Correlation between copy number variation genes and molecular subtypes
Overview
Introduction

This pipeline computes the correlation between significant copy number variation (cnv) genes and molecular subtypes.

Summary

Testing the association between copy number variation of 82 peak regions and 12 molecular subtypes across 489 patients, 191 significant findings detected with Q value < 0.25.

  • Amp Peak 1(1q21.2) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 2(2p16.1) cnvs correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • Amp Peak 3(2q31.2) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • Amp Peak 5(3q26.33) cnvs correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 6(4q12) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 7(5p15.33) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 8(5p12) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 9(6p12.1) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 10(6q12) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 11(7p11.2) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 12(7q21.2) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Amp Peak 15(9p13.3) cnvs correlated to 'MRNASEQ_CHIERARCHICAL'.

  • Amp Peak 16(11q13.3) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 17(12p13.33) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Amp Peak 18(12q15) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 21(15q26.3) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Amp Peak 22(17q25.1) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Amp Peak 23(18p11.32) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Amp Peak 24(18q11.2) cnvs correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Amp Peak 25(19q12) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 26(19q13.2) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 27(20p12.2) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • Amp Peak 28(20q11.21) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 29(22q11.21) cnvs correlated to 'MRNASEQ_CNMF'.

  • Del Peak 1(1p36.32) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 2(1p13.1) cnvs correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 4(2q22.1) cnvs correlated to 'CN_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • Del Peak 5(2q37.1) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 7(3p13) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 8(3p12.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Del Peak 10(4p15.2) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • Del Peak 11(4q22.1) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • Del Peak 12(4q32.3) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 13(4q35.2) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 14(5q11.2) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 15(6p25.3) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Del Peak 16(6q22.31) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • Del Peak 17(6q26) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Del Peak 20(8p23.2) cnvs correlated to 'CN_CNMF'.

  • Del Peak 21(9p23) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • Del Peak 22(9p21.3) cnvs correlated to 'CN_CNMF'.

  • Del Peak 23(9p21.1) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • Del Peak 24(9q21.11) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 25(10p15.3) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 26(10p15.1) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 27(10q23.31) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • Del Peak 28(11p15.5) cnvs correlated to 'MRNA_CNMF',  'CN_CNMF', and 'RPPA_CHIERARCHICAL'.

  • Del Peak 29(11q22.1) cnvs correlated to 'CN_CNMF'.

  • Del Peak 34(14q11.2) cnvs correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • Del Peak 39(17p11.2) cnvs correlated to 'CN_CNMF'.

  • Del Peak 40(17q11.2) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Del Peak 44(19q13.32) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Del Peak 46(21q22.3) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.

  • Del Peak 48(22q13.32) cnvs correlated to 'MRNA_CNMF'.

  • Del Peak 49(Xp22.2) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 50(Xp21.1) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 51(Xp11.3) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 52(Xq22.3) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 82 regions and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 191 significant findings detected.

