Correlation between copy number variation genes (focal events) and molecular subtypes
Colorectal Adenocarcinoma (Primary solid tumor)
15 July 2014  |  analyses__2014_07_15
Maintainer Information
Citation Information
doi:10.7908/C1B56HGN
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1B56HGN
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 75 focal events and 12 molecular subtypes across 600 patients, 267 significant findings detected with P value < 0.05 and Q value < 0.25.

  • amp_1q31.1 cnv correlated to 'CN_CNMF'.

  • amp_2q33.1 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • amp_5p12 cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.

  • amp_6p21.1 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_8p11.23 cnv correlated to 'CN_CNMF'.

  • amp_8p11.21 cnv correlated to 'CN_CNMF'.

  • amp_8q12.1 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • amp_8q24.21 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_11p15.5 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_13q12.13 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_13q12.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • amp_16p11.2 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • amp_17q24.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • amp_19p13.2 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • amp_19q12 cnv correlated to 'CN_CNMF'.

  • amp_20p11.23 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_20p11.21 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_20q11.21 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_20q12 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_20q13.31 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_xq28 cnv correlated to 'CN_CNMF'.

  • del_1p36.11 cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_1p33 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • del_1p13.2 cnv correlated to 'CN_CNMF'.

  • del_4p16.1 cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • del_4q35.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • del_5q11.2 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_5q22.2 cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • del_8p22 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_8p11.21 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • del_8q11.1 cnv correlated to 'CN_CNMF'.

  • del_9p24.2 cnv correlated to 'CN_CNMF'.

  • del_10q21.1 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • del_10q23.31 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_10q25.2 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_12p13.1 cnv correlated to 'CN_CNMF'.

  • del_12q21.33 cnv correlated to 'CN_CNMF'.

  • del_14q11.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_14q31.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_14q31.1 cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_15q11.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_15q15.2 cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_15q21.1 cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_15q22.33 cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_17p12 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_18p11.31 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_18q12.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • del_18q22.1 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_19p13.3 cnv correlated to 'CN_CNMF'.

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

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

  • del_21q11.2 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • del_22q13.32 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 75 focal events and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 267 significant findings detected.

