), Q value = 0.043

Table S220.  Gene #55: 'del_10p15.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
DEL PEAK 24(10P15.3) MUTATED 12 7 28 7
DEL PEAK 24(10P15.3) WILD-TYPE 50 19 34 26

Figure S220.  Get High-res Image Gene #55: 'del_10p15.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_10p11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S221.  Gene #56: 'del_10p11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
DEL PEAK 25(10P11.21) MUTATED 9 5 38
DEL PEAK 25(10P11.21) WILD-TYPE 56 39 37

Figure S221.  Get High-res Image Gene #56: 'del_10p11.21' versus Molecular Subtype #1: 'CN_CNMF'

'del_10p11.21' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 6e-04

Table S222.  Gene #56: 'del_10p11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
DEL PEAK 25(10P11.21) MUTATED 9 10 33
DEL PEAK 25(10P11.21) WILD-TYPE 67 22 43

Figure S222.  Get High-res Image Gene #56: 'del_10p11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10p11.21' versus 'RPPA_CNMF'

P value = 0.036 (Fisher's exact test), Q value = 0.093

Table S223.  Gene #56: 'del_10p11.21' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 24 16 17 23 17 24 5
DEL PEAK 25(10P11.21) MUTATED 2 5 6 7 7 13 2
DEL PEAK 25(10P11.21) WILD-TYPE 22 11 11 16 10 11 3

Figure S223.  Get High-res Image Gene #56: 'del_10p11.21' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_10p11.21' versus 'RPPA_CHIERARCHICAL'

P value = 0.0297 (Fisher's exact test), Q value = 0.082

Table S224.  Gene #56: 'del_10p11.21' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
DEL PEAK 25(10P11.21) MUTATED 2 7 7 13 13
DEL PEAK 25(10P11.21) WILD-TYPE 21 14 15 13 21

Figure S224.  Get High-res Image Gene #56: 'del_10p11.21' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_10p11.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S225.  Gene #56: 'del_10p11.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 68 31
DEL PEAK 25(10P11.21) MUTATED 10 27 14
DEL PEAK 25(10P11.21) WILD-TYPE 74 41 17

Figure S225.  Get High-res Image Gene #56: 'del_10p11.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10p11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00027

Table S226.  Gene #56: 'del_10p11.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
DEL PEAK 25(10P11.21) MUTATED 7 3 41
DEL PEAK 25(10P11.21) WILD-TYPE 60 17 55

Figure S226.  Get High-res Image Gene #56: 'del_10p11.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10p11.21' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S227.  Gene #56: 'del_10p11.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
DEL PEAK 25(10P11.21) MUTATED 10 40 1
DEL PEAK 25(10P11.21) WILD-TYPE 74 47 11

Figure S227.  Get High-res Image Gene #56: 'del_10p11.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_10p11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00049

Table S228.  Gene #56: 'del_10p11.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
DEL PEAK 25(10P11.21) MUTATED 7 3 27 14
DEL PEAK 25(10P11.21) WILD-TYPE 55 23 35 19

Figure S228.  Get High-res Image Gene #56: 'del_10p11.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_10p11.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.0038

Table S229.  Gene #56: 'del_10p11.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 66 35 11
DEL PEAK 25(10P11.21) MUTATED 8 29 10 4
DEL PEAK 25(10P11.21) WILD-TYPE 58 37 25 7

Figure S229.  Get High-res Image Gene #56: 'del_10p11.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_10p11.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00039

Table S230.  Gene #56: 'del_10p11.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
DEL PEAK 25(10P11.21) MUTATED 7 3 41
DEL PEAK 25(10P11.21) WILD-TYPE 55 19 53

Figure S230.  Get High-res Image Gene #56: 'del_10p11.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q21.1' versus 'CN_CNMF'

P value = 0.002 (Fisher's exact test), Q value = 0.012

Table S231.  Gene #57: 'del_10q21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
DEL PEAK 26(10Q21.1) MUTATED 11 6 29
DEL PEAK 26(10Q21.1) WILD-TYPE 54 38 46

Figure S231.  Get High-res Image Gene #57: 'del_10q21.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q21.1' versus 'METHLYATION_CNMF'

P value = 0.0219 (Fisher's exact test), Q value = 0.07

Table S232.  Gene #57: 'del_10q21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
DEL PEAK 26(10Q21.1) MUTATED 12 7 27
DEL PEAK 26(10Q21.1) WILD-TYPE 64 25 49

Figure S232.  Get High-res Image Gene #57: 'del_10q21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q21.1' versus 'MRNASEQ_CNMF'

P value = 0.0443 (Fisher's exact test), Q value = 0.11

Table S233.  Gene #57: 'del_10q21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 68 31
DEL PEAK 26(10Q21.1) MUTATED 14 22 10
DEL PEAK 26(10Q21.1) WILD-TYPE 70 46 21

Figure S233.  Get High-res Image Gene #57: 'del_10q21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10q21.1' versus 'MIRSEQ_CNMF'

P value = 0.0158 (Fisher's exact test), Q value = 0.056

Table S234.  Gene #57: 'del_10q21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
DEL PEAK 26(10Q21.1) MUTATED 15 30 1
DEL PEAK 26(10Q21.1) WILD-TYPE 69 57 11

Figure S234.  Get High-res Image Gene #57: 'del_10q21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_10q21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0489 (Fisher's exact test), Q value = 0.12

Table S235.  Gene #57: 'del_10q21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
DEL PEAK 26(10Q21.1) MUTATED 10 4 31
DEL PEAK 26(10Q21.1) WILD-TYPE 52 18 63

Figure S235.  Get High-res Image Gene #57: 'del_10q21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q23.31' versus 'CN_CNMF'

P value = 0.0208 (Fisher's exact test), Q value = 0.067

Table S236.  Gene #58: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
DEL PEAK 27(10Q23.31) MUTATED 22 9 34
DEL PEAK 27(10Q23.31) WILD-TYPE 43 35 41

Figure S236.  Get High-res Image Gene #58: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q23.31' versus 'METHLYATION_CNMF'

P value = 0.0356 (Fisher's exact test), Q value = 0.093

Table S237.  Gene #58: 'del_10q23.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
DEL PEAK 27(10Q23.31) MUTATED 20 10 35
DEL PEAK 27(10Q23.31) WILD-TYPE 56 22 41

Figure S237.  Get High-res Image Gene #58: 'del_10q23.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11p15.4' versus 'METHLYATION_CNMF'