Molecular
subtypes 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
Del Peak 1(1p36 32) 0 (0%) 277 1.49e-06
(0.00136) 		1.22e-07
(0.000114) 		7.51e-35
(7.39e-32) 		1.96e-19
(1.92e-16) 		0.373
(1.00) 		0.0129
(1.00) 		3.79e-20
(3.72e-17) 		1.06e-20
(1.04e-17) 		2.12e-06
(0.00192) 		1.11e-05
(0.0097) 		0.00232
(1.00) 		3.84e-07
(0.000356)
Del Peak 2(1p13 1) 0 (0%) 281 0.000956
(0.726) 		6.31e-05
(0.053) 		3.83e-20
(3.76e-17) 		2.04e-12
(1.98e-09) 		0.0391
(1.00) 		0.0673
(1.00) 		2.36e-11
(2.28e-08) 		1.66e-13
(1.62e-10) 		4.79e-08
(4.52e-05) 		6.69e-06
(0.00592) 		0.00558
(1.00) 		5.63e-06
(0.00499)
Del Peak 24(9q21 11) 0 (0%) 247 8.38e-05
(0.0698) 		1.96e-05
(0.017) 		5.61e-13
(5.45e-10) 		1.41e-09
(1.35e-06) 		0.653
(1.00) 		0.239
(1.00) 		2.45e-15
(2.4e-12) 		6.64e-15
(6.49e-12) 		1.4e-05
(0.0122) 		5.56e-08
(5.24e-05) 		0.000947
(0.72) 		0.0462
(1.00)
Amp Peak 5(3q26 33) 0 (0%) 47 0.000425
(0.333) 		1.03e-05
(0.009) 		3.91e-15
(3.83e-12) 		7.78e-09
(7.41e-06) 		0.193
(1.00) 		0.0776
(1.00) 		1.98e-10
(1.91e-07) 		4.02e-08
(3.8e-05) 		6.45e-07
(0.000595) 		1.01e-06
(0.000928) 		0.0181
(1.00) 		0.00124
(0.928)
Amp Peak 22(17q25 1) 0 (0%) 258 0.0133
(1.00) 		0.0338
(1.00) 		1.54e-13
(1.5e-10) 		2.45e-08
(2.31e-05) 		0.479
(1.00) 		0.249
(1.00) 		3.01e-06
(0.0027) 		1.21e-07
(0.000113) 		0.000281
(0.224) 		0.0148
(1.00) 		1.19e-05
(0.0104) 		4.66e-06
(0.00415)
Amp Peak 24(18q11 2) 0 (0%) 344 0.000151
(0.123) 		0.0114
(1.00) 		6.51e-09
(6.21e-06) 		1.91e-05
(0.0165) 		0.197
(1.00) 		0.711
(1.00) 		7.51e-06
(0.00663) 		7.26e-07
(0.000668) 		0.00692
(1.00) 		0.00236
(1.00) 		0.000182
(0.147) 		0.000111
(0.0917)
Del Peak 5(2q37 1) 0 (0%) 335 0.00257
(1.00) 		0.00342
(1.00) 		4.19e-09
(4.01e-06) 		7.61e-07
(0.000699) 		0.523
(1.00) 		0.234
(1.00) 		2.07e-06
(0.00188) 		7.02e-06
(0.0062) 		2.81e-05
(0.0241) 		0.594
(1.00) 		1.46e-05
(0.0127) 		0.000193
(0.156)
Amp Peak 2(2p16 1) 0 (0%) 221 0.00212
(1.00) 		0.000275
(0.22) 		4.35e-14
(4.25e-11) 		2.79e-06
(0.00251) 		0.95
(1.00) 		0.643
(1.00) 		9.21e-10
(8.86e-07) 		4.83e-07
(0.000446) 		8.41e-05
(0.0699) 		0.000554
(0.428) 		0.00124
(0.932) 		0.000529
(0.412)
Del Peak 25(10p15 3) 0 (0%) 272 0.403
(1.00) 		0.572
(1.00) 		1.33e-07
(0.000124) 		8.77e-10
(8.45e-07) 		0.312
(1.00) 		0.39
(1.00) 		3.92e-05
(0.0332) 		4.28e-06
(0.00382) 		1.89e-06
(0.00171) 		1.14e-05
(0.00993) 		0.0246
(1.00) 		0.0139
(1.00)
Del Peak 26(10p15 1) 0 (0%) 284 0.109
(1.00) 		0.633
(1.00) 		1.83e-06
(0.00166) 		2.6e-10
(2.52e-07) 		0.469
(1.00) 		0.353
(1.00) 		1.59e-06
(0.00144) 		2.33e-06
(0.0021) 		1.58e-06
(0.00144) 		3.6e-06
(0.00322) 		0.173
(1.00) 		0.00975
(1.00)
Del Peak 40(17q11 2) 0 (0%) 367 3.03e-05
(0.0259) 		0.000101
(0.0837) 		1.55e-06
(0.00142) 		4.56e-05
(0.0384) 		0.495
(1.00) 		0.378
(1.00) 		7.33e-09
(6.98e-06) 		3.86e-09
(3.69e-06) 		0.275
(1.00) 		0.0053
(1.00) 		0.0124
(1.00) 		0.00178
(1.00)
Amp Peak 1(1q21 2) 0 (0%) 239 0.0448
(1.00) 		0.0304
(1.00) 		3.22e-12
(3.13e-09) 		7.11e-07
(0.000655) 		0.16
(1.00) 		0.0492
(1.00) 		1.48e-07
(0.000138) 		4.92e-10
(4.74e-07) 		0.00106
(0.798) 		3.03e-05
(0.0259) 		0.026
(1.00) 		0.0201
(1.00)
Amp Peak 3(2q31 2) 0 (0%) 324 0.0154
(1.00) 		0.0275
(1.00) 		2.93e-06
(0.00264) 		5.78e-06
(0.00512) 		0.826
(1.00) 		0.812
(1.00) 		4.83e-06
(0.00429) 		4.17e-05
(0.0353) 		0.0392
(1.00) 		0.62
(1.00) 		0.000309
(0.246) 		0.00191
(1.00)
Del Peak 12(4q32 3) 0 (0%) 171 0.0113
(1.00) 		0.0203
(1.00) 		5.63e-09
(5.38e-06) 		7.36e-05
(0.0616) 		0.101
(1.00) 		0.523
(1.00) 		4.7e-06
(0.00418) 		8.9e-05
(0.0739) 		0.000385
(0.303) 		0.00947
(1.00) 		0.0059
(1.00) 		7.55e-05
(0.0629)
Del Peak 13(4q35 2) 0 (0%) 169 0.0987
(1.00) 		0.396
(1.00) 		7.6e-08
(7.14e-05) 		3.56e-05
(0.0302) 		0.455
(1.00) 		0.47
(1.00) 		3.97e-06
(0.00355) 		0.000174
(0.142) 		0.00261
(1.00) 		0.0434
(1.00) 		0.0442
(1.00) 		0.000197
(0.159)
Del Peak 27(10q23 31) 0 (0%) 237 0.0148
(1.00) 		0.0131
(1.00) 		4.34e-08
(4.1e-05) 		2.36e-07
(0.00022) 		0.36
(1.00) 		0.39
(1.00) 		6.5e-08
(6.12e-05) 		9.78e-10
(9.4e-07) 		0.00477
(1.00) 		0.00309
(1.00) 		3.37e-05
(0.0286) 		0.00543
(1.00)
Del Peak 50(Xp21 1) 0 (0%) 333 0.386
(1.00) 		0.414
(1.00) 		3.82e-07
(0.000354) 		1.29e-05
(0.0112) 		0.197
(1.00) 		0.702
(1.00) 		0.000869
(0.662) 		0.00122
(0.917) 		2.01e-05
(0.0174) 		0.0544
(1.00) 		0.000246
(0.197) 		8.65e-09
(8.21e-06)
Del Peak 51(Xp11 3) 0 (0%) 336 0.11
(1.00) 		0.414
(1.00) 		1.22e-07
(0.000114) 		4.05e-06
(0.00362) 		0.0923
(1.00) 		0.124
(1.00) 		0.000787
(0.601) 		0.000352
(0.278) 		1.38e-06
(0.00126) 		0.0455
(1.00) 		3.21e-05
(0.0274) 		1.47e-08
(1.39e-05)
Amp Peak 12(7q21 2) 0 (0%) 233 0.175
(1.00) 		0.116
(1.00) 		4.52e-13
(4.4e-10) 		3.42e-06
(0.00307) 		0.0573
(1.00) 		0.389
(1.00) 		5.62e-06
(0.00499) 		1.09e-05
(0.00951) 		0.00292
(1.00) 		0.0251
(1.00) 		0.00411
(1.00) 		0.00127
(0.949)
Amp Peak 17(12p13 33) 0 (0%) 241 0.0263
(1.00) 		0.0936
(1.00) 		4.56e-07
(0.000422) 		7.03e-05
(0.0588) 		0.313
(1.00) 		0.729
(1.00) 		2.13e-08
(2.02e-05) 		4.59e-05
(0.0386) 		0.0121
(1.00) 		0.0205
(1.00) 		0.134
(1.00) 		0.0263
(1.00)
Amp Peak 21(15q26 3) 0 (0%) 316 0.253
(1.00) 		0.0414
(1.00) 		2.65e-06
(0.00239) 		0.000229
(0.185) 		0.354
(1.00) 		0.0183
(1.00) 		2.47e-05
(0.0212) 		0.000219
(0.177) 		0.00716
(1.00) 		0.0017
(1.00) 		0.0126
(1.00) 		0.0356
(1.00)
Del Peak 7(3p13) 0 (0%) 70 0.298
(1.00) 		0.949
(1.00) 		1.25e-06
(0.00114) 		0.000314
(0.25) 		0.775
(1.00) 		0.0387
(1.00) 		0.00143
(1.00) 		0.00684
(1.00) 		4.76e-05
(0.0401) 		0.0118
(1.00) 		0.00403
(1.00) 		5.83e-05
(0.049)
Del Peak 15(6p25 3) 0 (0%) 364 0.319
(1.00) 		0.0462
(1.00) 		0.000114
(0.0935) 		0.000102
(0.0844) 		0.393
(1.00) 		0.013
(1.00) 		2.82e-06
(0.00254) 		6.82e-08
(6.41e-05) 		0.0926
(1.00) 		0.0201
(1.00) 		0.0767
(1.00) 		0.00767
(1.00)
Del Peak 17(6q26) 0 (0%) 360 0.0421
(1.00) 		0.0154
(1.00) 		2.95e-05
(0.0252) 		0.000115
(0.0949) 		0.921
(1.00) 		0.69
(1.00) 		0.000276
(0.22) 		0.000219
(0.177) 		0.0208
(1.00) 		0.029
(1.00) 		0.0211
(1.00) 		0.0159
(1.00)
Del Peak 4(2q22 1) 0 (0%) 368 0.208
(1.00) 		0.245
(1.00) 		1.69e-05
(0.0147) 		0.000358
(0.282) 		0.546
(1.00) 		0.0829
(1.00) 		0.00785
(1.00) 		0.000962
(0.729) 		0.000126
(0.104) 		0.029
(1.00) 		0.000293
(0.233) 		0.0191
(1.00)
Del Peak 10(4p15 2) 0 (0%) 190 0.000325
(0.258) 		0.00153
(1.00) 		2.32e-09
(2.22e-06) 		6.04e-06
(0.00535) 		0.662
(1.00) 		0.0343
(1.00) 		9.06e-05
(0.0751) 		0.000341
(0.27) 		0.00352
(1.00) 		0.974
(1.00) 		0.005
(1.00) 		0.00059
(0.454)
Del Peak 14(5q11 2) 0 (0%) 136 0.706
(1.00) 		0.656
(1.00) 		2.55e-11
(2.47e-08) 		0.0001
(0.0832) 		0.959
(1.00) 		0.244
(1.00) 		0.00353
(1.00) 		0.00878
(1.00) 		0.0237
(1.00) 		3.21e-05
(0.0274) 		0.00364
(1.00) 		0.000523
(0.407)
Del Peak 28(11p15 5) 0 (0%) 259 0.000261
(0.209) 		0.0341
(1.00) 		1.39e-07
(0.000129) 		0.0237
(1.00) 		0.000764
(0.584) 		2.02e-05
(0.0174) 		0.0109
(1.00) 		0.0322
(1.00) 		0.0124
(1.00) 		0.213
(1.00) 		0.0203
(1.00) 		0.0195
(1.00)
Del Peak 52(Xq22 3) 0 (0%) 370 0.00842
(1.00) 		0.015
(1.00) 		2.71e-07
(0.000252) 		1.02e-05
(0.00897) 		0.663
(1.00) 		0.92
(1.00) 		0.00195
(1.00) 		0.0514
(1.00) 		3.57e-05
(0.0303) 		0.624
(1.00) 		0.000444
(0.348) 		0.013
(1.00)
Amp Peak 23(18p11 32) 0 (0%) 319 0.0582
(1.00) 		0.0147
(1.00) 		2.38e-07
(0.000221) 		2.17e-05
(0.0187) 		0.261
(1.00) 		0.735
(1.00) 		0.0839
(1.00) 		0.1
(1.00) 		0.0311
(1.00) 		0.0578
(1.00) 		0.0219
(1.00) 		0.0361
(1.00)
Amp Peak 27(20p12 2) 0 (0%) 221 0.00106
(0.798) 		0.0142
(1.00) 		5.15e-10
(4.96e-07) 		0.000539
(0.418) 		0.967
(1.00) 		0.221
(1.00) 		0.00307
(1.00) 		0.000136
(0.111) 		0.0107
(1.00) 		0.398
(1.00) 		0.0339
(1.00) 		0.372
(1.00)
Del Peak 8(3p12 3) 0 (0%) 81 0.164
(1.00) 		0.954
(1.00) 		2.32e-05
(0.02) 		0.000187
(0.151) 		1
(1.00) 		0.092
(1.00) 		0.00452
(1.00) 		0.00783
(1.00) 		0.000542
(0.419) 		0.0704
(1.00) 		0.0306
(1.00) 		0.00282
(1.00)
Del Peak 11(4q22 1) 0 (0%) 216 0.00688
(1.00) 		0.0456
(1.00) 		1.92e-06
(0.00175) 		0.00169
(1.00) 		0.123
(1.00) 		0.381
(1.00) 		0.00012
(0.0985) 		0.00125
(0.935) 		0.0298
(1.00) 		0.0958
(1.00) 		0.196
(1.00) 		0.12
(1.00)
Del Peak 16(6q22 31) 0 (0%) 372 0.0278
(1.00) 		0.0123
(1.00) 		4.19e-05
(0.0354) 		0.000726
(0.556) 		0.629
(1.00) 		0.354
(1.00) 		0.000154
(0.126) 		0.000571
(0.44) 		0.0327
(1.00) 		0.0398
(1.00) 		0.0434
(1.00) 		0.0264
(1.00)
Del Peak 21(9p23) 0 (0%) 172 0.0103
(1.00) 		0.00676
(1.00) 		3.09e-06
(0.00277) 		0.0718
(1.00) 		0.146
(1.00) 		0.208
(1.00) 		4.33e-05
(0.0365) 		0.0144
(1.00) 		0.00186
(1.00) 		0.00151
(1.00) 		0.0318
(1.00) 		0.728
(1.00)
Del Peak 23(9p21 1) 0 (0%) 177 0.121
(1.00) 		0.0364
(1.00) 		9.11e-06
(0.008) 		0.276
(1.00) 		0.673
(1.00) 		0.391
(1.00) 		0.00011
(0.0905) 		0.0108
(1.00) 		0.267
(1.00) 		0.0515
(1.00) 		0.0527
(1.00) 		0.416
(1.00)
Del Peak 34(14q11 2) 0 (0%) 322 0.0724
(1.00) 		0.237
(1.00) 		0.336
(1.00) 		0.864
(1.00) 		0.206
(1.00) 		0.159
(1.00) 		3.27e-05
(0.0278) 		1.37e-07
(0.000128) 		0.00508
(1.00) 		0.103
(1.00) 		0.422
(1.00) 		0.243
(1.00)
Del Peak 44(19q13 32) 0 (0%) 348 0.749
(1.00) 		0.247
(1.00) 		1.13e-06
(0.00104) 		2.32e-05
(0.02) 		0.183
(1.00) 		0.704
(1.00) 		0.0038
(1.00) 		0.0229
(1.00) 		0.00795
(1.00) 		0.767
(1.00) 		0.152
(1.00) 		0.0276
(1.00)
Del Peak 46(21q22 3) 0 (0%) 216 0.876
(1.00) 		0.189
(1.00) 		9.46e-08
(8.87e-05) 		0.0191
(1.00) 		0.396
(1.00) 		0.0991
(1.00) 		0.154
(1.00) 		0.006
(1.00) 		8.61e-05
(0.0716) 		0.123
(1.00) 		0.163
(1.00) 		0.0263
(1.00)
Del Peak 49(Xp22 2) 0 (0%) 332 0.616
(1.00) 		0.679
(1.00) 		1.23e-05
(0.0107) 		0.00111
(0.839) 		0.354
(1.00) 		0.8
(1.00) 		0.0214
(1.00) 		0.0339
(1.00) 		0.000818
(0.624) 		0.0869
(1.00) 		0.000491
(0.384) 		1.95e-06
(0.00177)
Amp Peak 6(4q12) 0 (0%) 378 0.809
(1.00) 		0.2
(1.00) 		0.00017
(0.138) 		0.0861
(1.00) 		0.356
(1.00) 		0.131
(1.00) 		0.101
(1.00) 		0.0697
(1.00) 		0.00308
(1.00) 		0.455
(1.00) 		0.0657
(1.00) 		1
(1.00)
Amp Peak 7(5p15 33) 0 (0%) 112 0.852
(1.00) 		0.983
(1.00) 		3.16e-09
(3.03e-06) 		0.0337
(1.00) 		0.405
(1.00) 		0.502
(1.00) 		0.5
(1.00) 		0.189
(1.00) 		0.806
(1.00) 		0.00869
(1.00) 		0.428
(1.00) 		0.237
(1.00)
Amp Peak 8(5p12) 0 (0%) 147 0.959
(1.00) 		1
(1.00) 		1.6e-08
(1.52e-05) 		0.0402
(1.00) 		0.217
(1.00) 		0.988
(1.00) 		0.511
(1.00) 		0.947
(1.00) 		0.946
(1.00) 		0.0711
(1.00) 		0.709
(1.00) 		0.811
(1.00)
Amp Peak 9(6p12 1) 0 (0%) 329 0.551
(1.00) 		0.737
(1.00) 		1.48e-05
(0.0129) 		0.0365
(1.00) 		0.962
(1.00) 		0.3
(1.00) 		0.00127
(0.95) 		0.251
(1.00) 		0.593
(1.00) 		0.107
(1.00) 		0.0366
(1.00) 		0.00435
(1.00)
Amp Peak 10(6q12) 0 (0%) 343 0.946
(1.00) 		0.748
(1.00) 		7.43e-05
(0.062) 		0.00192
(1.00) 		0.405
(1.00) 		0.392
(1.00) 		0.00602
(1.00) 		0.0158
(1.00) 		0.397
(1.00) 		0.0974
(1.00) 		0.288
(1.00) 		0.00736
(1.00)
Amp Peak 11(7p11 2) 0 (0%) 244 0.164
(1.00) 		0.0996
(1.00) 		8.85e-06
(0.00779) 		0.00298
(1.00) 		0.687
(1.00) 		0.801
(1.00) 		0.00805
(1.00) 		0.000385
(0.303) 		0.0863
(1.00) 		0.127
(1.00) 		0.0238
(1.00) 		0.0594
(1.00)
Amp Peak 15(9p13 3) 0 (0%) 354 0.124
(1.00) 		0.838
(1.00) 		0.00103
(0.778) 		0.00131
(0.974) 		0.0708
(1.00) 		0.00898
(1.00) 		0.000492
(0.384) 		0.000184
(0.149) 		0.0253
(1.00) 		0.351
(1.00) 		0.0811
(1.00) 		0.0627
(1.00)
Amp Peak 16(11q13 3) 0 (0%) 311 0.0582
(1.00) 		0.0872
(1.00) 		0.000134
(0.11) 		0.000629
(0.484) 		0.19
(1.00) 		0.0358
(1.00) 		0.0134
(1.00) 		0.0206
(1.00) 		0.0022
(1.00) 		0.111
(1.00) 		0.0152
(1.00) 		0.305
(1.00)
Amp Peak 18(12q15) 0 (0%) 316 0.235
(1.00) 		0.326
(1.00) 		3.26e-05
(0.0278) 		0.00693
(1.00) 		0.764
(1.00) 		0.524
(1.00) 		0.012
(1.00) 		0.00319
(1.00) 		0.647
(1.00) 		0.412
(1.00) 		0.0878
(1.00) 		0.131
(1.00)
Amp Peak 25(19q12) 0 (0%) 277 0.438
(1.00) 		0.693
(1.00) 		8.3e-09
(7.9e-06) 		0.00264
(1.00) 		0.231
(1.00) 		0.0287
(1.00) 		0.0238
(1.00) 		0.00647
(1.00) 		0.311
(1.00) 		0.586
(1.00) 		0.0718
(1.00) 		0.0572
(1.00)
Amp Peak 26(19q13 2) 0 (0%) 272 0.678
(1.00) 		0.86
(1.00) 		7.93e-07
(0.000728) 		0.00221
(1.00) 		0.356
(1.00) 		0.117
(1.00) 		0.0503
(1.00) 		0.0031
(1.00) 		0.445
(1.00) 		0.535
(1.00) 		0.284
(1.00) 		0.222
(1.00)
Amp Peak 28(20q11 21) 0 (0%) 198 0.86
(1.00) 		0.948
(1.00) 		4.62e-07
(0.000427) 		0.00646
(1.00) 		0.669
(1.00) 		0.588
(1.00) 		0.706
(1.00) 		0.436
(1.00) 		0.139
(1.00) 		0.0561
(1.00) 		0.0517
(1.00) 		0.652
(1.00)
Amp Peak 29(22q11 21) 0 (0%) 239 0.141
(1.00) 		0.204
(1.00) 		0.000374
(0.295) 		0.00473
(1.00) 		0.888
(1.00) 		0.349
(1.00) 		0.000284
(0.227) 		0.00415
(1.00) 		0.0157
(1.00) 		0.311
(1.00) 		0.00814
(1.00) 		0.269
(1.00)
Del Peak 20(8p23 2) 0 (0%) 158 0.667
(1.00) 		0.847
(1.00) 		6.89e-05
(0.0578) 		0.0334
(1.00) 		0.345
(1.00) 		0.141
(1.00) 		0.173
(1.00) 		0.0855
(1.00) 		0.0973
(1.00) 		0.117
(1.00) 		0.644
(1.00) 		0.0594
(1.00)
Del Peak 22(9p21 3) 0 (0%) 118 0.326
(1.00) 		0.311
(1.00) 		7.87e-06
(0.00693) 		0.512
(1.00) 		0.695
(1.00) 		0.388
(1.00) 		0.000539
(0.418) 		0.387
(1.00) 		0.217
(1.00) 		0.17
(1.00) 		0.0713
(1.00) 		0.896
(1.00)
Del Peak 29(11q22 1) 0 (0%) 338 0.708
(1.00) 		0.379
(1.00) 		0.000171
(0.139) 		0.00111
(0.835) 		0.101
(1.00) 		0.991
(1.00) 		0.106
(1.00) 		0.112
(1.00) 		0.000537
(0.417) 		0.569
(1.00) 		0.0218
(1.00) 		0.00303
(1.00)
Del Peak 39(17p11 2) 0 (0%) 231 0.217
(1.00) 		0.0324
(1.00) 		0.000255
(0.205) 		0.699
(1.00) 		0.15
(1.00) 		0.0182
(1.00) 		0.0734
(1.00) 		0.0769
(1.00) 		0.35
(1.00) 		0.0494
(1.00) 		0.941
(1.00) 		1
(1.00)
Del Peak 48(22q13 32) 0 (0%) 364 0.00022
(0.177) 		0.00221
(1.00) 		0.109
(1.00) 		0.0844
(1.00) 		0.543
(1.00) 		0.0759
(1.00) 		0.00228
(1.00) 		0.00291
(1.00) 		0.0676
(1.00) 		0.00175
(1.00) 		0.715
(1.00) 		0.372
(1.00)
Amp Peak 4(3p11 1) 0 (0%) 393 0.104
(1.00) 		0.836
(1.00) 		0.771
(1.00) 		0.757
(1.00) 		0.214
(1.00) 		0.0013
(0.966) 		0.312
(1.00) 		0.331
(1.00) 		0.24
(1.00) 		0.579
(1.00) 		0.738
(1.00) 		0.251
(1.00)
Amp Peak 13(8p11 23) 0 (0%) 258 0.0137
(1.00) 		0.467
(1.00) 		0.000648
(0.497) 		0.0237
(1.00) 		0.192
(1.00) 		0.0988
(1.00) 		0.00963
(1.00) 		0.716
(1.00) 		0.658
(1.00) 		0.149
(1.00) 		0.656
(1.00) 		0.183
(1.00)
Amp Peak 14(8q24 21) 0 (0%) 149 0.919
(1.00) 		0.788
(1.00) 		0.0255
(1.00) 		0.319
(1.00) 		0.917
(1.00) 		0.708
(1.00) 		0.878
(1.00) 		0.991
(1.00) 		0.544
(1.00) 		0.484
(1.00) 		0.229
(1.00) 		1
(1.00)
Amp Peak 19(13q34) 0 (0%) 404 0.981
(1.00) 		0.0207
(1.00) 		0.214
(1.00) 		0.521
(1.00) 		0.87
(1.00) 		0.0834
(1.00) 		0.917
(1.00) 		0.612
(1.00) 		0.62
(1.00) 		0.332
(1.00) 		0.573
(1.00) 		0.885
(1.00)
Amp Peak 20(14q13 3) 0 (0%) 338 0.316
(1.00) 		0.194
(1.00) 		0.0951
(1.00) 		0.112
(1.00) 		0.57
(1.00) 		0.00826
(1.00) 		0.0982
(1.00) 		0.0256
(1.00) 		0.0171
(1.00) 		0.321
(1.00) 		0.146
(1.00) 		1
(1.00)
Amp Peak 30(Xq28) 0 (0%) 359 0.793
(1.00) 		0.71
(1.00) 		0.0184
(1.00) 		0.0416
(1.00) 		0.0701
(1.00) 		0.069
(1.00) 		0.0255
(1.00) 		0.0368
(1.00) 		0.00599
(1.00) 		0.0978
(1.00) 		0.0388
(1.00) 		0.0177
(1.00)
Del Peak 3(2p25 3) 0 (0%) 443 0.0858
(1.00) 		0.0152
(1.00) 		0.169
(1.00) 		0.267
(1.00) 		0.11
(1.00) 		0.838
(1.00) 		0.329
(1.00) 		0.0308
(1.00) 		0.0262
(1.00) 		0.14
(1.00) 		0.168
(1.00) 		0.319
(1.00)
Del Peak 6(3p25 3) 0 (0%) 104 0.674
(1.00) 		0.63
(1.00) 		0.00942
(1.00) 		0.00125
(0.937) 		0.637
(1.00) 		0.18
(1.00) 		0.0208
(1.00) 		0.00844
(1.00) 		0.000934
(0.711) 		0.0141
(1.00) 		0.152
(1.00) 		0.015
(1.00)
Del Peak 9(3q11 1) 0 (0%) 412 0.762
(1.00) 		0.625
(1.00) 		0.3
(1.00) 		0.949
(1.00) 		0.765
(1.00) 		0.282
(1.00) 		0.753
(1.00) 		0.866
(1.00) 		0.769
(1.00) 		0.493
(1.00) 		0.426
(1.00) 		0.227
(1.00)
Del Peak 18(7q11 22) 0 (0%) 443 0.802
(1.00) 		0.106
(1.00) 		0.000502
(0.392) 		0.444
(1.00) 		0.958
(1.00) 		0.75
(1.00) 		0.00636
(1.00) 		0.124
(1.00) 		0.882
(1.00) 		0.862
(1.00) 		0.784
(1.00) 		1
(1.00)
Del Peak 19(7q36 3) 0 (0%) 386 0.17
(1.00) 		0.131
(1.00) 		0.000557
(0.43) 		0.272
(1.00) 		1
(1.00) 		0.315
(1.00) 		0.000659
(0.505) 		0.0012
(0.903) 		0.443
(1.00) 		0.503
(1.00) 		0.107
(1.00) 		0.788
(1.00)
Del Peak 30(11q25) 0 (0%) 311 0.874
(1.00) 		0.578
(1.00) 		0.00367
(1.00) 		0.0759
(1.00) 		0.113
(1.00) 		0.908
(1.00) 		0.074
(1.00) 		0.174
(1.00) 		0.0123
(1.00) 		0.568
(1.00) 		0.107
(1.00) 		0.0155
(1.00)
Del Peak 31(12q24 31) 0 (0%) 404 0.987
(1.00) 		0.372
(1.00) 		0.461
(1.00) 		0.249
(1.00) 		0.323
(1.00) 		0.207
(1.00) 		0.82
(1.00) 		0.729
(1.00) 		0.356
(1.00) 		0.0879
(1.00) 		0.55
(1.00) 		1
(1.00)
Del Peak 32(13q12 11) 0 (0%) 170 0.0859
(1.00) 		0.501
(1.00) 		0.00855
(1.00) 		0.148
(1.00) 		0.891
(1.00) 		0.16
(1.00) 		0.728
(1.00) 		0.261
(1.00) 		0.77
(1.00) 		0.386
(1.00) 		0.0862
(1.00) 		0.0801
(1.00)
Del Peak 33(13q14 2) 0 (0%) 157 0.0997
(1.00) 		0.321
(1.00) 		0.00861
(1.00) 		0.0352
(1.00) 		0.707
(1.00) 		0.682
(1.00) 		0.554
(1.00) 		0.0734
(1.00) 		0.147
(1.00) 		0.305
(1.00) 		0.0162
(1.00) 		0.0129
(1.00)
Del Peak 35(15q12) 0 (0%) 325 0.47
(1.00) 		0.469
(1.00) 		0.0821
(1.00) 		0.321
(1.00) 		0.0344
(1.00) 		0.0132
(1.00) 		0.19
(1.00) 		0.00448
(1.00) 		0.00848
(1.00) 		0.928
(1.00) 		0.284
(1.00) 		0.472
(1.00)
Del Peak 36(15q21 1) 0 (0%) 329 0.382
(1.00) 		0.415
(1.00) 		0.0155
(1.00) 		0.293
(1.00) 		0.138
(1.00) 		0.00763
(1.00) 		0.262
(1.00) 		0.00598
(1.00) 		0.00444
(1.00) 		0.611
(1.00) 		0.12
(1.00) 		0.551
(1.00)
Del Peak 37(16p13 3) 0 (0%) 311 0.348
(1.00) 		0.339
(1.00) 		0.00721
(1.00) 		0.058
(1.00) 		0.149
(1.00) 		0.606
(1.00) 		0.776
(1.00) 		0.108
(1.00) 		0.0252
(1.00) 		0.982
(1.00) 		0.126
(1.00) 		0.3
(1.00)
Del Peak 38(16q23 1) 0 (0%) 288 0.874
(1.00) 		0.336
(1.00) 		0.0359
(1.00) 		0.362
(1.00) 		0.354
(1.00) 		0.761
(1.00) 		0.147
(1.00) 		0.149
(1.00) 		0.0545
(1.00) 		0.418
(1.00) 		0.0018
(1.00) 		0.00497
(1.00)
Del Peak 41(17q25 3) 0 (0%) 389 0.0046
(1.00) 		0.015
(1.00) 		0.00196
(1.00) 		0.0291
(1.00) 		0.622
(1.00) 		0.994
(1.00) 		0.00624
(1.00) 		0.00192
(1.00) 		0.884
(1.00) 		0.0319
(1.00) 		0.372
(1.00) 		0.0138
(1.00)
Del Peak 42(18q23) 0 (0%) 262 0.454
(1.00) 		0.217
(1.00) 		0.0337
(1.00) 		0.284
(1.00) 		0.801
(1.00) 		0.397
(1.00) 		0.648
(1.00) 		0.0728
(1.00) 		0.237
(1.00) 		0.662
(1.00) 		0.1
(1.00) 		0.374
(1.00)
Del Peak 43(19p13 3) 0 (0%) 268 0.223
(1.00) 		0.00269
(1.00) 		0.00298
(1.00) 		0.834
(1.00) 		0.0799
(1.00) 		0.358
(1.00) 		0.171
(1.00) 		0.0501
(1.00) 		0.0483
(1.00) 		0.0022
(1.00) 		0.424
(1.00) 		0.576
(1.00)
Del Peak 45(21q21 1) 0 (0%) 253 0.571
(1.00) 		0.395
(1.00) 		0.000323
(0.256) 		0.0832
(1.00) 		0.585
(1.00) 		0.89
(1.00) 		0.394
(1.00) 		0.0961
(1.00) 		0.000467
(0.366) 		0.0643
(1.00) 		0.0175
(1.00) 		0.0357
(1.00)
Del Peak 47(22q11 21) 0 (0%) 399 0.0298
(1.00) 		0.16
(1.00) 		0.227
(1.00) 		0.299
(1.00) 		0.145
(1.00) 		0.129
(1.00) 		0.581
(1.00) 		0.542
(1.00) 		0.312
(1.00) 		1
(1.00) 		0.33
(1.00) 		0.3
(1.00)
'Amp Peak 1(1q21.2)' versus 'CN_CNMF'