Clinical
Features 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
amp 13q12 13 390 (65%) 210 1e-05
(0.009) 		1e-05
(0.009) 		1e-05
(0.009) 		1e-05
(0.009) 		0.0166
(1.00) 		0.0164
(1.00) 		1e-05
(0.009) 		1e-05
(0.009) 		0.00024
(0.156) 		0.485
(1.00) 		1e-05
(0.009) 		1e-05
(0.009)
amp 20q11 21 457 (76%) 143 1e-05
(0.009) 		1e-05
(0.009) 		1e-05
(0.009) 		1e-05
(0.009) 		0.00711
(1.00) 		0.0133
(1.00) 		1e-05
(0.009) 		1e-05
(0.009) 		0.0182
(1.00) 		0.00027
(0.174) 		1e-05
(0.009) 		1e-05
(0.009)
amp 20q12 459 (76%) 141 1e-05
(0.009) 		1e-05
(0.009) 		1e-05
(0.009) 		1e-05
(0.009) 		0.0112
(1.00) 		0.00643
(1.00) 		1e-05
(0.009) 		1e-05
(0.009) 		0.00752
(1.00) 		0.00017
(0.112) 		1e-05
(0.009) 		1e-05
(0.009)
amp 20q13 31 461 (77%) 139 1e-05
(0.009) 		1e-05
(0.009) 		1e-05
(0.009) 		1e-05
(0.009) 		0.0145
(1.00) 		0.00551
(1.00) 		1e-05
(0.009) 		1e-05
(0.009) 		0.0156
(1.00) 		0.00032
(0.205) 		1e-05
(0.009) 		1e-05
(0.009)
del 18q21 2 420 (70%) 180 1e-05
(0.009) 		1e-05
(0.009) 		1e-05
(0.009) 		1e-05
(0.009) 		0.0149
(1.00) 		0.0258
(1.00) 		1e-05
(0.009) 		1e-05
(0.009) 		0.0001
(0.0678) 		0.0292
(1.00) 		1e-05
(0.009) 		1e-05
(0.009)
del 18q22 1 415 (69%) 185 1e-05
(0.009) 		1e-05
(0.009) 		1e-05
(0.009) 		1e-05
(0.009) 		0.0311
(1.00) 		0.0385
(1.00) 		1e-05
(0.009) 		1e-05
(0.009) 		0.00013
(0.0871) 		0.0876
(1.00) 		1e-05
(0.009) 		1e-05
(0.009)
amp 13q12 2 385 (64%) 215 1e-05
(0.009) 		1e-05
(0.009) 		1e-05
(0.009) 		1e-05
(0.009) 		0.0192
(1.00) 		0.0404
(1.00) 		1e-05
(0.009) 		1e-05
(0.009) 		0.00055
(0.344) 		0.71
(1.00) 		1e-05
(0.009) 		1e-05
(0.009)
amp 13q22 1 387 (64%) 213 1e-05
(0.009) 		1e-05
(0.009) 		1e-05
(0.009) 		1e-05
(0.009) 		0.0847
(1.00) 		0.0962
(1.00) 		1e-05
(0.009) 		1e-05
(0.009) 		0.00108
(0.644) 		0.343
(1.00) 		1e-05
(0.009) 		1e-05
(0.009)
amp 20p11 21 354 (59%) 246 0.00015
(0.0999) 		2e-05
(0.0145) 		1e-05
(0.009) 		3e-05
(0.0213) 		0.00559
(1.00) 		0.138
(1.00) 		1e-05
(0.009) 		1e-05
(0.009) 		0.02
(1.00) 		0.00782
(1.00) 		1e-05
(0.009) 		1e-05
(0.009)
del 14q11 2 204 (34%) 396 4e-05
(0.028) 		1e-05
(0.009) 		1e-05
(0.009) 		4e-05
(0.028) 		0.00741
(1.00) 		0.142
(1.00) 		1e-05
(0.009) 		1e-05
(0.009) 		0.0587
(1.00) 		0.123
(1.00) 		1e-05
(0.009) 		1e-05
(0.009)
del 17p12 360 (60%) 240 1e-05
(0.009) 		1e-05
(0.009) 		1e-05
(0.009) 		1e-05
(0.009) 		0.0183
(1.00) 		0.00646
(1.00) 		1e-05
(0.009) 		1e-05
(0.009) 		0.0127
(1.00) 		0.0127
(1.00) 		1e-05
(0.009) 		1e-05
(0.009)
del 18p11 31 358 (60%) 242 1e-05
(0.009) 		1e-05
(0.009) 		1e-05
(0.009) 		1e-05
(0.009) 		0.0579
(1.00) 		0.116
(1.00) 		1e-05
(0.009) 		1e-05
(0.009) 		0.00313
(1.00) 		0.00686
(1.00) 		1e-05
(0.009) 		1e-05
(0.009)
del 18q12 2 402 (67%) 198 1e-05
(0.009) 		1e-05
(0.009) 		1e-05
(0.009) 		1e-05
(0.009) 		0.0353
(1.00) 		0.0654
(1.00) 		1e-05
(0.009) 		1e-05
(0.009) 		0.0011
(0.654) 		0.00737
(1.00) 		1e-05
(0.009) 		1e-05
(0.009)
amp 11p15 5 135 (22%) 465 0.00144
(0.841) 		0.00192
(1.00) 		2e-05
(0.0145) 		0.00037
(0.235) 		0.0302
(1.00) 		0.0831
(1.00) 		1e-05
(0.009) 		3e-05
(0.0213) 		0.428
(1.00) 		1e-05
(0.009) 		0.00022
(0.144) 		1e-05
(0.009)
del 8p23 2 282 (47%) 318 0.00025
(0.163) 		0.00099
(0.595) 		1e-05
(0.009) 		1e-05
(0.009) 		0.15
(1.00) 		0.0305
(1.00) 		1e-05
(0.009) 		1e-05
(0.009) 		0.163
(1.00) 		0.0302
(1.00) 		4e-05
(0.028) 		1e-05
(0.009)
del 8p22 297 (50%) 303 0.00121
(0.715) 		0.00037
(0.235) 		1e-05
(0.009) 		1e-05
(0.009) 		0.108
(1.00) 		0.00873
(1.00) 		2e-05
(0.0145) 		1e-05
(0.009) 		0.272
(1.00) 		0.0306
(1.00) 		3e-05
(0.0213) 		1e-05
(0.009)
del 14q31 1 212 (35%) 388 0.00036
(0.229) 		0.00043
(0.27) 		1e-05
(0.009) 		3e-05
(0.0213) 		0.00102
(0.609) 		0.131
(1.00) 		1e-05
(0.009) 		1e-05
(0.009) 		0.207
(1.00) 		0.0847
(1.00) 		1e-05
(0.009) 		1e-05
(0.009)
del 15q22 33 231 (38%) 369 0.00015
(0.0999) 		0.00126
(0.741) 		1e-05
(0.009) 		8e-05
(0.0546) 		0.555
(1.00) 		0.328
(1.00) 		1e-05
(0.009) 		1e-05
(0.009) 		0.788
(1.00) 		0.898
(1.00) 		1e-05
(0.009) 		1e-05
(0.009)
del 14q31 1 211 (35%) 389 0.00044
(0.276) 		0.00041
(0.26) 		1e-05
(0.009) 		6e-05
(0.0411) 		0.00112
(0.665) 		0.142
(1.00) 		1e-05
(0.009) 		1e-05
(0.009) 		0.271
(1.00) 		0.102
(1.00) 		1e-05
(0.009) 		1e-05
(0.009)
del 15q11 2 245 (41%) 355 0.0006
(0.373) 		0.00375
(1.00) 		1e-05
(0.009) 		0.00032
(0.205) 		0.132
(1.00) 		0.367
(1.00) 		2e-05
(0.0145) 		1e-05
(0.009) 		0.434
(1.00) 		0.43
(1.00) 		1e-05
(0.009) 		2e-05
(0.0145)
del 15q15 2 243 (40%) 357 4e-05
(0.028) 		0.00178
(1.00) 		1e-05
(0.009) 		0.00049
(0.307) 		0.0943
(1.00) 		0.37
(1.00) 		5e-05
(0.0346) 		1e-05
(0.009) 		0.626
(1.00) 		0.416
(1.00) 		5e-05
(0.0346) 		3e-05
(0.0213)
del 15q21 1 240 (40%) 360 0.00032
(0.205) 		0.0238
(1.00) 		1e-05
(0.009) 		0.00067
(0.41) 		0.095
(1.00) 		0.348
(1.00) 		0.00014
(0.0937) 		1e-05
(0.009) 		0.673
(1.00) 		0.466
(1.00) 		7e-05
(0.0478) 		3e-05
(0.0213)
amp 20p11 23 315 (52%) 285 0.00417
(1.00) 		0.00404
(1.00) 		1e-05
(0.009) 		0.00879
(1.00) 		0.00306
(1.00) 		0.0521
(1.00) 		0.00011
(0.0745) 		1e-05
(0.009) 		0.183
(1.00) 		0.0241
(1.00) 		3e-05
(0.0213) 		0.00011
(0.0745)
del 1p36 11 238 (40%) 362 5e-05
(0.0346) 		0.00057
(0.355) 		1e-05
(0.009) 		2e-05
(0.0145) 		0.112
(1.00) 		0.106
(1.00) 		2e-05
(0.0145) 		1e-05
(0.009) 		0.402
(1.00) 		0.0104
(1.00) 		0.00354
(1.00) 		0.00082
(0.497)
del 4q22 1 216 (36%) 384 0.017
(1.00) 		0.0296
(1.00) 		1e-05
(0.009) 		5e-05
(0.0346) 		0.587
(1.00) 		0.671
(1.00) 		0.0003
(0.193) 		2e-05
(0.0145) 		0.0183
(1.00) 		0.13
(1.00) 		0.00122
(0.72) 		0.00015
(0.0999)
del 10q23 31 156 (26%) 444 0.114
(1.00) 		0.243
(1.00) 		1e-05
(0.009) 		0.041
(1.00) 		0.0862
(1.00) 		0.304
(1.00) 		0.00034
(0.217) 		0.00014
(0.0937) 		0.529
(1.00) 		0.136
(1.00) 		5e-05
(0.0346) 		0.00021
(0.138)
del 10q25 2 152 (25%) 448 0.223
(1.00) 		0.296
(1.00) 		1e-05
(0.009) 		0.0169
(1.00) 		0.00551
(1.00) 		0.152
(1.00) 		3e-05
(0.0213) 		1e-05
(0.009) 		0.991
(1.00) 		0.206
(1.00) 		0.00015
(0.0999) 		9e-05
(0.0611)
amp 6p21 1 151 (25%) 449 0.0302
(1.00) 		0.00017
(0.112) 		1e-05
(0.009) 		0.209
(1.00) 		0.59
(1.00) 		0.733
(1.00) 		0.0597
(1.00) 		0.00036
(0.229) 		0.182
(1.00) 		0.705
(1.00) 		0.00254
(1.00) 		2e-05
(0.0145)
amp 16p11 2 166 (28%) 434 0.0177
(1.00) 		0.00215
(1.00) 		1e-05
(0.009) 		0.00074
(0.452) 		0.0268
(1.00) 		0.0541
(1.00) 		0.00011
(0.0745) 		5e-05
(0.0346) 		0.446
(1.00) 		0.72
(1.00) 		0.00061
(0.378) 		2e-05
(0.0145)
amp 17q24 1 138 (23%) 462 0.00951
(1.00) 		0.00767
(1.00) 		1e-05
(0.009) 		0.0003
(0.193) 		0.0886
(1.00) 		0.0247
(1.00) 		0.00041
(0.26) 		1e-05
(0.009) 		0.00021
(0.138) 		0.0318
(1.00) 		0.412
(1.00) 		0.0041
(1.00)
del 4p16 1 195 (32%) 405 0.0528
(1.00) 		0.0362
(1.00) 		1e-05
(0.009) 		0.00267
(1.00) 		0.43
(1.00) 		0.299
(1.00) 		0.00956
(1.00) 		0.00014
(0.0937) 		0.359
(1.00) 		0.33
(1.00) 		0.00016
(0.106) 		0.00025
(0.163)
del 4q35 1 225 (38%) 375 0.0198
(1.00) 		0.0577
(1.00) 		1e-05
(0.009) 		2e-05
(0.0145) 		0.282
(1.00) 		0.579
(1.00) 		0.00028
(0.181) 		0.00118
(0.699) 		0.195
(1.00) 		0.324
(1.00) 		8e-05
(0.0546) 		0.00042
(0.265)
del 5q11 2 151 (25%) 449 0.00064
(0.394) 		0.00025
(0.163) 		1e-05
(0.009) 		0.00316
(1.00) 		0.0313
(1.00) 		0.173
(1.00) 		0.00205
(1.00) 		0.00063
(0.389) 		0.771
(1.00) 		0.943
(1.00) 		2e-05
(0.0145) 		1e-05
(0.009)
del 20p12 1 184 (31%) 416 0.0197
(1.00) 		0.00066
(0.405) 		1e-05
(0.009) 		1e-05
(0.009) 		0.79
(1.00) 		0.697
(1.00) 		0.00077
(0.469) 		8e-05
(0.0546) 		0.0769
(1.00) 		0.00732
(1.00) 		0.112
(1.00) 		0.00025
(0.163)
del 20p12 1 184 (31%) 416 0.0201
(1.00) 		0.00087
(0.525) 		1e-05
(0.009) 		2e-05
(0.0145) 		0.788
(1.00) 		0.698
(1.00) 		0.00065
(0.4) 		4e-05
(0.028) 		0.0741
(1.00) 		0.00747
(1.00) 		0.109
(1.00) 		0.00017
(0.112)
del 22q13 32 222 (37%) 378 0.00253
(1.00) 		0.00012
(0.0805) 		1e-05
(0.009) 		0.0175
(1.00) 		0.513
(1.00) 		0.593
(1.00) 		0.00076
(0.464) 		4e-05
(0.028) 		0.938
(1.00) 		0.228
(1.00) 		4e-05
(0.028) 		0.00228
(1.00)
amp 2q33 1 134 (22%) 466 0.067
(1.00) 		0.00042
(0.265) 		1e-05
(0.009) 		0.00128
(0.751) 		0.238
(1.00) 		0.657
(1.00) 		0.00011
(0.0745) 		5e-05
(0.0346) 		0.0559
(1.00) 		0.0435
(1.00) 		0.182
(1.00) 		0.00065
(0.4)
amp 8q24 21 357 (60%) 243 0.24
(1.00) 		0.0513
(1.00) 		1e-05
(0.009) 		0.00056
(0.349) 		0.0265
(1.00) 		0.0401
(1.00) 		1e-05
(0.009) 		0.00203
(1.00) 		0.142
(1.00) 		0.0331
(1.00) 		0.00122
(0.72) 		0.00011
(0.0745)
amp 17q12 152 (25%) 448 0.0249
(1.00) 		0.00724
(1.00) 		1e-05
(0.009) 		0.00058
(0.361) 		0.161
(1.00) 		0.0886
(1.00) 		0.00034
(0.217) 		1e-05
(0.009) 		0.00576
(1.00) 		0.0225
(1.00) 		0.263
(1.00) 		0.0401
(1.00)
del 21q11 2 208 (35%) 392 0.0197
(1.00) 		0.00173
(1) 		1e-05
(0.009) 		0.028
(1.00) 		0.455
(1.00) 		0.708
(1.00) 		2e-05
(0.0145) 		0.00687
(1.00) 		0.0389
(1.00) 		0.316
(1.00) 		0.00011
(0.0745) 		0.00133
(0.779)
amp 5p12 112 (19%) 488 0.131
(1.00) 		0.0202
(1.00) 		2e-05
(0.0145) 		0.808
(1.00) 		0.00151
(0.879) 		0.136
(1.00) 		0.00096
(0.578) 		0.00977
(1.00) 		0.913
(1.00) 		0.343
(1.00) 		3e-05
(0.0213) 		0.00529
(1.00)
amp 8q12 1 322 (54%) 278 0.143
(1.00) 		0.0425
(1.00) 		1e-05
(0.009) 		0.0236
(1.00) 		0.0276
(1.00) 		0.0232
(1.00) 		6e-05
(0.0411) 		0.00062
(0.384) 		0.111
(1.00) 		0.0155
(1.00) 		0.00312
(1.00) 		0.00046
(0.288)
amp 19p13 2 105 (18%) 495 0.108
(1.00) 		0.0079
(1.00) 		1e-05
(0.009) 		0.0177
(1.00) 		0.462
(1.00) 		0.677
(1.00) 		0.0175
(1.00) 		0.00017
(0.112) 		0.113
(1.00) 		0.671
(1.00) 		0.0856
(1.00) 		0.0187
(1.00)
del 1p33 171 (28%) 429 0.0203
(1.00) 		0.0828
(1.00) 		1e-05
(0.009) 		0.00062
(0.384) 		0.831
(1.00) 		0.557
(1.00) 		0.00017
(0.112) 		0.00641
(1.00) 		0.454
(1.00) 		0.11
(1.00) 		0.00191
(1.00) 		0.00082
(0.497)
del 5q22 2 182 (30%) 418 0.00081
(0.492) 		0.00081
(0.492) 		1e-05
(0.009) 		0.117
(1.00) 		0.272
(1.00) 		0.377
(1.00) 		0.0332
(1.00) 		0.00162
(0.94) 		0.467
(1.00) 		0.35
(1.00) 		0.00145
(0.845) 		4e-05
(0.028)
del 8p11 21 130 (22%) 470 0.0358
(1.00) 		0.00236
(1.00) 		1e-05
(0.009) 		0.0327
(1.00) 		0.0821
(1.00) 		0.0859
(1.00) 		0.00025
(0.163) 		0.00101
(0.605) 		0.201
(1.00) 		0.00482
(1.00) 		0.465
(1.00) 		0.0781
(1.00)
del 10q21 1 128 (21%) 472 0.112
(1.00) 		0.177
(1.00) 		1e-05
(0.009) 		0.0154
(1.00) 		0.0831
(1.00) 		0.0855
(1.00) 		2e-05
(0.0145) 		0.00329
(1.00) 		0.69
(1.00) 		0.223
(1.00) 		0.00397
(1.00) 		0.0309
(1.00)
amp 1q31 1 142 (24%) 458 0.583
(1.00) 		0.552
(1.00) 		3e-05
(0.0213) 		0.487
(1.00) 		0.361
(1.00) 		0.124
(1.00) 		0.913
(1.00) 		0.154
(1.00) 		0.347
(1.00) 		0.254
(1.00) 		0.0246
(1.00) 		0.115
(1.00)
amp 8p11 23 206 (34%) 394 0.396
(1.00) 		0.21
(1.00) 		1e-05
(0.009) 		0.344
(1.00) 		0.768
(1.00) 		0.987
(1.00) 		0.00372
(1.00) 		0.00637
(1.00) 		0.0127
(1.00) 		0.0821
(1.00) 		0.0826
(1.00) 		0.0586
(1.00)
amp 8p11 21 250 (42%) 350 0.171
(1.00) 		0.11
(1.00) 		1e-05
(0.009) 		0.202
(1.00) 		0.723
(1.00) 		0.358
(1.00) 		0.0154
(1.00) 		0.0336
(1.00) 		0.0805
(1.00) 		0.249
(1.00) 		0.383
(1.00) 		0.117
(1.00)
amp 19q12 132 (22%) 468 0.029
(1.00) 		0.00158
(0.918) 		1e-05
(0.009) 		0.285
(1.00) 		0.0752
(1.00) 		0.431
(1.00) 		0.068
(1.00) 		0.00133
(0.779) 		0.188
(1.00) 		0.877
(1.00) 		0.245
(1.00) 		0.0247
(1.00)
amp xq28 121 (20%) 479 0.309
(1.00) 		0.548
(1.00) 		2e-05
(0.0145) 		0.258
(1.00) 		0.00482
(1.00) 		0.024
(1.00) 		0.705
(1.00) 		0.774
(1.00) 		0.911
(1.00) 		0.871
(1.00) 		0.0877
(1.00) 		0.144
(1.00)
del 1p13 2 171 (28%) 429 0.268
(1.00) 		0.403
(1.00) 		1e-05
(0.009) 		0.0154
(1.00) 		0.763
(1.00) 		0.83
(1.00) 		0.00092
(0.555) 		0.00101
(0.605) 		0.511
(1.00) 		0.118
(1.00) 		0.0109
(1.00) 		0.013
(1.00)
del 8q11 1 46 (8%) 554 0.582
(1.00) 		0.181
(1.00) 		1e-05
(0.009) 		0.38
(1.00) 		0.285
(1.00) 		0.304
(1.00) 		0.27
(1.00) 		0.0621
(1.00) 		0.166
(1.00) 		0.0927
(1.00) 		0.59
(1.00) 		0.642
(1.00)
del 9p24 2 81 (14%) 519 0.218
(1.00) 		0.299
(1.00) 		0.00021
(0.138) 		0.129
(1.00) 		0.6
(1.00) 		1
(1.00) 		0.00314
(1.00) 		0.00337
(1.00) 		0.216
(1.00) 		0.0232
(1.00) 		0.0381
(1.00) 		0.0921
(1.00)
del 12p13 1 90 (15%) 510 0.00509
(1.00) 		0.00167
(0.967) 		1e-05
(0.009) 		0.0333
(1.00) 		0.91
(1.00) 		0.472
(1.00) 		0.0935
(1.00) 		0.0137
(1.00) 		0.71
(1.00) 		0.755
(1.00) 		0.00471
(1.00) 		0.00113
(0.67)
del 12q21 33 88 (15%) 512 0.0348
(1.00) 		0.0351
(1.00) 		1e-05
(0.009) 		0.0252
(1.00) 		0.542
(1.00) 		0.891
(1.00) 		0.0473
(1.00) 		0.00894
(1.00) 		0.834
(1.00) 		0.77
(1.00) 		0.018
(1.00) 		0.0406
(1.00)
del 19p13 3 97 (16%) 503 0.118
(1.00) 		0.465
(1.00) 		1e-05
(0.009) 		0.379
(1.00) 		0.882
(1.00) 		0.101
(1.00) 		0.191
(1.00) 		0.118
(1.00) 		0.645
(1.00) 		0.00531
(1.00) 		0.0154
(1.00) 		0.0623
(1.00)
amp 5q22 3 63 (10%) 537 0.602
(1.00) 		0.58
(1.00) 		0.00535
(1.00) 		0.513
(1.00) 		0.465
(1.00) 		0.308
(1.00) 		0.666
(1.00) 		0.144
(1.00) 		0.617
(1.00) 		0.126
(1.00) 		0.236
(1.00) 		0.0761
(1.00)
amp 10q22 3 36 (6%) 564 1
(1.00) 		0.86
(1.00) 		0.414
(1.00) 		0.597
(1.00) 		0.296
(1.00) 		0.688
(1.00) 		0.653
(1.00) 		0.306
(1.00) 		0.435
(1.00) 		0.974
(1.00) 		0.00606
(1.00) 		0.355
(1.00)
amp 12p13 32 147 (24%) 453 0.65
(1.00) 		0.593
(1.00) 		0.243
(1.00) 		0.0196
(1.00) 		0.478
(1.00) 		0.303
(1.00) 		0.691
(1.00) 		0.698
(1.00) 		0.716
(1.00) 		1
(1.00) 		0.416
(1.00) 		0.727
(1.00)
amp 15q26 1 42 (7%) 558 0.709
(1.00) 		0.662
(1.00) 		0.394
(1.00) 		0.609
(1.00) 		0.236
(1.00) 		0.47
(1.00) 		0.518
(1.00) 		0.152
(1.00) 		0.716
(1.00) 		0.826
(1.00) 		0.772
(1.00) 		0.979
(1.00)
del 2p12 21 (4%) 579 1
(1.00) 		0.963
(1.00) 		0.001
(0.6) 		0.00381
(1.00) 		0.365
(1.00) 		1
(1.00) 		0.0499
(1.00) 		0.0597
(1.00) 		0.00628
(1.00) 		0.0926
(1.00) 		1
(1.00) 		0.616
(1.00)
del 2q22 1 34 (6%) 566 0.925
(1.00) 		0.608
(1.00) 		0.0808
(1.00) 		0.725
(1.00) 		0.342
(1.00) 		0.351
(1.00) 		0.491
(1.00) 		0.135
(1.00) 		0.579
(1.00) 		0.113
(1.00) 		0.709
(1.00) 		1
(1.00)
del 2q37 2 31 (5%) 569 0.984
(1.00) 		0.55
(1.00) 		0.471
(1.00) 		0.832
(1.00) 		0.937
(1.00) 		0.0613
(1.00) 		0.747
(1.00) 		0.21
(1.00) 		0.476
(1.00) 		0.0156
(1.00) 		0.208
(1.00) 		0.891
(1.00)
del 3p26 3 91 (15%) 509 0.358
(1.00) 		0.494
(1.00) 		0.103
(1.00) 		0.921
(1.00) 		0.652
(1.00) 		0.979
(1.00) 		0.304
(1.00) 		0.162
(1.00) 		0.476
(1.00) 		0.576
(1.00) 		0.0627
(1.00) 		0.513
(1.00)
del 3p14 2 112 (19%) 488 0.621
(1.00) 		0.467
(1.00) 		0.755
(1.00) 		0.798
(1.00) 		0.47
(1.00) 		0.245
(1.00) 		0.373
(1.00) 		0.491
(1.00) 		0.383
(1.00) 		0.304
(1.00) 		0.081
(1.00) 		0.322
(1.00)
del 3q26 31 62 (10%) 538 0.605
(1.00) 		0.876
(1.00) 		0.241
(1.00) 		0.545
(1.00) 		0.251
(1.00) 		0.3
(1.00) 		0.229
(1.00) 		0.361
(1.00) 		0.453
(1.00) 		0.0744
(1.00) 		0.251
(1.00) 		0.0179
(1.00)
del 6p25 3 79 (13%) 521 0.906
(1.00) 		0.348
(1.00) 		0.0414
(1.00) 		0.241
(1.00) 		0.0357
(1.00) 		0.635
(1.00) 		0.615
(1.00) 		0.745
(1.00) 		0.584
(1.00) 		0.723
(1.00) 		0.5
(1.00) 		0.847
(1.00)
del 6q26 90 (15%) 510 0.799
(1.00) 		0.854
(1.00) 		0.0773
(1.00) 		0.904
(1.00) 		0.0438
(1.00) 		0.124
(1.00) 		0.101
(1.00) 		0.0971
(1.00) 		0.376
(1.00) 		0.365
(1.00) 		0.528
(1.00) 		0.575
(1.00)
del 7q31 1 16 (3%) 584 0.291
(1.00) 		0.691
(1.00) 		0.958
(1.00) 		1
(1.00) 		0.684
(1.00) 		0.216
(1.00) 		0.742
(1.00) 		0.659
(1.00) 		0.108
(1.00) 		0.948
(1.00) 		0.142
(1.00) 		0.263
(1.00)
del 11q22 3 111 (18%) 489 0.385
(1.00) 		0.234
(1.00) 		0.0245
(1.00) 		0.131
(1.00) 		0.25
(1.00) 		0.981
(1.00) 		0.793
(1.00) 		0.623
(1.00) 		0.839
(1.00) 		0.428
(1.00) 		0.238
(1.00) 		0.249
(1.00)
del 16p13 3 68 (11%) 532 0.0933
(1.00) 		0.0775
(1.00) 		0.0955
(1.00) 		0.329
(1.00) 		0.542
(1.00) 		0.971
(1.00) 		0.389
(1.00) 		0.535
(1.00) 		0.671
(1.00) 		0.132
(1.00) 		0.565
(1.00) 		0.862
(1.00)
del 16q23 1 82 (14%) 518 0.0445
(1.00) 		0.00362
(1.00) 		0.291
(1.00) 		0.376
(1.00) 		0.253
(1.00) 		0.801
(1.00) 		0.56
(1.00) 		0.123
(1.00) 		0.606
(1.00) 		0.269
(1.00) 		0.73
(1.00) 		0.524
(1.00)
del 17q24 3 90 (15%) 510 0.976
(1.00) 		0.728
(1.00) 		0.0189
(1.00) 		0.965
(1.00) 		0.875
(1.00) 		0.557
(1.00) 		0.336
(1.00) 		0.0324
(1.00) 		0.843
(1.00) 		0.446
(1.00) 		0.0249
(1.00) 		0.262
(1.00)
'amp_1q31.1' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.021

