Correlation between copy number variation genes (focal events) and molecular subtypes
Overview
Introduction

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

Summary

Testing the association between copy number variation 55 focal events and 10 molecular subtypes across 331 patients, 109 significant findings detected with P value < 0.05 and Q value < 0.25.

  • amp_1q21.3 cnv correlated to 'CN_CNMF'.

  • amp_3q22.1 cnv correlated to 'CN_CNMF'.

  • amp_3q26.2 cnv correlated to 'CN_CNMF'.

  • amp_4p16.3 cnv correlated to 'CN_CNMF'.

  • amp_5q35.3 cnv correlated to 'CN_CNMF'.

  • amp_7p15.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

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

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

  • amp_9q34.3 cnv correlated to 'CN_CNMF'.

  • amp_11q13.3 cnv correlated to 'CN_CNMF'.

  • amp_12q24.32 cnv correlated to 'CN_CNMF'.

  • amp_14q21.1 cnv correlated to 'CN_CNMF'.

  • amp_19q13.43 cnv correlated to 'CN_CNMF'.

  • amp_20q13.31 cnv correlated to 'CN_CNMF'.

  • del_1p31.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_1q42.2 cnv correlated to 'METHLYATION_CNMF'.

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

  • del_2q22.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_3p13 cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_4q28.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • del_5q11.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • del_5q21.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_6q14.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

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

  • del_8p11.21 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_9p23 cnv correlated to 'CN_CNMF'.

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

  • del_12p13.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • del_12q24.31 cnv correlated to 'CN_CNMF'.

  • del_13q14.12 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_13q22.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • del_15q21.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • del_16q22.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • del_16q23.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • del_17p13.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • del_17q21.31 cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_18q22.1 cnv correlated to 'CN_CNMF'.

  • del_21q22.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 55 focal events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 109 significant findings detected.