P value = 3.22e-12 (Fisher's exact test), Q value = 3.1e-09

Table S1.  Gene #1: 'Amp Peak 1(1q21.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
AMP PEAK 1(1Q21.2) CNV 80 120 50
AMP PEAK 1(1Q21.2) WILD-TYPE 114 42 83

Figure S1.  Get High-res Image Gene #1: 'Amp Peak 1(1q21.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 1(1q21.2)' versus 'METHLYATION_CNMF'

P value = 7.11e-07 (Fisher's exact test), Q value = 0.00065

Table S2.  Gene #1: 'Amp Peak 1(1q21.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 99
AMP PEAK 1(1Q21.2) CNV 50 78 48
AMP PEAK 1(1Q21.2) WILD-TYPE 92 36 51

Figure S2.  Get High-res Image Gene #1: 'Amp Peak 1(1q21.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 1(1q21.2)' versus 'MRNASEQ_CNMF'

P value = 1.48e-07 (Fisher's exact test), Q value = 0.00014

Table S3.  Gene #1: 'Amp Peak 1(1q21.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 142 75
AMP PEAK 1(1Q21.2) CNV 44 100 71 29
AMP PEAK 1(1Q21.2) WILD-TYPE 74 43 71 46

Figure S3.  Get High-res Image Gene #1: 'Amp Peak 1(1q21.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 1(1q21.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.92e-10 (Fisher's exact test), Q value = 4.7e-07

Table S4.  Gene #1: 'Amp Peak 1(1q21.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 245
AMP PEAK 1(1Q21.2) CNV 52 100 92
AMP PEAK 1(1Q21.2) WILD-TYPE 41 40 153

Figure S4.  Get High-res Image Gene #1: 'Amp Peak 1(1q21.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 1(1q21.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.03e-05 (Fisher's exact test), Q value = 0.026

Table S5.  Gene #1: 'Amp Peak 1(1q21.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 71 163 229
AMP PEAK 1(1Q21.2) CNV 53 70 114
AMP PEAK 1(1Q21.2) WILD-TYPE 18 93 115

Figure S5.  Get High-res Image Gene #1: 'Amp Peak 1(1q21.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 2(2p16.1)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000275 (Fisher's exact test), Q value = 0.22

Table S6.  Gene #2: 'Amp Peak 2(2p16.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 22 56 23 53
AMP PEAK 2(2P16.1) CNV 7 42 15 22
AMP PEAK 2(2P16.1) WILD-TYPE 15 14 8 31

Figure S6.  Get High-res Image Gene #2: 'Amp Peak 2(2p16.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 2(2p16.1)' versus 'CN_CNMF'

P value = 4.35e-14 (Fisher's exact test), Q value = 4.2e-11

Table S7.  Gene #2: 'Amp Peak 2(2p16.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
AMP PEAK 2(2P16.1) CNV 72 126 70
AMP PEAK 2(2P16.1) WILD-TYPE 122 36 63

Figure S7.  Get High-res Image Gene #2: 'Amp Peak 2(2p16.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 2(2p16.1)' versus 'METHLYATION_CNMF'

P value = 2.79e-06 (Fisher's exact test), Q value = 0.0025

Table S8.  Gene #2: 'Amp Peak 2(2p16.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 99
AMP PEAK 2(2P16.1) CNV 61 84 51
AMP PEAK 2(2P16.1) WILD-TYPE 81 30 48

Figure S8.  Get High-res Image Gene #2: 'Amp Peak 2(2p16.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 2(2p16.1)' versus 'MRNASEQ_CNMF'

P value = 9.21e-10 (Fisher's exact test), Q value = 8.9e-07

Table S9.  Gene #2: 'Amp Peak 2(2p16.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 142 75
AMP PEAK 2(2P16.1) CNV 51 106 81 24
AMP PEAK 2(2P16.1) WILD-TYPE 67 37 61 51

Figure S9.  Get High-res Image Gene #2: 'Amp Peak 2(2p16.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 2(2p16.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.83e-07 (Fisher's exact test), Q value = 0.00045

Table S10.  Gene #2: 'Amp Peak 2(2p16.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 245
AMP PEAK 2(2P16.1) CNV 53 101 108
AMP PEAK 2(2P16.1) WILD-TYPE 40 39 137

Figure S10.  Get High-res Image Gene #2: 'Amp Peak 2(2p16.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 2(2p16.1)' versus 'MIRSEQ_CNMF'

P value = 8.41e-05 (Fisher's exact test), Q value = 0.07

Table S11.  Gene #2: 'Amp Peak 2(2p16.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 130 124 64
AMP PEAK 2(2P16.1) CNV 80 88 49 39
AMP PEAK 2(2P16.1) WILD-TYPE 65 42 75 25

Figure S11.  Get High-res Image Gene #2: 'Amp Peak 2(2p16.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 3(2q31.2)' versus 'CN_CNMF'

P value = 2.93e-06 (Fisher's exact test), Q value = 0.0026

Table S12.  Gene #3: 'Amp Peak 3(2q31.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
AMP PEAK 3(2Q31.2) CNV 43 77 45
AMP PEAK 3(2Q31.2) WILD-TYPE 151 85 88

Figure S12.  Get High-res Image Gene #3: 'Amp Peak 3(2q31.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 3(2q31.2)' versus 'METHLYATION_CNMF'

P value = 5.78e-06 (Fisher's exact test), Q value = 0.0051

Table S13.  Gene #3: 'Amp Peak 3(2q31.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 99
AMP PEAK 3(2Q31.2) CNV 36 60 26
AMP PEAK 3(2Q31.2) WILD-TYPE 106 54 73

Figure S13.  Get High-res Image Gene #3: 'Amp Peak 3(2q31.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 3(2q31.2)' versus 'MRNASEQ_CNMF'

P value = 4.83e-06 (Fisher's exact test), Q value = 0.0043

Table S14.  Gene #3: 'Amp Peak 3(2q31.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 142 75
AMP PEAK 3(2Q31.2) CNV 30 72 45 15
AMP PEAK 3(2Q31.2) WILD-TYPE 88 71 97 60

Figure S14.  Get High-res Image Gene #3: 'Amp Peak 3(2q31.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 3(2q31.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.17e-05 (Fisher's exact test), Q value = 0.035

Table S15.  Gene #3: 'Amp Peak 3(2q31.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 245
AMP PEAK 3(2Q31.2) CNV 33 67 62
AMP PEAK 3(2Q31.2) WILD-TYPE 60 73 183

Figure S15.  Get High-res Image Gene #3: 'Amp Peak 3(2q31.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 3(2q31.2)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000309 (Fisher's exact test), Q value = 0.25

Table S16.  Gene #3: 'Amp Peak 3(2q31.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 111 91
AMP PEAK 3(2Q31.2) CNV 56 29 19
AMP PEAK 3(2Q31.2) WILD-TYPE 69 82 72

Figure S16.  Get High-res Image Gene #3: 'Amp Peak 3(2q31.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 5(3q26.33)' versus 'MRNA_CHIERARCHICAL'

P value = 1.03e-05 (Fisher's exact test), Q value = 0.009

Table S17.  Gene #5: 'Amp Peak 5(3q26.33)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 22 56 23 53
AMP PEAK 5(3Q26.33) CNV 14 56 20 50
AMP PEAK 5(3Q26.33) WILD-TYPE 8 0 3 3

Figure S17.  Get High-res Image Gene #5: 'Amp Peak 5(3q26.33)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 5(3q26.33)' versus 'CN_CNMF'

P value = 3.91e-15 (Fisher's exact test), Q value = 3.8e-12

Table S18.  Gene #5: 'Amp Peak 5(3q26.33)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
AMP PEAK 5(3Q26.33) CNV 151 162 129
AMP PEAK 5(3Q26.33) WILD-TYPE 43 0 4

Figure S18.  Get High-res Image Gene #5: 'Amp Peak 5(3q26.33)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 5(3q26.33)' versus 'METHLYATION_CNMF'