Table S1.  Gene #1: 'amp_1q31.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 235 217 113 35
AMP PEAK 1(1Q31.1) MUTATED 33 66 30 13
AMP PEAK 1(1Q31.1) WILD-TYPE 202 151 83 22

Figure S1.  Get High-res Image Gene #1: 'amp_1q31.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_2q33.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S2.  Gene #2: 'amp_2q33.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 235 217 113 35
AMP PEAK 2(2Q33.1) MUTATED 29 66 24 15
AMP PEAK 2(2Q33.1) WILD-TYPE 206 151 89 20

Figure S2.  Get High-res Image Gene #2: 'amp_2q33.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_2q33.1' versus 'MRNASEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.074

Table S3.  Gene #2: 'amp_2q33.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 130 139 188
AMP PEAK 2(2Q33.1) MUTATED 33 14 47 36
AMP PEAK 2(2Q33.1) WILD-TYPE 94 116 92 152

Figure S3.  Get High-res Image Gene #2: 'amp_2q33.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_2q33.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.035

Table S4.  Gene #2: 'amp_2q33.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 64 107 45 65 66 96 141
AMP PEAK 2(2Q33.1) MUTATED 12 22 4 22 25 9 36
AMP PEAK 2(2Q33.1) WILD-TYPE 52 85 41 43 41 87 105

Figure S4.  Get High-res Image Gene #2: 'amp_2q33.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_5p12' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S5.  Gene #3: 'amp_5p12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 235 217 113 35
AMP PEAK 3(5P12) MUTATED 20 55 27 10
AMP PEAK 3(5P12) WILD-TYPE 215 162 86 25

Figure S5.  Get High-res Image Gene #3: 'amp_5p12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_5p12' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.021

Table S6.  Gene #3: 'amp_5p12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
AMP PEAK 3(5P12) MUTATED 26 6 19
AMP PEAK 3(5P12) WILD-TYPE 74 103 66

Figure S6.  Get High-res Image Gene #3: 'amp_5p12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_6p21.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.11

Table S7.  Gene #5: 'amp_6p21.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
AMP PEAK 5(6P21.1) MUTATED 4 12 13 22
AMP PEAK 5(6P21.1) WILD-TYPE 45 29 63 27

Figure S7.  Get High-res Image Gene #5: 'amp_6p21.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_6p21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S8.  Gene #5: 'amp_6p21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 235 217 113 35
AMP PEAK 5(6P21.1) MUTATED 21 88 33 9
AMP PEAK 5(6P21.1) WILD-TYPE 214 129 80 26

Figure S8.  Get High-res Image Gene #5: 'amp_6p21.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_6p21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00036 (Fisher's exact test), Q value = 0.23

Table S9.  Gene #5: 'amp_6p21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 64 107 45 65 66 96 141
AMP PEAK 5(6P21.1) MUTATED 14 28 5 19 26 12 45
AMP PEAK 5(6P21.1) WILD-TYPE 50 79 40 46 40 84 96

Figure S9.  Get High-res Image Gene #5: 'amp_6p21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_6p21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S10.  Gene #5: 'amp_6p21.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 82 52 67 33 60
AMP PEAK 5(6P21.1) MUTATED 25 17 25 14 3
AMP PEAK 5(6P21.1) WILD-TYPE 57 35 42 19 57

Figure S10.  Get High-res Image Gene #5: 'amp_6p21.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8p11.23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S11.  Gene #6: 'amp_8p11.23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 235 217 113 35
AMP PEAK 6(8P11.23) MUTATED 42 63 86 15
AMP PEAK 6(8P11.23) WILD-TYPE 193 154 27 20

Figure S11.  Get High-res Image Gene #6: 'amp_8p11.23' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8p11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S12.  Gene #7: 'amp_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 235 217 113 35
AMP PEAK 7(8P11.21) MUTATED 50 83 101 16
AMP PEAK 7(8P11.21) WILD-TYPE 185 134 12 19

Figure S12.  Get High-res Image Gene #7: 'amp_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8q12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S13.  Gene #8: 'amp_8q12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 235 217 113 35
AMP PEAK 8(8Q12.1) MUTATED 67 119 110 26
AMP PEAK 8(8Q12.1) WILD-TYPE 168 98 3 9

Figure S13.  Get High-res Image Gene #8: 'amp_8q12.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8q12.1' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.041

Table S14.  Gene #8: 'amp_8q12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 130 139 188
AMP PEAK 8(8Q12.1) MUTATED 77 49 92 96
AMP PEAK 8(8Q12.1) WILD-TYPE 50 81 47 92

Figure S14.  Get High-res Image Gene #8: 'amp_8q12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8q24.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S15.  Gene #9: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 235 217 113 35
AMP PEAK 9(8Q24.21) MUTATED 78 140 112 27
AMP PEAK 9(8Q24.21) WILD-TYPE 157 77 1 8

Figure S15.  Get High-res Image Gene #9: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S16.  Gene #9: 'amp_8q24.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 130 139 188
AMP PEAK 9(8Q24.21) MUTATED 83 56 102 109
AMP PEAK 9(8Q24.21) WILD-TYPE 44 74 37 79

Figure S16.  Get High-res Image Gene #9: 'amp_8q24.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.074

Table S17.  Gene #9: 'amp_8q24.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 82 52 67 33 60
AMP PEAK 9(8Q24.21) MUTATED 51 41 46 24 23
AMP PEAK 9(8Q24.21) WILD-TYPE 31 11 21 9 37

Figure S17.  Get High-res Image Gene #9: 'amp_8q24.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_11p15.5' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S18.  Gene #11: 'amp_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 235 217 113 35
AMP PEAK 11(11P15.5) MUTATED 29 66 27 13
AMP PEAK 11(11P15.5) WILD-TYPE 206 151 86 22

Figure S18.  Get High-res Image Gene #11: 'amp_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

'amp_11p15.5' versus 'METHLYATION_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.23

Table S19.  Gene #11: 'amp_11p15.5' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 155 121
AMP PEAK 11(11P15.5) MUTATED 19 46 13
AMP PEAK 11(11P15.5) WILD-TYPE 79 109 108

Figure S19.  Get High-res Image Gene #11: 'amp_11p15.5' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_11p15.5' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S20.  Gene #11: 'amp_11p15.5' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 130 139 188
AMP PEAK 11(11P15.5) MUTATED 24 12 48 47
AMP PEAK 11(11P15.5) WILD-TYPE 103 118 91 141

Figure S20.  Get High-res Image Gene #11: 'amp_11p15.5' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_11p15.5' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.021

Table S21.  Gene #11: 'amp_11p15.5' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 64 107 45 65 66 96 141
AMP PEAK 11(11P15.5) MUTATED 11 19 2 22 18 12 47
AMP PEAK 11(11P15.5) WILD-TYPE 53 88 43 43 48 84 94

Figure S21.  Get High-res Image Gene #11: 'amp_11p15.5' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_11p15.5' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S22.  Gene #11: 'amp_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 139 171
AMP PEAK 11(11P15.5) MUTATED 35 67 22
AMP PEAK 11(11P15.5) WILD-TYPE 193 72 149

Figure S22.  Get High-res Image Gene #11: 'amp_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_11p15.5' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.14

Table S23.  Gene #11: 'amp_11p15.5' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
AMP PEAK 11(11P15.5) MUTATED 30 10 22
AMP PEAK 11(11P15.5) WILD-TYPE 70 99 63

Figure S23.  Get High-res Image Gene #11: 'amp_11p15.5' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_11p15.5' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S24.  Gene #11: 'amp_11p15.5' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 82 52 67 33 60
AMP PEAK 11(11P15.5) MUTATED 15 7 14 21 5
AMP PEAK 11(11P15.5) WILD-TYPE 67 45 53 12 55

Figure S24.  Get High-res Image Gene #11: 'amp_11p15.5' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_13q12.13' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S25.  Gene #13: 'amp_13q12.13' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
AMP PEAK 13(13Q12.13) MUTATED 19 48 57 16
AMP PEAK 13(13Q12.13) WILD-TYPE 24 14 12 25

Figure S25.  Get High-res Image Gene #13: 'amp_13q12.13' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_13q12.13' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S26.  Gene #13: 'amp_13q12.13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
AMP PEAK 13(13Q12.13) MUTATED 15 30 51 44
AMP PEAK 13(13Q12.13) WILD-TYPE 34 11 25 5

Figure S26.  Get High-res Image Gene #13: 'amp_13q12.13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_13q12.13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S27.  Gene #13: 'amp_13q12.13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 235 217 113 35
AMP PEAK 13(13Q12.13) MUTATED 83 208 78 21
AMP PEAK 13(13Q12.13) WILD-TYPE 152 9 35 14

Figure S27.  Get High-res Image Gene #13: 'amp_13q12.13' versus Molecular Subtype #3: 'CN_CNMF'

'amp_13q12.13' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S28.  Gene #13: 'amp_13q12.13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 155 121
AMP PEAK 13(13Q12.13) MUTATED 57 132 58
AMP PEAK 13(13Q12.13) WILD-TYPE 41 23 63

Figure S28.  Get High-res Image Gene #13: 'amp_13q12.13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_13q12.13' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S29.  Gene #13: 'amp_13q12.13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 130 139 188
AMP PEAK 13(13Q12.13) MUTATED 80 60 111 130
AMP PEAK 13(13Q12.13) WILD-TYPE 47 70 28 58

Figure S29.  Get High-res Image Gene #13: 'amp_13q12.13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_13q12.13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S30.  Gene #13: 'amp_13q12.13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 64 107 45 65 66 96 141
AMP PEAK 13(13Q12.13) MUTATED 28 77 14 52 59 37 114
AMP PEAK 13(13Q12.13) WILD-TYPE 36 30 31 13 7 59 27

Figure S30.  Get High-res Image Gene #13: 'amp_13q12.13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_13q12.13' versus 'MIRSEQ_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.16

Table S31.  Gene #13: 'amp_13q12.13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 211 95 232
AMP PEAK 13(13Q12.13) MUTATED 159 52 141
AMP PEAK 13(13Q12.13) WILD-TYPE 52 43 91

Figure S31.  Get High-res Image Gene #13: 'amp_13q12.13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_13q12.13' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S32.  Gene #13: 'amp_13q12.13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
AMP PEAK 13(13Q12.13) MUTATED 87 49 65
AMP PEAK 13(13Q12.13) WILD-TYPE 13 60 20

Figure S32.  Get High-res Image Gene #13: 'amp_13q12.13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_13q12.13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S33.  Gene #13: 'amp_13q12.13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 82 52 67 33 60
AMP PEAK 13(13Q12.13) MUTATED 58 46 57 24 16
AMP PEAK 13(13Q12.13) WILD-TYPE 24 6 10 9 44

Figure S33.  Get High-res Image Gene #13: 'amp_13q12.13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_13q12.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S34.  Gene #14: 'amp_13q12.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
AMP PEAK 14(13Q12.2) MUTATED 19 47 55 17
AMP PEAK 14(13Q12.2) WILD-TYPE 24 15 14 24

Figure S34.  Get High-res Image Gene #14: 'amp_13q12.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_13q12.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S35.  Gene #14: 'amp_13q12.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
AMP PEAK 14(13Q12.2) MUTATED 16 29 50 43
AMP PEAK 14(13Q12.2) WILD-TYPE 33 12 26 6

Figure S35.  Get High-res Image Gene #14: 'amp_13q12.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_13q12.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S36.  Gene #14: 'amp_13q12.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 235 217 113 35
AMP PEAK 14(13Q12.2) MUTATED 81 207 75 22
AMP PEAK 14(13Q12.2) WILD-TYPE 154 10 38 13

Figure S36.  Get High-res Image Gene #14: 'amp_13q12.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_13q12.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S37.  Gene #14: 'amp_13q12.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 155 121
AMP PEAK 14(13Q12.2) MUTATED 57 132 56
AMP PEAK 14(13Q12.2) WILD-TYPE 41 23 65

Figure S37.  Get High-res Image Gene #14: 'amp_13q12.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_13q12.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S38.  Gene #14: 'amp_13q12.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 130 139 188
AMP PEAK 14(13Q12.2) MUTATED 79 59 110 128
AMP PEAK 14(13Q12.2) WILD-TYPE 48 71 29 60

Figure S38.  Get High-res Image Gene #14: 'amp_13q12.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_13q12.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S39.  Gene #14: 'amp_13q12.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 64 107 45 65 66 96 141
AMP PEAK 14(13Q12.2) MUTATED 27 76 14 51 59 37 112
AMP PEAK 14(13Q12.2) WILD-TYPE 37 31 31 14 7 59 29