P value = 0.0465 (Fisher's exact test), Q value = 0.11

Table S238.  Gene #59: 'del_11p15.4' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
DEL PEAK 28(11P15.4) MUTATED 30 9 40
DEL PEAK 28(11P15.4) WILD-TYPE 46 23 36

Figure S238.  Get High-res Image Gene #59: 'del_11p15.4' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11q25' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00027

Table S239.  Gene #60: 'del_11q25' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
DEL PEAK 29(11Q25) MUTATED 24 9 48
DEL PEAK 29(11Q25) WILD-TYPE 41 35 27

Figure S239.  Get High-res Image Gene #60: 'del_11q25' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q25' versus 'METHLYATION_CNMF'

P value = 0.0294 (Fisher's exact test), Q value = 0.082

Table S240.  Gene #60: 'del_11q25' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
DEL PEAK 29(11Q25) MUTATED 29 10 42
DEL PEAK 29(11Q25) WILD-TYPE 47 22 34

Figure S240.  Get High-res Image Gene #60: 'del_11q25' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11q25' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0498 (Fisher's exact test), Q value = 0.12

Table S241.  Gene #60: 'del_11q25' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
DEL PEAK 29(11Q25) MUTATED 22 8 50
DEL PEAK 29(11Q25) WILD-TYPE 45 12 46

Figure S241.  Get High-res Image Gene #60: 'del_11q25' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11q25' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0262 (Fisher's exact test), Q value = 0.077

Table S242.  Gene #60: 'del_11q25' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 66 35 11
DEL PEAK 29(11Q25) MUTATED 23 37 16 2
DEL PEAK 29(11Q25) WILD-TYPE 43 29 19 9

Figure S242.  Get High-res Image Gene #60: 'del_11q25' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_11q25' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0294 (Fisher's exact test), Q value = 0.082

Table S243.  Gene #60: 'del_11q25' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
DEL PEAK 29(11Q25) MUTATED 19 10 49
DEL PEAK 29(11Q25) WILD-TYPE 43 12 45

Figure S243.  Get High-res Image Gene #60: 'del_11q25' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_12q23.1' versus 'METHLYATION_CNMF'

P value = 0.0186 (Fisher's exact test), Q value = 0.063

Table S244.  Gene #61: 'del_12q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
DEL PEAK 30(12Q23.1) MUTATED 28 10 13
DEL PEAK 30(12Q23.1) WILD-TYPE 48 22 63

Figure S244.  Get High-res Image Gene #61: 'del_12q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_12q23.1' versus 'MRNASEQ_CNMF'

P value = 0.0422 (Fisher's exact test), Q value = 0.1

Table S245.  Gene #61: 'del_12q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 68 31
DEL PEAK 30(12Q23.1) MUTATED 31 13 7
DEL PEAK 30(12Q23.1) WILD-TYPE 53 55 24

Figure S245.  Get High-res Image Gene #61: 'del_12q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_12q23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0467 (Fisher's exact test), Q value = 0.11

Table S246.  Gene #61: 'del_12q23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
DEL PEAK 30(12Q23.1) MUTATED 20 10 20
DEL PEAK 30(12Q23.1) WILD-TYPE 42 12 74

Figure S246.  Get High-res Image Gene #61: 'del_12q23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_13q12.11' versus 'CN_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.0031

Table S247.  Gene #62: 'del_13q12.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
DEL PEAK 31(13Q12.11) MUTATED 24 9 43
DEL PEAK 31(13Q12.11) WILD-TYPE 41 35 32

Figure S247.  Get High-res Image Gene #62: 'del_13q12.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q12.11' versus 'METHLYATION_CNMF'

P value = 0.0149 (Fisher's exact test), Q value = 0.054

Table S248.  Gene #62: 'del_13q12.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
DEL PEAK 31(13Q12.11) MUTATED 24 11 41
DEL PEAK 31(13Q12.11) WILD-TYPE 52 21 35

Figure S248.  Get High-res Image Gene #62: 'del_13q12.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_13q12.11' versus 'RPPA_CNMF'

P value = 0.0308 (Fisher's exact test), Q value = 0.084

Table S249.  Gene #62: 'del_13q12.11' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 24 16 17 23 17 24 5
DEL PEAK 31(13Q12.11) MUTATED 6 5 5 10 8 17 3
DEL PEAK 31(13Q12.11) WILD-TYPE 18 11 12 13 9 7 2

Figure S249.  Get High-res Image Gene #62: 'del_13q12.11' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_13q12.11' versus 'RPPA_CHIERARCHICAL'

P value = 0.0383 (Fisher's exact test), Q value = 0.096

Table S250.  Gene #62: 'del_13q12.11' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
DEL PEAK 31(13Q12.11) MUTATED 7 5 9 17 16
DEL PEAK 31(13Q12.11) WILD-TYPE 16 16 13 9 18

Figure S250.  Get High-res Image Gene #62: 'del_13q12.11' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_13q12.11' versus 'MRNASEQ_CNMF'

P value = 0.00874 (Fisher's exact test), Q value = 0.037

Table S251.  Gene #62: 'del_13q12.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 68 31
DEL PEAK 31(13Q12.11) MUTATED 25 37 13
DEL PEAK 31(13Q12.11) WILD-TYPE 59 31 18

Figure S251.  Get High-res Image Gene #62: 'del_13q12.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_13q12.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00368 (Fisher's exact test), Q value = 0.019

Table S252.  Gene #62: 'del_13q12.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
DEL PEAK 31(13Q12.11) MUTATED 23 3 49
DEL PEAK 31(13Q12.11) WILD-TYPE 44 17 47

Figure S252.  Get High-res Image Gene #62: 'del_13q12.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_13q12.11' versus 'MIRSEQ_CNMF'

P value = 0.00813 (Fisher's exact test), Q value = 0.035

Table S253.  Gene #62: 'del_13q12.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
DEL PEAK 31(13Q12.11) MUTATED 25 46 5
DEL PEAK 31(13Q12.11) WILD-TYPE 59 41 7

Figure S253.  Get High-res Image Gene #62: 'del_13q12.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_13q12.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00947 (Fisher's exact test), Q value = 0.038

Table S254.  Gene #62: 'del_13q12.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
DEL PEAK 31(13Q12.11) MUTATED 19 7 30 20
DEL PEAK 31(13Q12.11) WILD-TYPE 43 19 32 13