P value = 7.78e-09 (Fisher's exact test), Q value = 7.4e-06

Table S19.  Gene #5: 'Amp Peak 5(3q26.33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 99
AMP PEAK 5(3Q26.33) CNV 113 114 93
AMP PEAK 5(3Q26.33) WILD-TYPE 29 0 6

Figure S19.  Get High-res Image Gene #5: 'Amp Peak 5(3q26.33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 5(3q26.33)' versus 'MRNASEQ_CNMF'

P value = 1.98e-10 (Fisher's exact test), Q value = 1.9e-07

Table S20.  Gene #5: 'Amp Peak 5(3q26.33)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 142 75
AMP PEAK 5(3Q26.33) CNV 110 143 124 55
AMP PEAK 5(3Q26.33) WILD-TYPE 8 0 18 20

Figure S20.  Get High-res Image Gene #5: 'Amp Peak 5(3q26.33)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 5(3q26.33)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.02e-08 (Fisher's exact test), Q value = 3.8e-05

Table S21.  Gene #5: 'Amp Peak 5(3q26.33)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 245
AMP PEAK 5(3Q26.33) CNV 85 140 207
AMP PEAK 5(3Q26.33) WILD-TYPE 8 0 38

Figure S21.  Get High-res Image Gene #5: 'Amp Peak 5(3q26.33)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 5(3q26.33)' versus 'MIRSEQ_CNMF'

P value = 6.45e-07 (Fisher's exact test), Q value = 0.00059

Table S22.  Gene #5: 'Amp Peak 5(3q26.33)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 130 124 64
AMP PEAK 5(3Q26.33) CNV 131 127 98 63
AMP PEAK 5(3Q26.33) WILD-TYPE 14 3 26 1

Figure S22.  Get High-res Image Gene #5: 'Amp Peak 5(3q26.33)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 5(3q26.33)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.01e-06 (Fisher's exact test), Q value = 0.00093

Table S23.  Gene #5: 'Amp Peak 5(3q26.33)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 71 163 229
AMP PEAK 5(3Q26.33) CNV 71 156 192
AMP PEAK 5(3Q26.33) WILD-TYPE 0 7 37

Figure S23.  Get High-res Image Gene #5: 'Amp Peak 5(3q26.33)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 6(4q12)' versus 'CN_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.14

Table S24.  Gene #6: 'Amp Peak 6(4q12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
AMP PEAK 6(4Q12) CNV 27 40 44
AMP PEAK 6(4Q12) WILD-TYPE 167 122 89

Figure S24.  Get High-res Image Gene #6: 'Amp Peak 6(4q12)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 7(5p15.33)' versus 'CN_CNMF'

P value = 3.16e-09 (Fisher's exact test), Q value = 3e-06

Table S25.  Gene #7: 'Amp Peak 7(5p15.33)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
AMP PEAK 7(5P15.33) CNV 135 116 126
AMP PEAK 7(5P15.33) WILD-TYPE 59 46 7

Figure S25.  Get High-res Image Gene #7: 'Amp Peak 7(5p15.33)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 8(5p12)' versus 'CN_CNMF'

P value = 1.6e-08 (Fisher's exact test), Q value = 1.5e-05

Table S26.  Gene #8: 'Amp Peak 8(5p12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
AMP PEAK 8(5P12) CNV 113 112 117
AMP PEAK 8(5P12) WILD-TYPE 81 50 16

Figure S26.  Get High-res Image Gene #8: 'Amp Peak 8(5p12)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 9(6p12.1)' versus 'CN_CNMF'

P value = 1.48e-05 (Fisher's exact test), Q value = 0.013

Table S27.  Gene #9: 'Amp Peak 9(6p12.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
AMP PEAK 9(6P12.1) CNV 40 65 55
AMP PEAK 9(6P12.1) WILD-TYPE 154 97 78

Figure S27.  Get High-res Image Gene #9: 'Amp Peak 9(6p12.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 10(6q12)' versus 'CN_CNMF'

P value = 7.43e-05 (Fisher's exact test), Q value = 0.062

Table S28.  Gene #10: 'Amp Peak 10(6q12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
AMP PEAK 10(6Q12) CNV 37 57 52
AMP PEAK 10(6Q12) WILD-TYPE 157 105 81

Figure S28.  Get High-res Image Gene #10: 'Amp Peak 10(6q12)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 11(7p11.2)' versus 'CN_CNMF'

P value = 8.85e-06 (Fisher's exact test), Q value = 0.0078

Table S29.  Gene #11: 'Amp Peak 11(7p11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
AMP PEAK 11(7P11.2) CNV 80 106 59
AMP PEAK 11(7P11.2) WILD-TYPE 114 56 74

Figure S29.  Get High-res Image Gene #11: 'Amp Peak 11(7p11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 12(7q21.2)' versus 'CN_CNMF'

P value = 4.52e-13 (Fisher's exact test), Q value = 4.4e-10

Table S30.  Gene #12: 'Amp Peak 12(7q21.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
AMP PEAK 12(7Q21.2) CNV 67 120 69
AMP PEAK 12(7Q21.2) WILD-TYPE 127 42 64

Figure S30.  Get High-res Image Gene #12: 'Amp Peak 12(7q21.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 12(7q21.2)' versus 'METHLYATION_CNMF'

P value = 3.42e-06 (Fisher's exact test), Q value = 0.0031

Table S31.  Gene #12: 'Amp Peak 12(7q21.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 99
AMP PEAK 12(7Q21.2) CNV 50 75 55
AMP PEAK 12(7Q21.2) WILD-TYPE 92 39 44

Figure S31.  Get High-res Image Gene #12: 'Amp Peak 12(7q21.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 12(7q21.2)' versus 'MRNASEQ_CNMF'

P value = 5.62e-06 (Fisher's exact test), Q value = 0.005

Table S32.  Gene #12: 'Amp Peak 12(7q21.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 142 75
AMP PEAK 12(7Q21.2) CNV 59 100 64 29
AMP PEAK 12(7Q21.2) WILD-TYPE 59 43 78 46

Figure S32.  Get High-res Image Gene #12: 'Amp Peak 12(7q21.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 12(7q21.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.09e-05 (Fisher's exact test), Q value = 0.0095

Table S33.  Gene #12: 'Amp Peak 12(7q21.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 245
AMP PEAK 12(7Q21.2) CNV 46 97 109
AMP PEAK 12(7Q21.2) WILD-TYPE 47 43 136

Figure S33.  Get High-res Image Gene #12: 'Amp Peak 12(7q21.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 15(9p13.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000184 (Fisher's exact test), Q value = 0.15

Table S34.  Gene #15: 'Amp Peak 15(9p13.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 245
AMP PEAK 15(9P13.3) CNV 26 57 51
AMP PEAK 15(9P13.3) WILD-TYPE 67 83 194

Figure S34.  Get High-res Image Gene #15: 'Amp Peak 15(9p13.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 16(11q13.3)' versus 'CN_CNMF'

P value = 0.000134 (Fisher's exact test), Q value = 0.11

Table S35.  Gene #16: 'Amp Peak 16(11q13.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
AMP PEAK 16(11Q13.3) CNV 51 62 65
AMP PEAK 16(11Q13.3) WILD-TYPE 143 100 68

Figure S35.  Get High-res Image Gene #16: 'Amp Peak 16(11q13.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 17(12p13.33)' versus 'CN_CNMF'

P value = 4.56e-07 (Fisher's exact test), Q value = 0.00042

Table S36.  Gene #17: 'Amp Peak 17(12p13.33)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
AMP PEAK 17(12P13.33) CNV 71 105 72
AMP PEAK 17(12P13.33) WILD-TYPE 123 57 61

Figure S36.  Get High-res Image Gene #17: 'Amp Peak 17(12p13.33)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 17(12p13.33)' versus 'METHLYATION_CNMF'

P value = 7.03e-05 (Fisher's exact test), Q value = 0.059

Table S37.  Gene #17: 'Amp Peak 17(12p13.33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 99
AMP PEAK 17(12P13.33) CNV 57 75 60
AMP PEAK 17(12P13.33) WILD-TYPE 85 39 39

Figure S37.  Get High-res Image Gene #17: 'Amp Peak 17(12p13.33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 17(12p13.33)' versus 'MRNASEQ_CNMF'

P value = 2.13e-08 (Fisher's exact test), Q value = 2e-05

Table S38.  Gene #17: 'Amp Peak 17(12p13.33)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 142 75
AMP PEAK 17(12P13.33) CNV 40 93 84 25
AMP PEAK 17(12P13.33) WILD-TYPE 78 50 58 50

Figure S38.  Get High-res Image Gene #17: 'Amp Peak 17(12p13.33)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 17(12p13.33)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.59e-05 (Fisher's exact test), Q value = 0.039

Table S39.  Gene #17: 'Amp Peak 17(12p13.33)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 245
AMP PEAK 17(12P13.33) CNV 54 88 100
AMP PEAK 17(12P13.33) WILD-TYPE 39 52 145

Figure S39.  Get High-res Image Gene #17: 'Amp Peak 17(12p13.33)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 18(12q15)' versus 'CN_CNMF'

P value = 3.26e-05 (Fisher's exact test), Q value = 0.028

Table S40.  Gene #18: 'Amp Peak 18(12q15)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
AMP PEAK 18(12Q15) CNV 50 79 44
AMP PEAK 18(12Q15) WILD-TYPE 144 83 89

Figure S40.  Get High-res Image Gene #18: 'Amp Peak 18(12q15)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 21(15q26.3)' versus 'CN_CNMF'

P value = 2.65e-06 (Fisher's exact test), Q value = 0.0024

Table S41.  Gene #21: 'Amp Peak 21(15q26.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
AMP PEAK 21(15Q26.3) CNV 45 79 49
AMP PEAK 21(15Q26.3) WILD-TYPE 149 83 84

Figure S41.  Get High-res Image Gene #21: 'Amp Peak 21(15q26.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 21(15q26.3)' versus 'METHLYATION_CNMF'

P value = 0.000229 (Fisher's exact test), Q value = 0.18

Table S42.  Gene #21: 'Amp Peak 21(15q26.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 99
AMP PEAK 21(15Q26.3) CNV 32 53 36
AMP PEAK 21(15Q26.3) WILD-TYPE 110 61 63

Figure S42.  Get High-res Image Gene #21: 'Amp Peak 21(15q26.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 21(15q26.3)' versus 'MRNASEQ_CNMF'

P value = 2.47e-05 (Fisher's exact test), Q value = 0.021

Table S43.  Gene #21: 'Amp Peak 21(15q26.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 142 75
AMP PEAK 21(15Q26.3) CNV 28 73 45 22
AMP PEAK 21(15Q26.3) WILD-TYPE 90 70 97 53

Figure S43.  Get High-res Image Gene #21: 'Amp Peak 21(15q26.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 21(15q26.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000219 (Fisher's exact test), Q value = 0.18

Table S44.  Gene #21: 'Amp Peak 21(15q26.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 245
AMP PEAK 21(15Q26.3) CNV 27 69 72
AMP PEAK 21(15Q26.3) WILD-TYPE 66 71 173

Figure S44.  Get High-res Image Gene #21: 'Amp Peak 21(15q26.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 22(17q25.1)' versus 'CN_CNMF'

P value = 1.54e-13 (Fisher's exact test), Q value = 1.5e-10

Table S45.  Gene #22: 'Amp Peak 22(17q25.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
AMP PEAK 22(17Q25.1) CNV 54 110 67
AMP PEAK 22(17Q25.1) WILD-TYPE 140 52 66

Figure S45.  Get High-res Image Gene #22: 'Amp Peak 22(17q25.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 22(17q25.1)' versus 'METHLYATION_CNMF'

P value = 2.45e-08 (Fisher's exact test), Q value = 2.3e-05

Table S46.  Gene #22: 'Amp Peak 22(17q25.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 99
AMP PEAK 22(17Q25.1) CNV 40 73 51
AMP PEAK 22(17Q25.1) WILD-TYPE 102 41 48

Figure S46.  Get High-res Image Gene #22: 'Amp Peak 22(17q25.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 22(17q25.1)' versus 'MRNASEQ_CNMF'

P value = 3.01e-06 (Fisher's exact test), Q value = 0.0027

Table S47.  Gene #22: 'Amp Peak 22(17q25.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 142 75
AMP PEAK 22(17Q25.1) CNV 45 93 60 26
AMP PEAK 22(17Q25.1) WILD-TYPE 73 50 82 49

Figure S47.  Get High-res Image Gene #22: 'Amp Peak 22(17q25.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 22(17q25.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.21e-07 (Fisher's exact test), Q value = 0.00011

Table S48.  Gene #22: 'Amp Peak 22(17q25.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 245
AMP PEAK 22(17Q25.1) CNV 48 90 86
AMP PEAK 22(17Q25.1) WILD-TYPE 45 50 159

Figure S48.  Get High-res Image Gene #22: 'Amp Peak 22(17q25.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 22(17q25.1)' versus 'MIRSEQ_CNMF'

P value = 0.000281 (Fisher's exact test), Q value = 0.22

Table S49.  Gene #22: 'Amp Peak 22(17q25.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 130 124 64
AMP PEAK 22(17Q25.1) CNV 71 78 41 29
AMP PEAK 22(17Q25.1) WILD-TYPE 74 52 83 35

Figure S49.  Get High-res Image Gene #22: 'Amp Peak 22(17q25.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 22(17q25.1)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.19e-05 (Fisher's exact test), Q value = 0.01

Table S50.  Gene #22: 'Amp Peak 22(17q25.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 111 91
AMP PEAK 22(17Q25.1) CNV 79 38 36
AMP PEAK 22(17Q25.1) WILD-TYPE 46 73 55

Figure S50.  Get High-res Image Gene #22: 'Amp Peak 22(17q25.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 22(17q25.1)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.66e-06 (Fisher's exact test), Q value = 0.0042

Table S51.  Gene #22: 'Amp Peak 22(17q25.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 150 177
AMP PEAK 22(17Q25.1) CNV 91 62
AMP PEAK 22(17Q25.1) WILD-TYPE 59 115

Figure S51.  Get High-res Image Gene #22: 'Amp Peak 22(17q25.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 23(18p11.32)' versus 'CN_CNMF'

P value = 2.38e-07 (Fisher's exact test), Q value = 0.00022

Table S52.  Gene #23: 'Amp Peak 23(18p11.32)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
AMP PEAK 23(18P11.32) CNV 42 80 48
AMP PEAK 23(18P11.32) WILD-TYPE 152 82 85

Figure S52.  Get High-res Image Gene #23: 'Amp Peak 23(18p11.32)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 23(18p11.32)' versus 'METHLYATION_CNMF'

P value = 2.17e-05 (Fisher's exact test), Q value = 0.019

Table S53.  Gene #23: 'Amp Peak 23(18p11.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 99
AMP PEAK 23(18P11.32) CNV 30 49 46
AMP PEAK 23(18P11.32) WILD-TYPE 112 65 53