Figure S39.  Get High-res Image Gene #14: 'amp_13q12.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_13q12.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S40.  Gene #14: 'amp_13q12.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
AMP PEAK 14(13Q12.2) MUTATED 85 48 65
AMP PEAK 14(13Q12.2) WILD-TYPE 15 61 20

Figure S40.  Get High-res Image Gene #14: 'amp_13q12.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_13q12.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S41.  Gene #14: 'amp_13q12.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 82 52 67 33 60
AMP PEAK 14(13Q12.2) MUTATED 58 45 57 23 15
AMP PEAK 14(13Q12.2) WILD-TYPE 24 7 10 10 45

Figure S41.  Get High-res Image Gene #14: 'amp_13q12.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_13q22.1' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S42.  Gene #15: 'amp_13q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
AMP PEAK 15(13Q22.1) MUTATED 18 48 54 17
AMP PEAK 15(13Q22.1) WILD-TYPE 25 14 15 24

Figure S42.  Get High-res Image Gene #15: 'amp_13q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_13q22.1' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S43.  Gene #15: 'amp_13q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
AMP PEAK 15(13Q22.1) MUTATED 14 29 52 42
AMP PEAK 15(13Q22.1) WILD-TYPE 35 12 24 7

Figure S43.  Get High-res Image Gene #15: 'amp_13q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_13q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S44.  Gene #15: 'amp_13q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 235 217 113 35
AMP PEAK 15(13Q22.1) MUTATED 86 205 76 20
AMP PEAK 15(13Q22.1) WILD-TYPE 149 12 37 15

Figure S44.  Get High-res Image Gene #15: 'amp_13q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_13q22.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S45.  Gene #15: 'amp_13q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 155 121
AMP PEAK 15(13Q22.1) MUTATED 57 130 60
AMP PEAK 15(13Q22.1) WILD-TYPE 41 25 61

Figure S45.  Get High-res Image Gene #15: 'amp_13q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_13q22.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S46.  Gene #15: 'amp_13q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 130 139 188
AMP PEAK 15(13Q22.1) MUTATED 79 59 111 129
AMP PEAK 15(13Q22.1) WILD-TYPE 48 71 28 59

Figure S46.  Get High-res Image Gene #15: 'amp_13q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_13q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S47.  Gene #15: 'amp_13q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 64 107 45 65 66 96 141
AMP PEAK 15(13Q22.1) MUTATED 30 76 15 51 56 36 114
AMP PEAK 15(13Q22.1) WILD-TYPE 34 31 30 14 10 60 27

Figure S47.  Get High-res Image Gene #15: 'amp_13q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_13q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S48.  Gene #15: 'amp_13q22.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
AMP PEAK 15(13Q22.1) MUTATED 83 53 65
AMP PEAK 15(13Q22.1) WILD-TYPE 17 56 20

Figure S48.  Get High-res Image Gene #15: 'amp_13q22.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_13q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S49.  Gene #15: 'amp_13q22.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 82 52 67 33 60
AMP PEAK 15(13Q22.1) MUTATED 59 43 56 24 19
AMP PEAK 15(13Q22.1) WILD-TYPE 23 9 11 9 41

Figure S49.  Get High-res Image Gene #15: 'amp_13q22.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_16p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S50.  Gene #17: 'amp_16p11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 235 217 113 35
AMP PEAK 17(16P11.2) MUTATED 22 109 26 9
AMP PEAK 17(16P11.2) WILD-TYPE 213 108 87 26

Figure S50.  Get High-res Image Gene #17: 'amp_16p11.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_16p11.2' versus 'MRNASEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.074

Table S51.  Gene #17: 'amp_16p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 130 139 188
AMP PEAK 17(16P11.2) MUTATED 33 18 53 59
AMP PEAK 17(16P11.2) WILD-TYPE 94 112 86 129

Figure S51.  Get High-res Image Gene #17: 'amp_16p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_16p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.035

Table S52.  Gene #17: 'amp_16p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 64 107 45 65 66 96 141
AMP PEAK 17(16P11.2) MUTATED 18 25 3 19 26 18 54
AMP PEAK 17(16P11.2) WILD-TYPE 46 82 42 46 40 78 87

Figure S52.  Get High-res Image Gene #17: 'amp_16p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_16p11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S53.  Gene #17: 'amp_16p11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 82 52 67 33 60
AMP PEAK 17(16P11.2) MUTATED 26 18 27 12 3
AMP PEAK 17(16P11.2) WILD-TYPE 56 34 40 21 57

Figure S53.  Get High-res Image Gene #17: 'amp_16p11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S54.  Gene #18: 'amp_17q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 235 217 113 35
AMP PEAK 18(17Q12) MUTATED 28 78 39 7
AMP PEAK 18(17Q12) WILD-TYPE 207 139 74 28

Figure S54.  Get High-res Image Gene #18: 'amp_17q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q12' versus 'MRNASEQ_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.22

Table S55.  Gene #18: 'amp_17q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 130 139 188
AMP PEAK 18(17Q12) MUTATED 25 21 52 50
AMP PEAK 18(17Q12) WILD-TYPE 102 109 87 138

Figure S55.  Get High-res Image Gene #18: 'amp_17q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S56.  Gene #18: 'amp_17q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 64 107 45 65 66 96 141
AMP PEAK 18(17Q12) MUTATED 9 26 4 24 21 13 51
AMP PEAK 18(17Q12) WILD-TYPE 55 81 41 41 45 83 90

Figure S56.  Get High-res Image Gene #18: 'amp_17q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_17q24.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S57.  Gene #19: 'amp_17q24.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 235 217 113 35
AMP PEAK 19(17Q24.1) MUTATED 23 78 31 6
AMP PEAK 19(17Q24.1) WILD-TYPE 212 139 82 29

Figure S57.  Get High-res Image Gene #19: 'amp_17q24.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q24.1' versus 'METHLYATION_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.19

Table S58.  Gene #19: 'amp_17q24.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 155 121
AMP PEAK 19(17Q24.1) MUTATED 14 52 21
AMP PEAK 19(17Q24.1) WILD-TYPE 84 103 100

Figure S58.  Get High-res Image Gene #19: 'amp_17q24.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17q24.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S59.  Gene #19: 'amp_17q24.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 64 107 45 65 66 96 141
AMP PEAK 19(17Q24.1) MUTATED 7 23 3 23 21 11 45
AMP PEAK 19(17Q24.1) WILD-TYPE 57 84 42 42 45 85 96

Figure S59.  Get High-res Image Gene #19: 'amp_17q24.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_17q24.1' versus 'MIRSEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.14

Table S60.  Gene #19: 'amp_17q24.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 211 95 232
AMP PEAK 19(17Q24.1) MUTATED 61 8 53
AMP PEAK 19(17Q24.1) WILD-TYPE 150 87 179

Figure S60.  Get High-res Image Gene #19: 'amp_17q24.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_19p13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S61.  Gene #20: 'amp_19p13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 235 217 113 35
AMP PEAK 20(19P13.2) MUTATED 17 60 21 7
AMP PEAK 20(19P13.2) WILD-TYPE 218 157 92 28

Figure S61.  Get High-res Image Gene #20: 'amp_19p13.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.11

Table S62.  Gene #20: 'amp_19p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 64 107 45 65 66 96 141
AMP PEAK 20(19P13.2) MUTATED 8 21 2 12 23 8 30
AMP PEAK 20(19P13.2) WILD-TYPE 56 86 43 53 43 88 111

Figure S62.  Get High-res Image Gene #20: 'amp_19p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_19q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S63.  Gene #21: 'amp_19q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 235 217 113 35
AMP PEAK 21(19Q12) MUTATED 25 75 24 8
AMP PEAK 21(19Q12) WILD-TYPE 210 142 89 27

Figure S63.  Get High-res Image Gene #21: 'amp_19q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20p11.23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S64.  Gene #22: 'amp_20p11.23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 235 217 113 35
AMP PEAK 22(20P11.23) MUTATED 82 134 64 35
AMP PEAK 22(20P11.23) WILD-TYPE 153 83 49 0

Figure S64.  Get High-res Image Gene #22: 'amp_20p11.23' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20p11.23' versus 'MRNASEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.074

Table S65.  Gene #22: 'amp_20p11.23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 130 139 188
AMP PEAK 22(20P11.23) MUTATED 63 49 90 104
AMP PEAK 22(20P11.23) WILD-TYPE 64 81 49 84

Figure S65.  Get High-res Image Gene #22: 'amp_20p11.23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20p11.23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S66.  Gene #22: 'amp_20p11.23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 64 107 45 65 66 96 141
AMP PEAK 22(20P11.23) MUTATED 27 60 12 43 41 36 87
AMP PEAK 22(20P11.23) WILD-TYPE 37 47 33 22 25 60 54

Figure S66.  Get High-res Image Gene #22: 'amp_20p11.23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20p11.23' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.021

Table S67.  Gene #22: 'amp_20p11.23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
AMP PEAK 22(20P11.23) MUTATED 67 40 50
AMP PEAK 22(20P11.23) WILD-TYPE 33 69 35

Figure S67.  Get High-res Image Gene #22: 'amp_20p11.23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_20p11.23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.074

Table S68.  Gene #22: 'amp_20p11.23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 82 52 67 33 60
AMP PEAK 22(20P11.23) MUTATED 45 34 40 22 16
AMP PEAK 22(20P11.23) WILD-TYPE 37 18 27 11 44

Figure S68.  Get High-res Image Gene #22: 'amp_20p11.23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20p11.21' versus 'MRNA_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.1

Table S69.  Gene #23: 'amp_20p11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
AMP PEAK 23(20P11.21) MUTATED 16 43 49 17
AMP PEAK 23(20P11.21) WILD-TYPE 27 19 20 24

Figure S69.  Get High-res Image Gene #23: 'amp_20p11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20p11.21' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S70.  Gene #23: 'amp_20p11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
AMP PEAK 23(20P11.21) MUTATED 14 27 48 36
AMP PEAK 23(20P11.21) WILD-TYPE 35 14 28 13

Figure S70.  Get High-res Image Gene #23: 'amp_20p11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20p11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S71.  Gene #23: 'amp_20p11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 235 217 113 35
AMP PEAK 23(20P11.21) MUTATED 85 164 70 35
AMP PEAK 23(20P11.21) WILD-TYPE 150 53 43 0

Figure S71.  Get High-res Image Gene #23: 'amp_20p11.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20p11.21' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.021

Table S72.  Gene #23: 'amp_20p11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 155 121
AMP PEAK 23(20P11.21) MUTATED 50 116 58
AMP PEAK 23(20P11.21) WILD-TYPE 48 39 63

Figure S72.  Get High-res Image Gene #23: 'amp_20p11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20p11.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S73.  Gene #23: 'amp_20p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 130 139 188
AMP PEAK 23(20P11.21) MUTATED 73 51 106 114
AMP PEAK 23(20P11.21) WILD-TYPE 54 79 33 74

Figure S73.  Get High-res Image Gene #23: 'amp_20p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20p11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S74.  Gene #23: 'amp_20p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 64 107 45 65 66 96 141
AMP PEAK 23(20P11.21) MUTATED 30 68 11 49 49 36 101
AMP PEAK 23(20P11.21) WILD-TYPE 34 39 34 16 17 60 40

Figure S74.  Get High-res Image Gene #23: 'amp_20p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20p11.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S75.  Gene #23: 'amp_20p11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
AMP PEAK 23(20P11.21) MUTATED 76 44 58
AMP PEAK 23(20P11.21) WILD-TYPE 24 65 27

Figure S75.  Get High-res Image Gene #23: 'amp_20p11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_20p11.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S76.  Gene #23: 'amp_20p11.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 82 52 67 33 60
AMP PEAK 23(20P11.21) MUTATED 51 41 45 26 15
AMP PEAK 23(20P11.21) WILD-TYPE 31 11 22 7 45

Figure S76.  Get High-res Image Gene #23: 'amp_20p11.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20q11.21' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S77.  Gene #24: 'amp_20q11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
AMP PEAK 24(20Q11.21) MUTATED 18 60 63 23
AMP PEAK 24(20Q11.21) WILD-TYPE 25 2 6 18

Figure S77.  Get High-res Image Gene #24: 'amp_20q11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20q11.21' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S78.  Gene #24: 'amp_20q11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
AMP PEAK 24(20Q11.21) MUTATED 15 39 62 48
AMP PEAK 24(20Q11.21) WILD-TYPE 34 2 14 1

Figure S78.  Get High-res Image Gene #24: 'amp_20q11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20q11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S79.  Gene #24: 'amp_20q11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 235 217 113 35
AMP PEAK 24(20Q11.21) MUTATED 112 215 95 35
AMP PEAK 24(20Q11.21) WILD-TYPE 123 2 18 0

Figure S79.  Get High-res Image Gene #24: 'amp_20q11.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20q11.21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S80.  Gene #24: 'amp_20q11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 155 121
AMP PEAK 24(20Q11.21) MUTATED 68 151 68
AMP PEAK 24(20Q11.21) WILD-TYPE 30 4 53

Figure S80.  Get High-res Image Gene #24: 'amp_20q11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20q11.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S81.  Gene #24: 'amp_20q11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 130 139 188
AMP PEAK 24(20Q11.21) MUTATED 94 68 136 147
AMP PEAK 24(20Q11.21) WILD-TYPE 33 62 3 41

Figure S81.  Get High-res Image Gene #24: 'amp_20q11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20q11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S82.  Gene #24: 'amp_20q11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 64 107 45 65 66 96 141
AMP PEAK 24(20Q11.21) MUTATED 39 86 13 62 65 45 135
AMP PEAK 24(20Q11.21) WILD-TYPE 25 21 32 3 1 51 6

Figure S82.  Get High-res Image Gene #24: 'amp_20q11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20q11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 0.17

Table S83.  Gene #24: 'amp_20q11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 139 171
AMP PEAK 24(20Q11.21) MUTATED 167 122 120
AMP PEAK 24(20Q11.21) WILD-TYPE 61 17 51

Figure S83.  Get High-res Image Gene #24: 'amp_20q11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20q11.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S84.  Gene #24: 'amp_20q11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
AMP PEAK 24(20Q11.21) MUTATED 94 59 75
AMP PEAK 24(20Q11.21) WILD-TYPE 6 50 10