Clinical
Features 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Chi-square test Fisher's exact test Chi-square test Fisher's exact test
del 16q22 3 119 (36%) 212 1.38e-16
(7.49e-14) 		1.87e-07
(9.38e-05) 		0.405
(1.00) 		0.207
(1.00) 		2.27e-05
(0.0109) 		1.46e-06
(0.000725) 		1.18e-05
(0.00571) 		4.51e-08
(2.31e-05) 		4.29e-05
(0.0201) 		0.00229
(0.952)
del 6q14 3 105 (32%) 226 5.25e-17
(2.86e-14) 		5.25e-23
(2.87e-20) 		0.00716
(1.00) 		0.0375
(1.00) 		6.65e-08
(3.36e-05) 		1.19e-09
(6.18e-07) 		0.000543
(0.239) 		0.0318
(1.00) 		2.52e-05
(0.0121) 		0.462
(1.00)
del 8p21 3 182 (55%) 149 4.19e-09
(2.17e-06) 		5.51e-09
(2.84e-06) 		0.0304
(1.00) 		0.0834
(1.00) 		3.08e-07
(0.000154) 		8.41e-06
(0.00409) 		4.48e-10
(2.34e-07) 		0.0301
(1.00) 		3.79e-07
(0.000189) 		0.0971
(1.00)
del 10q23 31 101 (31%) 230 2.31e-10
(1.21e-07) 		5.23e-11
(2.77e-08) 		0.0687
(1.00) 		0.306
(1.00) 		1.32e-14
(7.08e-12) 		5.67e-12
(3.02e-09) 		0.000226
(0.103) 		0.0157
(1.00) 		4.05e-05
(0.019) 		0.00253
(1.00)
del 17p13 1 90 (27%) 241 3.37e-14
(1.81e-11) 		5.85e-08
(2.97e-05) 		0.029
(1.00) 		0.0385
(1.00) 		4.65e-10
(2.43e-07) 		3.31e-10
(1.73e-07) 		0.00475
(1.00) 		8.68e-07
(0.000431) 		0.000282
(0.126) 		0.012
(1.00)
del 21q22 3 99 (30%) 232 5.08e-09
(2.62e-06) 		9.18e-22
(5.02e-19) 		0.123
(1.00) 		0.235
(1.00) 		4.08e-20
(2.23e-17) 		5.83e-16
(3.16e-13) 		0.00763
(1.00) 		0.000124
(0.057) 		0.00184
(0.772) 		0.000554
(0.244)
del 2q22 1 50 (15%) 281 4.56e-15
(2.45e-12) 		6.62e-11
(3.5e-08) 		0.015
(1.00) 		0.0897
(1.00) 		9.14e-05
(0.0422) 		2.34e-05
(0.0112) 		0.0859
(1.00) 		0.0608
(1.00) 		0.00013
(0.0594) 		0.000657
(0.287)
del 15q21 3 38 (11%) 293 1.04e-08
(5.35e-06) 		0.000148
(0.0678) 		0.00162
(0.685) 		0.0793
(1.00) 		0.000517
(0.229) 		0.000159
(0.0723) 		0.0208
(1.00) 		8.43e-05
(0.0391) 		0.00419
(1.00) 		0.127
(1.00)
del 16q23 3 130 (39%) 201 3.78e-18
(2.06e-15) 		5.76e-08
(2.92e-05) 		0.784
(1.00) 		0.703
(1.00) 		0.000181
(0.0823) 		4.52e-05
(0.0211) 		0.000595
(0.261) 		4.46e-06
(0.00218) 		0.00704
(1.00) 		0.0471
(1.00)
del 1p31 3 38 (11%) 293 0.000375
(0.167) 		2.32e-05
(0.0112) 		0.312
(1.00) 		0.714
(1.00) 		3.18e-05
(0.0151) 		2.41e-06
(0.00119) 		0.0394
(1.00) 		0.0375
(1.00) 		0.0199
(1.00) 		0.103
(1.00)
del 2q22 3 44 (13%) 287 1.18e-15
(6.36e-13) 		3.58e-08
(1.83e-05) 		0.129
(1.00) 		0.0412
(1.00) 		0.000272
(0.122) 		2.71e-05
(0.013) 		0.395
(1.00) 		0.0474
(1.00) 		0.0566
(1.00) 		0.0621
(1.00)
del 5q21 1 57 (17%) 274 1.45e-15
(7.83e-13) 		2.28e-10
(1.2e-07) 		0.118
(1.00) 		0.228
(1.00) 		0.000459
(0.204) 		6.6e-05
(0.0308) 		0.0457
(1.00) 		0.125
(1.00) 		0.0325
(1.00) 		0.0768
(1.00)
del 8p11 21 105 (32%) 226 9.84e-07
(0.000488) 		8.55e-10
(4.45e-07) 		0.846
(1.00) 		0.59
(1.00) 		1.18e-05
(0.00573) 		0.00026
(0.117) 		0.00142
(0.603) 		0.00398
(1.00) 		0.00316
(1.00) 		0.204
(1.00)
del 13q14 12 139 (42%) 192 4.88e-12
(2.6e-09) 		4.96e-08
(2.53e-05) 		0.0747
(1.00) 		0.207
(1.00) 		8.3e-06
(0.00404) 		7.12e-06
(0.00347) 		0.00107
(0.458) 		0.0244
(1.00) 		0.00257
(1.00) 		0.0865
(1.00)
amp 7p15 3 61 (18%) 270 2.48e-10
(1.3e-07) 		8.74e-08
(4.41e-05) 		0.309
(1.00) 		0.462
(1.00) 		7.08e-05
(0.033) 		0.00489
(1.00) 		0.154
(1.00) 		0.283
(1.00) 		0.195
(1.00) 		0.853
(1.00)
amp 8q24 21 84 (25%) 247 1.48e-16
(8e-14) 		1.96e-05
(0.00949) 		0.00642
(1.00) 		0.0247
(1.00) 		0.000311
(0.139) 		0.000786
(0.34) 		0.00156
(0.663) 		0.0229
(1.00) 		0.00124
(0.529) 		0.477
(1.00)
del 3p13 54 (16%) 277 0.066
(1.00) 		1.37e-07
(6.91e-05) 		0.803
(1.00) 		0.855
(1.00) 		0.000137
(0.0625) 		1.36e-07
(6.85e-05) 		0.0491
(1.00) 		0.0573
(1.00) 		0.00992
(1.00) 		0.0175
(1.00)
del 17q21 31 65 (20%) 266 0.0397
(1.00) 		9.14e-09
(4.7e-06) 		0.529
(1.00) 		0.846
(1.00) 		3.3e-09
(1.71e-06) 		2.87e-05
(0.0137) 		0.0341
(1.00) 		0.00544
(1.00) 		0.0938
(1.00) 		0.144
(1.00)
amp 8p11 23 32 (10%) 299 5e-08
(2.54e-05) 		7.44e-05
(0.0346) 		0.0844
(1.00) 		0.31
(1.00) 		0.0476
(1.00) 		0.0995
(1.00) 		0.142
(1.00) 		0.233
(1.00) 		0.101
(1.00) 		0.274
(1.00)
del 4q28 2 25 (8%) 306 8.45e-05
(0.0391) 		2.78e-05
(0.0133) 		0.138
(1.00) 		0.359
(1.00) 		0.0608
(1.00) 		0.02
(1.00) 		0.193
(1.00) 		0.335
(1.00) 		0.176
(1.00) 		0.167
(1.00)
del 5q11 2 52 (16%) 279 1.09e-10
(5.75e-08) 		2.56e-06
(0.00126) 		0.00457
(1.00) 		0.024
(1.00) 		0.0115
(1.00) 		0.00206
(0.864) 		0.0353
(1.00) 		0.00687
(1.00) 		0.02
(1.00) 		0.0639
(1.00)
del 12p13 1 71 (21%) 260 3.68e-05
(0.0174) 		0.000159
(0.0723) 		0.125
(1.00) 		0.429
(1.00) 		0.00148
(0.628) 		0.00584
(1.00) 		0.0163
(1.00) 		0.0103
(1.00) 		0.0468
(1.00) 		0.247
(1.00)
del 13q22 1 107 (32%) 224 4.69e-14
(2.51e-11) 		3.82e-05
(0.018) 		0.00886
(1.00) 		0.0609
(1.00) 		0.000919
(0.397) 		0.00241
(1.00) 		0.00164
(0.693) 		0.0483
(1.00) 		0.00633
(1.00) 		0.329
(1.00)
amp 1q21 3 22 (7%) 309 2.87e-06
(0.00141) 		0.00482
(1.00) 		0.00369
(1.00) 		0.16
(1.00) 		0.0029
(1.00) 		0.00108
(0.461) 		0.0548
(1.00) 		0.0838
(1.00) 		0.186
(1.00) 		0.655
(1.00)
amp 3q22 1 40 (12%) 291 4.34e-11
(2.3e-08) 		0.00447
(1.00) 		0.174
(1.00) 		0.406
(1.00) 		0.00642
(1.00) 		0.0154
(1.00) 		0.388
(1.00) 		0.862
(1.00) 		0.319
(1.00) 		0.619
(1.00)
amp 3q26 2 47 (14%) 284 3.46e-09
(1.79e-06) 		0.156
(1.00) 		0.142
(1.00) 		0.506
(1.00) 		0.0454
(1.00) 		0.135
(1.00) 		0.335
(1.00) 		0.588
(1.00) 		0.246
(1.00) 		0.509
(1.00)
amp 4p16 3 13 (4%) 318 0.000244
(0.11) 		0.01
(1.00) 		0.505
(1.00) 		0.188
(1.00) 		0.0151
(1.00) 		0.119
(1.00) 		0.786
(1.00) 		0.528
(1.00) 		0.448
(1.00) 		0.671
(1.00)
amp 5q35 3 16 (5%) 315 6.03e-07
(3e-04) 		0.0453
(1.00) 		0.112
(1.00) 		0.158
(1.00) 		0.0881
(1.00) 		0.0819
(1.00) 		0.102
(1.00) 		0.0857
(1.00) 		0.79
(1.00) 		0.694
(1.00)
amp 9q34 3 35 (11%) 296 4.93e-14
(2.63e-11) 		0.0362
(1.00) 		0.0541
(1.00) 		0.0411
(1.00) 		0.00217
(0.906) 		0.00518
(1.00) 		0.0853
(1.00) 		0.0264
(1.00) 		0.225
(1.00) 		0.546
(1.00)
amp 11q13 3 20 (6%) 311 1.7e-06
(0.000841) 		0.0581
(1.00) 		0.521
(1.00) 		0.39
(1.00) 		0.0226
(1.00) 		0.16
(1.00) 		0.789
(1.00) 		0.198
(1.00) 		0.163
(1.00) 		0.6
(1.00)
amp 12q24 32 12 (4%) 319 9.15e-05
(0.0422) 		0.317
(1.00) 		0.228
(1.00) 		0.264
(1.00) 		0.872
(1.00) 		0.0614
(1.00) 		0.256
(1.00) 		0.621
(1.00) 		0.2
(1.00) 		0.396
(1.00)
amp 14q21 1 17 (5%) 314 2.9e-05
(0.0138) 		0.0108
(1.00) 		0.166
(1.00) 		0.139
(1.00) 		0.182
(1.00) 		0.279
(1.00) 		0.417
(1.00) 		0.144
(1.00) 		0.439
(1.00) 		0.984
(1.00)
amp 19q13 43 8 (2%) 323 0.00023
(0.104) 		0.101
(1.00) 		0.452
(1.00) 		0.314
(1.00) 		0.101
(1.00) 		0.0118
(1.00) 		0.471
(1.00) 		0.0993
(1.00) 		0.462
(1.00) 		0.366
(1.00)
amp 20q13 31 21 (6%) 310 0.000309
(0.138) 		0.00104
(0.446) 		0.303
(1.00) 		0.304
(1.00) 		0.0837
(1.00) 		0.126
(1.00) 		0.56
(1.00) 		0.458
(1.00) 		0.284
(1.00) 		0.324
(1.00)
del 1q42 2 27 (8%) 304 0.00077
(0.334) 		0.000471
(0.209) 		0.933
(1.00) 		0.391
(1.00) 		0.464
(1.00) 		0.266
(1.00) 		0.38
(1.00) 		0.819
(1.00) 		0.395
(1.00) 		0.805
(1.00)
del 9p23 26 (8%) 305 3.41e-05
(0.0161) 		0.219
(1.00) 		0.00358
(1.00) 		0.071
(1.00) 		0.0204
(1.00) 		0.0228
(1.00) 		0.408
(1.00) 		0.756
(1.00) 		0.146
(1.00) 		0.74
(1.00)
del 12q24 31 28 (8%) 303 3.8e-06
(0.00186) 		0.0887
(1.00) 		1
(1.00) 		1
(1.00) 		0.0521
(1.00) 		0.116
(1.00) 		0.13
(1.00) 		0.248
(1.00) 		0.304
(1.00) 		0.83
(1.00)
del 18q22 1 83 (25%) 248 1.71e-07
(8.56e-05) 		0.109
(1.00) 		0.319
(1.00) 		0.0644
(1.00) 		0.00845
(1.00) 		0.0141
(1.00) 		0.37
(1.00) 		0.0794
(1.00) 		0.201
(1.00) 		0.0506
(1.00)
amp 4q13 3 6 (2%) 325 0.0351
(1.00) 		0.22
(1.00) 		0.471
(1.00) 		0.635
(1.00) 		0.03
(1.00) 		0.39
(1.00) 		0.347
(1.00) 		0.212
(1.00) 		0.488
(1.00) 		0.355
(1.00)
amp 15q11 2 9 (3%) 322 0.794
(1.00) 		0.635
(1.00) 		1
(1.00) 		1
(1.00) 		0.837
(1.00) 		0.637
(1.00) 		0.357
(1.00) 		1
(1.00) 		0.752
(1.00) 		0.917
(1.00)
amp xp22 11 12 (4%) 319 0.000759
(0.331) 		0.872
(1.00) 		0.372
(1.00) 		0.618
(1.00) 		0.0468
(1.00) 		0.125
(1.00) 		0.0463
(1.00) 		0.0905
(1.00)
amp xp22 11 12 (4%) 319 0.000759
(0.331) 		0.934
(1.00) 		0.0933
(1.00) 		0.275
(1.00) 		0.155
(1.00) 		0.758
(1.00) 		0.286
(1.00) 		0.156
(1.00) 		0.182
(1.00) 		0.439
(1.00)
amp xp21 1 11 (3%) 320 0.00277
(1.00) 		0.232
(1.00) 		0.848
(1.00) 		0.735
(1.00) 		0.268
(1.00) 		0.805
(1.00) 		0.0736
(1.00) 		0.0789
(1.00) 		0.094
(1.00) 		0.384
(1.00)
amp xq21 1 9 (3%) 322 0.0582
(1.00) 		0.362
(1.00) 		0.484
(1.00) 		0.495
(1.00) 		0.104
(1.00) 		0.358
(1.00) 		0.0742
(1.00) 		0.374
(1.00) 		0.248
(1.00) 		0.395
(1.00)
amp xq21 1 7 (2%) 324 0.00379
(1.00) 		0.00166
(0.699) 		0.452
(1.00) 		1
(1.00) 		0.509
(1.00) 		0.159
(1.00) 		0.853
(1.00) 		0.91
(1.00) 		0.754
(1.00) 		0.653
(1.00)
amp xq21 31 7 (2%) 324 0.0134
(1.00) 		0.308
(1.00) 		0.848
(1.00) 		0.735
(1.00) 		0.124
(1.00) 		0.185
(1.00) 		0.756
(1.00) 		0.872
(1.00) 		0.699
(1.00) 		0.949
(1.00)
amp xq25 6 (2%) 325 0.224
(1.00) 		0.0367
(1.00) 		0.624
(1.00) 		1
(1.00) 		0.141
(1.00) 		0.0971
(1.00) 		0.179
(1.00) 		0.575
(1.00) 		0.2
(1.00) 		0.192
(1.00)
amp xq25 9 (3%) 322 0.0902
(1.00) 		0.195
(1.00) 		1
(1.00) 		0.771
(1.00) 		0.202
(1.00) 		0.0224
(1.00) 		0.835
(1.00) 		0.374
(1.00) 		0.63
(1.00) 		0.395
(1.00)
amp xq27 1 11 (3%) 320 0.0143
(1.00) 		0.121
(1.00) 		0.418
(1.00) 		0.308
(1.00) 		0.927
(1.00) 		0.692
(1.00) 		0.00868
(1.00) 		0.0338
(1.00) 		0.0129
(1.00) 		0.00927
(1.00)
del 1q23 1 15 (5%) 316 0.111
(1.00) 		0.00399
(1.00) 		0.297
(1.00) 		0.176
(1.00) 		0.036
(1.00) 		0.0022
(0.916) 		0.169
(1.00) 		0.147
(1.00) 		0.0406
(1.00) 		0.459
(1.00)
del 2p22 1 24 (7%) 307 0.0104
(1.00) 		0.0749
(1.00) 		0.0247
(1.00) 		0.786
(1.00) 		0.00528
(1.00) 		0.0292
(1.00) 		0.23
(1.00) 		0.543
(1.00) 		0.0829
(1.00) 		0.518
(1.00)
del 3q29 19 (6%) 312 0.399
(1.00) 		0.0361
(1.00) 		0.73
(1.00) 		0.415
(1.00) 		0.00763
(1.00) 		0.171
(1.00) 		0.302
(1.00) 		0.914
(1.00) 		0.417
(1.00) 		0.91
(1.00)
del 11q23 2 31 (9%) 300 0.0106
(1.00) 		0.0472
(1.00) 		0.155
(1.00) 		0.109
(1.00) 		0.803
(1.00) 		0.962
(1.00) 		0.18
(1.00) 		0.535
(1.00) 		0.483
(1.00) 		0.45
(1.00)
del 19q13 2 29 (9%) 302 0.0206
(1.00) 		0.113
(1.00) 		0.352
(1.00) 		0.502
(1.00) 		0.0444
(1.00) 		0.367
(1.00) 		0.544
(1.00) 		0.0108
(1.00) 		0.128
(1.00) 		0.167
(1.00)
del 21q22 2 34 (10%) 297 0.0729
(1.00) 		0.0101
(1.00) 		0.394
(1.00) 		0.763
(1.00) 		0.00095
(0.409) 		0.000586
(0.257) 		0.861
(1.00) 		0.574
(1.00) 		0.983
(1.00) 		0.585
(1.00)
'amp_1q21.3' versus 'CN_CNMF'