Figure S53.  Get High-res Image Gene #23: 'Amp Peak 23(18p11.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 24(18q11.2)' versus 'MRNA_CNMF'

P value = 0.000151 (Fisher's exact test), Q value = 0.12

Table S54.  Gene #24: 'Amp Peak 24(18q11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
AMP PEAK 24(18Q11.2) CNV 7 25 5 15
AMP PEAK 24(18Q11.2) WILD-TYPE 35 27 27 13

Figure S54.  Get High-res Image Gene #24: 'Amp Peak 24(18q11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 24(18q11.2)' versus 'CN_CNMF'

P value = 6.51e-09 (Fisher's exact test), Q value = 6.2e-06

Table S55.  Gene #24: 'Amp Peak 24(18q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
AMP PEAK 24(18Q11.2) CNV 32 75 38
AMP PEAK 24(18Q11.2) WILD-TYPE 162 87 95

Figure S55.  Get High-res Image Gene #24: 'Amp Peak 24(18q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 24(18q11.2)' versus 'METHLYATION_CNMF'

P value = 1.91e-05 (Fisher's exact test), Q value = 0.017

Table S56.  Gene #24: 'Amp Peak 24(18q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 99
AMP PEAK 24(18Q11.2) CNV 23 48 31
AMP PEAK 24(18Q11.2) WILD-TYPE 119 66 68

Figure S56.  Get High-res Image Gene #24: 'Amp Peak 24(18q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 24(18q11.2)' versus 'MRNASEQ_CNMF'

P value = 7.51e-06 (Fisher's exact test), Q value = 0.0066

Table S57.  Gene #24: 'Amp Peak 24(18q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 142 75
AMP PEAK 24(18Q11.2) CNV 26 60 46 9
AMP PEAK 24(18Q11.2) WILD-TYPE 92 83 96 66

Figure S57.  Get High-res Image Gene #24: 'Amp Peak 24(18q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 24(18q11.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.26e-07 (Fisher's exact test), Q value = 0.00067

Table S58.  Gene #24: 'Amp Peak 24(18q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 245
AMP PEAK 24(18Q11.2) CNV 37 58 46
AMP PEAK 24(18Q11.2) WILD-TYPE 56 82 199

Figure S58.  Get High-res Image Gene #24: 'Amp Peak 24(18q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 24(18q11.2)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000182 (Fisher's exact test), Q value = 0.15

Table S59.  Gene #24: 'Amp Peak 24(18q11.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 111 91
AMP PEAK 24(18Q11.2) CNV 49 17 24
AMP PEAK 24(18Q11.2) WILD-TYPE 76 94 67

Figure S59.  Get High-res Image Gene #24: 'Amp Peak 24(18q11.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 24(18q11.2)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000111 (Fisher's exact test), Q value = 0.092

Table S60.  Gene #24: 'Amp Peak 24(18q11.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 150 177
AMP PEAK 24(18Q11.2) CNV 57 33
AMP PEAK 24(18Q11.2) WILD-TYPE 93 144

Figure S60.  Get High-res Image Gene #24: 'Amp Peak 24(18q11.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 25(19q12)' versus 'CN_CNMF'

P value = 8.3e-09 (Fisher's exact test), Q value = 7.9e-06

Table S61.  Gene #25: 'Amp Peak 25(19q12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
AMP PEAK 25(19Q12) CNV 58 100 54
AMP PEAK 25(19Q12) WILD-TYPE 136 62 79

Figure S61.  Get High-res Image Gene #25: 'Amp Peak 25(19q12)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 26(19q13.2)' versus 'CN_CNMF'

P value = 7.93e-07 (Fisher's exact test), Q value = 0.00073

Table S62.  Gene #26: 'Amp Peak 26(19q13.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
AMP PEAK 26(19Q13.2) CNV 62 97 58
AMP PEAK 26(19Q13.2) WILD-TYPE 132 65 75

Figure S62.  Get High-res Image Gene #26: 'Amp Peak 26(19q13.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 27(20p12.2)' versus 'CN_CNMF'

P value = 5.15e-10 (Fisher's exact test), Q value = 5e-07

Table S63.  Gene #27: 'Amp Peak 27(20p12.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
AMP PEAK 27(20P12.2) CNV 74 117 77
AMP PEAK 27(20P12.2) WILD-TYPE 120 45 56

Figure S63.  Get High-res Image Gene #27: 'Amp Peak 27(20p12.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 27(20p12.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000136 (Fisher's exact test), Q value = 0.11

Table S64.  Gene #27: 'Amp Peak 27(20p12.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 245
AMP PEAK 27(20P12.2) CNV 53 96 114
AMP PEAK 27(20P12.2) WILD-TYPE 40 44 131

Figure S64.  Get High-res Image Gene #27: 'Amp Peak 27(20p12.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 28(20q11.21)' versus 'CN_CNMF'

P value = 4.62e-07 (Fisher's exact test), Q value = 0.00043

Table S65.  Gene #28: 'Amp Peak 28(20q11.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
AMP PEAK 28(20Q11.21) CNV 87 109 95
AMP PEAK 28(20Q11.21) WILD-TYPE 107 53 38

Figure S65.  Get High-res Image Gene #28: 'Amp Peak 28(20q11.21)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 29(22q11.21)' versus 'MRNASEQ_CNMF'

P value = 0.000284 (Fisher's exact test), Q value = 0.23

Table S66.  Gene #29: 'Amp Peak 29(22q11.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 142 75
AMP PEAK 29(22Q11.21) CNV 56 94 66 29
AMP PEAK 29(22Q11.21) WILD-TYPE 62 49 76 46

Figure S66.  Get High-res Image Gene #29: 'Amp Peak 29(22q11.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 1(1p36.32)' versus 'MRNA_CNMF'

P value = 1.49e-06 (Fisher's exact test), Q value = 0.0014

Table S67.  Gene #31: 'Del Peak 1(1p36.32)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
DEL PEAK 1(1P36.32) CNV 9 38 14 8
DEL PEAK 1(1P36.32) WILD-TYPE 33 14 18 20

Figure S67.  Get High-res Image Gene #31: 'Del Peak 1(1p36.32)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 1(1p36.32)' versus 'MRNA_CHIERARCHICAL'

P value = 1.22e-07 (Fisher's exact test), Q value = 0.00011

Table S68.  Gene #31: 'Del Peak 1(1p36.32)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 22 56 23 53
DEL PEAK 1(1P36.32) CNV 8 42 7 12
DEL PEAK 1(1P36.32) WILD-TYPE 14 14 16 41

Figure S68.  Get High-res Image Gene #31: 'Del Peak 1(1p36.32)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 1(1p36.32)' versus 'CN_CNMF'

P value = 7.51e-35 (Fisher's exact test), Q value = 7.4e-32

Table S69.  Gene #31: 'Del Peak 1(1p36.32)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
DEL PEAK 1(1P36.32) CNV 53 133 26
DEL PEAK 1(1P36.32) WILD-TYPE 141 29 107

Figure S69.  Get High-res Image Gene #31: 'Del Peak 1(1p36.32)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 1(1p36.32)' versus 'METHLYATION_CNMF'

P value = 1.96e-19 (Fisher's exact test), Q value = 1.9e-16

Table S70.  Gene #31: 'Del Peak 1(1p36.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 99
DEL PEAK 1(1P36.32) CNV 26 85 38
DEL PEAK 1(1P36.32) WILD-TYPE 116 29 61

Figure S70.  Get High-res Image Gene #31: 'Del Peak 1(1p36.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 1(1p36.32)' versus 'MRNASEQ_CNMF'

P value = 3.79e-20 (Fisher's exact test), Q value = 3.7e-17

Table S71.  Gene #31: 'Del Peak 1(1p36.32)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 142 75
DEL PEAK 1(1P36.32) CNV 34 110 43 22
DEL PEAK 1(1P36.32) WILD-TYPE 84 33 99 53

Figure S71.  Get High-res Image Gene #31: 'Del Peak 1(1p36.32)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 1(1p36.32)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.06e-20 (Fisher's exact test), Q value = 1e-17

Table S72.  Gene #31: 'Del Peak 1(1p36.32)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 245
DEL PEAK 1(1P36.32) CNV 28 108 73
DEL PEAK 1(1P36.32) WILD-TYPE 65 32 172

Figure S72.  Get High-res Image Gene #31: 'Del Peak 1(1p36.32)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 1(1p36.32)' versus 'MIRSEQ_CNMF'

P value = 2.12e-06 (Fisher's exact test), Q value = 0.0019

Table S73.  Gene #31: 'Del Peak 1(1p36.32)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 130 124 64
DEL PEAK 1(1P36.32) CNV 61 62 34 43
DEL PEAK 1(1P36.32) WILD-TYPE 84 68 90 21

Figure S73.  Get High-res Image Gene #31: 'Del Peak 1(1p36.32)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 1(1p36.32)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.11e-05 (Fisher's exact test), Q value = 0.0097

Table S74.  Gene #31: 'Del Peak 1(1p36.32)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 71 163 229
DEL PEAK 1(1P36.32) CNV 49 65 86
DEL PEAK 1(1P36.32) WILD-TYPE 22 98 143

Figure S74.  Get High-res Image Gene #31: 'Del Peak 1(1p36.32)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 1(1p36.32)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.84e-07 (Fisher's exact test), Q value = 0.00036

Table S75.  Gene #31: 'Del Peak 1(1p36.32)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 150 177
DEL PEAK 1(1P36.32) CNV 86 52
DEL PEAK 1(1P36.32) WILD-TYPE 64 125

Figure S75.  Get High-res Image Gene #31: 'Del Peak 1(1p36.32)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 2(1p13.1)' versus 'MRNA_CHIERARCHICAL'

P value = 6.31e-05 (Fisher's exact test), Q value = 0.053

Table S76.  Gene #32: 'Del Peak 2(1p13.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 22 56 23 53
DEL PEAK 2(1P13.1) CNV 9 37 12 12
DEL PEAK 2(1P13.1) WILD-TYPE 13 19 11 41

Figure S76.  Get High-res Image Gene #32: 'Del Peak 2(1p13.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 2(1p13.1)' versus 'CN_CNMF'

P value = 3.83e-20 (Fisher's exact test), Q value = 3.8e-17

Table S77.  Gene #32: 'Del Peak 2(1p13.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
DEL PEAK 2(1P13.1) CNV 50 117 41
DEL PEAK 2(1P13.1) WILD-TYPE 144 45 92

Figure S77.  Get High-res Image Gene #32: 'Del Peak 2(1p13.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 2(1p13.1)' versus 'METHLYATION_CNMF'

P value = 2.04e-12 (Fisher's exact test), Q value = 2e-09

Table S78.  Gene #32: 'Del Peak 2(1p13.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 99
DEL PEAK 2(1P13.1) CNV 35 78 33
DEL PEAK 2(1P13.1) WILD-TYPE 107 36 66

Figure S78.  Get High-res Image Gene #32: 'Del Peak 2(1p13.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 2(1p13.1)' versus 'MRNASEQ_CNMF'

P value = 2.36e-11 (Fisher's exact test), Q value = 2.3e-08

Table S79.  Gene #32: 'Del Peak 2(1p13.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 142 75
DEL PEAK 2(1P13.1) CNV 37 97 49 22
DEL PEAK 2(1P13.1) WILD-TYPE 81 46 93 53

Figure S79.  Get High-res Image Gene #32: 'Del Peak 2(1p13.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 2(1p13.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.66e-13 (Fisher's exact test), Q value = 1.6e-10

Table S80.  Gene #32: 'Del Peak 2(1p13.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 245
DEL PEAK 2(1P13.1) CNV 39 96 70
DEL PEAK 2(1P13.1) WILD-TYPE 54 44 175

Figure S80.  Get High-res Image Gene #32: 'Del Peak 2(1p13.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 2(1p13.1)' versus 'MIRSEQ_CNMF'

P value = 4.79e-08 (Fisher's exact test), Q value = 4.5e-05

Table S81.  Gene #32: 'Del Peak 2(1p13.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 130 124 64
DEL PEAK 2(1P13.1) CNV 66 61 28 42
DEL PEAK 2(1P13.1) WILD-TYPE 79 69 96 22

Figure S81.  Get High-res Image Gene #32: 'Del Peak 2(1p13.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 2(1p13.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.69e-06 (Fisher's exact test), Q value = 0.0059

Table S82.  Gene #32: 'Del Peak 2(1p13.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 71 163 229
DEL PEAK 2(1P13.1) CNV 49 62 86
DEL PEAK 2(1P13.1) WILD-TYPE 22 101 143

Figure S82.  Get High-res Image Gene #32: 'Del Peak 2(1p13.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 2(1p13.1)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.63e-06 (Fisher's exact test), Q value = 0.005

Table S83.  Gene #32: 'Del Peak 2(1p13.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 150 177
DEL PEAK 2(1P13.1) CNV 82 52
DEL PEAK 2(1P13.1) WILD-TYPE 68 125

Figure S83.  Get High-res Image Gene #32: 'Del Peak 2(1p13.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 4(2q22.1)' versus 'CN_CNMF'

P value = 1.69e-05 (Fisher's exact test), Q value = 0.015

Table S84.  Gene #34: 'Del Peak 4(2q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
DEL PEAK 4(2Q22.1) CNV 29 59 33
DEL PEAK 4(2Q22.1) WILD-TYPE 165 103 100

Figure S84.  Get High-res Image Gene #34: 'Del Peak 4(2q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 4(2q22.1)' versus 'MIRSEQ_CNMF'

P value = 0.000126 (Fisher's exact test), Q value = 0.1

Table S85.  Gene #34: 'Del Peak 4(2q22.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 130 124 64
DEL PEAK 4(2Q22.1) CNV 47 34 14 21
DEL PEAK 4(2Q22.1) WILD-TYPE 98 96 110 43

Figure S85.  Get High-res Image Gene #34: 'Del Peak 4(2q22.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 4(2q22.1)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000293 (Fisher's exact test), Q value = 0.23

Table S86.  Gene #34: 'Del Peak 4(2q22.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 111 91
DEL PEAK 4(2Q22.1) CNV 45 20 13
DEL PEAK 4(2Q22.1) WILD-TYPE 80 91 78

Figure S86.  Get High-res Image Gene #34: 'Del Peak 4(2q22.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 5(2q37.1)' versus 'CN_CNMF'

P value = 4.19e-09 (Fisher's exact test), Q value = 4e-06

Table S87.  Gene #35: 'Del Peak 5(2q37.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
DEL PEAK 5(2Q37.1) CNV 39 81 34
DEL PEAK 5(2Q37.1) WILD-TYPE 155 81 99

Figure S87.  Get High-res Image Gene #35: 'Del Peak 5(2q37.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 5(2q37.1)' versus 'METHLYATION_CNMF'