Figure S84.  Get High-res Image Gene #24: 'amp_20q11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_20q11.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S85.  Gene #24: 'amp_20q11.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 82 52 67 33 60
AMP PEAK 24(20Q11.21) MUTATED 69 48 62 31 18
AMP PEAK 24(20Q11.21) WILD-TYPE 13 4 5 2 42

Figure S85.  Get High-res Image Gene #24: 'amp_20q11.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20q12' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S86.  Gene #25: 'amp_20q12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
AMP PEAK 25(20Q12) MUTATED 17 60 63 22
AMP PEAK 25(20Q12) WILD-TYPE 26 2 6 19

Figure S86.  Get High-res Image Gene #25: 'amp_20q12' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20q12' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S87.  Gene #25: 'amp_20q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
AMP PEAK 25(20Q12) MUTATED 14 39 61 48
AMP PEAK 25(20Q12) WILD-TYPE 35 2 15 1

Figure S87.  Get High-res Image Gene #25: 'amp_20q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S88.  Gene #25: 'amp_20q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 235 217 113 35
AMP PEAK 25(20Q12) MUTATED 112 215 97 35
AMP PEAK 25(20Q12) WILD-TYPE 123 2 16 0

Figure S88.  Get High-res Image Gene #25: 'amp_20q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S89.  Gene #25: 'amp_20q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 155 121
AMP PEAK 25(20Q12) MUTATED 69 151 71
AMP PEAK 25(20Q12) WILD-TYPE 29 4 50

Figure S89.  Get High-res Image Gene #25: 'amp_20q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20q12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S90.  Gene #25: 'amp_20q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 130 139 188
AMP PEAK 25(20Q12) MUTATED 96 69 136 146
AMP PEAK 25(20Q12) WILD-TYPE 31 61 3 42

Figure S90.  Get High-res Image Gene #25: 'amp_20q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S91.  Gene #25: 'amp_20q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 64 107 45 65 66 96 141
AMP PEAK 25(20Q12) MUTATED 41 87 14 62 65 43 135
AMP PEAK 25(20Q12) WILD-TYPE 23 20 31 3 1 53 6

Figure S91.  Get High-res Image Gene #25: 'amp_20q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.11

Table S92.  Gene #25: 'amp_20q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 139 171
AMP PEAK 25(20Q12) MUTATED 169 123 119
AMP PEAK 25(20Q12) WILD-TYPE 59 16 52

Figure S92.  Get High-res Image Gene #25: 'amp_20q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20q12' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S93.  Gene #25: 'amp_20q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
AMP PEAK 25(20Q12) MUTATED 95 60 76
AMP PEAK 25(20Q12) WILD-TYPE 5 49 9

Figure S93.  Get High-res Image Gene #25: 'amp_20q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_20q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S94.  Gene #25: 'amp_20q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 82 52 67 33 60
AMP PEAK 25(20Q12) MUTATED 69 49 63 31 19
AMP PEAK 25(20Q12) WILD-TYPE 13 3 4 2 41

Figure S94.  Get High-res Image Gene #25: 'amp_20q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20q13.31' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S95.  Gene #26: 'amp_20q13.31' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
AMP PEAK 26(20Q13.31) MUTATED 18 60 64 24
AMP PEAK 26(20Q13.31) WILD-TYPE 25 2 5 17

Figure S95.  Get High-res Image Gene #26: 'amp_20q13.31' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20q13.31' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S96.  Gene #26: 'amp_20q13.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
AMP PEAK 26(20Q13.31) MUTATED 15 39 64 48
AMP PEAK 26(20Q13.31) WILD-TYPE 34 2 12 1

Figure S96.  Get High-res Image Gene #26: 'amp_20q13.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20q13.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S97.  Gene #26: 'amp_20q13.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 235 217 113 35
AMP PEAK 26(20Q13.31) MUTATED 113 214 99 35
AMP PEAK 26(20Q13.31) WILD-TYPE 122 3 14 0

Figure S97.  Get High-res Image Gene #26: 'amp_20q13.31' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20q13.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S98.  Gene #26: 'amp_20q13.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 155 121
AMP PEAK 26(20Q13.31) MUTATED 68 150 71
AMP PEAK 26(20Q13.31) WILD-TYPE 30 5 50

Figure S98.  Get High-res Image Gene #26: 'amp_20q13.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20q13.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S99.  Gene #26: 'amp_20q13.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 130 139 188
AMP PEAK 26(20Q13.31) MUTATED 96 71 135 148
AMP PEAK 26(20Q13.31) WILD-TYPE 31 59 4 40

Figure S99.  Get High-res Image Gene #26: 'amp_20q13.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20q13.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S100.  Gene #26: 'amp_20q13.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 64 107 45 65 66 96 141
AMP PEAK 26(20Q13.31) MUTATED 41 88 13 61 65 46 136
AMP PEAK 26(20Q13.31) WILD-TYPE 23 19 32 4 1 50 5

Figure S100.  Get High-res Image Gene #26: 'amp_20q13.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20q13.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00032 (Fisher's exact test), Q value = 0.21

Table S101.  Gene #26: 'amp_20q13.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 139 171
AMP PEAK 26(20Q13.31) MUTATED 170 123 121
AMP PEAK 26(20Q13.31) WILD-TYPE 58 16 50

Figure S101.  Get High-res Image Gene #26: 'amp_20q13.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20q13.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S102.  Gene #26: 'amp_20q13.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
AMP PEAK 26(20Q13.31) MUTATED 94 61 76
AMP PEAK 26(20Q13.31) WILD-TYPE 6 48 9

Figure S102.  Get High-res Image Gene #26: 'amp_20q13.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_20q13.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S103.  Gene #26: 'amp_20q13.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 82 52 67 33 60
AMP PEAK 26(20Q13.31) MUTATED 70 48 63 31 19
AMP PEAK 26(20Q13.31) WILD-TYPE 12 4 4 2 41

Figure S103.  Get High-res Image Gene #26: 'amp_20q13.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_xq28' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S104.  Gene #27: 'amp_xq28' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 235 217 113 35
AMP PEAK 27(XQ28) MUTATED 24 54 36 7
AMP PEAK 27(XQ28) WILD-TYPE 211 163 77 28

Figure S104.  Get High-res Image Gene #27: 'amp_xq28' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p36.11' versus 'MRNA_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.035

Table S105.  Gene #28: 'del_1p36.11' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
DEL PEAK 1(1P36.11) MUTATED 14 36 36 7
DEL PEAK 1(1P36.11) WILD-TYPE 29 26 33 34

Figure S105.  Get High-res Image Gene #28: 'del_1p36.11' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_1p36.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S106.  Gene #28: 'del_1p36.11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 235 217 113 35
DEL PEAK 1(1P36.11) MUTATED 49 124 39 26
DEL PEAK 1(1P36.11) WILD-TYPE 186 93 74 9

Figure S106.  Get High-res Image Gene #28: 'del_1p36.11' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p36.11' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S107.  Gene #28: 'del_1p36.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 155 121
DEL PEAK 1(1P36.11) MUTATED 34 81 29
DEL PEAK 1(1P36.11) WILD-TYPE 64 74 92

Figure S107.  Get High-res Image Gene #28: 'del_1p36.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p36.11' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S108.  Gene #28: 'del_1p36.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 130 139 188
DEL PEAK 1(1P36.11) MUTATED 52 26 71 82
DEL PEAK 1(1P36.11) WILD-TYPE 75 104 68 106

Figure S108.  Get High-res Image Gene #28: 'del_1p36.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p36.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S109.  Gene #28: 'del_1p36.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 64 107 45 65 66 96 141
DEL PEAK 1(1P36.11) MUTATED 17 36 6 33 37 27 75
DEL PEAK 1(1P36.11) WILD-TYPE 47 71 39 32 29 69 66

Figure S109.  Get High-res Image Gene #28: 'del_1p36.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S110.  Gene #29: 'del_1p33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 235 217 113 35
DEL PEAK 2(1P33) MUTATED 34 95 19 23
DEL PEAK 2(1P33) WILD-TYPE 201 122 94 12

Figure S110.  Get High-res Image Gene #29: 'del_1p33' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p33' versus 'MRNASEQ_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.11

Table S111.  Gene #29: 'del_1p33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 130 139 188
DEL PEAK 2(1P33) MUTATED 37 20 55 52
DEL PEAK 2(1P33) WILD-TYPE 90 110 84 136

Figure S111.  Get High-res Image Gene #29: 'del_1p33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S112.  Gene #30: 'del_1p13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 235 217 113 35
DEL PEAK 3(1P13.2) MUTATED 36 94 23 18
DEL PEAK 3(1P13.2) WILD-TYPE 199 123 90 17

Figure S112.  Get High-res Image Gene #30: 'del_1p13.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_4p16.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S113.  Gene #37: 'del_4p16.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 235 217 113 35
DEL PEAK 10(4P16.1) MUTATED 36 102 31 26
DEL PEAK 10(4P16.1) WILD-TYPE 199 115 82 9

Figure S113.  Get High-res Image Gene #37: 'del_4p16.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_4p16.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.094

Table S114.  Gene #37: 'del_4p16.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 64 107 45 65 66 96 141
DEL PEAK 10(4P16.1) MUTATED 16 30 4 26 30 26 57
DEL PEAK 10(4P16.1) WILD-TYPE 48 77 41 39 36 70 84

Figure S114.  Get High-res Image Gene #37: 'del_4p16.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4p16.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.11

Table S115.  Gene #37: 'del_4p16.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
DEL PEAK 10(4P16.1) MUTATED 40 18 33
DEL PEAK 10(4P16.1) WILD-TYPE 60 91 52

Figure S115.  Get High-res Image Gene #37: 'del_4p16.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_4p16.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00025 (Fisher's exact test), Q value = 0.16

Table S116.  Gene #37: 'del_4p16.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 82 52 67 33 60
DEL PEAK 10(4P16.1) MUTATED 26 24 25 10 6
DEL PEAK 10(4P16.1) WILD-TYPE 56 28 42 23 54

Figure S116.  Get High-res Image Gene #37: 'del_4p16.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S117.  Gene #38: 'del_4q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 235 217 113 35
DEL PEAK 11(4Q22.1) MUTATED 43 111 37 25
DEL PEAK 11(4Q22.1) WILD-TYPE 192 106 76 10

Figure S117.  Get High-res Image Gene #38: 'del_4q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q22.1' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.035

Table S118.  Gene #38: 'del_4q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 155 121
DEL PEAK 11(4Q22.1) MUTATED 37 74 27
DEL PEAK 11(4Q22.1) WILD-TYPE 61 81 94

Figure S118.  Get High-res Image Gene #38: 'del_4q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q22.1' versus 'MRNASEQ_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.19

Table S119.  Gene #38: 'del_4q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 130 139 188
DEL PEAK 11(4Q22.1) MUTATED 46 26 60 75
DEL PEAK 11(4Q22.1) WILD-TYPE 81 104 79 113

Figure S119.  Get High-res Image Gene #38: 'del_4q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S120.  Gene #38: 'del_4q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 64 107 45 65 66 96 141
DEL PEAK 11(4Q22.1) MUTATED 16 34 5 32 32 26 62
DEL PEAK 11(4Q22.1) WILD-TYPE 48 73 40 33 34 70 79

Figure S120.  Get High-res Image Gene #38: 'del_4q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.1

Table S121.  Gene #38: 'del_4q22.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 82 52 67 33 60
DEL PEAK 11(4Q22.1) MUTATED 30 24 29 15 7
DEL PEAK 11(4Q22.1) WILD-TYPE 52 28 38 18 53

Figure S121.  Get High-res Image Gene #38: 'del_4q22.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q35.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S122.  Gene #39: 'del_4q35.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 235 217 113 35
DEL PEAK 12(4Q35.1) MUTATED 45 115 42 23
DEL PEAK 12(4Q35.1) WILD-TYPE 190 102 71 12

Figure S122.  Get High-res Image Gene #39: 'del_4q35.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q35.1' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S123.  Gene #39: 'del_4q35.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 155 121
DEL PEAK 12(4Q35.1) MUTATED 40 75 27
DEL PEAK 12(4Q35.1) WILD-TYPE 58 80 94

Figure S123.  Get High-res Image Gene #39: 'del_4q35.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q35.1' versus 'MRNASEQ_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.18

Table S124.  Gene #39: 'del_4q35.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 130 139 188
DEL PEAK 12(4Q35.1) MUTATED 52 28 60 77
DEL PEAK 12(4Q35.1) WILD-TYPE 75 102 79 111

Figure S124.  Get High-res Image Gene #39: 'del_4q35.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4q35.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.055

Table S125.  Gene #39: 'del_4q35.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
DEL PEAK 12(4Q35.1) MUTATED 48 23 38
DEL PEAK 12(4Q35.1) WILD-TYPE 52 86 47

Figure S125.  Get High-res Image Gene #39: 'del_4q35.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_5q11.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00025 (Fisher's exact test), Q value = 0.16

Table S126.  Gene #40: 'del_5q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
DEL PEAK 13(5Q11.2) MUTATED 9 18 8 16
DEL PEAK 13(5Q11.2) WILD-TYPE 40 23 68 33

Figure S126.  Get High-res Image Gene #40: 'del_5q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_5q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S127.  Gene #40: 'del_5q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 235 217 113 35
DEL PEAK 13(5Q11.2) MUTATED 22 73 36 20
DEL PEAK 13(5Q11.2) WILD-TYPE 213 144 77 15

Figure S127.  Get High-res Image Gene #40: 'del_5q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S128.  Gene #40: 'del_5q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
DEL PEAK 13(5Q11.2) MUTATED 35 11 29
DEL PEAK 13(5Q11.2) WILD-TYPE 65 98 56

Figure S128.  Get High-res Image Gene #40: 'del_5q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_5q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S129.  Gene #40: 'del_5q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 82 52 67 33 60
DEL PEAK 13(5Q11.2) MUTATED 22 23 23 6 1
DEL PEAK 13(5Q11.2) WILD-TYPE 60 29 44 27 59

Figure S129.  Get High-res Image Gene #40: 'del_5q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q22.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S130.  Gene #41: 'del_5q22.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 235 217 113 35
DEL PEAK 14(5Q22.2) MUTATED 36 82 43 21
DEL PEAK 14(5Q22.2) WILD-TYPE 199 135 70 14

Figure S130.  Get High-res Image Gene #41: 'del_5q22.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q22.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.028