P value = 2.87e-06 (Fisher's exact test), Q value = 0.0014

Table S1.  Gene #1: 'amp_1q21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 183 104
AMP PEAK 1(1Q21.3) MUTATED 1 3 18
AMP PEAK 1(1Q21.3) WILD-TYPE 43 180 86

Figure S1.  Get High-res Image Gene #1: 'amp_1q21.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3q22.1' versus 'CN_CNMF'

P value = 4.34e-11 (Fisher's exact test), Q value = 2.3e-08

Table S2.  Gene #2: 'amp_3q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 183 104
AMP PEAK 2(3Q22.1) MUTATED 9 3 28
AMP PEAK 2(3Q22.1) WILD-TYPE 35 180 76

Figure S2.  Get High-res Image Gene #2: 'amp_3q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3q26.2' versus 'CN_CNMF'

P value = 3.46e-09 (Fisher's exact test), Q value = 1.8e-06

Table S3.  Gene #3: 'amp_3q26.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 183 104
AMP PEAK 3(3Q26.2) MUTATED 11 7 29
AMP PEAK 3(3Q26.2) WILD-TYPE 33 176 75

Figure S3.  Get High-res Image Gene #3: 'amp_3q26.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_4p16.3' versus 'CN_CNMF'

P value = 0.000244 (Fisher's exact test), Q value = 0.11

Table S4.  Gene #4: 'amp_4p16.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 183 104
AMP PEAK 4(4P16.3) MUTATED 0 2 11
AMP PEAK 4(4P16.3) WILD-TYPE 44 181 93

Figure S4.  Get High-res Image Gene #4: 'amp_4p16.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5q35.3' versus 'CN_CNMF'

P value = 6.03e-07 (Fisher's exact test), Q value = 3e-04

Table S5.  Gene #6: 'amp_5q35.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 183 104
AMP PEAK 6(5Q35.3) MUTATED 0 1 15
AMP PEAK 6(5Q35.3) WILD-TYPE 44 182 89

Figure S5.  Get High-res Image Gene #6: 'amp_5q35.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7p15.3' versus 'CN_CNMF'

P value = 2.48e-10 (Fisher's exact test), Q value = 1.3e-07

Table S6.  Gene #7: 'amp_7p15.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 183 104
AMP PEAK 7(7P15.3) MUTATED 15 11 35
AMP PEAK 7(7P15.3) WILD-TYPE 29 172 69

Figure S6.  Get High-res Image Gene #7: 'amp_7p15.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7p15.3' versus 'METHLYATION_CNMF'

P value = 8.74e-08 (Fisher's exact test), Q value = 4.4e-05

Table S7.  Gene #7: 'amp_7p15.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 106 129
AMP PEAK 7(7P15.3) MUTATED 35 6 20
AMP PEAK 7(7P15.3) WILD-TYPE 61 100 109

Figure S7.  Get High-res Image Gene #7: 'amp_7p15.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7p15.3' versus 'MRNASEQ_CNMF'

P value = 7.08e-05 (Fisher's exact test), Q value = 0.033

Table S8.  Gene #7: 'amp_7p15.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 97 112
AMP PEAK 7(7P15.3) MUTATED 36 7 18
AMP PEAK 7(7P15.3) WILD-TYPE 85 90 94

Figure S8.  Get High-res Image Gene #7: 'amp_7p15.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_8p11.23' versus 'CN_CNMF'

P value = 5e-08 (Fisher's exact test), Q value = 2.5e-05

Table S9.  Gene #8: 'amp_8p11.23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 183 104
AMP PEAK 8(8P11.23) MUTATED 8 3 21
AMP PEAK 8(8P11.23) WILD-TYPE 36 180 83