Figure S254.  Get High-res Image Gene #62: 'del_13q12.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_13q12.11' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.013 (Fisher's exact test), Q value = 0.049

Table S255.  Gene #62: 'del_13q12.11' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 66 35 11
DEL PEAK 31(13Q12.11) MUTATED 20 37 11 5
DEL PEAK 31(13Q12.11) WILD-TYPE 46 29 24 6

Figure S255.  Get High-res Image Gene #62: 'del_13q12.11' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_13q12.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0159 (Fisher's exact test), Q value = 0.056

Table S256.  Gene #62: 'del_13q12.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
DEL PEAK 31(13Q12.11) MUTATED 18 7 48
DEL PEAK 31(13Q12.11) WILD-TYPE 44 15 46

Figure S256.  Get High-res Image Gene #62: 'del_13q12.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_13q14.2' versus 'CN_CNMF'

P value = 0.00172 (Fisher's exact test), Q value = 0.011

Table S257.  Gene #63: 'del_13q14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
DEL PEAK 32(13Q14.2) MUTATED 23 10 41
DEL PEAK 32(13Q14.2) WILD-TYPE 42 34 34

Figure S257.  Get High-res Image Gene #63: 'del_13q14.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q14.2' versus 'METHLYATION_CNMF'

P value = 0.00482 (Fisher's exact test), Q value = 0.023

Table S258.  Gene #63: 'del_13q14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
DEL PEAK 32(13Q14.2) MUTATED 25 8 41
DEL PEAK 32(13Q14.2) WILD-TYPE 51 24 35

Figure S258.  Get High-res Image Gene #63: 'del_13q14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_13q14.2' versus 'MRNASEQ_CNMF'

P value = 0.0198 (Fisher's exact test), Q value = 0.065

Table S259.  Gene #63: 'del_13q14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 68 31
DEL PEAK 32(13Q14.2) MUTATED 25 35 14
DEL PEAK 32(13Q14.2) WILD-TYPE 59 33 17

Figure S259.  Get High-res Image Gene #63: 'del_13q14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_13q14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0216 (Fisher's exact test), Q value = 0.07

Table S260.  Gene #63: 'del_13q14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
DEL PEAK 32(13Q14.2) MUTATED 21 5 48
DEL PEAK 32(13Q14.2) WILD-TYPE 46 15 48

Figure S260.  Get High-res Image Gene #63: 'del_13q14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_CNMF'

P value = 0.0172 (Fisher's exact test), Q value = 0.059

Table S261.  Gene #63: 'del_13q14.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
DEL PEAK 32(13Q14.2) MUTATED 25 44 4
DEL PEAK 32(13Q14.2) WILD-TYPE 59 43 8

Figure S261.  Get High-res Image Gene #63: 'del_13q14.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_13q14.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0243 (Fisher's exact test), Q value = 0.073

Table S262.  Gene #63: 'del_13q14.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
DEL PEAK 32(13Q14.2) MUTATED 21 5 31 16
DEL PEAK 32(13Q14.2) WILD-TYPE 41 21 31 17

Figure S262.  Get High-res Image Gene #63: 'del_13q14.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0228 (Fisher's exact test), Q value = 0.071

Table S263.  Gene #63: 'del_13q14.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 66 35 11
DEL PEAK 32(13Q14.2) MUTATED 21 36 10 4
DEL PEAK 32(13Q14.2) WILD-TYPE 45 30 25 7

Figure S263.  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 = 0.0249 (Fisher's exact test), Q value = 0.074

Table S264.  Gene #63: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
DEL PEAK 32(13Q14.2) MUTATED 20 5 46
DEL PEAK 32(13Q14.2) WILD-TYPE 42 17 48

Figure S264.  Get High-res Image Gene #63: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_13q21.31' versus 'CN_CNMF'

P value = 0.0131 (Fisher's exact test), Q value = 0.049

Table S265.  Gene #64: 'del_13q21.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
DEL PEAK 33(13Q21.31) MUTATED 22 10 37
DEL PEAK 33(13Q21.31) WILD-TYPE 43 34 38

Figure S265.  Get High-res Image Gene #64: 'del_13q21.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q23.3' versus 'CN_CNMF'

P value = 0.00323 (Fisher's exact test), Q value = 0.017

Table S266.  Gene #65: 'del_14q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
DEL PEAK 34(14Q23.3) MUTATED 28 8 15
DEL PEAK 34(14Q23.3) WILD-TYPE 37 36 60

Figure S266.  Get High-res Image Gene #65: 'del_14q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q23.3' versus 'METHLYATION_CNMF'

P value = 0.015 (Fisher's exact test), Q value = 0.054

Table S267.  Gene #65: 'del_14q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
DEL PEAK 34(14Q23.3) MUTATED 29 9 13
DEL PEAK 34(14Q23.3) WILD-TYPE 47 23 63

Figure S267.  Get High-res Image Gene #65: 'del_14q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_14q23.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0248 (Fisher's exact test), Q value = 0.074

Table S268.  Gene #65: 'del_14q23.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
DEL PEAK 34(14Q23.3) MUTATED 6 11 7 6 4
DEL PEAK 34(14Q23.3) WILD-TYPE 17 10 15 20 30

Figure S268.  Get High-res Image Gene #65: 'del_14q23.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_14q23.3' versus 'MRNASEQ_CNMF'

P value = 0.00048 (Fisher's exact test), Q value = 0.0038

Table S269.  Gene #65: 'del_14q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 68 31
DEL PEAK 34(14Q23.3) MUTATED 31 19 1
DEL PEAK 34(14Q23.3) WILD-TYPE 53 49 30

Figure S269.  Get High-res Image Gene #65: 'del_14q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_14q23.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0432 (Fisher's exact test), Q value = 0.11

Table S270.  Gene #65: 'del_14q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
DEL PEAK 34(14Q23.3) MUTATED 26 5 20
DEL PEAK 34(14Q23.3) WILD-TYPE 41 15 76

Figure S270.  Get High-res Image Gene #65: 'del_14q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_14q23.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0133 (Fisher's exact test), Q value = 0.049

Table S271.  Gene #65: 'del_14q23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
DEL PEAK 34(14Q23.3) MUTATED 27 5 13 6
DEL PEAK 34(14Q23.3) WILD-TYPE 35 21 49 27

Figure S271.  Get High-res Image Gene #65: 'del_14q23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_14q23.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0282 (Fisher's exact test), Q value = 0.08