Table S131.  Gene #41: 'del_5q22.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 82 52 67 33 60
DEL PEAK 14(5Q22.2) MUTATED 30 27 20 11 6
DEL PEAK 14(5Q22.2) WILD-TYPE 52 25 47 22 54

Figure S131.  Get High-res Image Gene #41: 'del_5q22.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p23.2' versus 'MRNA_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.16

Table S132.  Gene #45: 'del_8p23.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
DEL PEAK 18(8P23.2) MUTATED 17 42 37 11
DEL PEAK 18(8P23.2) WILD-TYPE 26 20 32 30

Figure S132.  Get High-res Image Gene #45: 'del_8p23.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_8p23.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S133.  Gene #45: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 235 217 113 35
DEL PEAK 18(8P23.2) MUTATED 42 144 82 14
DEL PEAK 18(8P23.2) WILD-TYPE 193 73 31 21

Figure S133.  Get High-res Image Gene #45: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_8p23.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S134.  Gene #45: 'del_8p23.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 155 121
DEL PEAK 18(8P23.2) MUTATED 38 99 37
DEL PEAK 18(8P23.2) WILD-TYPE 60 56 84

Figure S134.  Get High-res Image Gene #45: 'del_8p23.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_8p23.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S135.  Gene #45: 'del_8p23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 130 139 188
DEL PEAK 18(8P23.2) MUTATED 64 33 80 98
DEL PEAK 18(8P23.2) WILD-TYPE 63 97 59 90

Figure S135.  Get High-res Image Gene #45: 'del_8p23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_8p23.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S136.  Gene #45: 'del_8p23.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 64 107 45 65 66 96 141
DEL PEAK 18(8P23.2) MUTATED 28 42 6 34 45 36 84
DEL PEAK 18(8P23.2) WILD-TYPE 36 65 39 31 21 60 57

Figure S136.  Get High-res Image Gene #45: 'del_8p23.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.028

Table S137.  Gene #45: 'del_8p23.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
DEL PEAK 18(8P23.2) MUTATED 61 32 45
DEL PEAK 18(8P23.2) WILD-TYPE 39 77 40

Figure S137.  Get High-res Image Gene #45: 'del_8p23.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_8p23.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S138.  Gene #45: 'del_8p23.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 82 52 67 33 60
DEL PEAK 18(8P23.2) MUTATED 41 32 36 20 9
DEL PEAK 18(8P23.2) WILD-TYPE 41 20 31 13 51

Figure S138.  Get High-res Image Gene #45: 'del_8p23.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p22' versus 'MRNA_CHIERARCHICAL'

P value = 0.00037 (Fisher's exact test), Q value = 0.23

Table S139.  Gene #46: 'del_8p22' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
DEL PEAK 19(8P22) MUTATED 13 28 40 29
DEL PEAK 19(8P22) WILD-TYPE 36 13 36 20

Figure S139.  Get High-res Image Gene #46: 'del_8p22' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_8p22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S140.  Gene #46: 'del_8p22' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 235 217 113 35
DEL PEAK 19(8P22) MUTATED 45 151 85 16
DEL PEAK 19(8P22) WILD-TYPE 190 66 28 19

Figure S140.  Get High-res Image Gene #46: 'del_8p22' versus Molecular Subtype #3: 'CN_CNMF'

'del_8p22' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S141.  Gene #46: 'del_8p22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 155 121
DEL PEAK 19(8P22) MUTATED 40 104 42
DEL PEAK 19(8P22) WILD-TYPE 58 51 79

Figure S141.  Get High-res Image Gene #46: 'del_8p22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_8p22' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S142.  Gene #46: 'del_8p22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 130 139 188
DEL PEAK 19(8P22) MUTATED 68 38 83 100
DEL PEAK 19(8P22) WILD-TYPE 59 92 56 88

Figure S142.  Get High-res Image Gene #46: 'del_8p22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_8p22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S143.  Gene #46: 'del_8p22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 64 107 45 65 66 96 141
DEL PEAK 19(8P22) MUTATED 31 45 6 37 47 36 87
DEL PEAK 19(8P22) WILD-TYPE 33 62 39 28 19 60 54

Figure S143.  Get High-res Image Gene #46: 'del_8p22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_8p22' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.021

Table S144.  Gene #46: 'del_8p22' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
DEL PEAK 19(8P22) MUTATED 63 36 49
DEL PEAK 19(8P22) WILD-TYPE 37 73 36

Figure S144.  Get High-res Image Gene #46: 'del_8p22' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_8p22' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S145.  Gene #46: 'del_8p22' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 82 52 67 33 60
DEL PEAK 19(8P22) MUTATED 43 35 40 21 9
DEL PEAK 19(8P22) WILD-TYPE 39 17 27 12 51

Figure S145.  Get High-res Image Gene #46: 'del_8p22' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S146.  Gene #47: 'del_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 235 217 113 35
DEL PEAK 20(8P11.21) MUTATED 26 75 20 9
DEL PEAK 20(8P11.21) WILD-TYPE 209 142 93 26

Figure S146.  Get High-res Image Gene #47: 'del_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

'del_8p11.21' versus 'MRNASEQ_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.16

Table S147.  Gene #47: 'del_8p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 130 139 188
DEL PEAK 20(8P11.21) MUTATED 27 13 30 56
DEL PEAK 20(8P11.21) WILD-TYPE 100 117 109 132

Figure S147.  Get High-res Image Gene #47: 'del_8p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_8q11.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S148.  Gene #48: 'del_8q11.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 235 217 113 35
DEL PEAK 21(8Q11.1) MUTATED 10 31 1 4
DEL PEAK 21(8Q11.1) WILD-TYPE 225 186 112 31

Figure S148.  Get High-res Image Gene #48: 'del_8q11.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p24.2' versus 'CN_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.14

Table S149.  Gene #49: 'del_9p24.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 235 217 113 35
DEL PEAK 22(9P24.2) MUTATED 16 44 14 7
DEL PEAK 22(9P24.2) WILD-TYPE 219 173 99 28

Figure S149.  Get High-res Image Gene #49: 'del_9p24.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S150.  Gene #50: 'del_10q21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 235 217 113 35
DEL PEAK 23(10Q21.1) MUTATED 20 56 34 18
DEL PEAK 23(10Q21.1) WILD-TYPE 215 161 79 17

Figure S150.  Get High-res Image Gene #50: 'del_10q21.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q21.1' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S151.  Gene #50: 'del_10q21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 130 139 188
DEL PEAK 23(10Q21.1) MUTATED 25 12 47 41
DEL PEAK 23(10Q21.1) WILD-TYPE 102 118 92 147

Figure S151.  Get High-res Image Gene #50: 'del_10q21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S152.  Gene #51: 'del_10q23.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 235 217 113 35
DEL PEAK 24(10Q23.31) MUTATED 31 64 40 21
DEL PEAK 24(10Q23.31) WILD-TYPE 204 153 73 14

Figure S152.  Get High-res Image Gene #51: 'del_10q23.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q23.31' versus 'MRNASEQ_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.22

Table S153.  Gene #51: 'del_10q23.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 130 139 188
DEL PEAK 24(10Q23.31) MUTATED 32 21 54 44
DEL PEAK 24(10Q23.31) WILD-TYPE 95 109 85 144

Figure S153.  Get High-res Image Gene #51: 'del_10q23.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.094

Table S154.  Gene #51: 'del_10q23.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 64 107 45 65 66 96 141
DEL PEAK 24(10Q23.31) MUTATED 11 27 4 21 32 23 33
DEL PEAK 24(10Q23.31) WILD-TYPE 53 80 41 44 34 73 108

Figure S154.  Get High-res Image Gene #51: 'del_10q23.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.035

Table S155.  Gene #51: 'del_10q23.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
DEL PEAK 24(10Q23.31) MUTATED 35 14 31
DEL PEAK 24(10Q23.31) WILD-TYPE 65 95 54

Figure S155.  Get High-res Image Gene #51: 'del_10q23.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_10q23.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.14

Table S156.  Gene #51: 'del_10q23.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 82 52 67 33 60
DEL PEAK 24(10Q23.31) MUTATED 21 21 26 7 5
DEL PEAK 24(10Q23.31) WILD-TYPE 61 31 41 26 55

Figure S156.  Get High-res Image Gene #51: 'del_10q23.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q25.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S157.  Gene #52: 'del_10q25.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 235 217 113 35
DEL PEAK 25(10Q25.2) MUTATED 30 65 34 23
DEL PEAK 25(10Q25.2) WILD-TYPE 205 152 79 12

Figure S157.  Get High-res Image Gene #52: 'del_10q25.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q25.2' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.021

Table S158.  Gene #52: 'del_10q25.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 130 139 188
DEL PEAK 25(10Q25.2) MUTATED 32 14 49 51
DEL PEAK 25(10Q25.2) WILD-TYPE 95 116 90 137

Figure S158.  Get High-res Image Gene #52: 'del_10q25.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10q25.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S159.  Gene #52: 'del_10q25.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 64 107 45 65 66 96 141
DEL PEAK 25(10Q25.2) MUTATED 11 18 2 19 33 28 35
DEL PEAK 25(10Q25.2) WILD-TYPE 53 89 43 46 33 68 106

Figure S159.  Get High-res Image Gene #52: 'del_10q25.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10q25.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.1

Table S160.  Gene #52: 'del_10q25.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
DEL PEAK 25(10Q25.2) MUTATED 32 12 27
DEL PEAK 25(10Q25.2) WILD-TYPE 68 97 58

Figure S160.  Get High-res Image Gene #52: 'del_10q25.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_10q25.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.061

Table S161.  Gene #52: 'del_10q25.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 82 52 67 33 60
DEL PEAK 25(10Q25.2) MUTATED 19 20 23 5 4
DEL PEAK 25(10Q25.2) WILD-TYPE 63 32 44 28 56

Figure S161.  Get High-res Image Gene #52: 'del_10q25.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_12p13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S162.  Gene #54: 'del_12p13.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 235 217 113 35
DEL PEAK 27(12P13.1) MUTATED 9 52 20 9
DEL PEAK 27(12P13.1) WILD-TYPE 226 165 93 26

Figure S162.  Get High-res Image Gene #54: 'del_12p13.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_12q21.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S163.  Gene #55: 'del_12q21.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 235 217 113 35
DEL PEAK 28(12Q21.33) MUTATED 11 48 19 10
DEL PEAK 28(12Q21.33) WILD-TYPE 224 169 94 25

Figure S163.  Get High-res Image Gene #55: 'del_12q21.33' versus Molecular Subtype #3: 'CN_CNMF'

'del_14q11.2' versus 'MRNA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.028

Table S164.  Gene #56: 'del_14q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
DEL PEAK 29(14Q11.2) MUTATED 8 31 34 6
DEL PEAK 29(14Q11.2) WILD-TYPE 35 31 35 35

Figure S164.  Get High-res Image Gene #56: 'del_14q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_14q11.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S165.  Gene #56: 'del_14q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
DEL PEAK 29(14Q11.2) MUTATED 5 21 28 25
DEL PEAK 29(14Q11.2) WILD-TYPE 44 20 48 24

Figure S165.  Get High-res Image Gene #56: 'del_14q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_14q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S166.  Gene #56: 'del_14q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 235 217 113 35
DEL PEAK 29(14Q11.2) MUTATED 27 144 20 13
DEL PEAK 29(14Q11.2) WILD-TYPE 208 73 93 22

Figure S166.  Get High-res Image Gene #56: 'del_14q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_14q11.2' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.028

Table S167.  Gene #56: 'del_14q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 155 121
DEL PEAK 29(14Q11.2) MUTATED 29 71 24
DEL PEAK 29(14Q11.2) WILD-TYPE 69 84 97

Figure S167.  Get High-res Image Gene #56: 'del_14q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_14q11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S168.  Gene #56: 'del_14q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 130 139 188
DEL PEAK 29(14Q11.2) MUTATED 28 21 73 75
DEL PEAK 29(14Q11.2) WILD-TYPE 99 109 66 113

Figure S168.  Get High-res Image Gene #56: 'del_14q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_14q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S169.  Gene #56: 'del_14q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 64 107 45 65 66 96 141
DEL PEAK 29(14Q11.2) MUTATED 11 36 3 29 33 15 70
DEL PEAK 29(14Q11.2) WILD-TYPE 53 71 42 36 33 81 71

Figure S169.  Get High-res Image Gene #56: 'del_14q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_14q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S170.  Gene #56: 'del_14q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
DEL PEAK 29(14Q11.2) MUTATED 49 17 32
DEL PEAK 29(14Q11.2) WILD-TYPE 51 92 53

Figure S170.  Get High-res Image Gene #56: 'del_14q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_14q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S171.  Gene #56: 'del_14q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 82 52 67 33 60
DEL PEAK 29(14Q11.2) MUTATED 31 22 28 15 2
DEL PEAK 29(14Q11.2) WILD-TYPE 51 30 39 18 58

Figure S171.  Get High-res Image Gene #56: 'del_14q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_14q31.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S172.  Gene #57: 'del_14q31.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 235 217 113 35
DEL PEAK 30(14Q31.1) MUTATED 31 145 21 14
DEL PEAK 30(14Q31.1) WILD-TYPE 204 72 92 21

Figure S172.  Get High-res Image Gene #57: 'del_14q31.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_14q31.1' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.041

Table S173.  Gene #57: 'del_14q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 155 121
DEL PEAK 30(14Q31.1) MUTATED 28 73 26
DEL PEAK 30(14Q31.1) WILD-TYPE 70 82 95

Figure S173.  Get High-res Image Gene #57: 'del_14q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_14q31.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S174.  Gene #57: 'del_14q31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 130 139 188
DEL PEAK 30(14Q31.1) MUTATED 30 22 73 79
DEL PEAK 30(14Q31.1) WILD-TYPE 97 108 66 109

Figure S174.  Get High-res Image Gene #57: 'del_14q31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_14q31.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S175.  Gene #57: 'del_14q31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 64 107 45 65 66 96 141
DEL PEAK 30(14Q31.1) MUTATED 12 38 5 26 32 19 72
DEL PEAK 30(14Q31.1) WILD-TYPE 52 69 40 39 34 77 69

Figure S175.  Get High-res Image Gene #57: 'del_14q31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_14q31.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S176.  Gene #57: 'del_14q31.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
DEL PEAK 30(14Q31.1) MUTATED 50 16 32
DEL PEAK 30(14Q31.1) WILD-TYPE 50 93 53