Figure S9.  Get High-res Image Gene #8: 'amp_8p11.23' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8p11.23' versus 'METHLYATION_CNMF'

P value = 7.44e-05 (Fisher's exact test), Q value = 0.035

Table S10.  Gene #8: 'amp_8p11.23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 106 129
AMP PEAK 8(8P11.23) MUTATED 20 3 9
AMP PEAK 8(8P11.23) WILD-TYPE 76 103 120

Figure S10.  Get High-res Image Gene #8: 'amp_8p11.23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'CN_CNMF'

P value = 1.48e-16 (Fisher's exact test), Q value = 8e-14

Table S11.  Gene #9: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 183 104
AMP PEAK 9(8Q24.21) MUTATED 8 18 58
AMP PEAK 9(8Q24.21) WILD-TYPE 36 165 46

Figure S11.  Get High-res Image Gene #9: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

P value = 1.96e-05 (Fisher's exact test), Q value = 0.0095

Table S12.  Gene #9: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 106 129
AMP PEAK 9(8Q24.21) MUTATED 39 13 32
AMP PEAK 9(8Q24.21) WILD-TYPE 57 93 97

Figure S12.  Get High-res Image Gene #9: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CNMF'

P value = 0.000311 (Fisher's exact test), Q value = 0.14

Table S13.  Gene #9: 'amp_8q24.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 97 112
AMP PEAK 9(8Q24.21) MUTATED 40 11 33
AMP PEAK 9(8Q24.21) WILD-TYPE 81 86 79

Figure S13.  Get High-res Image Gene #9: 'amp_8q24.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_9q34.3' versus 'CN_CNMF'

P value = 4.93e-14 (Fisher's exact test), Q value = 2.6e-11

Table S14.  Gene #10: 'amp_9q34.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 183 104
AMP PEAK 10(9Q34.3) MUTATED 0 3 32
AMP PEAK 10(9Q34.3) WILD-TYPE 44 180 72

Figure S14.  Get High-res Image Gene #10: 'amp_9q34.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11q13.3' versus 'CN_CNMF'

P value = 1.7e-06 (Fisher's exact test), Q value = 0.00084

Table S15.  Gene #11: 'amp_11q13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 183 104
AMP PEAK 11(11Q13.3) MUTATED 1 2 17
AMP PEAK 11(11Q13.3) WILD-TYPE 43 181 87

Figure S15.  Get High-res Image Gene #11: 'amp_11q13.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12q24.32' versus 'CN_CNMF'

P value = 9.15e-05 (Fisher's exact test), Q value = 0.042

Table S16.  Gene #12: 'amp_12q24.32' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 183 104
AMP PEAK 12(12Q24.32) MUTATED 0 1 11
AMP PEAK 12(12Q24.32) WILD-TYPE 44 182 93

Figure S16.  Get High-res Image Gene #12: 'amp_12q24.32' versus Molecular Subtype #1: 'CN_CNMF'

'amp_14q21.1' versus 'CN_CNMF'

P value = 2.9e-05 (Fisher's exact test), Q value = 0.014

Table S17.  Gene #13: 'amp_14q21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 183 104
AMP PEAK 13(14Q21.1) MUTATED 4 1 12
AMP PEAK 13(14Q21.1) WILD-TYPE 40 182 92

Figure S17.  Get High-res Image Gene #13: 'amp_14q21.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19q13.43' versus 'CN_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.1

Table S18.  Gene #15: 'amp_19q13.43' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 183 104
AMP PEAK 15(19Q13.43) MUTATED 0 0 8
AMP PEAK 15(19Q13.43) WILD-TYPE 44 183 96

Figure S18.  Get High-res Image Gene #15: 'amp_19q13.43' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20q13.31' versus 'CN_CNMF'

P value = 0.000309 (Fisher's exact test), Q value = 0.14

Table S19.  Gene #16: 'amp_20q13.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 183 104
AMP PEAK 16(20Q13.31) MUTATED 2 4 15
AMP PEAK 16(20Q13.31) WILD-TYPE 42 179 89

Figure S19.  Get High-res Image Gene #16: 'amp_20q13.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p31.3' versus 'CN_CNMF'

P value = 0.000375 (Fisher's exact test), Q value = 0.17

Table S20.  Gene #26: 'del_1p31.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 183 104
DEL PEAK 1(1P31.3) MUTATED 2 13 23
DEL PEAK 1(1P31.3) WILD-TYPE 42 170 81

Figure S20.  Get High-res Image Gene #26: 'del_1p31.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p31.3' versus 'METHLYATION_CNMF'

P value = 2.32e-05 (Fisher's exact test), Q value = 0.011

Table S21.  Gene #26: 'del_1p31.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 106 129
DEL PEAK 1(1P31.3) MUTATED 10 2 26
DEL PEAK 1(1P31.3) WILD-TYPE 86 104 103

Figure S21.  Get High-res Image Gene #26: 'del_1p31.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p31.3' versus 'MRNASEQ_CNMF'

P value = 3.18e-05 (Fisher's exact test), Q value = 0.015

Table S22.  Gene #26: 'del_1p31.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 97 112
DEL PEAK 1(1P31.3) MUTATED 12 2 24
DEL PEAK 1(1P31.3) WILD-TYPE 109 95 88

Figure S22.  Get High-res Image Gene #26: 'del_1p31.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_1p31.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.41e-06 (Fisher's exact test), Q value = 0.0012

Table S23.  Gene #26: 'del_1p31.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 93 122
DEL PEAK 1(1P31.3) MUTATED 8 2 28
DEL PEAK 1(1P31.3) WILD-TYPE 107 91 94

Figure S23.  Get High-res Image Gene #26: 'del_1p31.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1q42.2' versus 'METHLYATION_CNMF'

P value = 0.000471 (Fisher's exact test), Q value = 0.21

Table S24.  Gene #28: 'del_1q42.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 106 129
DEL PEAK 3(1Q42.2) MUTATED 17 3 7
DEL PEAK 3(1Q42.2) WILD-TYPE 79 103 122

Figure S24.  Get High-res Image Gene #28: 'del_1q42.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q22.1' versus 'CN_CNMF'

P value = 4.56e-15 (Fisher's exact test), Q value = 2.5e-12

Table S25.  Gene #30: 'del_2q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 183 104
DEL PEAK 5(2Q22.1) MUTATED 16 3 31
DEL PEAK 5(2Q22.1) WILD-TYPE 28 180 73

Figure S25.  Get High-res Image Gene #30: 'del_2q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q22.1' versus 'METHLYATION_CNMF'

P value = 6.62e-11 (Fisher's exact test), Q value = 3.5e-08

Table S26.  Gene #30: 'del_2q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 106 129
DEL PEAK 5(2Q22.1) MUTATED 34 2 14
DEL PEAK 5(2Q22.1) WILD-TYPE 62 104 115

Figure S26.  Get High-res Image Gene #30: 'del_2q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q22.1' versus 'MRNASEQ_CNMF'

P value = 9.14e-05 (Fisher's exact test), Q value = 0.042

Table S27.  Gene #30: 'del_2q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 97 112
DEL PEAK 5(2Q22.1) MUTATED 31 5 14
DEL PEAK 5(2Q22.1) WILD-TYPE 90 92 98

Figure S27.  Get High-res Image Gene #30: 'del_2q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.34e-05 (Fisher's exact test), Q value = 0.011

Table S28.  Gene #30: 'del_2q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 93 122
DEL PEAK 5(2Q22.1) MUTATED 29 3 18
DEL PEAK 5(2Q22.1) WILD-TYPE 86 90 104

Figure S28.  Get High-res Image Gene #30: 'del_2q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_2q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00013 (Chi-square test), Q value = 0.059

Table S29.  Gene #30: 'del_2q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 80 28 89 95 29
DEL PEAK 5(2Q22.1) MUTATED 4 1 17 25 1
DEL PEAK 5(2Q22.1) WILD-TYPE 76 27 72 70 28

Figure S29.  Get High-res Image Gene #30: 'del_2q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_2q22.3' versus 'CN_CNMF'