P value = 7.61e-07 (Fisher's exact test), Q value = 7e-04

Table S88.  Gene #35: 'Del Peak 5(2q37.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 99
DEL PEAK 5(2Q37.1) CNV 25 55 34
DEL PEAK 5(2Q37.1) WILD-TYPE 117 59 65

Figure S88.  Get High-res Image Gene #35: 'Del Peak 5(2q37.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 5(2q37.1)' versus 'MRNASEQ_CNMF'

P value = 2.07e-06 (Fisher's exact test), Q value = 0.0019

Table S89.  Gene #35: 'Del Peak 5(2q37.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 142 75
DEL PEAK 5(2Q37.1) CNV 36 67 38 10
DEL PEAK 5(2Q37.1) WILD-TYPE 82 76 104 65

Figure S89.  Get High-res Image Gene #35: 'Del Peak 5(2q37.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 5(2q37.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.02e-06 (Fisher's exact test), Q value = 0.0062

Table S90.  Gene #35: 'Del Peak 5(2q37.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 245
DEL PEAK 5(2Q37.1) CNV 25 67 59
DEL PEAK 5(2Q37.1) WILD-TYPE 68 73 186

Figure S90.  Get High-res Image Gene #35: 'Del Peak 5(2q37.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 5(2q37.1)' versus 'MIRSEQ_CNMF'

P value = 2.81e-05 (Fisher's exact test), Q value = 0.024

Table S91.  Gene #35: 'Del Peak 5(2q37.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 130 124 64
DEL PEAK 5(2Q37.1) CNV 52 53 19 23
DEL PEAK 5(2Q37.1) WILD-TYPE 93 77 105 41

Figure S91.  Get High-res Image Gene #35: 'Del Peak 5(2q37.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 5(2q37.1)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.46e-05 (Fisher's exact test), Q value = 0.013

Table S92.  Gene #35: 'Del Peak 5(2q37.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 111 91
DEL PEAK 5(2Q37.1) CNV 58 24 19
DEL PEAK 5(2Q37.1) WILD-TYPE 67 87 72

Figure S92.  Get High-res Image Gene #35: 'Del Peak 5(2q37.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 5(2q37.1)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000193 (Fisher's exact test), Q value = 0.16

Table S93.  Gene #35: 'Del Peak 5(2q37.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 150 177
DEL PEAK 5(2Q37.1) CNV 62 39
DEL PEAK 5(2Q37.1) WILD-TYPE 88 138

Figure S93.  Get High-res Image Gene #35: 'Del Peak 5(2q37.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 7(3p13)' versus 'CN_CNMF'

P value = 1.25e-06 (Fisher's exact test), Q value = 0.0011

Table S94.  Gene #37: 'Del Peak 7(3p13)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
DEL PEAK 7(3P13) CNV 147 153 119
DEL PEAK 7(3P13) WILD-TYPE 47 9 14

Figure S94.  Get High-res Image Gene #37: 'Del Peak 7(3p13)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 7(3p13)' versus 'METHLYATION_CNMF'

P value = 0.000314 (Fisher's exact test), Q value = 0.25

Table S95.  Gene #37: 'Del Peak 7(3p13)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 99
DEL PEAK 7(3P13) CNV 109 107 88
DEL PEAK 7(3P13) WILD-TYPE 33 7 11

Figure S95.  Get High-res Image Gene #37: 'Del Peak 7(3p13)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 7(3p13)' versus 'MIRSEQ_CNMF'

P value = 4.76e-05 (Fisher's exact test), Q value = 0.04

Table S96.  Gene #37: 'Del Peak 7(3p13)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 130 124 64
DEL PEAK 7(3P13) CNV 127 119 90 60
DEL PEAK 7(3P13) WILD-TYPE 18 11 34 4

Figure S96.  Get High-res Image Gene #37: 'Del Peak 7(3p13)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 7(3p13)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.83e-05 (Fisher's exact test), Q value = 0.049

Table S97.  Gene #37: 'Del Peak 7(3p13)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 150 177
DEL PEAK 7(3P13) CNV 141 139
DEL PEAK 7(3P13) WILD-TYPE 9 38

Figure S97.  Get High-res Image Gene #37: 'Del Peak 7(3p13)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 8(3p12.3)' versus 'CN_CNMF'

P value = 2.32e-05 (Fisher's exact test), Q value = 0.02

Table S98.  Gene #38: 'Del Peak 8(3p12.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
DEL PEAK 8(3P12.3) CNV 144 149 115
DEL PEAK 8(3P12.3) WILD-TYPE 50 13 18

Figure S98.  Get High-res Image Gene #38: 'Del Peak 8(3p12.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 8(3p12.3)' versus 'METHLYATION_CNMF'

P value = 0.000187 (Fisher's exact test), Q value = 0.15

Table S99.  Gene #38: 'Del Peak 8(3p12.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 99
DEL PEAK 8(3P12.3) CNV 105 106 84
DEL PEAK 8(3P12.3) WILD-TYPE 37 8 15

Figure S99.  Get High-res Image Gene #38: 'Del Peak 8(3p12.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 10(4p15.2)' versus 'CN_CNMF'

P value = 2.32e-09 (Fisher's exact test), Q value = 2.2e-06

Table S100.  Gene #40: 'Del Peak 10(4p15.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
DEL PEAK 10(4P15.2) CNV 93 129 77
DEL PEAK 10(4P15.2) WILD-TYPE 101 33 56

Figure S100.  Get High-res Image Gene #40: 'Del Peak 10(4p15.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 10(4p15.2)' versus 'METHLYATION_CNMF'

P value = 6.04e-06 (Fisher's exact test), Q value = 0.0053

Table S101.  Gene #40: 'Del Peak 10(4p15.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 99
DEL PEAK 10(4P15.2) CNV 66 86 66
DEL PEAK 10(4P15.2) WILD-TYPE 76 28 33

Figure S101.  Get High-res Image Gene #40: 'Del Peak 10(4p15.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 10(4p15.2)' versus 'MRNASEQ_CNMF'

P value = 9.06e-05 (Fisher's exact test), Q value = 0.075

Table S102.  Gene #40: 'Del Peak 10(4p15.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 142 75
DEL PEAK 10(4P15.2) CNV 76 107 73 38
DEL PEAK 10(4P15.2) WILD-TYPE 42 36 69 37

Figure S102.  Get High-res Image Gene #40: 'Del Peak 10(4p15.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 11(4q22.1)' versus 'CN_CNMF'

P value = 1.92e-06 (Fisher's exact test), Q value = 0.0017

Table S103.  Gene #41: 'Del Peak 11(4q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
DEL PEAK 11(4Q22.1) CNV 88 116 69
DEL PEAK 11(4Q22.1) WILD-TYPE 106 46 64

Figure S103.  Get High-res Image Gene #41: 'Del Peak 11(4q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 11(4q22.1)' versus 'MRNASEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.098

Table S104.  Gene #41: 'Del Peak 11(4q22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 142 75
DEL PEAK 11(4Q22.1) CNV 65 99 73 29
DEL PEAK 11(4Q22.1) WILD-TYPE 53 44 69 46

Figure S104.  Get High-res Image Gene #41: 'Del Peak 11(4q22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 12(4q32.3)' versus 'CN_CNMF'

P value = 5.63e-09 (Fisher's exact test), Q value = 5.4e-06

Table S105.  Gene #42: 'Del Peak 12(4q32.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
DEL PEAK 12(4Q32.3) CNV 102 134 82
DEL PEAK 12(4Q32.3) WILD-TYPE 92 28 51

Figure S105.  Get High-res Image Gene #42: 'Del Peak 12(4q32.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 12(4q32.3)' versus 'METHLYATION_CNMF'

P value = 7.36e-05 (Fisher's exact test), Q value = 0.062

Table S106.  Gene #42: 'Del Peak 12(4q32.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 99
DEL PEAK 12(4Q32.3) CNV 73 87 70
DEL PEAK 12(4Q32.3) WILD-TYPE 69 27 29

Figure S106.  Get High-res Image Gene #42: 'Del Peak 12(4q32.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 12(4q32.3)' versus 'MRNASEQ_CNMF'

P value = 4.7e-06 (Fisher's exact test), Q value = 0.0042

Table S107.  Gene #42: 'Del Peak 12(4q32.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 142 75
DEL PEAK 12(4Q32.3) CNV 78 114 84 35
DEL PEAK 12(4Q32.3) WILD-TYPE 40 29 58 40

Figure S107.  Get High-res Image Gene #42: 'Del Peak 12(4q32.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 12(4q32.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.9e-05 (Fisher's exact test), Q value = 0.074

Table S108.  Gene #42: 'Del Peak 12(4q32.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 245
DEL PEAK 12(4Q32.3) CNV 61 110 140
DEL PEAK 12(4Q32.3) WILD-TYPE 32 30 105

Figure S108.  Get High-res Image Gene #42: 'Del Peak 12(4q32.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 12(4q32.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.55e-05 (Fisher's exact test), Q value = 0.063

Table S109.  Gene #42: 'Del Peak 12(4q32.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 150 177
DEL PEAK 12(4Q32.3) CNV 114 97
DEL PEAK 12(4Q32.3) WILD-TYPE 36 80

Figure S109.  Get High-res Image Gene #42: 'Del Peak 12(4q32.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 13(4q35.2)' versus 'CN_CNMF'

P value = 7.6e-08 (Fisher's exact test), Q value = 7.1e-05

Table S110.  Gene #43: 'Del Peak 13(4q35.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
DEL PEAK 13(4Q35.2) CNV 106 133 81
DEL PEAK 13(4Q35.2) WILD-TYPE 88 29 52

Figure S110.  Get High-res Image Gene #43: 'Del Peak 13(4q35.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 13(4q35.2)' versus 'METHLYATION_CNMF'

P value = 3.56e-05 (Fisher's exact test), Q value = 0.03

Table S111.  Gene #43: 'Del Peak 13(4q35.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 99
DEL PEAK 13(4Q35.2) CNV 74 90 66
DEL PEAK 13(4Q35.2) WILD-TYPE 68 24 33

Figure S111.  Get High-res Image Gene #43: 'Del Peak 13(4q35.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 13(4q35.2)' versus 'MRNASEQ_CNMF'

P value = 3.97e-06 (Fisher's exact test), Q value = 0.0035

Table S112.  Gene #43: 'Del Peak 13(4q35.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 142 75
DEL PEAK 13(4Q35.2) CNV 75 115 87 35
DEL PEAK 13(4Q35.2) WILD-TYPE 43 28 55 40

Figure S112.  Get High-res Image Gene #43: 'Del Peak 13(4q35.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 13(4q35.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000174 (Fisher's exact test), Q value = 0.14

Table S113.  Gene #43: 'Del Peak 13(4q35.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 245
DEL PEAK 13(4Q35.2) CNV 60 110 142
DEL PEAK 13(4Q35.2) WILD-TYPE 33 30 103

Figure S113.  Get High-res Image Gene #43: 'Del Peak 13(4q35.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 13(4q35.2)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000197 (Fisher's exact test), Q value = 0.16

Table S114.  Gene #43: 'Del Peak 13(4q35.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 150 177
DEL PEAK 13(4Q35.2) CNV 113 98
DEL PEAK 13(4Q35.2) WILD-TYPE 37 79

Figure S114.  Get High-res Image Gene #43: 'Del Peak 13(4q35.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 14(5q11.2)' versus 'CN_CNMF'

P value = 2.55e-11 (Fisher's exact test), Q value = 2.5e-08

Table S115.  Gene #44: 'Del Peak 14(5q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
DEL PEAK 14(5Q11.2) CNV 106 134 113
DEL PEAK 14(5Q11.2) WILD-TYPE 88 28 20

Figure S115.  Get High-res Image Gene #44: 'Del Peak 14(5q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 14(5q11.2)' versus 'METHLYATION_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.083

Table S116.  Gene #44: 'Del Peak 14(5q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 99
DEL PEAK 14(5Q11.2) CNV 84 92 79
DEL PEAK 14(5Q11.2) WILD-TYPE 58 22 20

Figure S116.  Get High-res Image Gene #44: 'Del Peak 14(5q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 14(5q11.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.21e-05 (Fisher's exact test), Q value = 0.027

Table S117.  Gene #44: 'Del Peak 14(5q11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 71 163 229
DEL PEAK 14(5Q11.2) CNV 54 137 146
DEL PEAK 14(5Q11.2) WILD-TYPE 17 26 83

Figure S117.  Get High-res Image Gene #44: 'Del Peak 14(5q11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 15(6p25.3)' versus 'CN_CNMF'

P value = 0.000114 (Fisher's exact test), Q value = 0.094

Table S118.  Gene #45: 'Del Peak 15(6p25.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
DEL PEAK 15(6P25.3) CNV 40 61 24
DEL PEAK 15(6P25.3) WILD-TYPE 154 101 109

Figure S118.  Get High-res Image Gene #45: 'Del Peak 15(6p25.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 15(6p25.3)' versus 'METHLYATION_CNMF'

P value = 0.000102 (Fisher's exact test), Q value = 0.084

Table S119.  Gene #45: 'Del Peak 15(6p25.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 99
DEL PEAK 15(6P25.3) CNV 25 47 23
DEL PEAK 15(6P25.3) WILD-TYPE 117 67 76

Figure S119.  Get High-res Image Gene #45: 'Del Peak 15(6p25.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 15(6p25.3)' versus 'MRNASEQ_CNMF'

P value = 2.82e-06 (Fisher's exact test), Q value = 0.0025

Table S120.  Gene #45: 'Del Peak 15(6p25.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 142 75
DEL PEAK 15(6P25.3) CNV 28 60 22 14
DEL PEAK 15(6P25.3) WILD-TYPE 90 83 120 61

Figure S120.  Get High-res Image Gene #45: 'Del Peak 15(6p25.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 15(6p25.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.82e-08 (Fisher's exact test), Q value = 6.4e-05

Table S121.  Gene #45: 'Del Peak 15(6p25.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 245
DEL PEAK 15(6P25.3) CNV 12 61 51
DEL PEAK 15(6P25.3) WILD-TYPE 81 79 194

Figure S121.  Get High-res Image Gene #45: 'Del Peak 15(6p25.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 16(6q22.31)' versus 'CN_CNMF'

P value = 4.19e-05 (Fisher's exact test), Q value = 0.035

Table S122.  Gene #46: 'Del Peak 16(6q22.31)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
DEL PEAK 16(6Q22.31) CNV 33 59 25
DEL PEAK 16(6Q22.31) WILD-TYPE 161 103 108

Figure S122.  Get High-res Image Gene #46: 'Del Peak 16(6q22.31)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 16(6q22.31)' versus 'MRNASEQ_CNMF'

P value = 0.000154 (Fisher's exact test), Q value = 0.13

Table S123.  Gene #46: 'Del Peak 16(6q22.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 142 75
DEL PEAK 16(6Q22.31) CNV 20 54 25 17
DEL PEAK 16(6Q22.31) WILD-TYPE 98 89 117 58