Figure S176.  Get High-res Image Gene #57: 'del_14q31.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_14q31.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S177.  Gene #57: 'del_14q31.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 82 52 67 33 60
DEL PEAK 30(14Q31.1) MUTATED 29 22 29 15 3
DEL PEAK 30(14Q31.1) WILD-TYPE 53 30 38 18 57

Figure S177.  Get High-res Image Gene #57: 'del_14q31.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_14q31.1' versus 'MRNA_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.23

Table S178.  Gene #58: 'del_14q31.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
DEL PEAK 31(14Q31.1) MUTATED 11 31 34 7
DEL PEAK 31(14Q31.1) WILD-TYPE 32 31 35 34

Figure S178.  Get High-res Image Gene #58: 'del_14q31.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_14q31.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S179.  Gene #58: 'del_14q31.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 235 217 113 35
DEL PEAK 31(14Q31.1) MUTATED 32 146 20 14
DEL PEAK 31(14Q31.1) WILD-TYPE 203 71 93 21

Figure S179.  Get High-res Image Gene #58: 'del_14q31.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_14q31.1' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.021

Table S180.  Gene #58: 'del_14q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 155 121
DEL PEAK 31(14Q31.1) MUTATED 28 73 27
DEL PEAK 31(14Q31.1) WILD-TYPE 70 82 94

Figure S180.  Get High-res Image Gene #58: 'del_14q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_14q31.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S181.  Gene #58: 'del_14q31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 130 139 188
DEL PEAK 31(14Q31.1) MUTATED 30 23 73 79
DEL PEAK 31(14Q31.1) WILD-TYPE 97 107 66 109

Figure S181.  Get High-res Image Gene #58: 'del_14q31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_14q31.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S182.  Gene #58: 'del_14q31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 64 107 45 65 66 96 141
DEL PEAK 31(14Q31.1) MUTATED 12 39 5 27 31 19 72
DEL PEAK 31(14Q31.1) WILD-TYPE 52 68 40 38 35 77 69

Figure S182.  Get High-res Image Gene #58: 'del_14q31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_14q31.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S183.  Gene #58: 'del_14q31.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
DEL PEAK 31(14Q31.1) MUTATED 51 17 32
DEL PEAK 31(14Q31.1) WILD-TYPE 49 92 53

Figure S183.  Get High-res Image Gene #58: 'del_14q31.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_14q31.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S184.  Gene #58: 'del_14q31.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 82 52 67 33 60
DEL PEAK 31(14Q31.1) MUTATED 29 23 29 15 4
DEL PEAK 31(14Q31.1) WILD-TYPE 53 29 38 18 56

Figure S184.  Get High-res Image Gene #58: 'del_14q31.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_15q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S185.  Gene #59: 'del_15q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 235 217 113 35
DEL PEAK 32(15Q11.2) MUTATED 40 132 47 26
DEL PEAK 32(15Q11.2) WILD-TYPE 195 85 66 9

Figure S185.  Get High-res Image Gene #59: 'del_15q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q11.2' versus 'METHLYATION_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.21

Table S186.  Gene #59: 'del_15q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 155 121
DEL PEAK 32(15Q11.2) MUTATED 37 81 35
DEL PEAK 32(15Q11.2) WILD-TYPE 61 74 86

Figure S186.  Get High-res Image Gene #59: 'del_15q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_15q11.2' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S187.  Gene #59: 'del_15q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 130 139 188
DEL PEAK 32(15Q11.2) MUTATED 53 30 72 84
DEL PEAK 32(15Q11.2) WILD-TYPE 74 100 67 104

Figure S187.  Get High-res Image Gene #59: 'del_15q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_15q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S188.  Gene #59: 'del_15q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 64 107 45 65 66 96 141
DEL PEAK 32(15Q11.2) MUTATED 18 37 4 33 44 35 68
DEL PEAK 32(15Q11.2) WILD-TYPE 46 70 41 32 22 61 73

Figure S188.  Get High-res Image Gene #59: 'del_15q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_15q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S189.  Gene #59: 'del_15q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
DEL PEAK 32(15Q11.2) MUTATED 54 25 43
DEL PEAK 32(15Q11.2) WILD-TYPE 46 84 42

Figure S189.  Get High-res Image Gene #59: 'del_15q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_15q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S190.  Gene #59: 'del_15q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 82 52 67 33 60
DEL PEAK 32(15Q11.2) MUTATED 36 23 41 13 9
DEL PEAK 32(15Q11.2) WILD-TYPE 46 29 26 20 51

Figure S190.  Get High-res Image Gene #59: 'del_15q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_15q15.2' versus 'MRNA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.028

Table S191.  Gene #60: 'del_15q15.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
DEL PEAK 33(15Q15.2) MUTATED 11 34 39 8
DEL PEAK 33(15Q15.2) WILD-TYPE 32 28 30 33

Figure S191.  Get High-res Image Gene #60: 'del_15q15.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_15q15.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S192.  Gene #60: 'del_15q15.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 235 217 113 35
DEL PEAK 33(15Q15.2) MUTATED 40 130 46 27
DEL PEAK 33(15Q15.2) WILD-TYPE 195 87 67 8

Figure S192.  Get High-res Image Gene #60: 'del_15q15.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q15.2' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.035

Table S193.  Gene #60: 'del_15q15.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 130 139 188
DEL PEAK 33(15Q15.2) MUTATED 49 32 72 82
DEL PEAK 33(15Q15.2) WILD-TYPE 78 98 67 106

Figure S193.  Get High-res Image Gene #60: 'del_15q15.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_15q15.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S194.  Gene #60: 'del_15q15.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 64 107 45 65 66 96 141
DEL PEAK 33(15Q15.2) MUTATED 18 37 2 33 41 36 68
DEL PEAK 33(15Q15.2) WILD-TYPE 46 70 43 32 25 60 73

Figure S194.  Get High-res Image Gene #60: 'del_15q15.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_15q15.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.035

Table S195.  Gene #60: 'del_15q15.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
DEL PEAK 33(15Q15.2) MUTATED 51 25 41
DEL PEAK 33(15Q15.2) WILD-TYPE 49 84 44

Figure S195.  Get High-res Image Gene #60: 'del_15q15.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_15q15.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.021

Table S196.  Gene #60: 'del_15q15.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 82 52 67 33 60
DEL PEAK 33(15Q15.2) MUTATED 36 23 37 13 8
DEL PEAK 33(15Q15.2) WILD-TYPE 46 29 30 20 52

Figure S196.  Get High-res Image Gene #60: 'del_15q15.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_15q21.1' versus 'MRNA_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.21

Table S197.  Gene #61: 'del_15q21.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
DEL PEAK 34(15Q21.1) MUTATED 14 33 38 8
DEL PEAK 34(15Q21.1) WILD-TYPE 29 29 31 33

Figure S197.  Get High-res Image Gene #61: 'del_15q21.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_15q21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S198.  Gene #61: 'del_15q21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 235 217 113 35
DEL PEAK 34(15Q21.1) MUTATED 41 127 46 26
DEL PEAK 34(15Q21.1) WILD-TYPE 194 90 67 9

Figure S198.  Get High-res Image Gene #61: 'del_15q21.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q21.1' versus 'MRNASEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.094

Table S199.  Gene #61: 'del_15q21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 130 139 188
DEL PEAK 34(15Q21.1) MUTATED 48 33 71 82
DEL PEAK 34(15Q21.1) WILD-TYPE 79 97 68 106

Figure S199.  Get High-res Image Gene #61: 'del_15q21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_15q21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S200.  Gene #61: 'del_15q21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 64 107 45 65 66 96 141
DEL PEAK 34(15Q21.1) MUTATED 18 37 2 32 40 38 67
DEL PEAK 34(15Q21.1) WILD-TYPE 46 70 43 33 26 58 74

Figure S200.  Get High-res Image Gene #61: 'del_15q21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_15q21.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.048

Table S201.  Gene #61: 'del_15q21.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
DEL PEAK 34(15Q21.1) MUTATED 50 25 41
DEL PEAK 34(15Q21.1) WILD-TYPE 50 84 44

Figure S201.  Get High-res Image Gene #61: 'del_15q21.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_15q21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.021

Table S202.  Gene #61: 'del_15q21.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 82 52 67 33 60
DEL PEAK 34(15Q21.1) MUTATED 35 23 37 13 8
DEL PEAK 34(15Q21.1) WILD-TYPE 47 29 30 20 52

Figure S202.  Get High-res Image Gene #61: 'del_15q21.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_15q22.33' versus 'MRNA_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.1

Table S203.  Gene #62: 'del_15q22.33' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
DEL PEAK 35(15Q22.33) MUTATED 12 31 36 6
DEL PEAK 35(15Q22.33) WILD-TYPE 31 31 33 35

Figure S203.  Get High-res Image Gene #62: 'del_15q22.33' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_15q22.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S204.  Gene #62: 'del_15q22.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 235 217 113 35
DEL PEAK 35(15Q22.33) MUTATED 35 123 47 26
DEL PEAK 35(15Q22.33) WILD-TYPE 200 94 66 9

Figure S204.  Get High-res Image Gene #62: 'del_15q22.33' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q22.33' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.055

Table S205.  Gene #62: 'del_15q22.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 155 121
DEL PEAK 35(15Q22.33) MUTATED 35 79 31
DEL PEAK 35(15Q22.33) WILD-TYPE 63 76 90

Figure S205.  Get High-res Image Gene #62: 'del_15q22.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_15q22.33' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S206.  Gene #62: 'del_15q22.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 130 139 188
DEL PEAK 35(15Q22.33) MUTATED 50 27 69 79
DEL PEAK 35(15Q22.33) WILD-TYPE 77 103 70 109

Figure S206.  Get High-res Image Gene #62: 'del_15q22.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_15q22.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S207.  Gene #62: 'del_15q22.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 64 107 45 65 66 96 141
DEL PEAK 35(15Q22.33) MUTATED 17 35 2 30 44 31 66
DEL PEAK 35(15Q22.33) WILD-TYPE 47 72 43 35 22 65 75

Figure S207.  Get High-res Image Gene #62: 'del_15q22.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_15q22.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S208.  Gene #62: 'del_15q22.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
DEL PEAK 35(15Q22.33) MUTATED 49 23 42
DEL PEAK 35(15Q22.33) WILD-TYPE 51 86 43

Figure S208.  Get High-res Image Gene #62: 'del_15q22.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_15q22.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S209.  Gene #62: 'del_15q22.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 82 52 67 33 60
DEL PEAK 35(15Q22.33) MUTATED 34 19 39 14 8
DEL PEAK 35(15Q22.33) WILD-TYPE 48 33 28 19 52

Figure S209.  Get High-res Image Gene #62: 'del_15q22.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17p12' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S210.  Gene #65: 'del_17p12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
DEL PEAK 38(17P12) MUTATED 16 50 52 15
DEL PEAK 38(17P12) WILD-TYPE 27 12 17 26

Figure S210.  Get High-res Image Gene #65: 'del_17p12' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_17p12' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S211.  Gene #65: 'del_17p12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
DEL PEAK 38(17P12) MUTATED 14 32 49 38
DEL PEAK 38(17P12) WILD-TYPE 35 9 27 11

Figure S211.  Get High-res Image Gene #65: 'del_17p12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_17p12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S212.  Gene #65: 'del_17p12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 235 217 113 35
DEL PEAK 38(17P12) MUTATED 67 184 83 26
DEL PEAK 38(17P12) WILD-TYPE 168 33 30 9

Figure S212.  Get High-res Image Gene #65: 'del_17p12' versus Molecular Subtype #3: 'CN_CNMF'

'del_17p12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S213.  Gene #65: 'del_17p12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 155 121
DEL PEAK 38(17P12) MUTATED 47 123 54
DEL PEAK 38(17P12) WILD-TYPE 51 32 67

Figure S213.  Get High-res Image Gene #65: 'del_17p12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_17p12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S214.  Gene #65: 'del_17p12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 130 139 188
DEL PEAK 38(17P12) MUTATED 71 48 108 122
DEL PEAK 38(17P12) WILD-TYPE 56 82 31 66

Figure S214.  Get High-res Image Gene #65: 'del_17p12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_17p12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S215.  Gene #65: 'del_17p12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 64 107 45 65 66 96 141
DEL PEAK 38(17P12) MUTATED 33 62 6 50 50 42 106
DEL PEAK 38(17P12) WILD-TYPE 31 45 39 15 16 54 35

Figure S215.  Get High-res Image Gene #65: 'del_17p12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_17p12' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S216.  Gene #65: 'del_17p12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
DEL PEAK 38(17P12) MUTATED 80 43 53
DEL PEAK 38(17P12) WILD-TYPE 20 66 32

Figure S216.  Get High-res Image Gene #65: 'del_17p12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_17p12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S217.  Gene #65: 'del_17p12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 82 52 67 33 60
DEL PEAK 38(17P12) MUTATED 54 40 48 24 10
DEL PEAK 38(17P12) WILD-TYPE 28 12 19 9 50

Figure S217.  Get High-res Image Gene #65: 'del_17p12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18p11.31' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S218.  Gene #67: 'del_18p11.31' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
DEL PEAK 40(18P11.31) MUTATED 11 51 52 13
DEL PEAK 40(18P11.31) WILD-TYPE 32 11 17 28

Figure S218.  Get High-res Image Gene #67: 'del_18p11.31' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_18p11.31' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S219.  Gene #67: 'del_18p11.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
DEL PEAK 40(18P11.31) MUTATED 9 34 43 41
DEL PEAK 40(18P11.31) WILD-TYPE 40 7 33 8

Figure S219.  Get High-res Image Gene #67: 'del_18p11.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_18p11.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S220.  Gene #67: 'del_18p11.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 235 217 113 35
DEL PEAK 40(18P11.31) MUTATED 58 194 74 32
DEL PEAK 40(18P11.31) WILD-TYPE 177 23 39 3

Figure S220.  Get High-res Image Gene #67: 'del_18p11.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_18p11.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S221.  Gene #67: 'del_18p11.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 155 121
DEL PEAK 40(18P11.31) MUTATED 53 135 41
DEL PEAK 40(18P11.31) WILD-TYPE 45 20 80

Figure S221.  Get High-res Image Gene #67: 'del_18p11.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_18p11.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S222.  Gene #67: 'del_18p11.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 130 139 188
DEL PEAK 40(18P11.31) MUTATED 72 35 126 116
DEL PEAK 40(18P11.31) WILD-TYPE 55 95 13 72