P value = 1.18e-15 (Fisher's exact test), Q value = 6.4e-13

Table S30.  Gene #31: 'del_2q22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 183 104
DEL PEAK 6(2Q22.3) MUTATED 15 1 28
DEL PEAK 6(2Q22.3) WILD-TYPE 29 182 76

Figure S30.  Get High-res Image Gene #31: 'del_2q22.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q22.3' versus 'METHLYATION_CNMF'

P value = 3.58e-08 (Fisher's exact test), Q value = 1.8e-05

Table S31.  Gene #31: 'del_2q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 106 129
DEL PEAK 6(2Q22.3) MUTATED 28 2 14
DEL PEAK 6(2Q22.3) WILD-TYPE 68 104 115

Figure S31.  Get High-res Image Gene #31: 'del_2q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q22.3' versus 'MRNASEQ_CNMF'

P value = 0.000272 (Fisher's exact test), Q value = 0.12

Table S32.  Gene #31: 'del_2q22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 97 112
DEL PEAK 6(2Q22.3) MUTATED 28 5 11
DEL PEAK 6(2Q22.3) WILD-TYPE 93 92 101

Figure S32.  Get High-res Image Gene #31: 'del_2q22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2q22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.71e-05 (Fisher's exact test), Q value = 0.013

Table S33.  Gene #31: 'del_2q22.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 93 122
DEL PEAK 6(2Q22.3) MUTATED 26 2 16
DEL PEAK 6(2Q22.3) WILD-TYPE 89 91 106

Figure S33.  Get High-res Image Gene #31: 'del_2q22.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p13' versus 'METHLYATION_CNMF'

P value = 1.37e-07 (Fisher's exact test), Q value = 6.9e-05

Table S34.  Gene #32: 'del_3p13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 106 129
DEL PEAK 7(3P13) MUTATED 4 11 39
DEL PEAK 7(3P13) WILD-TYPE 92 95 90

Figure S34.  Get High-res Image Gene #32: 'del_3p13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p13' versus 'MRNASEQ_CNMF'

P value = 0.000137 (Fisher's exact test), Q value = 0.063

Table S35.  Gene #32: 'del_3p13' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 97 112
DEL PEAK 7(3P13) MUTATED 14 8 32
DEL PEAK 7(3P13) WILD-TYPE 107 89 80

Figure S35.  Get High-res Image Gene #32: 'del_3p13' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.36e-07 (Fisher's exact test), Q value = 6.9e-05

Table S36.  Gene #32: 'del_3p13' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 93 122
DEL PEAK 7(3P13) MUTATED 6 10 38
DEL PEAK 7(3P13) WILD-TYPE 109 83 84

Figure S36.  Get High-res Image Gene #32: 'del_3p13' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q28.2' versus 'CN_CNMF'

P value = 8.45e-05 (Fisher's exact test), Q value = 0.039

Table S37.  Gene #34: 'del_4q28.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 183 104
DEL PEAK 9(4Q28.2) MUTATED 7 4 14
DEL PEAK 9(4Q28.2) WILD-TYPE 37 179 90

Figure S37.  Get High-res Image Gene #34: 'del_4q28.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q28.2' versus 'METHLYATION_CNMF'

P value = 2.78e-05 (Fisher's exact test), Q value = 0.013

Table S38.  Gene #34: 'del_4q28.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 106 129
DEL PEAK 9(4Q28.2) MUTATED 17 1 7
DEL PEAK 9(4Q28.2) WILD-TYPE 79 105 122

Figure S38.  Get High-res Image Gene #34: 'del_4q28.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q11.2' versus 'CN_CNMF'

P value = 1.09e-10 (Fisher's exact test), Q value = 5.7e-08

Table S39.  Gene #35: 'del_5q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 183 104
DEL PEAK 10(5Q11.2) MUTATED 6 9 37
DEL PEAK 10(5Q11.2) WILD-TYPE 38 174 67

Figure S39.  Get High-res Image Gene #35: 'del_5q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q11.2' versus 'METHLYATION_CNMF'

P value = 2.56e-06 (Fisher's exact test), Q value = 0.0013

Table S40.  Gene #35: 'del_5q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 106 129
DEL PEAK 10(5Q11.2) MUTATED 25 3 24
DEL PEAK 10(5Q11.2) WILD-TYPE 71 103 105

Figure S40.  Get High-res Image Gene #35: 'del_5q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q21.1' versus 'CN_CNMF'

P value = 1.45e-15 (Fisher's exact test), Q value = 7.8e-13

Table S41.  Gene #36: 'del_5q21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 183 104
DEL PEAK 11(5Q21.1) MUTATED 19 5 33
DEL PEAK 11(5Q21.1) WILD-TYPE 25 178 71

Figure S41.  Get High-res Image Gene #36: 'del_5q21.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q21.1' versus 'METHLYATION_CNMF'

P value = 2.28e-10 (Fisher's exact test), Q value = 1.2e-07

Table S42.  Gene #36: 'del_5q21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 106 129
DEL PEAK 11(5Q21.1) MUTATED 38 6 13
DEL PEAK 11(5Q21.1) WILD-TYPE 58 100 116

Figure S42.  Get High-res Image Gene #36: 'del_5q21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q21.1' versus 'MRNASEQ_CNMF'

P value = 0.000459 (Fisher's exact test), Q value = 0.2

Table S43.  Gene #36: 'del_5q21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 97 112
DEL PEAK 11(5Q21.1) MUTATED 34 9 14
DEL PEAK 11(5Q21.1) WILD-TYPE 87 88 98

Figure S43.  Get High-res Image Gene #36: 'del_5q21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_5q21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.6e-05 (Fisher's exact test), Q value = 0.031

Table S44.  Gene #36: 'del_5q21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 93 122
DEL PEAK 11(5Q21.1) MUTATED 34 7 16
DEL PEAK 11(5Q21.1) WILD-TYPE 81 86 106

Figure S44.  Get High-res Image Gene #36: 'del_5q21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6q14.3' versus 'CN_CNMF'

P value = 5.25e-17 (Fisher's exact test), Q value = 2.9e-14

Table S45.  Gene #37: 'del_6q14.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 183 104
DEL PEAK 12(6Q14.3) MUTATED 29 23 53
DEL PEAK 12(6Q14.3) WILD-TYPE 15 160 51

Figure S45.  Get High-res Image Gene #37: 'del_6q14.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q14.3' versus 'METHLYATION_CNMF'

P value = 5.25e-23 (Fisher's exact test), Q value = 2.9e-20

Table S46.  Gene #37: 'del_6q14.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 106 129
DEL PEAK 12(6Q14.3) MUTATED 68 8 29
DEL PEAK 12(6Q14.3) WILD-TYPE 28 98 100

Figure S46.  Get High-res Image Gene #37: 'del_6q14.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6q14.3' versus 'MRNASEQ_CNMF'

P value = 6.65e-08 (Fisher's exact test), Q value = 3.4e-05

Table S47.  Gene #37: 'del_6q14.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 97 112
DEL PEAK 12(6Q14.3) MUTATED 61 15 29
DEL PEAK 12(6Q14.3) WILD-TYPE 60 82 83

Figure S47.  Get High-res Image Gene #37: 'del_6q14.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6q14.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.19e-09 (Fisher's exact test), Q value = 6.2e-07

Table S48.  Gene #37: 'del_6q14.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 93 122
DEL PEAK 12(6Q14.3) MUTATED 60 11 34
DEL PEAK 12(6Q14.3) WILD-TYPE 55 82 88

Figure S48.  Get High-res Image Gene #37: 'del_6q14.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6q14.3' versus 'MIRSEQ_CNMF'

P value = 0.000543 (Chi-square test), Q value = 0.24

Table S49.  Gene #37: 'del_6q14.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 63 51 86 24 97
DEL PEAK 12(6Q14.3) MUTATED 22 4 31 5 40
DEL PEAK 12(6Q14.3) WILD-TYPE 41 47 55 19 57

Figure S49.  Get High-res Image Gene #37: 'del_6q14.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_6q14.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.52e-05 (Chi-square test), Q value = 0.012