Figure S123.  Get High-res Image Gene #46: 'Del Peak 16(6q22.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 17(6q26)' versus 'CN_CNMF'

P value = 2.95e-05 (Fisher's exact test), Q value = 0.025

Table S124.  Gene #47: 'Del Peak 17(6q26)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
DEL PEAK 17(6Q26) CNV 37 64 28
DEL PEAK 17(6Q26) WILD-TYPE 157 98 105

Figure S124.  Get High-res Image Gene #47: 'Del Peak 17(6q26)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 17(6q26)' versus 'METHLYATION_CNMF'

P value = 0.000115 (Fisher's exact test), Q value = 0.095

Table S125.  Gene #47: 'Del Peak 17(6q26)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 99
DEL PEAK 17(6Q26) CNV 27 48 22
DEL PEAK 17(6Q26) WILD-TYPE 115 66 77

Figure S125.  Get High-res Image Gene #47: 'Del Peak 17(6q26)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 17(6q26)' versus 'MRNASEQ_CNMF'

P value = 0.000276 (Fisher's exact test), Q value = 0.22

Table S126.  Gene #47: 'Del Peak 17(6q26)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 142 75
DEL PEAK 17(6Q26) CNV 23 58 31 16
DEL PEAK 17(6Q26) WILD-TYPE 95 85 111 59

Figure S126.  Get High-res Image Gene #47: 'Del Peak 17(6q26)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 17(6q26)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000219 (Fisher's exact test), Q value = 0.18

Table S127.  Gene #47: 'Del Peak 17(6q26)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 245
DEL PEAK 17(6Q26) CNV 19 56 53
DEL PEAK 17(6Q26) WILD-TYPE 74 84 192

Figure S127.  Get High-res Image Gene #47: 'Del Peak 17(6q26)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 20(8p23.2)' versus 'CN_CNMF'

P value = 6.89e-05 (Fisher's exact test), Q value = 0.058

Table S128.  Gene #50: 'Del Peak 20(8p23.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
DEL PEAK 20(8P23.2) CNV 109 121 101
DEL PEAK 20(8P23.2) WILD-TYPE 85 41 32

Figure S128.  Get High-res Image Gene #50: 'Del Peak 20(8p23.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 21(9p23)' versus 'CN_CNMF'

P value = 3.09e-06 (Fisher's exact test), Q value = 0.0028

Table S129.  Gene #51: 'Del Peak 21(9p23)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
DEL PEAK 21(9P23) CNV 111 97 109
DEL PEAK 21(9P23) WILD-TYPE 83 65 24

Figure S129.  Get High-res Image Gene #51: 'Del Peak 21(9p23)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 21(9p23)' versus 'MRNASEQ_CNMF'

P value = 4.33e-05 (Fisher's exact test), Q value = 0.037

Table S130.  Gene #51: 'Del Peak 21(9p23)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 142 75
DEL PEAK 21(9P23) CNV 90 79 103 38
DEL PEAK 21(9P23) WILD-TYPE 28 64 39 37

Figure S130.  Get High-res Image Gene #51: 'Del Peak 21(9p23)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 22(9p21.3)' versus 'CN_CNMF'

P value = 7.87e-06 (Fisher's exact test), Q value = 0.0069

Table S131.  Gene #52: 'Del Peak 22(9p21.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
DEL PEAK 22(9P21.3) CNV 130 122 119
DEL PEAK 22(9P21.3) WILD-TYPE 64 40 14

Figure S131.  Get High-res Image Gene #52: 'Del Peak 22(9p21.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 23(9p21.1)' versus 'CN_CNMF'

P value = 9.11e-06 (Fisher's exact test), Q value = 0.008

Table S132.  Gene #53: 'Del Peak 23(9p21.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
DEL PEAK 23(9P21.1) CNV 113 92 107
DEL PEAK 23(9P21.1) WILD-TYPE 81 70 26

Figure S132.  Get High-res Image Gene #53: 'Del Peak 23(9p21.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 23(9p21.1)' versus 'MRNASEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.09

Table S133.  Gene #53: 'Del Peak 23(9p21.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 142 75
DEL PEAK 23(9P21.1) CNV 90 77 99 39
DEL PEAK 23(9P21.1) WILD-TYPE 28 66 43 36

Figure S133.  Get High-res Image Gene #53: 'Del Peak 23(9p21.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 24(9q21.11)' versus 'MRNA_CNMF'

P value = 8.38e-05 (Fisher's exact test), Q value = 0.07

Table S134.  Gene #54: 'Del Peak 24(9q21.11)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
DEL PEAK 24(9Q21.11) CNV 28 12 19 15
DEL PEAK 24(9Q21.11) WILD-TYPE 14 40 13 13

Figure S134.  Get High-res Image Gene #54: 'Del Peak 24(9q21.11)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 24(9q21.11)' versus 'MRNA_CHIERARCHICAL'

P value = 1.96e-05 (Fisher's exact test), Q value = 0.017

Table S135.  Gene #54: 'Del Peak 24(9q21.11)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 22 56 23 53
DEL PEAK 24(9Q21.11) CNV 14 13 17 30
DEL PEAK 24(9Q21.11) WILD-TYPE 8 43 6 23

Figure S135.  Get High-res Image Gene #54: 'Del Peak 24(9q21.11)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 24(9q21.11)' versus 'CN_CNMF'

P value = 5.61e-13 (Fisher's exact test), Q value = 5.5e-10

Table S136.  Gene #54: 'Del Peak 24(9q21.11)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
DEL PEAK 24(9Q21.11) CNV 97 48 97
DEL PEAK 24(9Q21.11) WILD-TYPE 97 114 36

Figure S136.  Get High-res Image Gene #54: 'Del Peak 24(9q21.11)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 24(9q21.11)' versus 'METHLYATION_CNMF'

P value = 1.41e-09 (Fisher's exact test), Q value = 1.4e-06

Table S137.  Gene #54: 'Del Peak 24(9q21.11)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 99
DEL PEAK 24(9Q21.11) CNV 84 29 63
DEL PEAK 24(9Q21.11) WILD-TYPE 58 85 36

Figure S137.  Get High-res Image Gene #54: 'Del Peak 24(9q21.11)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 24(9q21.11)' versus 'MRNASEQ_CNMF'

P value = 2.45e-15 (Fisher's exact test), Q value = 2.4e-12

Table S138.  Gene #54: 'Del Peak 24(9q21.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 142 75
DEL PEAK 24(9Q21.11) CNV 78 31 90 37
DEL PEAK 24(9Q21.11) WILD-TYPE 40 112 52 38

Figure S138.  Get High-res Image Gene #54: 'Del Peak 24(9q21.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 24(9q21.11)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.64e-15 (Fisher's exact test), Q value = 6.5e-12

Table S139.  Gene #54: 'Del Peak 24(9q21.11)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 245
DEL PEAK 24(9Q21.11) CNV 60 30 146
DEL PEAK 24(9Q21.11) WILD-TYPE 33 110 99

Figure S139.  Get High-res Image Gene #54: 'Del Peak 24(9q21.11)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 24(9q21.11)' versus 'MIRSEQ_CNMF'

P value = 1.4e-05 (Fisher's exact test), Q value = 0.012

Table S140.  Gene #54: 'Del Peak 24(9q21.11)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 130 124 64
DEL PEAK 24(9Q21.11) CNV 62 78 71 17
DEL PEAK 24(9Q21.11) WILD-TYPE 83 52 53 47

Figure S140.  Get High-res Image Gene #54: 'Del Peak 24(9q21.11)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 24(9q21.11)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.56e-08 (Fisher's exact test), Q value = 5.2e-05

Table S141.  Gene #54: 'Del Peak 24(9q21.11)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 71 163 229
DEL PEAK 24(9Q21.11) CNV 17 104 107
DEL PEAK 24(9Q21.11) WILD-TYPE 54 59 122

Figure S141.  Get High-res Image Gene #54: 'Del Peak 24(9q21.11)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 25(10p15.3)' versus 'CN_CNMF'

P value = 1.33e-07 (Fisher's exact test), Q value = 0.00012

Table S142.  Gene #55: 'Del Peak 25(10p15.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
DEL PEAK 25(10P15.3) CNV 63 100 54
DEL PEAK 25(10P15.3) WILD-TYPE 131 62 79

Figure S142.  Get High-res Image Gene #55: 'Del Peak 25(10p15.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 25(10p15.3)' versus 'METHLYATION_CNMF'

P value = 8.77e-10 (Fisher's exact test), Q value = 8.4e-07

Table S143.  Gene #55: 'Del Peak 25(10p15.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 99
DEL PEAK 25(10P15.3) CNV 46 80 36
DEL PEAK 25(10P15.3) WILD-TYPE 96 34 63

Figure S143.  Get High-res Image Gene #55: 'Del Peak 25(10p15.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 25(10p15.3)' versus 'MRNASEQ_CNMF'

P value = 3.92e-05 (Fisher's exact test), Q value = 0.033

Table S144.  Gene #55: 'Del Peak 25(10p15.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 142 75
DEL PEAK 25(10P15.3) CNV 46 87 56 24
DEL PEAK 25(10P15.3) WILD-TYPE 72 56 86 51

Figure S144.  Get High-res Image Gene #55: 'Del Peak 25(10p15.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 25(10p15.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.28e-06 (Fisher's exact test), Q value = 0.0038

Table S145.  Gene #55: 'Del Peak 25(10p15.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 245
DEL PEAK 25(10P15.3) CNV 35 87 91
DEL PEAK 25(10P15.3) WILD-TYPE 58 53 154

Figure S145.  Get High-res Image Gene #55: 'Del Peak 25(10p15.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 25(10p15.3)' versus 'MIRSEQ_CNMF'

P value = 1.89e-06 (Fisher's exact test), Q value = 0.0017

Table S146.  Gene #55: 'Del Peak 25(10p15.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 130 124 64
DEL PEAK 25(10P15.3) CNV 67 67 34 42
DEL PEAK 25(10P15.3) WILD-TYPE 78 63 90 22

Figure S146.  Get High-res Image Gene #55: 'Del Peak 25(10p15.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 25(10p15.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.14e-05 (Fisher's exact test), Q value = 0.0099

Table S147.  Gene #55: 'Del Peak 25(10p15.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 71 163 229
DEL PEAK 25(10P15.3) CNV 50 72 88
DEL PEAK 25(10P15.3) WILD-TYPE 21 91 141

Figure S147.  Get High-res Image Gene #55: 'Del Peak 25(10p15.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 26(10p15.1)' versus 'CN_CNMF'

P value = 1.83e-06 (Fisher's exact test), Q value = 0.0017

Table S148.  Gene #56: 'Del Peak 26(10p15.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
DEL PEAK 26(10P15.1) CNV 62 94 49
DEL PEAK 26(10P15.1) WILD-TYPE 132 68 84

Figure S148.  Get High-res Image Gene #56: 'Del Peak 26(10p15.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 26(10p15.1)' versus 'METHLYATION_CNMF'

P value = 2.6e-10 (Fisher's exact test), Q value = 2.5e-07

Table S149.  Gene #56: 'Del Peak 26(10p15.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 99
DEL PEAK 26(10P15.1) CNV 45 78 30
DEL PEAK 26(10P15.1) WILD-TYPE 97 36 69

Figure S149.  Get High-res Image Gene #56: 'Del Peak 26(10p15.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 26(10p15.1)' versus 'MRNASEQ_CNMF'

P value = 1.59e-06 (Fisher's exact test), Q value = 0.0014

Table S150.  Gene #56: 'Del Peak 26(10p15.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 142 75
DEL PEAK 26(10P15.1) CNV 42 86 53 20
DEL PEAK 26(10P15.1) WILD-TYPE 76 57 89 55

Figure S150.  Get High-res Image Gene #56: 'Del Peak 26(10p15.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 26(10p15.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.33e-06 (Fisher's exact test), Q value = 0.0021

Table S151.  Gene #56: 'Del Peak 26(10p15.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 245
DEL PEAK 26(10P15.1) CNV 33 84 84
DEL PEAK 26(10P15.1) WILD-TYPE 60 56 161

Figure S151.  Get High-res Image Gene #56: 'Del Peak 26(10p15.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 26(10p15.1)' versus 'MIRSEQ_CNMF'

P value = 1.58e-06 (Fisher's exact test), Q value = 0.0014

Table S152.  Gene #56: 'Del Peak 26(10p15.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 130 124 64
DEL PEAK 26(10P15.1) CNV 65 61 31 41
DEL PEAK 26(10P15.1) WILD-TYPE 80 69 93 23

Figure S152.  Get High-res Image Gene #56: 'Del Peak 26(10p15.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 26(10p15.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.6e-06 (Fisher's exact test), Q value = 0.0032

Table S153.  Gene #56: 'Del Peak 26(10p15.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 71 163 229
DEL PEAK 26(10P15.1) CNV 49 68 81
DEL PEAK 26(10P15.1) WILD-TYPE 22 95 148

Figure S153.  Get High-res Image Gene #56: 'Del Peak 26(10p15.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 27(10q23.31)' versus 'CN_CNMF'

P value = 4.34e-08 (Fisher's exact test), Q value = 4.1e-05

Table S154.  Gene #57: 'Del Peak 27(10q23.31)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
DEL PEAK 27(10Q23.31) CNV 75 112 65
DEL PEAK 27(10Q23.31) WILD-TYPE 119 50 68

Figure S154.  Get High-res Image Gene #57: 'Del Peak 27(10q23.31)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 27(10q23.31)' versus 'METHLYATION_CNMF'

P value = 2.36e-07 (Fisher's exact test), Q value = 0.00022

Table S155.  Gene #57: 'Del Peak 27(10q23.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 99
DEL PEAK 27(10Q23.31) CNV 52 81 51
DEL PEAK 27(10Q23.31) WILD-TYPE 90 33 48

Figure S155.  Get High-res Image Gene #57: 'Del Peak 27(10q23.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 27(10q23.31)' versus 'MRNASEQ_CNMF'

P value = 6.5e-08 (Fisher's exact test), Q value = 6.1e-05

Table S156.  Gene #57: 'Del Peak 27(10q23.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 142 75
DEL PEAK 27(10Q23.31) CNV 51 103 61 30
DEL PEAK 27(10Q23.31) WILD-TYPE 67 40 81 45

Figure S156.  Get High-res Image Gene #57: 'Del Peak 27(10q23.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 27(10q23.31)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.78e-10 (Fisher's exact test), Q value = 9.4e-07

Table S157.  Gene #57: 'Del Peak 27(10q23.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 245
DEL PEAK 27(10Q23.31) CNV 47 102 96
DEL PEAK 27(10Q23.31) WILD-TYPE 46 38 149

Figure S157.  Get High-res Image Gene #57: 'Del Peak 27(10q23.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 27(10q23.31)' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.37e-05 (Fisher's exact test), Q value = 0.029