Table S272.  Gene #65: 'del_14q23.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 66 35 11
DEL PEAK 34(14Q23.3) MUTATED 27 16 5 3
DEL PEAK 34(14Q23.3) WILD-TYPE 39 50 30 8

Figure S272.  Get High-res Image Gene #65: 'del_14q23.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_14q23.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00215 (Fisher's exact test), Q value = 0.013

Table S273.  Gene #65: 'del_14q23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
DEL PEAK 34(14Q23.3) MUTATED 28 4 19
DEL PEAK 34(14Q23.3) WILD-TYPE 34 18 75

Figure S273.  Get High-res Image Gene #65: 'del_14q23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_15q11.2' versus 'MRNASEQ_CNMF'

P value = 0.0124 (Fisher's exact test), Q value = 0.048

Table S274.  Gene #66: 'del_15q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 68 31
DEL PEAK 35(15Q11.2) MUTATED 35 24 4
DEL PEAK 35(15Q11.2) WILD-TYPE 49 44 27

Figure S274.  Get High-res Image Gene #66: 'del_15q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_15q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0193 (Fisher's exact test), Q value = 0.063

Table S275.  Gene #66: 'del_15q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
DEL PEAK 35(15Q11.2) MUTATED 19 16 20 8
DEL PEAK 35(15Q11.2) WILD-TYPE 43 10 42 25

Figure S275.  Get High-res Image Gene #66: 'del_15q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_15q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0034 (Fisher's exact test), Q value = 0.018

Table S276.  Gene #66: 'del_15q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
DEL PEAK 35(15Q11.2) MUTATED 20 15 28
DEL PEAK 35(15Q11.2) WILD-TYPE 42 7 66

Figure S276.  Get High-res Image Gene #66: 'del_15q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S277.  Gene #67: 'del_16p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
DEL PEAK 36(16P13.3) MUTATED 39 10 16
DEL PEAK 36(16P13.3) WILD-TYPE 26 34 59

Figure S277.  Get High-res Image Gene #67: 'del_16p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_16p13.3' versus 'METHLYATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00096

Table S278.  Gene #67: 'del_16p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
DEL PEAK 36(16P13.3) MUTATED 41 8 16
DEL PEAK 36(16P13.3) WILD-TYPE 35 24 60

Figure S278.  Get High-res Image Gene #67: 'del_16p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16p13.3' versus 'MRNASEQ_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.0019

Table S279.  Gene #67: 'del_16p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 68 31
DEL PEAK 36(16P13.3) MUTATED 43 16 6
DEL PEAK 36(16P13.3) WILD-TYPE 41 52 25

Figure S279.  Get High-res Image Gene #67: 'del_16p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00068

Table S280.  Gene #67: 'del_16p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
DEL PEAK 36(16P13.3) MUTATED 34 11 20
DEL PEAK 36(16P13.3) WILD-TYPE 33 9 76

Figure S280.  Get High-res Image Gene #67: 'del_16p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_16p13.3' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00027

Table S281.  Gene #67: 'del_16p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
DEL PEAK 36(16P13.3) MUTATED 44 18 2
DEL PEAK 36(16P13.3) WILD-TYPE 40 69 10

Figure S281.  Get High-res Image Gene #67: 'del_16p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_16p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S282.  Gene #67: 'del_16p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
DEL PEAK 36(16P13.3) MUTATED 37 9 14 4
DEL PEAK 36(16P13.3) WILD-TYPE 25 17 48 29

Figure S282.  Get High-res Image Gene #67: 'del_16p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_16p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00076

Table S283.  Gene #67: 'del_16p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 66 35 11
DEL PEAK 36(16P13.3) MUTATED 38 13 9 3
DEL PEAK 36(16P13.3) WILD-TYPE 28 53 26 8

Figure S283.  Get High-res Image Gene #67: 'del_16p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_16p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S284.  Gene #67: 'del_16p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
DEL PEAK 36(16P13.3) MUTATED 36 9 18
DEL PEAK 36(16P13.3) WILD-TYPE 26 13 76

Figure S284.  Get High-res Image Gene #67: 'del_16p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q23.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S285.  Gene #68: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
DEL PEAK 37(16Q23.1) MUTATED 50 18 16
DEL PEAK 37(16Q23.1) WILD-TYPE 15 26 59

Figure S285.  Get High-res Image Gene #68: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S286.  Gene #68: 'del_16q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
DEL PEAK 37(16Q23.1) MUTATED 56 11 17
DEL PEAK 37(16Q23.1) WILD-TYPE 20 21 59

Figure S286.  Get High-res Image Gene #68: 'del_16q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16q23.1' versus 'RPPA_CNMF'

P value = 0.0391 (Fisher's exact test), Q value = 0.097

Table S287.  Gene #68: 'del_16q23.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 24 16 17 23 17 24 5
DEL PEAK 37(16Q23.1) MUTATED 13 7 7 9 10 3 2
DEL PEAK 37(16Q23.1) WILD-TYPE 11 9 10 14 7 21 3

Figure S287.  Get High-res Image Gene #68: 'del_16q23.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_16q23.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0384 (Fisher's exact test), Q value = 0.096

Table S288.  Gene #68: 'del_16q23.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
DEL PEAK 37(16Q23.1) MUTATED 11 13 11 7 9
DEL PEAK 37(16Q23.1) WILD-TYPE 12 8 11 19 25

Figure S288.  Get High-res Image Gene #68: 'del_16q23.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_16q23.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S289.  Gene #68: 'del_16q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 68 31
DEL PEAK 37(16Q23.1) MUTATED 59 18 7
DEL PEAK 37(16Q23.1) WILD-TYPE 25 50 24

Figure S289.  Get High-res Image Gene #68: 'del_16q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S290.  Gene #68: 'del_16q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
DEL PEAK 37(16Q23.1) MUTATED 49 12 23
DEL PEAK 37(16Q23.1) WILD-TYPE 18 8 73

Figure S290.  Get High-res Image Gene #68: 'del_16q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S291.  Gene #68: 'del_16q23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
DEL PEAK 37(16Q23.1) MUTATED 60 22 1
DEL PEAK 37(16Q23.1) WILD-TYPE 24 65 11

Figure S291.  Get High-res Image Gene #68: 'del_16q23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_16q23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S292.  Gene #68: 'del_16q23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
DEL PEAK 37(16Q23.1) MUTATED 46 16 14 7
DEL PEAK 37(16Q23.1) WILD-TYPE 16 10 48 26