Table S50.  Gene #37: 'del_6q14.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 80 28 89 95 29
DEL PEAK 12(6Q14.3) MUTATED 23 3 28 46 2
DEL PEAK 12(6Q14.3) WILD-TYPE 57 25 61 49 27

Figure S50.  Get High-res Image Gene #37: 'del_6q14.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_8p21.3' versus 'CN_CNMF'

P value = 4.19e-09 (Fisher's exact test), Q value = 2.2e-06

Table S51.  Gene #38: 'del_8p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 183 104
DEL PEAK 13(8P21.3) MUTATED 13 88 81
DEL PEAK 13(8P21.3) WILD-TYPE 31 95 23

Figure S51.  Get High-res Image Gene #38: 'del_8p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p21.3' versus 'METHLYATION_CNMF'

P value = 5.51e-09 (Fisher's exact test), Q value = 2.8e-06

Table S52.  Gene #38: 'del_8p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 106 129
DEL PEAK 13(8P21.3) MUTATED 53 35 94
DEL PEAK 13(8P21.3) WILD-TYPE 43 71 35

Figure S52.  Get High-res Image Gene #38: 'del_8p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_8p21.3' versus 'MRNASEQ_CNMF'

P value = 3.08e-07 (Fisher's exact test), Q value = 0.00015

Table S53.  Gene #38: 'del_8p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 97 112
DEL PEAK 13(8P21.3) MUTATED 69 33 80
DEL PEAK 13(8P21.3) WILD-TYPE 52 64 32

Figure S53.  Get High-res Image Gene #38: 'del_8p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_8p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.41e-06 (Fisher's exact test), Q value = 0.0041

Table S54.  Gene #38: 'del_8p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 93 122
DEL PEAK 13(8P21.3) MUTATED 54 40 88
DEL PEAK 13(8P21.3) WILD-TYPE 61 53 34

Figure S54.  Get High-res Image Gene #38: 'del_8p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_8p21.3' versus 'MIRSEQ_CNMF'

P value = 4.48e-10 (Chi-square test), Q value = 2.3e-07

Table S55.  Gene #38: 'del_8p21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 63 51 86 24 97
DEL PEAK 13(8P21.3) MUTATED 48 12 54 4 59
DEL PEAK 13(8P21.3) WILD-TYPE 15 39 32 20 38

Figure S55.  Get High-res Image Gene #38: 'del_8p21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_8p21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.79e-07 (Chi-square test), Q value = 0.00019

Table S56.  Gene #38: 'del_8p21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 80 28 89 95 29
DEL PEAK 13(8P21.3) MUTATED 51 9 56 58 3
DEL PEAK 13(8P21.3) WILD-TYPE 29 19 33 37 26

Figure S56.  Get High-res Image Gene #38: 'del_8p21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_8p11.21' versus 'CN_CNMF'

P value = 9.84e-07 (Fisher's exact test), Q value = 0.00049

Table S57.  Gene #39: 'del_8p11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 183 104
DEL PEAK 14(8P11.21) MUTATED 1 62 42
DEL PEAK 14(8P11.21) WILD-TYPE 43 121 62

Figure S57.  Get High-res Image Gene #39: 'del_8p11.21' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p11.21' versus 'METHLYATION_CNMF'

P value = 8.55e-10 (Fisher's exact test), Q value = 4.5e-07

Table S58.  Gene #39: 'del_8p11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 106 129
DEL PEAK 14(8P11.21) MUTATED 29 12 64
DEL PEAK 14(8P11.21) WILD-TYPE 67 94 65

Figure S58.  Get High-res Image Gene #39: 'del_8p11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_8p11.21' versus 'MRNASEQ_CNMF'

P value = 1.18e-05 (Fisher's exact test), Q value = 0.0057

Table S59.  Gene #39: 'del_8p11.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 97 112
DEL PEAK 14(8P11.21) MUTATED 42 14 49
DEL PEAK 14(8P11.21) WILD-TYPE 79 83 63

Figure S59.  Get High-res Image Gene #39: 'del_8p11.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_8p11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.12

Table S60.  Gene #39: 'del_8p11.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 93 122
DEL PEAK 14(8P11.21) MUTATED 31 19 55
DEL PEAK 14(8P11.21) WILD-TYPE 84 74 67

Figure S60.  Get High-res Image Gene #39: 'del_8p11.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9p23' versus 'CN_CNMF'

P value = 3.41e-05 (Fisher's exact test), Q value = 0.016

Table S61.  Gene #40: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 183 104
DEL PEAK 15(9P23) MUTATED 1 6 19
DEL PEAK 15(9P23) WILD-TYPE 43 177 85

Figure S61.  Get High-res Image Gene #40: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q23.31' versus 'CN_CNMF'

P value = 2.31e-10 (Fisher's exact test), Q value = 1.2e-07

Table S62.  Gene #41: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 183 104
DEL PEAK 16(10Q23.31) MUTATED 7 36 58
DEL PEAK 16(10Q23.31) WILD-TYPE 37 147 46

Figure S62.  Get High-res Image Gene #41: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q23.31' versus 'METHLYATION_CNMF'

P value = 5.23e-11 (Fisher's exact test), Q value = 2.8e-08

Table S63.  Gene #41: 'del_10q23.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 106 129
DEL PEAK 16(10Q23.31) MUTATED 23 12 66
DEL PEAK 16(10Q23.31) WILD-TYPE 73 94 63

Figure S63.  Get High-res Image Gene #41: 'del_10q23.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q23.31' versus 'MRNASEQ_CNMF'

P value = 1.32e-14 (Fisher's exact test), Q value = 7.1e-12

Table S64.  Gene #41: 'del_10q23.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 97 112
DEL PEAK 16(10Q23.31) MUTATED 23 12 66
DEL PEAK 16(10Q23.31) WILD-TYPE 98 85 46

Figure S64.  Get High-res Image Gene #41: 'del_10q23.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.67e-12 (Fisher's exact test), Q value = 3e-09

Table S65.  Gene #41: 'del_10q23.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 93 122
DEL PEAK 16(10Q23.31) MUTATED 15 20 66
DEL PEAK 16(10Q23.31) WILD-TYPE 100 73 56

Figure S65.  Get High-res Image Gene #41: 'del_10q23.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_CNMF'

P value = 0.000226 (Chi-square test), Q value = 0.1

Table S66.  Gene #41: 'del_10q23.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 63 51 86 24 97
DEL PEAK 16(10Q23.31) MUTATED 28 7 31 1 31
DEL PEAK 16(10Q23.31) WILD-TYPE 35 44 55 23 66

Figure S66.  Get High-res Image Gene #41: 'del_10q23.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_10q23.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.05e-05 (Chi-square test), Q value = 0.019

Table S67.  Gene #41: 'del_10q23.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 80 28 89 95 29
DEL PEAK 16(10Q23.31) MUTATED 31 1 35 30 1
DEL PEAK 16(10Q23.31) WILD-TYPE 49 27 54 65 28

Figure S67.  Get High-res Image Gene #41: 'del_10q23.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_12p13.1' versus 'CN_CNMF'

P value = 3.68e-05 (Fisher's exact test), Q value = 0.017

Table S68.  Gene #43: 'del_12p13.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 183 104
DEL PEAK 18(12P13.1) MUTATED 4 29 38
DEL PEAK 18(12P13.1) WILD-TYPE 40 154 66

Figure S68.  Get High-res Image Gene #43: 'del_12p13.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_12p13.1' versus 'METHLYATION_CNMF'

P value = 0.000159 (Fisher's exact test), Q value = 0.072

Table S69.  Gene #43: 'del_12p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 106 129
DEL PEAK 18(12P13.1) MUTATED 25 9 37
DEL PEAK 18(12P13.1) WILD-TYPE 71 97 92

Figure S69.  Get High-res Image Gene #43: 'del_12p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_12q24.31' versus 'CN_CNMF'