Figure S222.  Get High-res Image Gene #67: 'del_18p11.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_18p11.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S223.  Gene #67: 'del_18p11.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 64 107 45 65 66 96 141
DEL PEAK 40(18P11.31) MUTATED 25 63 5 56 59 32 109
DEL PEAK 40(18P11.31) WILD-TYPE 39 44 40 9 7 64 32

Figure S223.  Get High-res Image Gene #67: 'del_18p11.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_18p11.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S224.  Gene #67: 'del_18p11.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
DEL PEAK 40(18P11.31) MUTATED 84 34 59
DEL PEAK 40(18P11.31) WILD-TYPE 16 75 26

Figure S224.  Get High-res Image Gene #67: 'del_18p11.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_18p11.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S225.  Gene #67: 'del_18p11.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 82 52 67 33 60
DEL PEAK 40(18P11.31) MUTATED 51 39 51 28 8
DEL PEAK 40(18P11.31) WILD-TYPE 31 13 16 5 52

Figure S225.  Get High-res Image Gene #67: 'del_18p11.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18q12.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S226.  Gene #68: 'del_18q12.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
DEL PEAK 41(18Q12.2) MUTATED 17 54 56 17
DEL PEAK 41(18Q12.2) WILD-TYPE 26 8 13 24

Figure S226.  Get High-res Image Gene #68: 'del_18q12.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_18q12.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S227.  Gene #68: 'del_18q12.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
DEL PEAK 41(18Q12.2) MUTATED 14 36 52 42
DEL PEAK 41(18Q12.2) WILD-TYPE 35 5 24 7

Figure S227.  Get High-res Image Gene #68: 'del_18q12.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_18q12.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S228.  Gene #68: 'del_18q12.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 235 217 113 35
DEL PEAK 41(18Q12.2) MUTATED 72 203 94 33
DEL PEAK 41(18Q12.2) WILD-TYPE 163 14 19 2

Figure S228.  Get High-res Image Gene #68: 'del_18q12.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_18q12.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S229.  Gene #68: 'del_18q12.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 155 121
DEL PEAK 41(18Q12.2) MUTATED 58 144 52
DEL PEAK 41(18Q12.2) WILD-TYPE 40 11 69

Figure S229.  Get High-res Image Gene #68: 'del_18q12.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_18q12.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S230.  Gene #68: 'del_18q12.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 130 139 188
DEL PEAK 41(18Q12.2) MUTATED 84 50 127 132
DEL PEAK 41(18Q12.2) WILD-TYPE 43 80 12 56

Figure S230.  Get High-res Image Gene #68: 'del_18q12.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_18q12.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S231.  Gene #68: 'del_18q12.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 64 107 45 65 66 96 141
DEL PEAK 41(18Q12.2) MUTATED 31 73 7 56 65 44 117
DEL PEAK 41(18Q12.2) WILD-TYPE 33 34 38 9 1 52 24

Figure S231.  Get High-res Image Gene #68: 'del_18q12.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_18q12.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S232.  Gene #68: 'del_18q12.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
DEL PEAK 41(18Q12.2) MUTATED 90 44 66
DEL PEAK 41(18Q12.2) WILD-TYPE 10 65 19

Figure S232.  Get High-res Image Gene #68: 'del_18q12.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_18q12.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S233.  Gene #68: 'del_18q12.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 82 52 67 33 60
DEL PEAK 41(18Q12.2) MUTATED 61 45 56 28 10
DEL PEAK 41(18Q12.2) WILD-TYPE 21 7 11 5 50

Figure S233.  Get High-res Image Gene #68: 'del_18q12.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18q21.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S234.  Gene #69: 'del_18q21.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
DEL PEAK 42(18Q21.2) MUTATED 17 55 57 18
DEL PEAK 42(18Q21.2) WILD-TYPE 26 7 12 23

Figure S234.  Get High-res Image Gene #69: 'del_18q21.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_18q21.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S235.  Gene #69: 'del_18q21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
DEL PEAK 42(18Q21.2) MUTATED 14 36 55 42
DEL PEAK 42(18Q21.2) WILD-TYPE 35 5 21 7

Figure S235.  Get High-res Image Gene #69: 'del_18q21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_18q21.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S236.  Gene #69: 'del_18q21.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 235 217 113 35
DEL PEAK 42(18Q21.2) MUTATED 80 206 100 34
DEL PEAK 42(18Q21.2) WILD-TYPE 155 11 13 1

Figure S236.  Get High-res Image Gene #69: 'del_18q21.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_18q21.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S237.  Gene #69: 'del_18q21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 155 121
DEL PEAK 42(18Q21.2) MUTATED 60 146 63
DEL PEAK 42(18Q21.2) WILD-TYPE 38 9 58

Figure S237.  Get High-res Image Gene #69: 'del_18q21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_18q21.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S238.  Gene #69: 'del_18q21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 130 139 188
DEL PEAK 42(18Q21.2) MUTATED 88 59 129 134
DEL PEAK 42(18Q21.2) WILD-TYPE 39 71 10 54

Figure S238.  Get High-res Image Gene #69: 'del_18q21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_18q21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S239.  Gene #69: 'del_18q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 64 107 45 65 66 96 141
DEL PEAK 42(18Q21.2) MUTATED 34 77 12 58 65 45 119
DEL PEAK 42(18Q21.2) WILD-TYPE 30 30 33 7 1 51 22

Figure S239.  Get High-res Image Gene #69: 'del_18q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_18q21.2' versus 'MIRSEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.068

Table S240.  Gene #69: 'del_18q21.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 211 95 232
DEL PEAK 42(18Q21.2) MUTATED 169 55 153
DEL PEAK 42(18Q21.2) WILD-TYPE 42 40 79

Figure S240.  Get High-res Image Gene #69: 'del_18q21.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_18q21.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S241.  Gene #69: 'del_18q21.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
DEL PEAK 42(18Q21.2) MUTATED 92 52 68
DEL PEAK 42(18Q21.2) WILD-TYPE 8 57 17

Figure S241.  Get High-res Image Gene #69: 'del_18q21.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_18q21.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S242.  Gene #69: 'del_18q21.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 82 52 67 33 60
DEL PEAK 42(18Q21.2) MUTATED 64 46 57 29 16
DEL PEAK 42(18Q21.2) WILD-TYPE 18 6 10 4 44

Figure S242.  Get High-res Image Gene #69: 'del_18q21.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18q22.1' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S243.  Gene #70: 'del_18q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
DEL PEAK 43(18Q22.1) MUTATED 17 55 56 19
DEL PEAK 43(18Q22.1) WILD-TYPE 26 7 13 22

Figure S243.  Get High-res Image Gene #70: 'del_18q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_18q22.1' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S244.  Gene #70: 'del_18q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
DEL PEAK 43(18Q22.1) MUTATED 15 36 54 42
DEL PEAK 43(18Q22.1) WILD-TYPE 34 5 22 7

Figure S244.  Get High-res Image Gene #70: 'del_18q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_18q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S245.  Gene #70: 'del_18q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 235 217 113 35
DEL PEAK 43(18Q22.1) MUTATED 77 206 98 34
DEL PEAK 43(18Q22.1) WILD-TYPE 158 11 15 1

Figure S245.  Get High-res Image Gene #70: 'del_18q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_18q22.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S246.  Gene #70: 'del_18q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 155 121
DEL PEAK 43(18Q22.1) MUTATED 58 145 61
DEL PEAK 43(18Q22.1) WILD-TYPE 40 10 60

Figure S246.  Get High-res Image Gene #70: 'del_18q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_18q22.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S247.  Gene #70: 'del_18q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 130 139 188
DEL PEAK 43(18Q22.1) MUTATED 85 59 128 133
DEL PEAK 43(18Q22.1) WILD-TYPE 42 71 11 55

Figure S247.  Get High-res Image Gene #70: 'del_18q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_18q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S248.  Gene #70: 'del_18q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 64 107 45 65 66 96 141
DEL PEAK 43(18Q22.1) MUTATED 33 74 12 57 65 46 118
DEL PEAK 43(18Q22.1) WILD-TYPE 31 33 33 8 1 50 23

Figure S248.  Get High-res Image Gene #70: 'del_18q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_18q22.1' versus 'MIRSEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.087

Table S249.  Gene #70: 'del_18q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 211 95 232
DEL PEAK 43(18Q22.1) MUTATED 167 53 153
DEL PEAK 43(18Q22.1) WILD-TYPE 44 42 79

Figure S249.  Get High-res Image Gene #70: 'del_18q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_18q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S250.  Gene #70: 'del_18q22.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
DEL PEAK 43(18Q22.1) MUTATED 92 50 66
DEL PEAK 43(18Q22.1) WILD-TYPE 8 59 19

Figure S250.  Get High-res Image Gene #70: 'del_18q22.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_18q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S251.  Gene #70: 'del_18q22.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 82 52 67 33 60
DEL PEAK 43(18Q22.1) MUTATED 65 43 57 28 15
DEL PEAK 43(18Q22.1) WILD-TYPE 17 9 10 5 45

Figure S251.  Get High-res Image Gene #70: 'del_18q22.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S252.  Gene #71: 'del_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 235 217 113 35
DEL PEAK 44(19P13.3) MUTATED 16 48 24 9
DEL PEAK 44(19P13.3) WILD-TYPE 219 169 89 26

Figure S252.  Get High-res Image Gene #71: 'del_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_20p12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S253.  Gene #72: 'del_20p12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 235 217 113 35
DEL PEAK 45(20P12.1) MUTATED 45 103 36 0
DEL PEAK 45(20P12.1) WILD-TYPE 190 114 77 35

Figure S253.  Get High-res Image Gene #72: 'del_20p12.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_20p12.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S254.  Gene #72: 'del_20p12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 155 121
DEL PEAK 45(20P12.1) MUTATED 21 69 21
DEL PEAK 45(20P12.1) WILD-TYPE 77 86 100

Figure S254.  Get High-res Image Gene #72: 'del_20p12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_20p12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.055

Table S255.  Gene #72: 'del_20p12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 64 107 45 65 66 96 141
DEL PEAK 45(20P12.1) MUTATED 12 32 5 25 27 21 58
DEL PEAK 45(20P12.1) WILD-TYPE 52 75 40 40 39 75 83

Figure S255.  Get High-res Image Gene #72: 'del_20p12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_20p12.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00025 (Fisher's exact test), Q value = 0.16

Table S256.  Gene #72: 'del_20p12.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 82 52 67 33 60
DEL PEAK 45(20P12.1) MUTATED 27 27 21 10 7
DEL PEAK 45(20P12.1) WILD-TYPE 55 25 46 23 53

Figure S256.  Get High-res Image Gene #72: 'del_20p12.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_20p12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S257.  Gene #73: 'del_20p12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 235 217 113 35
DEL PEAK 46(20P12.1) MUTATED 45 103 36 0
DEL PEAK 46(20P12.1) WILD-TYPE 190 114 77 35

Figure S257.  Get High-res Image Gene #73: 'del_20p12.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_20p12.1' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S258.  Gene #73: 'del_20p12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 155 121
DEL PEAK 46(20P12.1) MUTATED 21 69 21
DEL PEAK 46(20P12.1) WILD-TYPE 77 86 100

Figure S258.  Get High-res Image Gene #73: 'del_20p12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_20p12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.028

Table S259.  Gene #73: 'del_20p12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 64 107 45 65 66 96 141
DEL PEAK 46(20P12.1) MUTATED 12 32 5 25 27 21 58
DEL PEAK 46(20P12.1) WILD-TYPE 52 75 40 40 39 75 83

Figure S259.  Get High-res Image Gene #73: 'del_20p12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_20p12.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.11

Table S260.  Gene #73: 'del_20p12.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 82 52 67 33 60
DEL PEAK 46(20P12.1) MUTATED 27 27 21 10 7
DEL PEAK 46(20P12.1) WILD-TYPE 55 25 46 23 53

Figure S260.  Get High-res Image Gene #73: 'del_20p12.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_21q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S261.  Gene #74: 'del_21q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 235 217 113 35
DEL PEAK 47(21Q11.2) MUTATED 50 105 32 21
DEL PEAK 47(21Q11.2) WILD-TYPE 185 112 81 14

Figure S261.  Get High-res Image Gene #74: 'del_21q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_21q11.2' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S262.  Gene #74: 'del_21q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 130 139 188
DEL PEAK 47(21Q11.2) MUTATED 39 28 71 64
DEL PEAK 47(21Q11.2) WILD-TYPE 88 102 68 124

Figure S262.  Get High-res Image Gene #74: 'del_21q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_21q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.074

Table S263.  Gene #74: 'del_21q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
DEL PEAK 47(21Q11.2) MUTATED 51 25 29
DEL PEAK 47(21Q11.2) WILD-TYPE 49 84 56

Figure S263.  Get High-res Image Gene #74: 'del_21q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_22q13.32' versus 'MRNA_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.081

Table S264.  Gene #75: 'del_22q13.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
DEL PEAK 48(22Q13.32) MUTATED 7 19 33 27
DEL PEAK 48(22Q13.32) WILD-TYPE 42 22 43 22

Figure S264.  Get High-res Image Gene #75: 'del_22q13.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_22q13.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.009

Table S265.  Gene #75: 'del_22q13.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 235 217 113 35
DEL PEAK 48(22Q13.32) MUTATED 41 123 37 21
DEL PEAK 48(22Q13.32) WILD-TYPE 194 94 76 14

Figure S265.  Get High-res Image Gene #75: 'del_22q13.32' versus Molecular Subtype #3: 'CN_CNMF'

'del_22q13.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.028

Table S266.  Gene #75: 'del_22q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 64 107 45 65 66 96 141
DEL PEAK 48(22Q13.32) MUTATED 18 40 5 29 29 27 68
DEL PEAK 48(22Q13.32) WILD-TYPE 46 67 40 36 37 69 73

Figure S266.  Get High-res Image Gene #75: 'del_22q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.028

Table S267.  Gene #75: 'del_22q13.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
DEL PEAK 48(22Q13.32) MUTATED 50 23 33
DEL PEAK 48(22Q13.32) WILD-TYPE 50 86 52

Figure S267.  Get High-res Image Gene #75: 'del_22q13.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

Methods & Data
Input

  • Copy number data file = transformed.cor.cli.txt

  • Molecular subtype file = COADREAD-TP.transferedmergedcluster.txt

  • Number of patients = 600

  • Number of significantly focal cnvs = 75

  • Number of molecular subtypes = 12

  • Exclude genes that fewer than K tumors have alterations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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