Figure S292.  Get High-res Image Gene #68: 'del_16q23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S293.  Gene #68: 'del_16q23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 66 35 11
DEL PEAK 37(16Q23.1) MUTATED 49 17 11 4
DEL PEAK 37(16Q23.1) WILD-TYPE 17 49 24 7

Figure S293.  Get High-res Image Gene #68: 'del_16q23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_16q23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S294.  Gene #68: 'del_16q23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
DEL PEAK 37(16Q23.1) MUTATED 46 14 21
DEL PEAK 37(16Q23.1) WILD-TYPE 16 8 73

Figure S294.  Get High-res Image Gene #68: 'del_16q23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17p12' versus 'CN_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.001

Table S295.  Gene #69: 'del_17p12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
DEL PEAK 38(17P12) MUTATED 44 19 23
DEL PEAK 38(17P12) WILD-TYPE 21 25 52

Figure S295.  Get High-res Image Gene #69: 'del_17p12' versus Molecular Subtype #1: 'CN_CNMF'

'del_17p12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S296.  Gene #69: 'del_17p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
DEL PEAK 38(17P12) MUTATED 54 10 22
DEL PEAK 38(17P12) WILD-TYPE 22 22 54

Figure S296.  Get High-res Image Gene #69: 'del_17p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17p12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S297.  Gene #69: 'del_17p12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 68 31
DEL PEAK 38(17P12) MUTATED 57 19 10
DEL PEAK 38(17P12) WILD-TYPE 27 49 21

Figure S297.  Get High-res Image Gene #69: 'del_17p12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_17p12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00027

Table S298.  Gene #69: 'del_17p12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
DEL PEAK 38(17P12) MUTATED 46 11 29
DEL PEAK 38(17P12) WILD-TYPE 21 9 67

Figure S298.  Get High-res Image Gene #69: 'del_17p12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_17p12' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S299.  Gene #69: 'del_17p12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
DEL PEAK 38(17P12) MUTATED 56 29 1
DEL PEAK 38(17P12) WILD-TYPE 28 58 11

Figure S299.  Get High-res Image Gene #69: 'del_17p12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_17p12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00027

Table S300.  Gene #69: 'del_17p12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
DEL PEAK 38(17P12) MUTATED 41 17 19 9
DEL PEAK 38(17P12) WILD-TYPE 21 9 43 24

Figure S300.  Get High-res Image Gene #69: 'del_17p12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_17p12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0102 (Fisher's exact test), Q value = 0.041

Table S301.  Gene #69: 'del_17p12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 66 35 11
DEL PEAK 38(17P12) MUTATED 42 26 12 5
DEL PEAK 38(17P12) WILD-TYPE 24 40 23 6

Figure S301.  Get High-res Image Gene #69: 'del_17p12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_17p12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S302.  Gene #69: 'del_17p12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
DEL PEAK 38(17P12) MUTATED 41 16 28
DEL PEAK 38(17P12) WILD-TYPE 21 6 66

Figure S302.  Get High-res Image Gene #69: 'del_17p12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17q25.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0357 (Fisher's exact test), Q value = 0.093

Table S303.  Gene #70: 'del_17q25.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 66 35 11
DEL PEAK 39(17Q25.3) MUTATED 14 21 3 1
DEL PEAK 39(17Q25.3) WILD-TYPE 52 45 32 10

Figure S303.  Get High-res Image Gene #70: 'del_17q25.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_18p11.23' versus 'METHLYATION_CNMF'

P value = 0.00608 (Fisher's exact test), Q value = 0.028

Table S304.  Gene #71: 'del_18p11.23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
DEL PEAK 40(18P11.23) MUTATED 35 7 18
DEL PEAK 40(18P11.23) WILD-TYPE 41 25 58

Figure S304.  Get High-res Image Gene #71: 'del_18p11.23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_18p11.23' versus 'MRNASEQ_CNMF'

P value = 0.0168 (Fisher's exact test), Q value = 0.058

Table S305.  Gene #71: 'del_18p11.23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 68 31
DEL PEAK 40(18P11.23) MUTATED 36 17 6
DEL PEAK 40(18P11.23) WILD-TYPE 48 51 25

Figure S305.  Get High-res Image Gene #71: 'del_18p11.23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_18p11.23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0311 (Fisher's exact test), Q value = 0.085

Table S306.  Gene #71: 'del_18p11.23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
DEL PEAK 40(18P11.23) MUTATED 29 7 23
DEL PEAK 40(18P11.23) WILD-TYPE 38 13 73

Figure S306.  Get High-res Image Gene #71: 'del_18p11.23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_18p11.23' versus 'MIRSEQ_CNMF'

P value = 0.0255 (Fisher's exact test), Q value = 0.075

Table S307.  Gene #71: 'del_18p11.23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
DEL PEAK 40(18P11.23) MUTATED 35 20 5
DEL PEAK 40(18P11.23) WILD-TYPE 49 67 7

Figure S307.  Get High-res Image Gene #71: 'del_18p11.23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_18p11.23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0483 (Fisher's exact test), Q value = 0.11

Table S308.  Gene #71: 'del_18p11.23' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
DEL PEAK 40(18P11.23) MUTATED 26 9 23
DEL PEAK 40(18P11.23) WILD-TYPE 36 13 71

Figure S308.  Get High-res Image Gene #71: 'del_18p11.23' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18q12.2' versus 'METHLYATION_CNMF'

P value = 0.0174 (Fisher's exact test), Q value = 0.059

Table S309.  Gene #72: 'del_18q12.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
DEL PEAK 41(18Q12.2) MUTATED 55 16 40
DEL PEAK 41(18Q12.2) WILD-TYPE 21 16 36

Figure S309.  Get High-res Image Gene #72: 'del_18q12.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_18q12.2' versus 'MRNASEQ_CNMF'

P value = 0.0237 (Fisher's exact test), Q value = 0.072

Table S310.  Gene #72: 'del_18q12.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 68 31
DEL PEAK 41(18Q12.2) MUTATED 59 37 14
DEL PEAK 41(18Q12.2) WILD-TYPE 25 31 17

Figure S310.  Get High-res Image Gene #72: 'del_18q12.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_18q12.2' versus 'MIRSEQ_CNMF'

P value = 0.0443 (Fisher's exact test), Q value = 0.11

Table S311.  Gene #72: 'del_18q12.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
DEL PEAK 41(18Q12.2) MUTATED 59 45 7
DEL PEAK 41(18Q12.2) WILD-TYPE 25 42 5