P value = 3.8e-06 (Fisher's exact test), Q value = 0.0019

Table S70.  Gene #44: 'del_12q24.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 183 104
DEL PEAK 19(12Q24.31) MUTATED 2 5 21
DEL PEAK 19(12Q24.31) WILD-TYPE 42 178 83

Figure S70.  Get High-res Image Gene #44: 'del_12q24.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q14.12' versus 'CN_CNMF'

P value = 4.88e-12 (Fisher's exact test), Q value = 2.6e-09

Table S71.  Gene #45: 'del_13q14.12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 183 104
DEL PEAK 20(13Q14.12) MUTATED 27 45 67
DEL PEAK 20(13Q14.12) WILD-TYPE 17 138 37

Figure S71.  Get High-res Image Gene #45: 'del_13q14.12' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q14.12' versus 'METHLYATION_CNMF'

P value = 4.96e-08 (Fisher's exact test), Q value = 2.5e-05

Table S72.  Gene #45: 'del_13q14.12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 106 129
DEL PEAK 20(13Q14.12) MUTATED 53 21 65
DEL PEAK 20(13Q14.12) WILD-TYPE 43 85 64

Figure S72.  Get High-res Image Gene #45: 'del_13q14.12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_13q14.12' versus 'MRNASEQ_CNMF'

P value = 8.3e-06 (Fisher's exact test), Q value = 0.004

Table S73.  Gene #45: 'del_13q14.12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 97 112
DEL PEAK 20(13Q14.12) MUTATED 53 23 63
DEL PEAK 20(13Q14.12) WILD-TYPE 68 74 49

Figure S73.  Get High-res Image Gene #45: 'del_13q14.12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_13q14.12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.12e-06 (Fisher's exact test), Q value = 0.0035

Table S74.  Gene #45: 'del_13q14.12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 93 122
DEL PEAK 20(13Q14.12) MUTATED 51 21 67
DEL PEAK 20(13Q14.12) WILD-TYPE 64 72 55

Figure S74.  Get High-res Image Gene #45: 'del_13q14.12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_13q22.1' versus 'CN_CNMF'

P value = 4.69e-14 (Fisher's exact test), Q value = 2.5e-11

Table S75.  Gene #46: 'del_13q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 183 104
DEL PEAK 21(13Q22.1) MUTATED 17 28 62
DEL PEAK 21(13Q22.1) WILD-TYPE 27 155 42

Figure S75.  Get High-res Image Gene #46: 'del_13q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q22.1' versus 'METHLYATION_CNMF'

P value = 3.82e-05 (Fisher's exact test), Q value = 0.018

Table S76.  Gene #46: 'del_13q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 106 129
DEL PEAK 21(13Q22.1) MUTATED 40 17 50
DEL PEAK 21(13Q22.1) WILD-TYPE 56 89 79

Figure S76.  Get High-res Image Gene #46: 'del_13q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_15q21.3' versus 'CN_CNMF'

P value = 1.04e-08 (Fisher's exact test), Q value = 5.3e-06

Table S77.  Gene #47: 'del_15q21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 183 104
DEL PEAK 22(15Q21.3) MUTATED 1 8 29
DEL PEAK 22(15Q21.3) WILD-TYPE 43 175 75

Figure S77.  Get High-res Image Gene #47: 'del_15q21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_15q21.3' versus 'METHLYATION_CNMF'

P value = 0.000148 (Fisher's exact test), Q value = 0.068

Table S78.  Gene #47: 'del_15q21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 106 129
DEL PEAK 22(15Q21.3) MUTATED 14 2 22
DEL PEAK 22(15Q21.3) WILD-TYPE 82 104 107

Figure S78.  Get High-res Image Gene #47: 'del_15q21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_15q21.3' versus 'MRNASEQ_CNMF'

P value = 0.000517 (Fisher's exact test), Q value = 0.23

Table S79.  Gene #47: 'del_15q21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 97 112
DEL PEAK 22(15Q21.3) MUTATED 17 2 19
DEL PEAK 22(15Q21.3) WILD-TYPE 104 95 93

Figure S79.  Get High-res Image Gene #47: 'del_15q21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_15q21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000159 (Fisher's exact test), Q value = 0.072

Table S80.  Gene #47: 'del_15q21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 93 122
DEL PEAK 22(15Q21.3) MUTATED 12 2 24
DEL PEAK 22(15Q21.3) WILD-TYPE 103 91 98

Figure S80.  Get High-res Image Gene #47: 'del_15q21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_15q21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.43e-05 (Fisher's exact test), Q value = 0.039

Table S81.  Gene #47: 'del_15q21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 86 104 79
DEL PEAK 22(15Q21.3) MUTATED 1 18 4 13
DEL PEAK 22(15Q21.3) WILD-TYPE 51 68 100 66

Figure S81.  Get High-res Image Gene #47: 'del_15q21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_16q22.3' versus 'CN_CNMF'

P value = 1.38e-16 (Fisher's exact test), Q value = 7.5e-14

Table S82.  Gene #48: 'del_16q22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 183 104
DEL PEAK 23(16Q22.3) MUTATED 7 40 72
DEL PEAK 23(16Q22.3) WILD-TYPE 37 143 32

Figure S82.  Get High-res Image Gene #48: 'del_16q22.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q22.3' versus 'METHLYATION_CNMF'

P value = 1.87e-07 (Fisher's exact test), Q value = 9.4e-05

Table S83.  Gene #48: 'del_16q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 106 129
DEL PEAK 23(16Q22.3) MUTATED 38 17 64
DEL PEAK 23(16Q22.3) WILD-TYPE 58 89 65

Figure S83.  Get High-res Image Gene #48: 'del_16q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16q22.3' versus 'MRNASEQ_CNMF'

P value = 2.27e-05 (Fisher's exact test), Q value = 0.011

Table S84.  Gene #48: 'del_16q22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 97 112
DEL PEAK 23(16Q22.3) MUTATED 44 19 56
DEL PEAK 23(16Q22.3) WILD-TYPE 77 78 56

Figure S84.  Get High-res Image Gene #48: 'del_16q22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16q22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.46e-06 (Fisher's exact test), Q value = 0.00072

Table S85.  Gene #48: 'del_16q22.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 93 122
DEL PEAK 23(16Q22.3) MUTATED 30 23 66
DEL PEAK 23(16Q22.3) WILD-TYPE 85 70 56

Figure S85.  Get High-res Image Gene #48: 'del_16q22.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_16q22.3' versus 'MIRSEQ_CNMF'

P value = 1.18e-05 (Chi-square test), Q value = 0.0057

Table S86.  Gene #48: 'del_16q22.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 63 51 86 24 97
DEL PEAK 23(16Q22.3) MUTATED 17 11 33 2 52
DEL PEAK 23(16Q22.3) WILD-TYPE 46 40 53 22 45

Figure S86.  Get High-res Image Gene #48: 'del_16q22.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_16q22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.51e-08 (Fisher's exact test), Q value = 2.3e-05

Table S87.  Gene #48: 'del_16q22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 86 104 79
DEL PEAK 23(16Q22.3) MUTATED 6 51 30 28
DEL PEAK 23(16Q22.3) WILD-TYPE 46 35 74 51

Figure S87.  Get High-res Image Gene #48: 'del_16q22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_16q22.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.29e-05 (Chi-square test), Q value = 0.02

Table S88.  Gene #48: 'del_16q22.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 80 28 89 95 29
DEL PEAK 23(16Q22.3) MUTATED 21 4 35 50 5
DEL PEAK 23(16Q22.3) WILD-TYPE 59 24 54 45 24

Figure S88.  Get High-res Image Gene #48: 'del_16q22.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_16q23.3' versus 'CN_CNMF'

P value = 3.78e-18 (Fisher's exact test), Q value = 2.1e-15

Table S89.  Gene #49: 'del_16q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 183 104
DEL PEAK 24(16Q23.3) MUTATED 4 50 76
DEL PEAK 24(16Q23.3) WILD-TYPE 40 133 28

Figure S89.  Get High-res Image Gene #49: 'del_16q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.3' versus 'METHLYATION_CNMF'