Table S158.  Gene #57: 'Del Peak 27(10q23.31)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 111 91
DEL PEAK 27(10Q23.31) CNV 84 45 39
DEL PEAK 27(10Q23.31) WILD-TYPE 41 66 52

Figure S158.  Get High-res Image Gene #57: 'Del Peak 27(10q23.31)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 28(11p15.5)' versus 'MRNA_CNMF'

P value = 0.000261 (Fisher's exact test), Q value = 0.21

Table S159.  Gene #58: 'Del Peak 28(11p15.5)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
DEL PEAK 28(11P15.5) CNV 30 20 9 18
DEL PEAK 28(11P15.5) WILD-TYPE 12 32 23 10

Figure S159.  Get High-res Image Gene #58: 'Del Peak 28(11p15.5)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 28(11p15.5)' versus 'CN_CNMF'

P value = 1.39e-07 (Fisher's exact test), Q value = 0.00013

Table S160.  Gene #58: 'Del Peak 28(11p15.5)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
DEL PEAK 28(11P15.5) CNV 66 77 87
DEL PEAK 28(11P15.5) WILD-TYPE 128 85 46

Figure S160.  Get High-res Image Gene #58: 'Del Peak 28(11p15.5)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 28(11p15.5)' versus 'RPPA_CHIERARCHICAL'

P value = 2.02e-05 (Fisher's exact test), Q value = 0.017

Table S161.  Gene #58: 'Del Peak 28(11p15.5)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 47 49 40
DEL PEAK 28(11P15.5) CNV 29 17 36 10
DEL PEAK 28(11P15.5) WILD-TYPE 29 30 13 30

Figure S161.  Get High-res Image Gene #58: 'Del Peak 28(11p15.5)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 29(11q22.1)' versus 'CN_CNMF'

P value = 0.000171 (Fisher's exact test), Q value = 0.14

Table S162.  Gene #59: 'Del Peak 29(11q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
DEL PEAK 29(11Q22.1) CNV 40 65 46
DEL PEAK 29(11Q22.1) WILD-TYPE 154 97 87

Figure S162.  Get High-res Image Gene #59: 'Del Peak 29(11q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 34(14q11.2)' versus 'MRNASEQ_CNMF'

P value = 3.27e-05 (Fisher's exact test), Q value = 0.028

Table S163.  Gene #64: 'Del Peak 34(14q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 142 75
DEL PEAK 34(14Q11.2) CNV 27 53 68 17
DEL PEAK 34(14Q11.2) WILD-TYPE 91 90 74 58

Figure S163.  Get High-res Image Gene #64: 'Del Peak 34(14q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 34(14q11.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.37e-07 (Fisher's exact test), Q value = 0.00013

Table S164.  Gene #64: 'Del Peak 34(14q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 245
DEL PEAK 34(14Q11.2) CNV 53 52 60
DEL PEAK 34(14Q11.2) WILD-TYPE 40 88 185

Figure S164.  Get High-res Image Gene #64: 'Del Peak 34(14q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 39(17p11.2)' versus 'CN_CNMF'

P value = 0.000255 (Fisher's exact test), Q value = 0.2

Table S165.  Gene #69: 'Del Peak 39(17p11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
DEL PEAK 39(17P11.2) CNV 86 83 89
DEL PEAK 39(17P11.2) WILD-TYPE 108 79 44

Figure S165.  Get High-res Image Gene #69: 'Del Peak 39(17p11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 40(17q11.2)' versus 'MRNA_CNMF'

P value = 3.03e-05 (Fisher's exact test), Q value = 0.026

Table S166.  Gene #70: 'Del Peak 40(17q11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
DEL PEAK 40(17Q11.2) CNV 21 4 11 6
DEL PEAK 40(17Q11.2) WILD-TYPE 21 48 21 22

Figure S166.  Get High-res Image Gene #70: 'Del Peak 40(17q11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 40(17q11.2)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000101 (Fisher's exact test), Q value = 0.084

Table S167.  Gene #70: 'Del Peak 40(17q11.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 22 56 23 53
DEL PEAK 40(17Q11.2) CNV 8 4 9 21
DEL PEAK 40(17Q11.2) WILD-TYPE 14 52 14 32

Figure S167.  Get High-res Image Gene #70: 'Del Peak 40(17q11.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 40(17q11.2)' versus 'CN_CNMF'

P value = 1.55e-06 (Fisher's exact test), Q value = 0.0014

Table S168.  Gene #70: 'Del Peak 40(17q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
DEL PEAK 40(17Q11.2) CNV 55 19 48
DEL PEAK 40(17Q11.2) WILD-TYPE 139 143 85

Figure S168.  Get High-res Image Gene #70: 'Del Peak 40(17q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 40(17q11.2)' versus 'METHLYATION_CNMF'

P value = 4.56e-05 (Fisher's exact test), Q value = 0.038

Table S169.  Gene #70: 'Del Peak 40(17q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 99
DEL PEAK 40(17Q11.2) CNV 45 11 27
DEL PEAK 40(17Q11.2) WILD-TYPE 97 103 72

Figure S169.  Get High-res Image Gene #70: 'Del Peak 40(17q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 40(17q11.2)' versus 'MRNASEQ_CNMF'

P value = 7.33e-09 (Fisher's exact test), Q value = 7e-06

Table S170.  Gene #70: 'Del Peak 40(17q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 118 143 142 75
DEL PEAK 40(17Q11.2) CNV 44 11 42 24
DEL PEAK 40(17Q11.2) WILD-TYPE 74 132 100 51

Figure S170.  Get High-res Image Gene #70: 'Del Peak 40(17q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 40(17q11.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.86e-09 (Fisher's exact test), Q value = 3.7e-06

Table S171.  Gene #70: 'Del Peak 40(17q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 140 245
DEL PEAK 40(17Q11.2) CNV 25 11 85
DEL PEAK 40(17Q11.2) WILD-TYPE 68 129 160

Figure S171.  Get High-res Image Gene #70: 'Del Peak 40(17q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 44(19q13.32)' versus 'CN_CNMF'

P value = 1.13e-06 (Fisher's exact test), Q value = 0.001

Table S172.  Gene #74: 'Del Peak 44(19q13.32)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
DEL PEAK 44(19Q13.32) CNV 33 68 40
DEL PEAK 44(19Q13.32) WILD-TYPE 161 94 93

Figure S172.  Get High-res Image Gene #74: 'Del Peak 44(19q13.32)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 44(19q13.32)' versus 'METHLYATION_CNMF'

P value = 2.32e-05 (Fisher's exact test), Q value = 0.02

Table S173.  Gene #74: 'Del Peak 44(19q13.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 99
DEL PEAK 44(19Q13.32) CNV 22 42 38
DEL PEAK 44(19Q13.32) WILD-TYPE 120 72 61

Figure S173.  Get High-res Image Gene #74: 'Del Peak 44(19q13.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 46(21q22.3)' versus 'CN_CNMF'

P value = 9.46e-08 (Fisher's exact test), Q value = 8.9e-05

Table S174.  Gene #76: 'Del Peak 46(21q22.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
DEL PEAK 46(21Q22.3) CNV 78 110 85
DEL PEAK 46(21Q22.3) WILD-TYPE 116 52 48

Figure S174.  Get High-res Image Gene #76: 'Del Peak 46(21q22.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 46(21q22.3)' versus 'MIRSEQ_CNMF'

P value = 8.61e-05 (Fisher's exact test), Q value = 0.072

Table S175.  Gene #76: 'Del Peak 46(21q22.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 130 124 64
DEL PEAK 46(21Q22.3) CNV 95 83 50 33
DEL PEAK 46(21Q22.3) WILD-TYPE 50 47 74 31

Figure S175.  Get High-res Image Gene #76: 'Del Peak 46(21q22.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 48(22q13.32)' versus 'MRNA_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.18

Table S176.  Gene #78: 'Del Peak 48(22q13.32)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
DEL PEAK 48(22Q13.32) CNV 8 8 8 17
DEL PEAK 48(22Q13.32) WILD-TYPE 34 44 24 11

Figure S176.  Get High-res Image Gene #78: 'Del Peak 48(22q13.32)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 49(Xp22.2)' versus 'CN_CNMF'

P value = 1.23e-05 (Fisher's exact test), Q value = 0.011

Table S177.  Gene #79: 'Del Peak 49(Xp22.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
DEL PEAK 49(XP22.2) CNV 39 68 50
DEL PEAK 49(XP22.2) WILD-TYPE 155 94 83

Figure S177.  Get High-res Image Gene #79: 'Del Peak 49(Xp22.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 49(Xp22.2)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.95e-06 (Fisher's exact test), Q value = 0.0018

Table S178.  Gene #79: 'Del Peak 49(Xp22.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 150 177
DEL PEAK 49(XP22.2) CNV 70 38
DEL PEAK 49(XP22.2) WILD-TYPE 80 139

Figure S178.  Get High-res Image Gene #79: 'Del Peak 49(Xp22.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 50(Xp21.1)' versus 'CN_CNMF'

P value = 3.82e-07 (Fisher's exact test), Q value = 0.00035

Table S179.  Gene #80: 'Del Peak 50(Xp21.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
DEL PEAK 50(XP21.1) CNV 36 72 48
DEL PEAK 50(XP21.1) WILD-TYPE 158 90 85

Figure S179.  Get High-res Image Gene #80: 'Del Peak 50(Xp21.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 50(Xp21.1)' versus 'METHLYATION_CNMF'

P value = 1.29e-05 (Fisher's exact test), Q value = 0.011

Table S180.  Gene #80: 'Del Peak 50(Xp21.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 99
DEL PEAK 50(XP21.1) CNV 25 48 39
DEL PEAK 50(XP21.1) WILD-TYPE 117 66 60

Figure S180.  Get High-res Image Gene #80: 'Del Peak 50(Xp21.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 50(Xp21.1)' versus 'MIRSEQ_CNMF'

P value = 2.01e-05 (Fisher's exact test), Q value = 0.017

Table S181.  Gene #80: 'Del Peak 50(Xp21.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 130 124 64
DEL PEAK 50(XP21.1) CNV 47 54 21 29
DEL PEAK 50(XP21.1) WILD-TYPE 98 76 103 35

Figure S181.  Get High-res Image Gene #80: 'Del Peak 50(Xp21.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 50(Xp21.1)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000246 (Fisher's exact test), Q value = 0.2

Table S182.  Gene #80: 'Del Peak 50(Xp21.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 111 91
DEL PEAK 50(XP21.1) CNV 57 24 25
DEL PEAK 50(XP21.1) WILD-TYPE 68 87 66

Figure S182.  Get High-res Image Gene #80: 'Del Peak 50(Xp21.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 50(Xp21.1)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8.65e-09 (Fisher's exact test), Q value = 8.2e-06

Table S183.  Gene #80: 'Del Peak 50(Xp21.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 150 177
DEL PEAK 50(XP21.1) CNV 73 33
DEL PEAK 50(XP21.1) WILD-TYPE 77 144

Figure S183.  Get High-res Image Gene #80: 'Del Peak 50(Xp21.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 51(Xp11.3)' versus 'CN_CNMF'

P value = 1.22e-07 (Fisher's exact test), Q value = 0.00011

Table S184.  Gene #81: 'Del Peak 51(Xp11.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
DEL PEAK 51(XP11.3) CNV 36 75 42
DEL PEAK 51(XP11.3) WILD-TYPE 158 87 91

Figure S184.  Get High-res Image Gene #81: 'Del Peak 51(Xp11.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 51(Xp11.3)' versus 'METHLYATION_CNMF'

P value = 4.05e-06 (Fisher's exact test), Q value = 0.0036

Table S185.  Gene #81: 'Del Peak 51(Xp11.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 99
DEL PEAK 51(XP11.3) CNV 24 51 35
DEL PEAK 51(XP11.3) WILD-TYPE 118 63 64

Figure S185.  Get High-res Image Gene #81: 'Del Peak 51(Xp11.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 51(Xp11.3)' versus 'MIRSEQ_CNMF'

P value = 1.38e-06 (Fisher's exact test), Q value = 0.0013

Table S186.  Gene #81: 'Del Peak 51(Xp11.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 130 124 64
DEL PEAK 51(XP11.3) CNV 44 53 19 31
DEL PEAK 51(XP11.3) WILD-TYPE 101 77 105 33

Figure S186.  Get High-res Image Gene #81: 'Del Peak 51(Xp11.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 51(Xp11.3)' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.21e-05 (Fisher's exact test), Q value = 0.027

Table S187.  Gene #81: 'Del Peak 51(Xp11.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 111 91
DEL PEAK 51(XP11.3) CNV 58 23 22
DEL PEAK 51(XP11.3) WILD-TYPE 67 88 69

Figure S187.  Get High-res Image Gene #81: 'Del Peak 51(Xp11.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 51(Xp11.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.47e-08 (Fisher's exact test), Q value = 1.4e-05

Table S188.  Gene #81: 'Del Peak 51(Xp11.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 150 177
DEL PEAK 51(XP11.3) CNV 71 32
DEL PEAK 51(XP11.3) WILD-TYPE 79 145

Figure S188.  Get High-res Image Gene #81: 'Del Peak 51(Xp11.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 52(Xq22.3)' versus 'CN_CNMF'

P value = 2.71e-07 (Fisher's exact test), Q value = 0.00025

Table S189.  Gene #82: 'Del Peak 52(Xq22.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 162 133
DEL PEAK 52(XQ22.3) CNV 25 42 52
DEL PEAK 52(XQ22.3) WILD-TYPE 169 120 81

Figure S189.  Get High-res Image Gene #82: 'Del Peak 52(Xq22.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 52(Xq22.3)' versus 'METHLYATION_CNMF'

P value = 1.02e-05 (Fisher's exact test), Q value = 0.009

Table S190.  Gene #82: 'Del Peak 52(Xq22.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 99
DEL PEAK 52(XQ22.3) CNV 16 27 37
DEL PEAK 52(XQ22.3) WILD-TYPE 126 87 62

Figure S190.  Get High-res Image Gene #82: 'Del Peak 52(Xq22.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 52(Xq22.3)' versus 'MIRSEQ_CNMF'

P value = 3.57e-05 (Fisher's exact test), Q value = 0.03

Table S191.  Gene #82: 'Del Peak 52(Xq22.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 130 124 64
DEL PEAK 52(XQ22.3) CNV 41 45 13 16
DEL PEAK 52(XQ22.3) WILD-TYPE 104 85 111 48

Figure S191.  Get High-res Image Gene #82: 'Del Peak 52(Xq22.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

Methods & Data
Input

  • Copy number data file = All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level). The all lesions file is from GISTIC pipeline and summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.

  • Molecular subtype file = LUSC-TP.transferedmergedcluster.txt

  • Number of patients = 489

  • Number of copy number variation regions = 82

  • Number of molecular subtypes = 12

  • Exclude regions 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.

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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