Figure S311.  Get High-res Image Gene #72: 'del_18q12.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_18q12.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00066 (Fisher's exact test), Q value = 0.005

Table S312.  Gene #72: 'del_18q12.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
DEL PEAK 41(18Q12.2) MUTATED 38 23 38 12
DEL PEAK 41(18Q12.2) WILD-TYPE 24 3 24 21

Figure S312.  Get High-res Image Gene #72: 'del_18q12.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_18q12.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0346 (Fisher's exact test), Q value = 0.091

Table S313.  Gene #72: 'del_18q12.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 66 35 11
DEL PEAK 41(18Q12.2) MUTATED 45 32 26 6
DEL PEAK 41(18Q12.2) WILD-TYPE 21 34 9 5

Figure S313.  Get High-res Image Gene #72: 'del_18q12.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_18q12.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.0024

Table S314.  Gene #72: 'del_18q12.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
DEL PEAK 41(18Q12.2) MUTATED 39 21 49
DEL PEAK 41(18Q12.2) WILD-TYPE 23 1 45

Figure S314.  Get High-res Image Gene #72: 'del_18q12.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18q21.2' versus 'METHLYATION_CNMF'

P value = 9e-04 (Fisher's exact test), Q value = 0.0064

Table S315.  Gene #73: 'del_18q21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
DEL PEAK 42(18Q21.2) MUTATED 61 17 41
DEL PEAK 42(18Q21.2) WILD-TYPE 15 15 35

Figure S315.  Get High-res Image Gene #73: 'del_18q21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_18q21.2' versus 'MRNASEQ_CNMF'

P value = 0.00321 (Fisher's exact test), Q value = 0.017

Table S316.  Gene #73: 'del_18q21.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 68 31
DEL PEAK 42(18Q21.2) MUTATED 65 37 16
DEL PEAK 42(18Q21.2) WILD-TYPE 19 31 15

Figure S316.  Get High-res Image Gene #73: 'del_18q21.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_18q21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00903 (Fisher's exact test), Q value = 0.037

Table S317.  Gene #73: 'del_18q21.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
DEL PEAK 42(18Q21.2) MUTATED 51 15 52
DEL PEAK 42(18Q21.2) WILD-TYPE 16 5 44

Figure S317.  Get High-res Image Gene #73: 'del_18q21.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_18q21.2' versus 'MIRSEQ_CNMF'

P value = 0.00462 (Fisher's exact test), Q value = 0.022

Table S318.  Gene #73: 'del_18q21.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
DEL PEAK 42(18Q21.2) MUTATED 65 47 7
DEL PEAK 42(18Q21.2) WILD-TYPE 19 40 5

Figure S318.  Get High-res Image Gene #73: 'del_18q21.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_18q21.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00202 (Fisher's exact test), Q value = 0.012

Table S319.  Gene #73: 'del_18q21.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
DEL PEAK 42(18Q21.2) MUTATED 43 23 39 14
DEL PEAK 42(18Q21.2) WILD-TYPE 19 3 23 19

Figure S319.  Get High-res Image Gene #73: 'del_18q21.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_18q21.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0153 (Fisher's exact test), Q value = 0.055

Table S320.  Gene #73: 'del_18q21.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 66 35 11
DEL PEAK 42(18Q21.2) MUTATED 49 33 26 8
DEL PEAK 42(18Q21.2) WILD-TYPE 17 33 9 3

Figure S320.  Get High-res Image Gene #73: 'del_18q21.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_18q21.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00048 (Fisher's exact test), Q value = 0.0038

Table S321.  Gene #73: 'del_18q21.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
DEL PEAK 42(18Q21.2) MUTATED 43 21 52
DEL PEAK 42(18Q21.2) WILD-TYPE 19 1 42

Figure S321.  Get High-res Image Gene #73: 'del_18q21.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18q22.3' versus 'METHLYATION_CNMF'

P value = 0.0357 (Fisher's exact test), Q value = 0.093

Table S322.  Gene #74: 'del_18q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
DEL PEAK 43(18Q22.3) MUTATED 54 15 43
DEL PEAK 43(18Q22.3) WILD-TYPE 22 17 33

Figure S322.  Get High-res Image Gene #74: 'del_18q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_18q22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00819 (Fisher's exact test), Q value = 0.035

Table S323.  Gene #74: 'del_18q22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
DEL PEAK 43(18Q22.3) MUTATED 35 23 38 16
DEL PEAK 43(18Q22.3) WILD-TYPE 27 3 24 17

Figure S323.  Get High-res Image Gene #74: 'del_18q22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_18q22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00086 (Fisher's exact test), Q value = 0.0062

Table S324.  Gene #74: 'del_18q22.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
DEL PEAK 43(18Q22.3) MUTATED 35 21 53
DEL PEAK 43(18Q22.3) WILD-TYPE 27 1 41

Figure S324.  Get High-res Image Gene #74: 'del_18q22.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19p13.3' versus 'CN_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.0025

Table S325.  Gene #75: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
DEL PEAK 44(19P13.3) MUTATED 43 12 38
DEL PEAK 44(19P13.3) WILD-TYPE 22 32 37

Figure S325.  Get High-res Image Gene #75: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_19p13.3' versus 'MIRSEQ_CNMF'

P value = 0.0361 (Fisher's exact test), Q value = 0.093

Table S326.  Gene #75: 'del_19p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
DEL PEAK 44(19P13.3) MUTATED 47 44 2
DEL PEAK 44(19P13.3) WILD-TYPE 37 43 10

Figure S326.  Get High-res Image Gene #75: 'del_19p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_19p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0226 (Fisher's exact test), Q value = 0.071

Table S327.  Gene #75: 'del_19p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
DEL PEAK 44(19P13.3) MUTATED 40 9 26 18
DEL PEAK 44(19P13.3) WILD-TYPE 22 17 36 15

Figure S327.  Get High-res Image Gene #75: 'del_19p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00686 (Fisher's exact test), Q value = 0.03

Table S328.  Gene #75: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
DEL PEAK 44(19P13.3) MUTATED 41 7 43
DEL PEAK 44(19P13.3) WILD-TYPE 21 15 51

Figure S328.  Get High-res Image Gene #75: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19q11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0145 (Fisher's exact test), Q value = 0.053