P value = 5.76e-08 (Fisher's exact test), Q value = 2.9e-05

Table S90.  Gene #49: 'del_16q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 106 129
DEL PEAK 24(16Q23.3) MUTATED 39 20 71
DEL PEAK 24(16Q23.3) WILD-TYPE 57 86 58

Figure S90.  Get High-res Image Gene #49: 'del_16q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16q23.3' versus 'MRNASEQ_CNMF'

P value = 0.000181 (Fisher's exact test), Q value = 0.082

Table S91.  Gene #49: 'del_16q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 97 112
DEL PEAK 24(16Q23.3) MUTATED 47 24 59
DEL PEAK 24(16Q23.3) WILD-TYPE 74 73 53

Figure S91.  Get High-res Image Gene #49: 'del_16q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16q23.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.52e-05 (Fisher's exact test), Q value = 0.021

Table S92.  Gene #49: 'del_16q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 93 122
DEL PEAK 24(16Q23.3) MUTATED 32 31 67
DEL PEAK 24(16Q23.3) WILD-TYPE 83 62 55

Figure S92.  Get High-res Image Gene #49: 'del_16q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_16q23.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.46e-06 (Fisher's exact test), Q value = 0.0022

Table S93.  Gene #49: 'del_16q23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 86 104 79
DEL PEAK 24(16Q23.3) MUTATED 8 50 35 32
DEL PEAK 24(16Q23.3) WILD-TYPE 44 36 69 47

Figure S93.  Get High-res Image Gene #49: 'del_16q23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_17p13.1' versus 'CN_CNMF'

P value = 3.37e-14 (Fisher's exact test), Q value = 1.8e-11

Table S94.  Gene #50: 'del_17p13.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 183 104
DEL PEAK 25(17P13.1) MUTATED 3 29 58
DEL PEAK 25(17P13.1) WILD-TYPE 41 154 46

Figure S94.  Get High-res Image Gene #50: 'del_17p13.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_17p13.1' versus 'METHLYATION_CNMF'

P value = 5.85e-08 (Fisher's exact test), Q value = 3e-05

Table S95.  Gene #50: 'del_17p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 106 129
DEL PEAK 25(17P13.1) MUTATED 17 15 58
DEL PEAK 25(17P13.1) WILD-TYPE 79 91 71

Figure S95.  Get High-res Image Gene #50: 'del_17p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17p13.1' versus 'MRNASEQ_CNMF'

P value = 4.65e-10 (Fisher's exact test), Q value = 2.4e-07

Table S96.  Gene #50: 'del_17p13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 97 112
DEL PEAK 25(17P13.1) MUTATED 21 13 56
DEL PEAK 25(17P13.1) WILD-TYPE 100 84 56

Figure S96.  Get High-res Image Gene #50: 'del_17p13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_17p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.31e-10 (Fisher's exact test), Q value = 1.7e-07

Table S97.  Gene #50: 'del_17p13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 93 122
DEL PEAK 25(17P13.1) MUTATED 14 17 59
DEL PEAK 25(17P13.1) WILD-TYPE 101 76 63

Figure S97.  Get High-res Image Gene #50: 'del_17p13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_17p13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.68e-07 (Fisher's exact test), Q value = 0.00043

Table S98.  Gene #50: 'del_17p13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 86 104 79
DEL PEAK 25(17P13.1) MUTATED 4 41 21 21
DEL PEAK 25(17P13.1) WILD-TYPE 48 45 83 58

Figure S98.  Get High-res Image Gene #50: 'del_17p13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_17p13.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000282 (Chi-square test), Q value = 0.13

Table S99.  Gene #50: 'del_17p13.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 80 28 89 95 29
DEL PEAK 25(17P13.1) MUTATED 20 2 27 37 1
DEL PEAK 25(17P13.1) WILD-TYPE 60 26 62 58 28

Figure S99.  Get High-res Image Gene #50: 'del_17p13.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_17q21.31' versus 'METHLYATION_CNMF'

P value = 9.14e-09 (Fisher's exact test), Q value = 4.7e-06

Table S100.  Gene #51: 'del_17q21.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 106 129
DEL PEAK 26(17Q21.31) MUTATED 5 14 46
DEL PEAK 26(17Q21.31) WILD-TYPE 91 92 83

Figure S100.  Get High-res Image Gene #51: 'del_17q21.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17q21.31' versus 'MRNASEQ_CNMF'

P value = 3.3e-09 (Fisher's exact test), Q value = 1.7e-06

Table S101.  Gene #51: 'del_17q21.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 97 112
DEL PEAK 26(17Q21.31) MUTATED 13 8 44
DEL PEAK 26(17Q21.31) WILD-TYPE 108 89 68

Figure S101.  Get High-res Image Gene #51: 'del_17q21.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_17q21.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.87e-05 (Fisher's exact test), Q value = 0.014

Table S102.  Gene #51: 'del_17q21.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 93 122
DEL PEAK 26(17Q21.31) MUTATED 10 16 39
DEL PEAK 26(17Q21.31) WILD-TYPE 105 77 83

Figure S102.  Get High-res Image Gene #51: 'del_17q21.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_18q22.1' versus 'CN_CNMF'

P value = 1.71e-07 (Fisher's exact test), Q value = 8.6e-05

Table S103.  Gene #52: 'del_18q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 183 104
DEL PEAK 27(18Q22.1) MUTATED 6 30 47
DEL PEAK 27(18Q22.1) WILD-TYPE 38 153 57

Figure S103.  Get High-res Image Gene #52: 'del_18q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_21q22.3' versus 'CN_CNMF'

P value = 5.08e-09 (Fisher's exact test), Q value = 2.6e-06

Table S104.  Gene #55: 'del_21q22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 183 104
DEL PEAK 30(21Q22.3) MUTATED 1 48 50
DEL PEAK 30(21Q22.3) WILD-TYPE 43 135 54

Figure S104.  Get High-res Image Gene #55: 'del_21q22.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_21q22.3' versus 'METHLYATION_CNMF'

P value = 9.18e-22 (Fisher's exact test), Q value = 5e-19

Table S105.  Gene #55: 'del_21q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 106 129
DEL PEAK 30(21Q22.3) MUTATED 7 14 78
DEL PEAK 30(21Q22.3) WILD-TYPE 89 92 51

Figure S105.  Get High-res Image Gene #55: 'del_21q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_21q22.3' versus 'MRNASEQ_CNMF'

P value = 4.08e-20 (Fisher's exact test), Q value = 2.2e-17

Table S106.  Gene #55: 'del_21q22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 97 112
DEL PEAK 30(21Q22.3) MUTATED 13 15 71
DEL PEAK 30(21Q22.3) WILD-TYPE 108 82 41

Figure S106.  Get High-res Image Gene #55: 'del_21q22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_21q22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.83e-16 (Fisher's exact test), Q value = 3.2e-13

Table S107.  Gene #55: 'del_21q22.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 93 122
DEL PEAK 30(21Q22.3) MUTATED 8 24 67
DEL PEAK 30(21Q22.3) WILD-TYPE 107 69 55

Figure S107.  Get High-res Image Gene #55: 'del_21q22.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_21q22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000124 (Fisher's exact test), Q value = 0.057

Table S108.  Gene #55: 'del_21q22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 86 104 79
DEL PEAK 30(21Q22.3) MUTATED 5 38 33 20
DEL PEAK 30(21Q22.3) WILD-TYPE 47 48 71 59

Figure S108.  Get High-res Image Gene #55: 'del_21q22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_21q22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000554 (Fisher's exact test), Q value = 0.24

Table S109.  Gene #55: 'del_21q22.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 41 88 125
DEL PEAK 30(21Q22.3) MUTATED 31 4 27 34
DEL PEAK 30(21Q22.3) WILD-TYPE 36 37 61 91

Figure S109.  Get High-res Image Gene #55: 'del_21q22.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data
Input

  • Copy number data file = transformed.cor.cli.txt

  • Molecular subtype file = PRAD-TP.transferedmergedcluster.txt

  • Number of patients = 331

  • Number of significantly focal cnvs = 55

  • Number of molecular subtypes = 10

  • Exclude genes that fewer than K tumors have alterations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.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] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[3] 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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