Table S329.  Gene #76: 'del_19q11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
DEL PEAK 45(19Q11) MUTATED 21 1 15 10
DEL PEAK 45(19Q11) WILD-TYPE 41 25 47 23

Figure S329.  Get High-res Image Gene #76: 'del_19q11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_19q11' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00104 (Fisher's exact test), Q value = 0.0073

Table S330.  Gene #76: 'del_19q11' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 66 35 11
DEL PEAK 45(19Q11) MUTATED 17 23 1 4
DEL PEAK 45(19Q11) WILD-TYPE 49 43 34 7

Figure S330.  Get High-res Image Gene #76: 'del_19q11' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_19q11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0275 (Fisher's exact test), Q value = 0.079

Table S331.  Gene #76: 'del_19q11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
DEL PEAK 45(19Q11) MUTATED 20 1 24
DEL PEAK 45(19Q11) WILD-TYPE 42 21 70

Figure S331.  Get High-res Image Gene #76: 'del_19q11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_20p12.1' versus 'CN_CNMF'

P value = 0.0335 (Fisher's exact test), Q value = 0.089

Table S332.  Gene #77: 'del_20p12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
DEL PEAK 46(20P12.1) MUTATED 18 7 8
DEL PEAK 46(20P12.1) WILD-TYPE 47 37 67

Figure S332.  Get High-res Image Gene #77: 'del_20p12.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_20p12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0082 (Fisher's exact test), Q value = 0.035

Table S333.  Gene #77: 'del_20p12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
DEL PEAK 46(20P12.1) MUTATED 20 2 11
DEL PEAK 46(20P12.1) WILD-TYPE 47 18 85

Figure S333.  Get High-res Image Gene #77: 'del_20p12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_20p12.1' versus 'MIRSEQ_CNMF'

P value = 0.0168 (Fisher's exact test), Q value = 0.058

Table S334.  Gene #77: 'del_20p12.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
DEL PEAK 46(20P12.1) MUTATED 22 11 0
DEL PEAK 46(20P12.1) WILD-TYPE 62 76 12

Figure S334.  Get High-res Image Gene #77: 'del_20p12.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_20p12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0496 (Fisher's exact test), Q value = 0.12

Table S335.  Gene #77: 'del_20p12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
DEL PEAK 46(20P12.1) MUTATED 15 7 5 6
DEL PEAK 46(20P12.1) WILD-TYPE 47 19 57 27

Figure S335.  Get High-res Image Gene #77: 'del_20p12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_20p12.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0425 (Fisher's exact test), Q value = 0.1

Table S336.  Gene #77: 'del_20p12.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
DEL PEAK 46(20P12.1) MUTATED 16 6 11
DEL PEAK 46(20P12.1) WILD-TYPE 46 16 83

Figure S336.  Get High-res Image Gene #77: 'del_20p12.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_21q11.2' versus 'METHLYATION_CNMF'

P value = 0.0286 (Fisher's exact test), Q value = 0.08

Table S337.  Gene #78: 'del_21q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
DEL PEAK 47(21Q11.2) MUTATED 53 16 38
DEL PEAK 47(21Q11.2) WILD-TYPE 23 16 38

Figure S337.  Get High-res Image Gene #78: 'del_21q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_21q11.2' versus 'MRNASEQ_CNMF'

P value = 0.0354 (Fisher's exact test), Q value = 0.093

Table S338.  Gene #78: 'del_21q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 68 31
DEL PEAK 47(21Q11.2) MUTATED 55 31 20
DEL PEAK 47(21Q11.2) WILD-TYPE 29 37 11

Figure S338.  Get High-res Image Gene #78: 'del_21q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_21q21.1' versus 'METHLYATION_CNMF'

P value = 0.00948 (Fisher's exact test), Q value = 0.038

Table S339.  Gene #79: 'del_21q21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
DEL PEAK 48(21Q21.1) MUTATED 54 14 39
DEL PEAK 48(21Q21.1) WILD-TYPE 22 18 37

Figure S339.  Get High-res Image Gene #79: 'del_21q21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_21q22.12' versus 'METHLYATION_CNMF'

P value = 0.0108 (Fisher's exact test), Q value = 0.042

Table S340.  Gene #80: 'del_21q22.12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
DEL PEAK 49(21Q22.12) MUTATED 54 14 40
DEL PEAK 49(21Q22.12) WILD-TYPE 22 18 36

Figure S340.  Get High-res Image Gene #80: 'del_21q22.12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_21q22.12' versus 'MRNASEQ_CNMF'

P value = 0.0109 (Fisher's exact test), Q value = 0.042

Table S341.  Gene #80: 'del_21q22.12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 68 31
DEL PEAK 49(21Q22.12) MUTATED 56 30 21
DEL PEAK 49(21Q22.12) WILD-TYPE 28 38 10

Figure S341.  Get High-res Image Gene #80: 'del_21q22.12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_21q22.12' versus 'MIRSEQ_CNMF'

P value = 0.0316 (Fisher's exact test), Q value = 0.086

Table S342.  Gene #80: 'del_21q22.12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
DEL PEAK 49(21Q22.12) MUTATED 57 47 4
DEL PEAK 49(21Q22.12) WILD-TYPE 27 40 8

Figure S342.  Get High-res Image Gene #80: 'del_21q22.12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_22q11.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S343.  Gene #81: 'del_22q11.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
DEL PEAK 50(22Q11.1) MUTATED 46 13 20
DEL PEAK 50(22Q11.1) WILD-TYPE 19 31 55

Figure S343.  Get High-res Image Gene #81: 'del_22q11.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q11.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S344.  Gene #81: 'del_22q11.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
DEL PEAK 50(22Q11.1) MUTATED 51 10 18
DEL PEAK 50(22Q11.1) WILD-TYPE 25 22 58

Figure S344.  Get High-res Image Gene #81: 'del_22q11.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_22q11.1' versus 'RPPA_CNMF'

P value = 0.0222 (Fisher's exact test), Q value = 0.07

Table S345.  Gene #81: 'del_22q11.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 24 16 17 23 17 24 5
DEL PEAK 50(22Q11.1) MUTATED 15 7 7 10 6 3 1
DEL PEAK 50(22Q11.1) WILD-TYPE 9 9 10 13 11 21 4

Figure S345.  Get High-res Image Gene #81: 'del_22q11.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_22q11.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.00448 (Fisher's exact test), Q value = 0.022

Table S346.  Gene #81: 'del_22q11.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
DEL PEAK 50(22Q11.1) MUTATED 14 12 9 8 6
DEL PEAK 50(22Q11.1) WILD-TYPE 9 9 13 18 28

Figure S346.  Get High-res Image Gene #81: 'del_22q11.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_22q11.1' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00049

Table S347.  Gene #81: 'del_22q11.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 68 31
DEL PEAK 50(22Q11.1) MUTATED 52 20 7
DEL PEAK 50(22Q11.1) WILD-TYPE 32 48 24

Figure S347.  Get High-res Image Gene #81: 'del_22q11.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_22q11.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S348.  Gene #81: 'del_22q11.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
DEL PEAK 50(22Q11.1) MUTATED 43 10 26
DEL PEAK 50(22Q11.1) WILD-TYPE 24 10 70

Figure S348.  Get High-res Image Gene #81: 'del_22q11.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_22q11.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S349.  Gene #81: 'del_22q11.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
DEL PEAK 50(22Q11.1) MUTATED 53 25 1
DEL PEAK 50(22Q11.1) WILD-TYPE 31 62 11

Figure S349.  Get High-res Image Gene #81: 'del_22q11.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_22q11.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S350.  Gene #81: 'del_22q11.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
DEL PEAK 50(22Q11.1) MUTATED 43 11 16 9
DEL PEAK 50(22Q11.1) WILD-TYPE 19 15 46 24

Figure S350.  Get High-res Image Gene #81: 'del_22q11.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_22q11.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S351.  Gene #81: 'del_22q11.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 66 35 11
DEL PEAK 50(22Q11.1) MUTATED 48 19 7 3
DEL PEAK 50(22Q11.1) WILD-TYPE 18 47 28 8

Figure S351.  Get High-res Image Gene #81: 'del_22q11.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_22q11.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S352.  Gene #81: 'del_22q11.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
DEL PEAK 50(22Q11.1) MUTATED 44 9 24
DEL PEAK 50(22Q11.1) WILD-TYPE 18 13 70

Figure S352.  Get High-res Image Gene #81: 'del_22q11.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xp21.1' versus 'CN_CNMF'

P value = 0.00092 (Fisher's exact test), Q value = 0.0065

Table S353.  Gene #82: 'del_xp21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
DEL PEAK 51(XP21.1) MUTATED 25 7 37
DEL PEAK 51(XP21.1) WILD-TYPE 40 37 38

Figure S353.  Get High-res Image Gene #82: 'del_xp21.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_xp21.1' versus 'METHLYATION_CNMF'

P value = 0.0371 (Fisher's exact test), Q value = 0.094

Table S354.  Gene #82: 'del_xp21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
DEL PEAK 51(XP21.1) MUTATED 26 7 36
DEL PEAK 51(XP21.1) WILD-TYPE 50 25 40

Figure S354.  Get High-res Image Gene #82: 'del_xp21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xp21.1' versus 'MRNASEQ_CNMF'

P value = 0.00226 (Fisher's exact test), Q value = 0.013

Table S355.  Gene #82: 'del_xp21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 68 31
DEL PEAK 51(XP21.1) MUTATED 27 36 6
DEL PEAK 51(XP21.1) WILD-TYPE 57 32 25

Figure S355.  Get High-res Image Gene #82: 'del_xp21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_xp11.3' versus 'CN_CNMF'

P value = 0.00069 (Fisher's exact test), Q value = 0.0051

Table S356.  Gene #83: 'del_xp11.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
DEL PEAK 52(XP11.3) MUTATED 24 9 41
DEL PEAK 52(XP11.3) WILD-TYPE 41 35 34

Figure S356.  Get High-res Image Gene #83: 'del_xp11.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_xp11.3' versus 'MRNASEQ_CNMF'

P value = 0.00511 (Fisher's exact test), Q value = 0.024

Table S357.  Gene #83: 'del_xp11.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 68 31
DEL PEAK 52(XP11.3) MUTATED 26 38 10
DEL PEAK 52(XP11.3) WILD-TYPE 58 30 21

Figure S357.  Get High-res Image Gene #83: 'del_xp11.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_xp11.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0224 (Fisher's exact test), Q value = 0.071

Table S358.  Gene #83: 'del_xp11.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
DEL PEAK 52(XP11.3) MUTATED 20 6 48
DEL PEAK 52(XP11.3) WILD-TYPE 47 14 48

Figure S358.  Get High-res Image Gene #83: 'del_xp11.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_xp11.3' versus 'MIRSEQ_CNMF'

P value = 0.00312 (Fisher's exact test), Q value = 0.017

Table S359.  Gene #83: 'del_xp11.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
DEL PEAK 52(XP11.3) MUTATED 26 46 2
DEL PEAK 52(XP11.3) WILD-TYPE 58 41 10

Figure S359.  Get High-res Image Gene #83: 'del_xp11.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_xp11.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0438 (Fisher's exact test), Q value = 0.11

Table S360.  Gene #83: 'del_xp11.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
DEL PEAK 52(XP11.3) MUTATED 21 6 29 18
DEL PEAK 52(XP11.3) WILD-TYPE 41 20 33 15

Figure S360.  Get High-res Image Gene #83: 'del_xp11.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_xp11.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0334 (Fisher's exact test), Q value = 0.089

Table S361.  Gene #83: 'del_xp11.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 66 35 11
DEL PEAK 52(XP11.3) MUTATED 21 36 11 4
DEL PEAK 52(XP11.3) WILD-TYPE 45 30 24 7

Figure S361.  Get High-res Image Gene #83: 'del_xp11.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_xp11.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0174 (Fisher's exact test), Q value = 0.059

Table S362.  Gene #83: 'del_xp11.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
DEL PEAK 52(XP11.3) MUTATED 20 5 47
DEL PEAK 52(XP11.3) WILD-TYPE 42 17 47

Figure S362.  Get High-res Image Gene #83: 'del_xp11.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xq21.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0291 (Fisher's exact test), Q value = 0.082

Table S363.  Gene #85: 'del_xq21.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
DEL PEAK 54(XQ21.33) MUTATED 20 3 8 9
DEL PEAK 54(XQ21.33) WILD-TYPE 42 23 54 24

Figure S363.  Get High-res Image Gene #85: '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/ESCA-TP/15084414/transformed.cor.cli.txt

  • Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/ESCA-TP/15092862/ESCA-TP.transferedmergedcluster.txt

  • Number of patients = 184

  • Number of significantly focal cnvs = 85

  • 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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